Literature for peptidase A02.001: HIV-1 retropepsin

Summary Alignment Sequences Sequence features Distribution Structure Literature Substrates Pharma

(Topics flags: A Assay, S Structure, T Target, P Specificity, E Expression, V Review, M Mutation, I Inhibitor, L Localization. To select only the references relevant to a single topic, click the link above. See explanation.)

2025

Banerjee,T., Akram,M.B., Choudhury,U. and Balasubramanian,G. Predicting binding strength and dissociation kinetics of HIV-1 protease inhibitors Ritonavir, XK-263, and AHA-001 by molecular simulations J Mol Graph Model (2025) 140, 109110-109110. PubMed Europe PubMed DOI I
Bonardi,A. Computational approaches for designing viral protease inhibitors Enzymes (2025) 58, 59-91. PubMed Europe PubMed DOI
Chen,J., Fang,R., Wang,Z., Jiang,H., Xu,J. and Xiong,F. Rational Design and Multi-tiered Computational Evaluation of Novel Darunavir Derivatives as HIV-1 Protease Inhibitors: an Integrated Approach Using QSAR Model, Molecular Docking, MD Simulations, DFT Analysis, and ADME Profiling Chem Biodivers (2025) , e03500-e03500. PubMed Europe PubMed DOI
Funicello,M., Chiummiento,L., Santarsiere,A., Poggio,F. and Lupattelli,P. Recent Advances in Heterocyclic HIV Protease Inhibitors Int J Mol Sci (2025) 26 PubMed Europe PubMed DOI PMC EPMC
Gaikwad,S.Y., More,A., Seniya,C., Verma,K., Chandane-Tak,M., Nema,V., Kumar,S. and Mukherjee,A. Synergistic inhibition of HIV-1 by Nelfinavir and Epigallocatechin Gallate: A novel nanoemulsion-based therapeutic approach Virology (2025) 603, 110391-110391. PubMed Europe PubMed DOI I
Ghosh,A.K., Yadav,M., Sharma,A., Johnson,M., Ghosh,A.K., Prasad,R., Amano,M., Gerlits,O., Kovalevsky,A. and Mitsuya,H. Potent HIVƒ_'1 protease inhibitors containing oxabicyclo octanol-derived P2-ligands: Design, synthesis, and Xƒ_'ray structural studies of inhibitor-HIV-1 protease complexes Bioorg Med Chem Lett (2025) 120, 130109-130109. PubMed Europe PubMed DOI I
Ghosh,A.K., Shaktah,R., Ghosh,A.K., Johnson,M.E., Bhandari,D., Amano,M., Aoki,M., Kovalevsky,A. and Mitsuya,H. Design, synthesis, evaluation and X-ray structural studies of potent HIV-1 protease inhibitors containing substituted oxaspirocyclic carbamates as the P2 ligands Eur J Med Chem (2025) 297, 117880-117880. PubMed Europe PubMed DOI PMC EPMC
Hsieh,S.H., Huang,K.J. and Wang,C.T. A virus-like particle assembly system for probing the HIV-1 Gag-Pol dimerization domain: supporting evidence for reverse transcriptase involvement in protease activation by influencing Gag-Pol/Gag-Pol interaction J Virol (2025) , e0223624-e0223624. PubMed Europe PubMed DOI
Hughes,I.K., Hood,J.B., Quinones-Molina,A.A., Akiyama,H. and Gummuluru,S. Evasion of CARD8 Activation During HIV-1 Assembly bioRxiv (2025) PubMed Europe PubMed DOI PMC EPMC
Hughes,I.K., Hood,J.B., Quinones-Molina,A.A., Akiyama,H. and Gummuluru,S. Evasion of CARD8 activation during HIV-1 assembly Sci Adv (2025) 11, eadz1069-eadz1069. PubMed Europe PubMed DOI PMC EPMC
Isaguliants,M., Zhitkevich,A., Petkov,S., Gorodnicheva,T., Mezale,D., Fridrihsone,I., Kuzmenko,Y., Kostyushev,D., Kostyusheva,A., Gordeychuk,I. and Bayurova,E. Enzymatic activity of HIV-1 protease defines migration of tumor cells in vitro and enhances their metastatic activity in vivo Biochimie (2025) 228, 32-43. PubMed Europe PubMed DOI
Khuzwayo,S.S., Selepe,M.A., Meyer,D. and Gama,N.H. The synthesis and investigation of novel 3-benzoylbenzofurans and pyrazole derivatives for anti-HIV activity RSC Med Chem (2025) PubMed Europe PubMed DOI PMC EPMC I
Kulsuptrakul,J., Emerman,M. and Mitchell,P.S. CARD8 inflammasome activation during HIV-1 cell-to-cell transmission elife (2025) 13 PubMed Europe PubMed DOI PMC EPMC
Panda,M., Purohit,P., Barik,D., Dansana,J. and Meher,B.R. Bioactive fungal compounds as potential anti-HIV agents against HIV-1 protease: a multi-faceted molecular modelling approach for drug discovery J Biomol Struct Dyn (2025) , 1-23. PubMed Europe PubMed DOI
Preece,B., Peppel,W., Durden,H., Gallegos,R., Clinger,G., Bohn,N., Huwendiek-Poser,A., Ysassi,G., Roman,A., Garcia,G., Cly,T., Belnap,D. and Saffarian,S. Cryo-ET Reveals Distinct Gag Lattice Architectures in Virus-like Particles and Immature HIV-1 bioRxiv (2025) PubMed Europe PubMed DOI PMC EPMC
Rusconi,S., Paoletti,N. and Supuran,C.T. HIV protease and its inhibition Enzymes (2025) 58, 129-149. PubMed Europe PubMed DOI
Sahibzada,K.I., Shahid,S., Akhter,M., Abid,R., Azhar,M., Hu,Y. and Wei,D.Q. HIV OctaScanner: A Machine Learning Approach to Unveil Proteolytic Cleavage Dynamics in HIV-1 Protease Substrates J Chem Inf Model (2025) PubMed Europe PubMed DOI
Sherry,D., Sheik Ismail,Z., Mokhantso,T. and Sayed,Y. Subtype-Specific HIV-1 Protease and the Role of Hinge and Flap Dynamics in Drug Resistance: A Subtype C Narrative Viruses (2025) 17 PubMed Europe PubMed DOI PMC EPMC
Venkatachalam,S., Krishnan,S.R., Sayed,Y. and Gromiha,M.M. Structural and Functional Studies on HIV Protease: Mechanism of Action, Subtypes, Inhibitors, and Drug Resistance Methods Mol Biol (2025) 2867, 185-200. PubMed Europe PubMed DOI V
Venkatachalam,S., Krishnan,S.R., Pandian,R., Sayed,Y. and Gromiha,M.M. Structural Implications of HIV-1 Protease Subtype C Bound to Darunavir: A Molecular Dynamics Study Proteins (2025) PubMed Europe PubMed DOI I
Vig,E., Sun,J. and Chang,C.A. Pathway Specific Unbinding Free Energy Profiles of Ritonavir Dissociation from HIV-1 Protease Biochemistry (2025) 64, 940-952. PubMed Europe PubMed DOI PMC EPMC I
Yoosefian,M. Designing new pharmaceutical derivatives for potential inhibition of human immunodeficiency virus protease enzyme inhibition; a comprehensive in silico study J Biomol Struct Dyn (2025) , 1-22. PubMed Europe PubMed DOI I
Zhou,H., Gao,Y., Yang,Q., Shan,Q., Meng,S., Ma,L., Dong,B., Wang,J., Zhang,G., Wang,M., Cen,S., Wang,Y., Che,Y. and Zhu,M. Design, Synthesis, and Biological Evaluation of Novel Core Scaffold-Modified HIV-1 Protease Inhibitors for Overcoming Drug Resistance J Med Chem (2025) PubMed Europe PubMed DOI I

2024

Abimbola Salubi,C., Abbo,H.S., Jahed,N. and Titinchi,S. Medicinal chemistry perspectives on the development of piperazine-containing HIV-1 inhibitors Bioorg Med Chem (2024) 99, 117605-117605. PubMed Europe PubMed DOI V
Albrijawi,M.T. and Alhajj,R. LSTM-driven drug design using SELFIES for target-focused de novo generation of HIV-1 protease inhibitor candidates for AIDS treatment PLoS ONE (2024) 19, e0303597-e0303597. PubMed Europe PubMed DOI PMC EPMC
Chagas,B.C.A., Zhou,X., Guerrero,M., Ilina,T.V. and Ishima,R. Interplay between protease and reverse transcriptase dimerization in a model HIV-1 polyprotein Protein Sci (2024) 33, e5080-e5080. PubMed Europe PubMed DOI PMC EPMC I
Chuntakaruk,H., Boonpalit,K., Kinchagawat,J., Nakarin,F., Khotavivattana,T., Aonbangkhen,C., Shigeta,Y., Hengphasatporn,K., Nutanong,S., Rungrotmongkol,T. and Hannongbua,S. Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery J Comput Chem (2024) 45, 953-968. PubMed Europe PubMed DOI I
Chuntakaruk,H., Hengphasatporn,K., Shigeta,Y., Aonbangkhen,C., Lee,V.S., Khotavivattana,T., Rungrotmongkol,T. and Hannongbua,S. FMO-guided design of darunavir analogs as HIV-1 protease inhibitors Sci Rep (2024) 14, 3639-3639. PubMed Europe PubMed DOI PMC EPMC I
Ghosh,A.K., Sharma,A. and Ghazi,S. An Enzymatic Route to the Synthesis of Tricyclic Fused Hexahydrofuranofuran P2-Ligand for a Series of Highly Potent HIV-1 Protease Inhibitors Tetrahedron Lett (2024) 140 PubMed Europe PubMed DOI PMC EPMC
Ghosh,A.K., Lee,D., Sharma,A., Johnson,M.E., Ghosh,A.K., Wang,Y.F., Agniswamy,J., Amano,M., Hattori,S.I., Weber,I.T. and Mitsuya,H. Design of substituted tetrahydrofuran derivatives for HIV-1 protease inhibitors: synthesis, biological evaluation, and X-ray structural studies Org Biomol Chem (2024) 22, 7354-7372. PubMed Europe PubMed DOI
Meng,S., Gao,Y., Qiang,G., Hu,Z., Shan,Q., Wang,J., Wang,Y. and Mou,J. Rational design, synthesis and biological evaluation of novel HIV-1 protease inhibitors containing 2-phenylacetamide derivatives as P2 ligands with potent activity against DRV-Resistant HIV-1 variants Bioorg Med Chem Lett (2024) 101, 129651-129651. PubMed Europe PubMed DOI I
Mokhantso,T., Sherry,D., Worth,R., Pandian,R., Achilonu,I. and Sayed,Y. Contrasting the effect of hinge region insertions and non-active site mutations on HIV protease-inhibitor interactions: Insights from altered flap dynamics J Mol Graph Model (2024) 133, 108850-108850. PubMed Europe PubMed DOI
Mulato,A., Lansdon,E., Aoyama,R., Voigt,J., Lee,M., Liclican,A., Lee,G., Singer,E., Stafford,B., Gong,R., Murray,B., Chan,J., Lee,J., Xu,Y., Ahmadyar,S., Gonzalez,A., Cho,A., Stepan,G.J., Schmitz,U., Schultz,B., Marchand,B., Brumshtein,B., Wang,R., Yu,H., Cihlar,T., Xu,L. and Yant,S.R. Preclinical characterization of a non-peptidomimetic HIV protease inhibitor with improved metabolic stability Antimicrob Agents Chemother (2024) 68, e0137323-e0137323. PubMed Europe PubMed DOI PMC EPMC I
Naumovich,V., Kandagalla,S. and Grishina,M. Machine learning-based prediction of bioactivity in HIV-1 protease: insights from electron density analysis Future Med Chem (2024) , 1-9. PubMed Europe PubMed DOI
Saez,J.A. and Vera,J.F. Compact Class-conditional Attribute Category Clustering: Amino Acid Grouping for Enhanced HIV-1 Protease Cleavage Classification IEEE/ACM Trans Comput Biol Bioinform (2024) PP PubMed Europe PubMed DOI
Sankaran,S.V., Krishnan,S.R., Sayed,Y. and Gromiha,M.M. Mechanism of drug resistance in HIV-1 protease subtype C in the presence of Atazanavir Curr Res Struct Biol (2024) 7, 100132-100132. PubMed Europe PubMed DOI PMC EPMC I
Sherry,D. and Sayed,Y. Unveiling a Hidden Pocket in HIV-1 Protease: New Insights Into Retroviral Protease Cantilever-Tip Region Characteristics Proteins (2024) 92, 1398-1412. PubMed Europe PubMed DOI
Tabler,C.O. and Tilton,J.C. Mechanism and Kinetics of HIV-1 Protease Activation Viruses (2024) 16 PubMed Europe PubMed DOI PMC EPMC
Tran,T.T. and Fanucci,G.E. Natural Polymorphisms D60E and I62V Stabilize a Closed Conformation in HIV-1 Protease in the Absence of an Inhibitor or Substrate Viruses (2024) 16 PubMed Europe PubMed DOI PMC EPMC
Zheng,L., Pan,B., Tang,T., Xu,H., Hu,W., Zhang,Y., Wei,X., Liu,X., Wu,Q., Shi,Y., Yang,J., Zhou,Y. and Wei,Y. Synthesis and evaluation of nitrogen-containing derivatives of 3,11-dioxo-olean-12-en-30-oic acid against HIV-1 protease Nat Prod Res (2024) , 1-10. PubMed Europe PubMed DOI I

2023

Arrigoni,R., Santacroce,L., Ballini,A. and Palese,L.L. AI-Aided Search for New HIV-1 Protease Ligands Biomolecules (2023) 13 PubMed Europe PubMed DOI PMC EPMC
Baassi,M., Moussaoui,M., Soufi,H., Rajkhowa,S., Sharma,A., Sinha,S. and Belaaouad,S. Towards designing of a potential new HIV-1 protease inhibitor using QSAR study in combination with Molecular docking and Molecular dynamics simulations PLoS ONE (2023) 18, e0284539-e0284539. PubMed Europe PubMed DOI PMC EPMC
Centazzo,M., Manganaro,L. and Alvisi,G. Cellular Targets of HIV-1 Protease: Just the Tip of the Iceberg? Viruses (2023) 15 PubMed Europe PubMed DOI PMC EPMC
Clark,K.M., Wang,Q. and Shan,L. CARD8 Inflammasome Activation by HIV-1 Protease Methods Mol Biol (2023) 2641, 67-79. PubMed Europe PubMed DOI
Clark,K.M., Kim,J.G., Wang,Q., Gao,H., Presti,R.M. and Shan,L. Chemical inhibition of DPP9 sensitizes the CARD8 inflammasome in HIV-1-infected cells Nat Chem Biol (2023) 19, 431-439. PubMed Europe PubMed DOI
Dakshinamoorthy,A., Asmita,A. and Senapati,S. Comprehending the Structure, Dynamics, and Mechanism of Action of Drug-Resistant HIV Protease ACS Omega (2023) 8, 9748-9763. PubMed Europe PubMed DOI PMC EPMC V
Falcioni,F. and Popelier,P.L.A. How to Compute Atomistic Insight in DFT Clusters: The REG-IQA Approach J Chem Inf Model (2023) 63, 4312-4327. PubMed Europe PubMed DOI PMC EPMC
Guo,S., Saha,I., Saffarian,S. and Johnson,M.E. Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions elife (2023) 12 PubMed Europe PubMed DOI PMC EPMC
Hsieh,S.H., Yu,F.H., Huang,K.J. and Wang,C.T. HIV-1 reverse transcriptase stability correlates with Gag cleavage efficiency: reverse transcriptase interaction implications for modulating protease activation J Virol (2023) 97, e0094823-e0094823. PubMed Europe PubMed DOI PMC EPMC
Kulsuptrakul,J., Turcotte,E.A., Emerman,M. and Mitchell,P.S. A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection elife (2023) 12 PubMed Europe PubMed DOI PMC EPMC
Okafor,S.N., Meyer,A., Gadsden,J., Ahmed,F., Guzman,L., Ahmed,H., Romero,J.A.F. and Angsantikul,P. Drug Reprofiling to Identify Potential HIV-1 Protease Inhibitors Molecules (2023) 28 PubMed Europe PubMed DOI PMC EPMC I
Pan,B.W., Zheng,L.L., Shi,Y., Dong,Z.C., Feng,T.T., Yang,J., Wei,Y. and Zhou,Y. Synthesis and Antiviral and Antitumor Activities of Novel 18beta-Glycyrrhetinic Acid Derivatives Int J Mol Sci (2023) 24 PubMed Europe PubMed DOI PMC EPMC
Rahimi,M., Taghdir,M. and Abasi Joozdani,F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease Sci Rep (2023) 13, 14179-14179. PubMed Europe PubMed DOI PMC EPMC
Rajendran,M., Ferran,M.C., Mouli,L., Babbitt,G.A. and Lynch,M.L. Evolution of drug resistance drives destabilization of flap region dynamics in HIV-1 protease Biophys Rep (N Y) (2023) 3, 100121-100121. PubMed Europe PubMed DOI PMC EPMC
Sheik Ismail,Z., Worth,R., Mosebi,S. and Sayed,Y. HIV Protease Hinge Region Insertions at Codon 38 Affect Enzyme Kinetics, Conformational Stability and Dynamics Protein J (2023) 42, 490-501. PubMed Europe PubMed DOI PMC EPMC
Souffrant,M., Yao,X.Q. and Hamelberg,D. Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance J Chem Inf Model (2023) 63, 3892-3902. PubMed Europe PubMed DOI PMC EPMC
Tang,T.T., Li,S.M., Pan,B.W., Xiao,J.W., Pang,Y.X., Xie,S.X., Zhou,Y., Yang,J. and Wei,Y. Identification of Flavonoids from Scutellaria barbata D. Don as Inhibitors of HIV-1 and Cathepsin L Proteases and Their Structure-Activity Relationships Molecules (2023) 28 PubMed Europe PubMed DOI PMC EPMC I
Zhou,H., Ma,L., Dong,B., Wang,J., Zhang,G., Wang,M., Cen,S., Zhu,M., Shan,Q. and Wang,Y. Design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors containing pyrrolidine-derived P2 ligands to combat drug-resistant variant Eur J Med Chem (2023) 255, 115389-115389. PubMed Europe PubMed DOI I
Zhu,M., Shan,Q., Ma,L., Dong,B., Wang,J., Zhang,G., Wang,M., Zhou,J., Cen,S. and Wang,Y. Structure based design and evaluation of benzoheterocycle derivatives as potential dual HIV-1 protease and reverse transcriptase inhibitors Eur J Med Chem (2023) 246, 114981-114981. PubMed Europe PubMed DOI I

2022

Ahsan,M., Pindi,C. and Senapati,S. Mechanism of darunavir binding to monomeric HIV-1 protease: a step forward in the rational design of dimerization inhibitors Phys Chem Chem Phys (2022) 24, 7107-7120. PubMed Europe PubMed DOI I
Coimbra,J.T.S., Neves,R.P.P., Cunha,A.V., Ramos,M.J. and Fernandes,P.A. Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease Chemistry (2022) 28, e202201066-e202201066. PubMed Europe PubMed DOI
Kim,J.G. and Shan,L. Beyond Inhibition: A Novel Strategy of Targeting HIV-1 Protease to Eliminate Viral Reservoirs Viruses (2022) 14 PubMed Europe PubMed DOI PMC EPMC V
Koivisto,J.M., Poulsen,N.R., Larsen,B.S., Weibull,M.G.M., Stein,A., Doro,F., Winther,J.R., Lindorff-Larsen,K. and Willemoes,M. Co-evolution of drug resistance and broadened substrate recognition in HIV protease variants isolated from an Escherichia coli genetic selection system Biochem J (2022) 479, 479-501. PubMed Europe PubMed DOI
Kojima,E., Iimuro,A., Nakajima,M., Kinuta,H., Asada,N., Sako,Y., Nakata,Z., Uemura,K., Arita,S., Miki,S., Wakasa-Morimoto,C. and Tachibana,Y. Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template J Med Chem (2022) 65, 6157-6170. PubMed Europe PubMed DOI I
Kusumoto,Y., Hayashi,K., Sato,S., Yamada,T., Kozono,I., Nakata,Z., Asada,N., Mitsuki,S., Watanabe,A., Wakasa-Morimoto,C., Uemura,K., Arita,S., Miki,S., Mizutare,T. and Mikamiyama,H. Highly Potent and Oral Macrocyclic Peptides as a HIV-1 Protease Inhibitor: mRNA Display-Derived Hit-to-Lead Optimization ACS Med Chem Lett (2022) 13, 1634-1641. PubMed Europe PubMed DOI PMC EPMC
Ma,L., Wen,J., Dong,B., Zhou,J., Hu,S., Wang,J., Wang,Y., Zhu,M. and Cen,S. Design and Evaluation of Novel HIV-1 Protease Inhibitors Containing Phenols or Polyphenols as P2 Ligands with High Activity against DRV-Resistant HIV-1 Variants Int J Mol Sci (2022) 23 PubMed Europe PubMed DOI PMC EPMC I
Majerova,T. and Konvalinka,J. Viral proteases as therapeutic targets Mol Aspects Med (2022) 88, 101159-101159. PubMed Europe PubMed DOI PMC EPMC V I
Onah,E., Uzor,P.F., Ugwoke,I.C., Eze,J.U., Ugwuanyi,S.T., Chukwudi,I.R. and Ibezim,A. Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors BMC Bioinformatics (2022) 23, 466-466. PubMed Europe PubMed DOI PMC EPMC
Padariya,M., Baginski,M., Babak,M. and Kalathiya,U. Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme Biophys Chem (2022) 291, 106909-106909. PubMed Europe PubMed DOI
Qian,C., Flemming,A., Muller,B. and Lamb,D.C. Dynamics of HIV-1 Gag Processing as Revealed by Fluorescence Lifetime Imaging Microscopy and Single Virus Tracking Viruses (2022) 14 PubMed Europe PubMed DOI PMC EPMC
Samant,N., Nachum,G., Tsepal,T. and Bolon,D.N.A. Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease Protein Sci (2022) 31, e4366-e4366. PubMed Europe PubMed DOI PMC EPMC
Sherry,D., Pandian,R. and Sayed,Y. Non-active site mutations in the HIV protease: Diminished drug binding affinity is achieved through modulating the hydrophobic sliding mechanism Int J Biol Macromol (2022) 217, 27-41. PubMed Europe PubMed DOI
Tabler,C.O., Wegman,S.J., Chen,J., Shroff,H., Alhusaini,N. and Tilton,J.C. The HIV-1 Viral Protease Is Activated during Assembly and Budding Prior to Particle Release J Virol (2022) 96, e0219821-e0219821. PubMed Europe PubMed DOI PMC EPMC
Wong-Sam,A., Wang,Y.F., Kneller,D.W., Kovalevsky,A.Y., Ghosh,A.K., Harrison,R.W. and Weber,I.T. HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics J Mol Graph Model (2022) 117, 108315-108315. PubMed Europe PubMed DOI I
Wu,S., Li,H. and Ma,A. Exact reaction coordinates for flap opening in HIV-1 protease Proc Natl Acad Sci U S A (2022) 119, e2214906119-e2214906119. PubMed Europe PubMed DOI PMC EPMC
Yu,F.H., Huang,K.J. and Wang,C.T. Amino acid substitutions at the HIV-1 transframe region significantly impair virus infectivity PLoS ONE (2022) 17, e0262477-e0262477. PubMed Europe PubMed DOI PMC EPMC

2021

Agniswamy,J., Kneller,D.W., Ghosh,A.K. and Weber,I.T. Novel HIV PR inhibitors with C4-substituted bis-THF and bis-fluoro-benzyl target the two active site mutations of highly drug resistant mutant PR(S17) Biochem Biophys Res Commun (2021) 566, 30-35. PubMed Europe PubMed DOI I
C S,V. and Munusami,P. Revealing the drug resistance mechanism of saquinavir due to G48V and V82F mutations in subtype CRF01_AE HIV-1 protease: molecular dynamics simulation and binding free energy calculations J Biomol Struct Dyn (2021) , 1-18. PubMed Europe PubMed DOI
Eche,S. and Gordon,M.L. Recombinant expression of HIV-1 protease using soluble fusion tags in Escherichia coli: A vital tool for functional characterization of HIV-1 protease Virus Res (2021) 295, 198289-198289. PubMed Europe PubMed DOI V
Han,D., Tan,J., Men,J., Li,C. and Zhang,X. Quantitative structure activity/pharmacokinetics relationship studies of HIV-1 protease inhibitors using three modelling methods Med Chem (2021) 17, 396-406. PubMed Europe PubMed DOI I
Heilmann,E., Kimpel,J., Hofer,B., Rossler,A., Blaas,I., Egerer,L., Nolden,T., Urbiola,C., Krausslich,H.G., Wollmann,G. and von Laer,D. Chemogenetic ON and OFF switches for RNA virus replication Nat Commun (2021) 12, 1362-1362. PubMed Europe PubMed DOI PMC EPMC
Imamichi,T., Bernbaum,J.G., Laverdure,S., Yang,J., Chen,Q., Highbarger,H., Hao,M., Sui,H., Dewar,R., Chang,W. and Lane,H.C. Natural Occurring Polymorphisms in HIV-1 Integrase and RNase H Regulate Viral Release and Autoprocessing J Virol (2021) , JVI0132321-JVI0132321. PubMed Europe PubMed DOI
Jeremiah,S.S., Miyakawa,K., Matsunaga,S., Nishi,M., Kudoh,A., Takaoka,A., Sawasaki,T. and Ryo,A. Cleavage of TANK-Binding Kinase 1 by HIV-1 Protease Triggers Viral Innate Immune Evasion Front Microbiol (2021) 12, 643407-643407. PubMed Europe PubMed DOI PMC EPMC
Kumar,P. and Dominiak,P.M. Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease Molecules (2021) 26 PubMed Europe PubMed DOI PMC EPMC
La Monica,G., Lauria,A., Bono,A. and Martorana,A. Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors Int J Mol Sci (2021) 22 PubMed Europe PubMed DOI PMC EPMC
Leidner,F., Kurt Yilmaz,N. and Schiffer,C.A. Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning J Chem Theory Comput (2021) 17, 2054-2064. PubMed Europe PubMed DOI I
Li,M., Li,W., Xiao,Y., Liu,Q., Liang,L., Wang,D., Huang,W. and Wang,L. Nanopore detects gamma-radiation inhibited HIV-1 protease activity Biosens Bioelectron (2021) 194, 113602-113602. PubMed Europe PubMed DOI
Lyonnais,S., Sadiq,S.K., Lorca-Oro,C., Dufau,L., Nieto-Marquez,S., Escriba,T., Gabrielli,N., Tan,X., Ouizougun-Oubari,M., Okoronkwo,J., Reboud-Ravaux,M., Gatell,J.M., Marquet,R., Paillart,J.C., Meyerhans,A., Tisne,C., Gorelick,R.J. and Mirambeau,G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation Viruses (2021) 13 PubMed Europe PubMed DOI PMC EPMC
Samsudin,F., Gan,S.K. and Bond,P.J. The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations Comput Struct Biotechnol J (2021) 19, 330-342. PubMed Europe PubMed DOI PMC EPMC
Wang,Q., Gao,H., Clark,K.M., Mugisha,C.S., Davis,K., Tang,J.P., Harlan,G.H., DeSelm,C.J., Presti,R.M., Kutluay,S.B. and Shan,L. CARD8 is an inflammasome sensor for HIV-1 protease activity Science (2021) 371, eabe1707-eabe1707. PubMed Europe PubMed DOI
Weber,I.T., Wang,Y.F. and Harrison,R.W. HIV Protease: Historical Perspective and Current Research Viruses (2021) 13 PubMed Europe PubMed DOI PMC EPMC V
Zhu,M., Shan,Q., Ma,L., Wen,J., Dong,B., Zhang,G., Wang,M., Wang,J., Zhou,J., Cen,S. and Wang,Y. Design and biological evaluation of cinnamic and phenylpropionic amide derivatives as novel dual inhibitors of HIV-1 protease and reverse transcriptase Eur J Med Chem (2021) 220, 113498-113498. PubMed Europe PubMed DOI I

2020

Ancy,I., Sivanandam,M. and Kumaradhas,P. Possibility of HIV-1 protease inhibitors-clinical trial drugs as repurposed drugs for SARS-CoV-2 main protease: a molecular docking, molecular dynamics and binding free energy simulation study J Biomol Struct Dyn (2020) , 1-8. PubMed Europe PubMed DOI I
Badaya,A. and Sasidhar,Y.U. Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations Sci Rep (2020) 10, 5501-5501. PubMed Europe PubMed DOI PMC EPMC
Bastys,T., Gapsys,V., Walter,H., Heger,E., Doncheva,N.T., Kaiser,R., de Groot,B.L. and Kalinina,O.V. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors Retrovirology (2020) 17, 13-13. PubMed Europe PubMed DOI PMC EPMC
Bulut,H., Hattori,S.I., Aoki-Ogata,H., Hayashi,H., Das,D., Aoki,M., Davis,D.A., Rao,K.V., Nyalapatla,P.R., Ghosh,A.K. and Mitsuya,H. Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity Sci Rep (2020) 10, 10664-10664. PubMed Europe PubMed DOI PMC EPMC
Chiang,M. and Wang,C. A Single Amino Acid Substitution at HIV-1 Protease Termini Dimer Interface Significantly Reduces Viral Particles Processing Efficiency Jpn J Infect Dis (2020) PubMed Europe PubMed DOI
Chou,C.Y., Lin,C.Y., Wu,C.H. and Tai,D.F. Sensing HIV Protease and Its Inhibitor Using "Helical Epitope"-Imprinted Polymers Sensors (Basel) (2020) 20 PubMed Europe PubMed DOI PMC EPMC
Ergin,H.E., Inga,E.E., Maung,T.Z., Javed,M. and Khan,S. HIV, Antiretroviral Therapy and Metabolic Alterations: A Review Cureus (2020) 12, e8059-e8059. PubMed Europe PubMed DOI PMC EPMC
Fokam,J., Takou,D., Teto,G., Nforbih,S.E., Kome,O.P., Santoro,M.M., Ngoufack,E.S., Eyongetah,M., Palmer,D., Fokunang,E.T., Fokunang,C.N., Colizzi,V., Perno,C.F. and Ndjolo,A. Pre-treatment drug resistance and HIV-1 genetic diversity in the rural and urban settings of Northwest-Cameroon PLoS ONE (2020) 15, e0235958-e0235958. PubMed Europe PubMed DOI
Ghosh,A.K., Kovela,S., Osswald,H.L., Amano,M., Aoki,M., Agniswamy,J., Wang,Y.F., Weber,I.T. and Mitsuya,H. Structure-based design of highly potent HIV-1 protease inhibitors containing new tricyclic ring P2-ligands: design, synthesis, biological, and X-ray structural studies J Med Chem (2020) 63, 4867-4879. PubMed Europe PubMed DOI I
Hu,L., Hu,P., Yuan,X., Luo,X. and You,Z.H. Incorporating the coevolving information of substrates in predicting HIV-1 protease cleavage sites IEEE/ACM Trans Comput Biol Bioinform (2020) 17, 2017-2028. PubMed Europe PubMed DOI
Kleinpeter,A.B. and Freed,E.O. HIV-1 Maturation: Lessons Learned from Inhibitors Viruses (2020) 12 PubMed Europe PubMed DOI V
Lawal,M.M., Sanusi,Z.K., Govender,T., Maguire,G.E.M., Honarparvar,B. and Kruger,H.G. From recognition to reaction mechanism: an overview on the interactions between HIV-1 protease and its natural targets Curr Med Chem (2020) 27, 2514-2549. PubMed Europe PubMed DOI
Lockbaum,G.J., Leidner,F., Royer,W.E., Kurt Yilmaz,N. and Schiffer,C.A. Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures Acta Crystallogr D Struct Biol (2020) 76, 302-310. PubMed Europe PubMed DOI PMC EPMC S
Panthong,S., Itharat,A., Naknarin,S., Kuropakornpong,P., Ooraikul,B. and Sakpakdeejaroen,I. Bactericidal Effect and Anti-Inflammatory Activity of Cassia garettiana Heartwood Extract ScientificWorldJournal (2020) 2020, 1653180-1653180. PubMed Europe PubMed DOI PMC EPMC I
Schmidt,T., Louis,J.M. and Clore,G.M. Probing the Interaction between HIV-1 Protease and the Homodimeric p66/p66' Reverse Transcriptase Precursor by Double Electron-Electron Resonance EPR Spectroscopy Chembiochem (2020) 21, 3051-3055. PubMed Europe PubMed DOI
Sherry,D., Worth,R. and Sayed,Y. Two-step preparation of highly pure, soluble HIV protease from inclusion bodies recombinantly expressed in Escherichia coli Curr Protoc Protein Sci (2020) 100, e106-e106. PubMed Europe PubMed DOI E
Subbaiah,M.A.M., Ramar,T., Subramani,L., Desai,S.D., Sinha,S., Mandlekar,S., Jenkins,S.M., Krystal,M.R., Subramanian,M., Sridhar,S., Padmanabhan,S., Bhutani,P., Arla,R., Kadow,J.F. and Meanwell,N.A. (Carbonyl)oxyalkyl linker-based amino acid prodrugs of the HIV-1 protease inhibitor atazanavir that enhance oral bioavailability and plasma trough concentration Eur J Med Chem (2020) 207, 112749-112749. PubMed Europe PubMed DOI I
Tran,T.T., Liu,Z. and Fanucci,G.E. Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study Biochem Biophys Res Commun (2020) 532, 219-224. PubMed Europe PubMed DOI
Yu,F.H., Huang,K.J. and Wang,C.T. Conditional activation of an HIV-1 protease attenuated mutant by a leucine zipper dimerization motif Virus Res (2020) , 198258-198258. PubMed Europe PubMed DOI
Zhou,H., Zhu,M., Ma,L., Zhou,J., Dong,B., Zhang,G., Cen,S., Wang,Y. and Wang,J. Piperidine scaffold as the novel P2-ligands in cyclopropyl-containing HIV-1 protease inhibitors: Structure-based design, synthesis, biological evaluation and docking study PLoS ONE (2020) 15, e0235483-e0235483. PubMed Europe PubMed DOI PMC EPMC
Zhu,M., Dou,Y., Ma,L., Dong,B., Zhang,F., Zhang,G., Wang,J., Zhou,J., Cen,S. and Wang,Y. Novel HIV-1 Protease Inhibitors with Morpholine as the P2 Ligand to Enhance Activity against DRV-Resistant Variants ACS Med Chem Lett (2020) 11, 1196-1204. PubMed Europe PubMed DOI PMC EPMC I

2019

Ahsan,M. and Senapati,S. Water plays a cocatalytic role in epoxide ring opening reaction in aspartate proteases: a QM/MM study J Phys Chem B (2019) 123, 7955-7964. PubMed Europe PubMed DOI
Boucher,J.I., Whitfield,T.W., Dauphin,A., Nachum,G., Hollins,C., Zeldovich,K.B., Swanstrom,R., Schiffer,C.A., Luban,J. and Bolon,D.N.A. Constrained mutational sampling of amino acids in HIV-1 protease evolution Mol Biol Evol (2019) 36, 798-810. PubMed Europe PubMed DOI
C S,V., Tamizhselvi,R. and Munusami,P. Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations J Biomol Struct Dyn (2019) 37, 2608-2626. PubMed Europe PubMed DOI
Gardner,J.M. and Abrams,C.F. Energetics of flap opening in HIV-1 protease: string method calculations J Phys Chem B (2019) 123, 9584-9591. PubMed Europe PubMed DOI
Ghosh,A.K., Williams,J.N., Kovela,S., Takayama,J., Simpson,H.M., Walters,D.E., Hattori,S.I., Aoki,M. and Mitsuya,H. Potent HIV-1 protease inhibitors incorporating squaramide-derived P2 ligands: design, synthesis, and biological evaluation Bioorg Med Chem Lett (2019) 29, 2565-2570. PubMed Europe PubMed DOI PMC EPMC I
Ghosh,A.K., Xia,Z., Kovela,S., Robinson,W.L., Johnson,M.E., Kneller,D.W., Wang,Y.F., Aoki,M., Takamatsu,Y., Weber,I.T. and Mitsuya,H. Potent HIV-1 protease inhibitors containing carboxylic and boronic acids: effect on enzyme inhibition and antiviral activity and protein-ligand X-ray structural studies ChemMedChem (2019) 14, 1863-1872. PubMed Europe PubMed DOI S I
Hattori,S.I., Hayashi,H., Bulut,H., Rao,K.V., Nyalapatla,P.R., Hasegawa,K., Aoki,M., Ghosh,A.K. and Mitsuya,H. Halogen bond interactions of novel HIV-1 protease inhibitors (PI)(GRL-001-15 and GRL-003-15) with the flap of protease are critical for their potent activity against wild-type and multi-PI-resistant HIV-1 variants Antimicrob Agents Chemother (2019) 63, e02635-18-e02635-18. PubMed Europe PubMed DOI I
Henes,M., Lockbaum,G.J., Kosovrasti,K., Leidner,F., Nachum,G.S., Nalivaika,E.A., Lee,S.K., Spielvogel,E., Zhou,S., Swanstrom,R., Bolon,D.N.A., Kurt Yilmaz,N. and Schiffer,C.A. Picomolar to micromolar: elucidating the role of distal mutations in HIV-1 protease in conferring drug resistance ACS Chem Biol (2019) 14, 2441-2452. PubMed Europe PubMed DOI I
Huang,L., Li,L., Tien,C., LaBarbera,D.V. and Chen,C. Targeting HIV-1 protease autoprocessing for high-throughput drug discovery and drug resistance assessment Sci Rep (2019) 9, 301-301. PubMed Europe PubMed DOI PMC EPMC
Huang,S., Zhang,D., Mei,H., Kevin,M., Qu,S., Pan,X. and Lu,L. SMD-based interaction-energy fingerprints can predict accurately the dissociation rate constants of HIV-1 protease inhibitors J Chem Inf Model (2019) 59, 159-169. PubMed Europe PubMed DOI I
Karnati,K.R. and Wang,Y. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis J Mol Graph Model (2019) 92, 112-122. PubMed Europe PubMed DOI S
Li,P., Wang,S., Wang,H. and Yan,H. Synthesis and biological evaluation of 3,9-dioxatetraasteranes as C2-symmetric HIV-1 protease inhibitors and docking study Biol Pharm Bull (2019) 42, 261-267. PubMed Europe PubMed DOI I
Lockbaum,G.J., Leidner,F., Rusere,L.N., Henes,M., Kosovrasti,K., Nachum,G.S., Nalivaika,E.A., Ali,A., Yilmaz,N.K. and Schiffer,C.A. Structural adaptation of darunavir analogues against primary mutations in HIV-1 protease ACS Infect Dis (2019) 5, 316-325. PubMed Europe PubMed DOI I
Maseko,S.B., Govender,D., Govender,T., Naicker,T., Lin,J., Maguire,G.E.M. and Kruger,H.G. Optimized procedure for recovering HIV-1 protease (C-SA) from inclusion bodies Protein J (2019) 38, 30-36. PubMed Europe PubMed DOI E
Maximova,K., Wojtczak,J. and Trylska,J. Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions Eur Biophys J (2019) 48, 685-689. PubMed Europe PubMed DOI
Medina-O'Donnell,M., Rivas,F., Reyes-Zurita,F.J., Cano-Munoz,M., Martinez,A., Lupianez,J.A. and Parra,A. Oleanolic acid derivatives as potential inhibitors of HIV-1 protease J Nat Prod (2019) 82, 2886-2896. PubMed Europe PubMed DOI I
Pawar,S., Wang,Y.F., Wong-Sam,A., Agniswamy,J., Ghosh,A.K., Harrison,R.W. and Weber,I.T. Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I Biochem Biophys Res Commun (2019) 514, 974-978. PubMed Europe PubMed DOI S I
Rusere,L.N., Lockbaum,G.J., Lee,S.K., Henes,M., Kosovrasti,K., Spielvogel,E., Nalivaika,E.A., Swanstrom,R., Yilmaz,N.K., Schiffer,C.A. and Ali,A. HIV-1 protease inhibitors incorporating stereochemically defined P2' ligands to optimize hydrogen bonding in the substrate envelope J Med Chem (2019) 62, 8062-8079. PubMed Europe PubMed DOI I
Takamatsu,Y., Aoki,M., Bulut,H., Das,D., Amano,M., Sheri,V.R., Kovari,L.C., Hayashi,H., Delino,N.S., Ghosh,A.K. and Mitsuya,H. Novel protease inhibitors containing C-5-modified bis-THF and aminobenzothiazole as P2 and P2' ligands that exert potent antiviral activity against highly multidrug-resistant HIV-1 with high genetic barrier against the emergence of drug resistance Antimicrob Agents Chemother (2019) 63, e00372-19-e00372-19. PubMed Europe PubMed DOI I
Tramutola,F., Armentano,M.F., Berti,F., Chiummiento,L., Lupattelli,P., D'Orsi,R., Miglionico,R., Milella,L., Bisaccia,F. and Funicello,M. New heteroaryl carbamates: synthesis and biological screening in vitro and in mammalian cells of wild-type and mutant HIV-protease inhibitors Bioorg Med Chem (2019) 27, 1863-1870. PubMed Europe PubMed DOI I
Williams,A., Basson,A., Achilonu,I., Dirr,H.W., Morris,L. and Sayed,Y. Double trouble? Gag in conjunction with double insert in HIV protease contributes to reduced DRV susceptibility Biochem J (2019) 476, 375-384. PubMed Europe PubMed DOI
Zhu,M., Du,X.N., Li,Y.G., Zhang,G.N., Wang,J.X. and Wang,Y.C. Design, synthesis and biological evaluation of novel HIV-1 protease inhibitors with pentacyclic triterpenoids as P2-ligands Bioorg Med Chem Lett (2019) 29, 357-361. PubMed Europe PubMed DOI I
Zhu,M., Dong,B., Zhang,G.N., Wang,J.X., Cen,S. and Wang,Y.C. Synthesis and biological evaluation of new HIV-1 protease inhibitors with purine bases as P2-ligands Bioorg Med Chem Lett (2019) 29, 1541-1545. PubMed Europe PubMed DOI I
Zondagh,J., Basson,A.E., Achilonu,I., Morris,L., Dirr,H.W. and Sayed,Y. Drug susceptibility and replication capacity of a rare HIV-1 subtype C protease hinge region variant Antivir Ther (2019) 24, 333-342. PubMed Europe PubMed DOI I

2018

Amin,S.A., Adhikari,N., Bhargava,S., Jha,T. and Gayen,S. Structural exploration of hydroxyethylamines as HIV-1 protease inhibitors: new features identified SAR QSAR Environ Res (2018) 29, 385-408. PubMed Europe PubMed DOI I
Aoki,M., Das,D., Hayashi,H., Aoki-Ogata,H., Takamatsu,Y., Ghosh,A.K. and Mitsuya,H. Mechanism of Darunavir (DRV)'s high genetic barrier to HIV-1 resistance: a key V32I substitution in protease rarely occurs, but once it occurs, it predisposes HIV-1 to develop DRV resistance MBio (2018) 9 PubMed Europe PubMed DOI I
Bastys,T., Gapsys,V., Doncheva,N.T., Kaiser,R., de Groot,B.L. and Kalinina,O.V. Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations J Chem Theory Comput (2018) 14, 3397-3408. PubMed Europe PubMed DOI
Delino,N.S., Aoki,M., Hayashi,H., Hattori,S.I., Chang,S.B., Takamatsu,Y., Martyr,C.D., Das,D., Ghosh,A.K. and Mitsuya,H. GRL-079, a novel P2-Tp-THF-C5-alkylamine- and P2' -Abt-containing HIV-1 protease inhibitor, is extremely potent against multi-drug-resistant HIV-1 variants including HIVDRV(R)p51 and has a high genetic barrier against the emergence of resistant variants Antimicrob Agents Chemother (2018) 62, e02060-17-e02060-17. PubMed Europe PubMed DOI I
Ghosh,A.K., Rao,K.V., Nyalapatla,P.R., Kovela,S., Brindisi,M., Osswald,H.L., Sekhara Reddy,B., Agniswamy,J., Wang,Y.F., Aoki,M., Hattori,S.I., Weber,I.T. and Mitsuya,H. Design of highly potent, dual-acting and central-nervous-system-penetrating HIV-1 protease inhibitors with excellent potency against multidrug-resistant HIV-1 variants ChemMedChem (2018) 13, 803-815. PubMed Europe PubMed DOI S I
Ghosh,A.K., R Nyalapatla,P., Kovela,S., Rao,K.V., Brindisi,M., Osswald,H.L., Amano,M., Aoki,M., Agniswamy,J., Wang,Y.F., Weber,I.T. and Mitsuya,H. Design and synthesis of highly potent HIV-1 protease inhibitors containing tricyclic fused ring systems as novel P2 ligands: structure-activity studies, biological and X-ray structural analysis J Med Chem (2018) 61, 4561-4577. PubMed Europe PubMed DOI I
Ghosh,A.K., Jadhav,R.D., Simpson,H., Kovela,S., Osswald,H., Agniswamy,J., Wang,Y.F., Hattori,S.I., Weber,I.T. and Mitsuya,H. Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands Eur J Med Chem (2018) 160, 171-182. PubMed Europe PubMed DOI S I
Ghosh,A.K., Williams,J.N., Ho,R.Y., Simpson,H.M., Hattori,S.I., Hayashi,H., Agniswamy,J., Wang,Y.F., Weber,I.T. and Mitsuya,H. Design and synthesis of potent HIV-1 protease inhibitors containing bicyclic oxazolidinone scaffold as the P2 ligands: structure-activity studies and biological and X-ray structural studies J Med Chem (2018) 61, 9722-9737. PubMed Europe PubMed DOI I
Halder,A.K. Finding the structural requirements of diverse HIV-1 protease inhibitors using multiple QSAR modelling for lead identification SAR QSAR Environ Res (2018) 29, 911-933. PubMed Europe PubMed DOI I
Hassan,S., Srikakulam,S.K., Chandramohan,Y., Thangam,M., Muthukumar,S., Gayathri Devi,P.K. and Hanna,L.E. Exploring the conformational landscapes of HIV protease structural ensembles using principal component analysis Proteins (2018) 86, 990-1000. PubMed Europe PubMed DOI I
Hidaka,K., Kimura,T., Sankaranarayanan,R., Wang,J., McDaniel,K.F., Kempf,D.J., Kameoka,M., Adachi,M., Kuroki,R., Nguyen,J.T., Hayashi,Y. and Kiso,Y. Identification of highly potent human immunodeficiency virus type-1 protease inhibitors against lopinavir and darunavir resistant viruses from allophenylnorstatine-based peptidomimetics with P2 tetrahydrofuranylglycine J Med Chem (2018) 61, 5138-5153. PubMed Europe PubMed DOI I
Khan,S.N., Persons,J.D., Paulsen,J.L., Guerrero,M., Schiffer,C.A., Kurt-Yilmaz,N. and Ishima,R. Probing structural changes among analogous inhibitor-bound forms of HIV-1 protease and a drug-resistant mutant in solution by nuclear magnetic resonance Biochemistry (2018) 57, 1652-1662. PubMed Europe PubMed DOI I
Leidner,F., Kurt Yilmaz,N., Paulsen,J., Muller,Y.A. and Schiffer,C.A. Hydration structure and dynamics of inhibitor-bound HIV-1 protease J Chem Theory Comput (2018) 14, 2784-2796. PubMed Europe PubMed DOI S
Li,Y., Tian,Y., Qin,Z. and Yan,A. Classification of HIV-1 protease inhibitors by machine learning methods ACS Omega (2018) 3, 15837-15849. PubMed Europe PubMed DOI PMC EPMC I
Maphumulo,S.I., Halder,A.K., Govender,T., Maseko,S., Maguire,G.E.M., Honarparvar,B. and Kruger,H.G. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study Chem Biol Drug Des (2018) 92, 1899-1913. PubMed Europe PubMed DOI
Miao,Y., Huang,Y.M., Walker,R.C., McCammon,J.A. and Chang,C.A. Ligand binding pathways and conformational transitions of the HIV protease Biochemistry (2018) 57, 1533-1541. PubMed Europe PubMed DOI
Pawar,S.D., Freas,C., Weber,I.T. and Harrison,R.W. Analysis of drug resistance in HIV protease BMC Bioinformatics (2018) 19, 362-362. PubMed Europe PubMed DOI PMC EPMC I
Potempa,M., Lee,S.K., Kurt Yilmaz,N., Nalivaika,E.A., Rogers,A., Spielvogel,E., Carter CW Jr, Schiffer,C.A. and Swanstrom,R. HIV-1 Protease uses bi-specific S2/S2' subsites to optimize cleavage of two classes of target sites J Mol Biol (2018) 430, 5182-5195. PubMed Europe PubMed DOI
Qureshi,A., Rajput,A., Kaur,G. and Kumar,M. HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors J Cheminform (2018) 10, 12-12. PubMed Europe PubMed DOI PMC EPMC I
Sanusi,Z.K., Govender,T., Maguire,G.E.M., Maseko,S.B., Lin,J., Kruger,H.G. and Honarparvar,B. An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L upward arrowN upward arrowL PR mutant J Comput Aided Mol Des (2018) 32, 459-471. PubMed Europe PubMed DOI M I
Tarasova,O., Biziukova,N., Filimonov,D. and Poroikov,V. A computational approach for the prediction of HIV resistance based on amino acid and nucleotide descriptors Molecules (2018) 23 PubMed Europe PubMed DOI I
Thacker,J.C.R., Vincent,M.A. and Popelier,P.L.A. Using the relative energy gradient method with interacting quantum atoms to determine the reaction mechanism and catalytic effects in the peptide hydrolysis in HIV-1 protease Chemistry (2018) 24, 11200-11210. PubMed Europe PubMed DOI
Tien,C., Huang,L., Watanabe,S.M., Speidel,J.T., Carter,C.A. and Chen,C. Context-dependent autoprocessing of human immunodeficiency virus type 1 protease precursors PLoS ONE (2018) 13, e0191372-e0191372. PubMed Europe PubMed DOI PMC EPMC
Triki,D., Billot,T., Visseaux,B., Descamps,D., Flatters,D., Camproux,A.C. and Regad,L. Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases Sci Rep (2018) 8, 5789-5789. PubMed Europe PubMed DOI PMC EPMC
Windsor,I.W. and Raines,R.T. A substrate selected by phage display exhibits enhanced side-chain hydrogen bonding to HIV-1 protease Acta Crystallogr D Struct Biol (2018) 74, 690-694. PubMed Europe PubMed DOI PMC EPMC S
Windsor,I.W., Palte,M.J., Lukesh JC 3rd, Gold,B., Forest,K.T. and Raines,R.T. Sub-picomolar inhibition of HIV-1 protease with a boronic acid J Am Chem Soc (2018) 140, 14015-14018. PubMed Europe PubMed DOI S I
Wong-Sam,A., Wang,Y.F., Zhang,Y., Ghosh,A.K., Harrison,R.W. and Weber,I.T. Drug resistance mutation L76V alters nonpolar interactions at the flap-core interface of HIV-1 protease ACS Omega (2018) 3, 12132-12140. PubMed Europe PubMed DOI PMC EPMC
Zhang,Y., Chen,X., Roozbahani,G.M. and Guan,X. Graphene oxide-based biosensing platform for rapid and sensitive detection of HIV-1 protease Anal Bioanal Chem (2018) 410, 6177-6185. PubMed Europe PubMed DOI A

2017

Amano,M., Miguel Salcedo-Gomez,P., Yedidi,R.S., Delino,N.S., Nakata,H., Venkateswara Rao,K., Ghosh,A.K. and Mitsuya,H. GRL-09510, a Unique P2-crown-tetrahydrofuranylurethane-containing HIV-1 protease inhibitor, maintains its favorable antiviral activity against highly-drug-resistant HIV-1 variants in vitr Sci Rep (2017) 7, 12235-12235. PubMed Europe PubMed DOI PMC EPMC I
Aoki,M., Hayashi,H., Rao,K.V., Das,D., Higashi-Kuwata,N., Bulut,H., Aoki-Ogata,H., Takamatsu,Y., Yedidi,R.S., Davis,D.A., Hattori,S.I., Nishida,N., Hasegawa,K., Takamune,N., Nyalapatla,P.R., Osswald,H.L., Jono,H., Saito,H., Yarchoan,R., Misumi,S., Ghosh,A.K. and Mitsuya,H. A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency elife (2017) 6 PubMed Europe PubMed DOI PMC EPMC I
Appadurai,R. and Senapati,S. How mutations can resist drug binding yet keep HIV-1 protease functional Biochemistry (2017) 56, 2907-2920. PubMed Europe PubMed DOI
Bai,X., Yang,Z., Zhu,M., Dong,B., Zhou,L., Zhang,G., Wang,J. and Wang,Y. Design and synthesis of potent HIV-1 protease inhibitors with (S)-tetrahydrofuran-tertiary amine-acetamide as P2-ligand: structure-activity studies and biological evaluation Eur J Med Chem (2017) 137, 30-44. PubMed Europe PubMed DOI I
Barzegar,A., Naghizadeh,E., Zakariazadeh,M. and Azamat,J. Molecular dynamics simulation study of the HIV-1 protease inhibition using fullerene and new fullerene derivatives of carbon nanostructures Mini Rev Med Chem (2017) 17, 633-647. PubMed Europe PubMed I
Bhargava,S., Adhikari,N., Amin,S.A., Das,K., Gayen,S. and Jha,T. Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization SAR QSAR Environ Res (2017) 28, 973-990. PubMed Europe PubMed DOI I
Bungard,C.J., Williams,P.D., Schulz,J., Wiscount,C.M., Holloway,M.K., Loughran,H.M., Manikowski,J.J., Su,H.P., Bennett,D.J., Chang,L., Chu,X.J., Crespo,A., Dwyer,M.P., Keertikar,K., Morriello,G.J., Stamford,A.W., Waddell,S.T., Zhong,B., Hu,B., Ji,T., Diamond,T.L., Bahnck-Teets,C., Carroll,S.S., Fay,J.F., Min,X., Morris,W., Ballard,J.E., Miller,M.D. and McCauley,J.A. Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors ACS Med Chem Lett (2017) 8, 1292-1297. PubMed Europe PubMed DOI PMC EPMC I
Deshmukh,L., Tugarinov,V., Louis,J.M. and Clore,G.M. Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR Proc Natl Acad Sci U S A (2017) 114, E9855-E9855. PubMed Europe PubMed DOI
Duan,L.L., Zhu,T., Li,Y.C., Zhang,Q.G. and Zhang,J.Z. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations Sci Rep (2017) 7, 42223-42223. PubMed Europe PubMed DOI PMC EPMC
Ehlert,F.G.R., Linde,K. and Diederich,W.E. What are we missing? The detergent Triton X-100 added to avoid compound aggregation can affect assay results in an unpredictable manner ChemMedChem (2017) 12, 1419-1423. PubMed Europe PubMed DOI A I
Funicello,M., Chiummiento,L., Tramutola,F., Armentano,M.F., Bisaccia,F., Miglionico,R., Milella,L., Benedetti,F., Berti,F. and Lupattelli,P. Synthesis and biological evaluation in vitro and in mammalian cells of new heteroaryl carboxyamides as HIV-protease inhibitors Bioorg Med Chem (2017) 25, 4715-4722. PubMed Europe PubMed DOI I
Gerlits,O., Keen,D.A., Blakeley,M.P., Louis,J.M., Weber,I.T. and Kovalevsky,A. Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100 K J Med Chem (2017) 60, 2018-2025. PubMed Europe PubMed DOI S I
Ghosh,A.K., Rao,K.V., Nyalapatla,P.R., Osswald,H.L., Martyr,C.D., Aoki,M., Hayashi,H., Agniswamy,J., Wang,Y.F., Bulut,H., Das,D., Weber,I.T. and Mitsuya,H. Design and development of highly potent HIV-1 protease inhibitors with a crown-like oxotricyclic core as the P2-ligand to combat multidrug-resistant HIV variants J Med Chem (2017) 60, 4267-4278. PubMed Europe PubMed DOI I
Ghosh,A.K., Sean Fyvie,W., Brindisi,M., Steffey,M., Agniswamy,J., Wang,Y.F., Aoki,M., Amano,M., Weber,I.T. and Mitsuya,H. Design, synthesis, X-ray studies, and biological evaluation of novel macrocyclic HIV-1 protease inhibitors involving the P1'-P2' ligands Bioorg Med Chem Lett (2017) 27, 4925-4931. PubMed Europe PubMed DOI I
Ghosh,A.K., Fyvie,W.S., Brindisi,M., Steffey,M., Agniswamy,J., Wang,Y.F., Aoki,M., Amano,M., Weber,I.T. and Mitsuya,H. Design, synthesis, biological evaluation, and X-ray studies of HIV-1 protease inhibitors with modified P2' ligands of Darunavir ChemMedChem (2017) 12, 1942-1952. PubMed Europe PubMed DOI I
Heidari,A. and Fatemi,M.H. Comparative molecular field analysis (CoMFA) topomer CoMFA and hologram QSAR studies on a series of novel HIV-1 protease inhibitors Chem Biol Drug Des (2017) 89, 918-931. PubMed Europe PubMed DOI I
Huang,Y.M., Raymundo,M.A., Chen,W. and Chang,C.A. Mechanism of the association pathways for a pair of fast and slow binding ligands of HIV-1 protease Biochemistry (2017) 56, 1311-1323. PubMed Europe PubMed DOI I
Inoue,M., Oyama,D., Hidaka,K. and Kameoka,M. Evaluation of novel protease inhibitors against darunavir-resistant variants of HIV type 1 FEBS Open Bio (2017) 7, 88-95. PubMed Europe PubMed DOI PMC EPMC I
Mitchell,M.L., Xu,L., Newby,Z.E. and Desai,M.C. Synthesis of novel HIV-1 protease inhibitors via diastereoselective Henry reaction with nitrocyclopropane Tetrahedron Lett (2017) 58, 1123-1126. DOI I
Mohammadi,A.A., Taheri,S., Amouzegar,A., Ahdenov,R., Halvagar,M.R. and Sadr,A.S. Diastereoselective synthesis and molecular docking studies of novel fused tetrahydropyridine derivatives as new inhibitors of HIV protease J Mol Struct (2017) 1139, 166-174. DOI I
Palese,L.L. Conformations of the HIV-1 protease: a crystal structure data set analysis Biochim Biophys Acta (2017) 1865, 1416-1422. PubMed Europe PubMed DOI S
Palese,L.L. Analysis of the conformations of the HIV-1 protease from a large crystallographic data set Data Brief (2017) 15, 696-700. PubMed Europe PubMed DOI PMC EPMC S
Paulsen,J.L., Leidner,F., Ragland,D.A., Kurt Yilmaz,N. and Schiffer,C.A. Interdependence of inhibitor recognition in HIV-1 protease J Chem Theory Comput (2017) 13, 2300-2309. PubMed Europe PubMed DOI I
Rosner,H.I., Caldarini,M., Prestel,A., Vanoni,M.A., Broglia,R.A., Aliverti,A., Tiana,G. and Kragelund,B.B. Cold denaturation of the HIV-1 protease monomer Biochemistry (2017) 56, 1029-1032. PubMed Europe PubMed DOI
Subbaiah,M.A.M., Meanwell,N.A. and Kadow,J.F. Design strategies in the prodrugs of HIV-1 protease inhibitors to improve the pharmaceutical properties Eur J Med Chem (2017) 139, 865-883. PubMed Europe PubMed DOI I
Tong,J., Wu,Y., Bai,M. and Zhan,P. 3D-QSAR and molecular docking studies on HIV protease inhibitors J Mol Struct (2017) 1129, 17-22. DOI I
Zakharova,M.Y., Kuznetsova,A.A., Kaliberda,E.N., Dronina,M.A., Kolesnikov,A.V., Kozyr,A.V., Smirnov,I.V., Rumsh,L.D., Fedorova,O.S., Knorre,D.G., Gabibov,A.G. and Kuznetsov,N.A. Evolution of inhibitor-resistant natural mutant forms of HIV-1 protease probed by pre-steady state kinetic analysis Biochimie (2017) 142, 125-134. PubMed Europe PubMed DOI I

2016

Amano,M., Salcedo-Gomez,P.M., Zhao,R., Yedidi,R.S., Das,D., Bulut,H., Delino,N.S., Sheri,V.R., Ghosh,A.K. and Mitsuya,H. A modified P1 moiety enhances in vitro antiviral activity against various multidrug-resistant HIV-1 variants and in vitro central nervous system penetration properties of a novel nonpeptidic protease inhibitor, GRL-10413 Antimicrob Agents Chemother (2016) 60, 7046-7059. PubMed Europe PubMed DOI I
Benko,Z., Elder,R.T., Li,G., Liang,D. and Zhao,R.Y. HIV-1 protease in the fission yeast Schizosaccharomyces pombe PLoS ONE (2016) 11, e0151286-e0151286. PubMed Europe PubMed DOI PMC EPMC
Bungard,C.J., Williams,P.D., Ballard,J.E., Bennett,D.J., Beaulieu,C., Bahnck-Teets,C., Carroll,S.S., Chang,R.K., Dubost,D.C., Fay,J.F., Diamond,T.L., Greshock,T.J., Hao,L., Holloway,M.K., Felock,P.J., Gesell,J.J., Su,H.P., Manikowski,J.J., McKay,D.J., Miller,M., Min,X., Molinaro,C., Moradei,O.M., Nantermet,P.G., Nadeau,C., Sanchez,R.I., Satyanarayana,T., Shipe,W.D., Singh,S.K., Truong,V.L., Vijayasaradhi,S., Wiscount,C.M., Vacca,J.P., Crane,S.N. and McCauley,J.A. Discovery of MK-8718, an HIV protease inhibitor containing a novel morpholine aspartate binding group ACS Med Chem Lett (2016) 7, 702-707. PubMed Europe PubMed DOI PMC EPMC I
Chetty,S., Bhakat,S., Martin,A.J. and Soliman,M.E. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights J Biomol Struct Dyn (2016) 34, 135-151. PubMed Europe PubMed DOI
Gerlits,O., Wymore,T., Das,A., Shen,C.H., Parks,J.M., Smith,J.C., Weiss,K.L., Keen,D.A., Blakeley,M.P., Louis,J.M., Langan,P., Weber,I.T. and Kovalevsky,A. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site Angew Chem Int Ed Engl (2016) 55, 4924-4927. PubMed Europe PubMed DOI S I
Ghosh,A.K., Osswald,H.L. and Prato,G. Recent progress in the development of HIV-1 protease inhibitors for the treatment of HIV/AIDS J Med Chem (2016) 59, 5172-5208. PubMed Europe PubMed DOI I
Hu,G., Ma,A., Dou,X., Zhao,L. and Wang,J. Computational studies of a mechanism for binding and drug resistance in the wild type and four mutations of HIV-1 protease with a GRL-0519 inhibitor Int J Mol Sci (2016) 17 PubMed Europe PubMed DOI I
Huang,J., Zhu,Y., Sun,B., Yao,Y. and Liu,J. Determination of the protonation state of the Asp dyad: conventional molecular dynamics versus thermodynamic integration J Mol Model (2016) 22, 58-58. PubMed Europe PubMed DOI
Krzeminska,A., Moliner,V. and Swiderek,K. Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease J Am Chem Soc (2016) 138, 16283-16298. PubMed Europe PubMed DOI PMC EPMC
Liu,Z., Huang,X., Hu,L., Pham,L., Poole,K.M., Tang,Y., Mahon,B.P., Tang,W., Li,K., Goldfarb,N.E., Dunn,B.M., McKenna,R. and Fanucci,G.E. Effects of hinge-region natural polymorphisms on human immunodeficiency virus-type 1 protease structure, dynamics and drug-pressure evolution J Biol Chem (2016) 291, 22741-22756. PubMed Europe PubMed DOI I
Lockhat,H.A., Silva,J.R., Alves,C.N., Govender,T., Lameira,J., Maguire,G.E., Sayed,Y. and Kruger,H.G. Binding free energy calculations of nine FDA-approved protease inhibitors against HIV-1 subtype C I36T containing 100 amino acids per monomer Chem Biol Drug Des (2016) 87, 487-498. PubMed Europe PubMed DOI I
Manning,T. and Walsh,P. The importance of physicochemical characteristics and nonlinear classifiers in determining HIV-1 protease specificity Bioengineered (2016) 7, 65-78. PubMed Europe PubMed DOI P
Maseko,S.B., Natarajan,S., Sharma,V., Bhattacharyya,N., Govender,T., Sayed,Y., Maguire,G.E., Lin,J. and Kruger,H.G. Purification and characterization of naturally occurring HIV-1 (South African subtype C) protease mutants from inclusion bodies Protein Expr Purif (2016) 122, 90-96. PubMed Europe PubMed DOI E
Mattei,S., Schur,F.K. and Briggs,J.A. Retrovirus maturation-an extraordinary structural transformation Curr Opin Virol (2016) 18, 27-35. PubMed Europe PubMed DOI
Nakashima,M., Ode,H., Suzuki,K., Fujino,M., Maejima,M., Kimura,Y., Masaoka,T., Hattori,J., Matsuda,M., Hachiya,A., Yokomaku,Y., Suzuki,A., Watanabe,N., Sugiura,W. and Iwatani,Y. Unique flap conformation in an HIV-1 protease with high-level darunavir resistance Front Microbiol (2016) 7, 61-61. PubMed Europe PubMed DOI PMC EPMC I
Qu,S., Huang,S., Pan,X., Yang,L. and Mei,H. Constructing interconsistent, reasonable, and predictive models for both the kinetic and thermodynamic properties of HIV-1 protease inhibitors J Chem Inf Model (2016) 56, 2061-2068. PubMed Europe PubMed DOI I
Ravichandran,V., Venkateskumar,K., Shalini,S. and Harish,R. Exploring the structure-activity relationship of oxazolidinones as HIV-1 protease inhibitors-QSAR and pharmacophore modelling studies Chemometr Intelligent Lab Syst (2016) 154, 52-61. DOI I
Singh,O. and Su,E.C. Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features BMC Bioinform (2016) 17, 478-478. PubMed Europe PubMed DOI
Soares,R.O., Torres,P.H., Da Silva,M.L. and Pascutti,P.G. Unraveling HIV protease flaps dynamics by constant pH molecular dynamics simulations J Struct Biol (2016) 195, 216-226. PubMed Europe PubMed DOI
Soares,R.O., Torres,P.H., Da Silva,M.L. and Pascutti,P.G. Dataset showing the impact of the protonation states on molecular dynamics of HIV protease Data Brief (2016) 8, 1144-1150. PubMed Europe PubMed DOI PMC EPMC
Su,C.T., Ling,W.L., Lua,W.H., Haw,Y.X. and Gan,S.K. Structural analyses of 2015-updated drug-resistant mutations in HIV-1 protease: an implication of protease inhibitor cross-resistance BMC Bioinform (2016) 17, 500-500. PubMed Europe PubMed DOI I
Tong,J., Zhan,P., Bai,M. and Yao,T. Molecular modeling studies of human immunodeficiency virus type 1 protease inhibitors using three-dimensional quantitative structure-activity relationship, virtual screening, and docking simulations J Chemometr (2016) 30, 523-536. DOI I
Xanthopoulos,D., Kritsi,E., Supuran,C.T., Papadopoulos,M.G., Leonis,G. and Zoumpoulakis,P. Discovery of HIV type 1 aspartic protease hit compounds through combined computational approaches ChemMedChem (2016) 11, 1646-1652. PubMed Europe PubMed DOI I

2015

J Comput Chem (2015) 36, i-iI. I
Agniswamy,J., Louis,J.M., Shen,C.H., Yashchuk,S., Ghosh,A.K. and Weber,I.T. Substituted bis-THF protease inhibitors with improved potency against highly resistant mature HIV-1 protease PR20 J Med Chem (2015) 58, 5088-5095. PubMed Europe PubMed DOI I
Amano,M., Tojo,Y., Salcedo-Gomez,P.M., Parham,G.L., Nyalapatla,P.R., Das,D., Ghosh,A.K. and Mitsuya,H. A novel tricyclic ligand-containing nonpeptidic HIV-1 protease inhibitor, GRL-0739, effectively inhibits the replication of multidrug-resistant HIV-1 variants and has a desirable central nervous system penetration property in vitro Antimicrob Agents Chemother (2015) 59, 2625-2635. PubMed Europe PubMed DOI I
Casey,T.M. and Fanucci,G.E. Spin labeling and double electron-electron resonance (DEER) to deconstruct conformational ensembles of HIV protease Methods Enzymol (2015) 564, 153-187. PubMed Europe PubMed DOI
Chauhan,J., Chen,S.E., Fenstermacher,K.J., Naser-Tavakolian,A., Reingewertz,T., Salmo,R., Lee,C., Williams,E., Raje,M., Sundberg,E., DeStefano,J.J., Freire,E. and Fletcher,S. Synthetic, structural mimetics of the beta-hairpin flap of HIV-1 protease inhibit enzyme function Bioorg Med Chem (2015) 23, 7095-7109. PubMed Europe PubMed DOI I
Chen,J., Wang,X., Zhu,T., Zhang,Q. and Zhang,J.Z. A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods J Chem Inf Model (2015) 55, 1903-1913. PubMed Europe PubMed DOI I
Counts,C.J., Ho,P.S., Donlin,M.J., Tavis,J.E. and Chen,C. A functional interplay between human immunodeficiency virus type 1 protease residues 77 and 93 involved in differential regulation of precursor autoprocessing and mature protease activity PLoS ONE (2015) 10, e0123561- PubMed Europe PubMed DOI
De Conto,V., Braz,A.S., Perahia,D. and Scott,L.P. Recovery of the wild type atomic flexibility in the HIV-1 protease double mutants J Mol Graph Model (2015) 59, 107-116. PubMed Europe PubMed DOI
Deng,N., Forli,S., He,P., Perryman,A., Wickstrom,L., Vijayan,R.S., Tiefenbrunn,T., Stout,D., Gallicchio,E., Olson,A.J. and Levy,R.M. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease J Phys Chem B (2015) 119, 976-988. PubMed Europe PubMed DOI I
Duan,R., Lazim,R. and Zhang,D. Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field J Comput Chem (2015) 36, 1885-1892. PubMed Europe PubMed DOI
Duclair,S., Gautam,A., Ellington,A. and Prasad,V.R. High-affinity RNA aptamers against the HIV-1 protease inhibit both in vitro protease activity and late events of viral replication Mol Ther Nucleic Acids (2015) 4, e228-e228. PubMed Europe PubMed DOI I
Fatemi,M.H., Heidari,A. and Gharaghani,S. QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors J Theor Biol (2015) 369C, 13-22. PubMed Europe PubMed DOI I
Ghosh,A.K., Yashchuk,S., Mizuno,A., Chakraborty,N., Agniswamy,J., Wang,Y.F., Aoki,M., Gomez,P.M., Amano,M., Weber,I.T. and Mitsuya,H. Design of gem-difluoro-bis-tetrahydrofuran as P2 ligand for HIV-1 protease inhibitors to improve brain penetration: synthesis, X-ray studies, and biological evaluation ChemMedChem (2015) 10, 107-115. PubMed Europe PubMed DOI I
Ghosh,A.K., Yu,X., Osswald,H.L., Agniswamy,J., Wang,Y.F., Amano,M., Weber,I.T. and Mitsuya,H. Structure-based design of potent HIV-1 protease inhibitors with modified P1-biphenyl ligands: synthesis, biological evaluation, and enzyme-inhibitor X-ray structural studies J Med Chem (2015) 58, 5334-5343. PubMed Europe PubMed DOI I
Ghosh,A.K., Takayama,J., Kassekert,L.A., Ella-Menye,J.R., Yashchuk,S., Agniswamy,J., Wang,Y.F., Aoki,M., Amano,M., Weber,I.T. and Mitsuya,H. Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands Bioorg Med Chem Lett (2015) 25, 4903-4909. PubMed Europe PubMed DOI I
Ghosh,A.K., Martyr,C.D., Kassekert,L.A., Nyalapatla,P.R., Steffey,M., Agniswamy,J., Wang,Y.F., Weber,I.T., Amano,M. and Mitsuya,H. Design, synthesis, biological evaluation and X-ray structural studies of HIV-1 protease inhibitors containing substituted fused-tetrahydropyranyl tetrahydrofuran as P2-ligands Org Biomol Chem (2015) 13, 11607-11621. PubMed Europe PubMed DOI I
Ghosh,A.K., Martyr,C.D., Osswald,H.L., Sheri,V.R., Kassekert,L.A., Chen,S., Agniswamy,J., Wang,Y.F., Hayashi,H., Aoki,M., Weber,I.T. and Mitsuya,H. Design of HIV-1 protease inhibitors with amino-bis-tetrahydrofuran derivatives as P2-ligands to enhance backbone-binding interactions: synthesis, biological evaluation, and protein-ligand X-ray studies J Med Chem (2015) 58, 6994-7006. PubMed Europe PubMed DOI S I
Goldfarb,N.E., Ohanessian,M., Biswas,S., McGee,T.D., Jr., Mahon,B.P., Ostrov,D.A., Garcia,J., Tang,Y., McKenna,R., Roitberg,A. and Dunn,B.M. Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency Biochemistry (2015) 54, 422-433. PubMed Europe PubMed DOI I
Gupta,A., Jamal,S., Goyal,S., Jain,R., Wahi,D. and Grover,A. Structural studies on molecular mechanisms of nelfinavir resistance caused by non-active site mutation V77I in HIV-1 protease BMC Bioinformatics (2015) 16 Suppl 19, S10-S10. PubMed Europe PubMed DOI PMC EPMC I
Hohlfeld,K., Wegner,J.K., Kesteleyn,B., Linclau,B. and Unge,J. Disubstituted bis-THF moieties as new P2 ligands in nonpeptidal HIV-1 protease inhibitors (II) J Med Chem (2015) 58, 4029-4038. PubMed Europe PubMed DOI I
Honarparvar,B., Pawar,S.A., Alves,C.N., Lameira,J., Maguire,G.E., Silva,J.R., Govender,T. and Kruger,H.G. Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study J Biomed Sci (2015) 22, 15- PubMed Europe PubMed DOI PMC EPMC I
Ingr,M., Lange,R., Halabalova,V., Yehya,A., Hrncirik,J., Chevalier-Lucia,D., Palmade,L., Blayo,C., Konvalinka,J. and Dumay,E. Inhibitor and substrate binding induced stability of HIV-1 protease against sequential dissociation and unfolding revealed by high pressure spectroscopy and kinetics PLoS ONE (2015) 10, e0119099-e0119099. PubMed Europe PubMed DOI PMC EPMC
Islam,M.A. and Pillay,T.S. Exploration of the structural requirements of HIV-protease inhibitors using pharmacophore, virtual screening and molecular docking approaches for lead identification J Mol Graph Model (2015) 56C, 20-30. PubMed Europe PubMed DOI I
Jaskolski,M., Miller,M., Mohana Rao,J.K., Gustchina,A. and Wlodawer,A. Elucidation of the structure of retroviral proteases: a reminiscence FEBS J (2015) 282, 4059-4066. PubMed Europe PubMed DOI S
Katebi,A.R., Sankar,K., Jia,K. and Jernigan,R.L. The use of experimental structures to model protein dynamics Methods Mol Biol (2015) 1215, 213-236. PubMed Europe PubMed DOI PMC EPMC S
Konvalinka,J., Krausslich,H.-G. and Muller,B. Retroviral proteases and their roles in virion maturation Virology (2015) 479-480, 403-417. PubMed Europe PubMed DOI V
Kuiper,B.D., Keusch,B.J., Dewdney,T.G., Chordia,P., Ross,K., Brunzelle,J.S., Kovari,I.A., MacArthur,R., Salimnia,H. and Kovari,L.C. The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops Biochem Biophys Rep (2015) 2, 160-165. PubMed Europe PubMed DOI
Laco,G.S. HIV-1 protease substrate-groove: role in substrate recognition and inhibitor resistance Biochimie (2015) 118, 90-103. PubMed Europe PubMed DOI
Li,N., Ainsworth,R.I., Ding,B., Hou,T. and Wang,W. Using hierarchical virtual screening to combat drug resistance of the HIV-1 protease J Chem Inf Model (2015) 55, 1400-1412. PubMed Europe PubMed DOI I
Liu,H., Shi,X., Guo,D., Zhao,Z. and Yimin Feature selection combined with neural network structure optimization for HIV-1 protease cleavage site prediction Biomed Res Int (2015) 2015, 263586- PubMed Europe PubMed DOI PMC EPMC
Louis,J.M., Deshmukh,L., Sayer,J.M., Aniana,A. and Clore,G.M. Mutations proximal to sites of autoproteolysis and the alpha-helix that co-evolve under drug pressure modulate the autoprocessing and vitality of HIV-1 protease Biochemistry (2015) 54, 5414-5424. PubMed Europe PubMed DOI
Meher,B.R. and Wang,Y. Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism J Mol Graph Model (2015) 56C, 60-73. PubMed Europe PubMed DOI I
Meng,J., Lai,M.T., Munshi,V., Grobler,J., McCauley,J., Zuck,P., Johnson,E.N., Uebele,V.N., Hermes,J.D. and Adam,G.C. Screening of HIV-1 protease using a combination of an ultra-high-throughput fluorescent-based assay and RapidFire mass spectrometry J Biomol Screen (2015) 20, 606-615. PubMed Europe PubMed DOI A
Ngo,S.T., Mai,B.K., Hiep,D.M. and Li,M.S. Estimation of the binding free energy of AC1NX476 to HIV-1 protease wild type and mutations using free energy perturbation method Chem Biol Drug Des (2015) 86, 546-558. PubMed Europe PubMed DOI I
Nguyen,H.L., Nguyen,T.T., Vu,Q.T., Le,H.T., Pham,Y., Trinh,P.L., Bui,T.P. and Phan,T.N. An efficient procedure for the expression and purification of HIV-1 protease from inclusion bodies Protein Expr Purif (2015) 116, 59-65. PubMed Europe PubMed DOI E
Ozahata,M., Sabino,E., Diaz,R., Cesar-Jr,R.M. and Ferreira,J. Data-intensive analysis of HIV mutations BMC Bioinformatics (2015) 16, 35-35. PubMed Europe PubMed DOI
Ozer,N., Ozen,A., Schiffer,C.A. and Haliloglu,T. Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution Evol Appl (2015) 8, 185-198. PubMed Europe PubMed DOI PMC EPMC
Pietrucci,F., Vargiu,A.V. and Kranjc,A. HIV-1 protease dimerization dynamics reveals a transient druggable binding pocket at the interface Sci Rep (2015) 5, 18555-18555. PubMed Europe PubMed DOI PMC EPMC
Potempa,M., Nalivaika,E., Ragland,D., Lee,S.K., Schiffer,C.A. and Swanstrom,R. A direct interaction with RNA dramatically enhances the catalytic activity of the HIV-1 protease in vitro J Mol Biol (2015) 427, 2360-2378. PubMed Europe PubMed DOI
Prashar,V., Bihani,S.C., Ferrer,J.L. and Hosur,M.V. Structural basis of why nelfinavir-resistant D30N mutant of HIV-1 protease remains susceptible to saquinavir Chem Biol Drug Des (2015) 86, 302-308. PubMed Europe PubMed DOI S I
Qi,Y.K., Chang,H.N., Pan,K.M., Tian,C.L. and Zheng,J.S. Total chemical synthesis of the site-selective azide-labeled [I66A]HIV-1 protease Chem Commun (Camb) (2015) 51, 14632-14635. PubMed Europe PubMed DOI
Razzaghi-Asl,N., Sepehri,S., Ebadi,A., Miri,R. and Shahabipour,S. Effect of biomolecular conformation on docking simulation: a case study on a potent HIV-1 protease inhibitor Iran J Pharm Res (2015) 14, 785-802. PubMed Europe PubMed PMC EPMC I
Roche,J., Louis,J.M. and Bax,A. Conformation of inhibitor-free HIV-1 protease derived from NMR spectroscopy in a weakly oriented solution Chembiochem (2015) 16, 214-218. PubMed Europe PubMed DOI S
Rognvaldsson,T., You,L. and Garwicz,D. State of the art prediction of HIV-1 protease cleavage sites Bioinformatics (2015) 31, 1204-1210. PubMed Europe PubMed DOI P
Schimer,J., Pavova,M., Anders,M., Pachl,P., Sacha,P., Cigler,P., Weber,J., Majer,P., Rezacova,P., Krausslich,H.G., Muller,B. and Konvalinka,J. Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor Nat Commun (2015) 6, 6461-6461. PubMed Europe PubMed DOI I
Shen,C.H., Chang,Y.C., Agniswamy,J., Harrison,R.W. and Weber,I.T. Conformational variation of an extreme drug resistant mutant of HIV protease J Mol Graph Model (2015) 62, 87-96. PubMed Europe PubMed DOI
Shen,Y., Radhakrishnan,M.L. and Tidor,B. Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition Proteins (2015) 83, 351-372. PubMed Europe PubMed DOI I
Singh,A. and Pal,T.K. Docking analysis of gallic acid derivatives as HIV-1 protease inhibitors Int J Bioinform Res Appl (2015) 11, 540-546. PubMed Europe PubMed I
Sroczynski,D., Malinowski,Z., Szczesniak,A.K. and Pakulska,W. New 1(2H)-phthalazinone derivatives as potent nonpeptidic HIV-1 protease inhibitors: molecular docking studies, molecular dynamics simulation, oral bioavailability and ADME prediction Mol Simul (2015) 42, 628-641. DOI I
Strom,T.A., Durdagi,S., Ersoz,S.S., Salmas,R.E., Supuran,C.T. and Barron,A.R. Fullerene-based inhibitors of HIV-1 protease J Pept Sci (2015) 21, 862-870. PubMed Europe PubMed DOI I
Wagner,R.N., Reed,J.C. and Chanda,S.K. HIV-1 protease cleaves the serine-threonine kinases RIPK1 and RIPK2 Retrovirology (2015) 12, 74-74. PubMed Europe PubMed DOI PMC EPMC
Weber,I.T., Kneller,D.W. and Wong-Sam,A. Highly resistant HIV-1 proteases and strategies for their inhibition Future Med Chem (2015) 7, 1023-1038. PubMed Europe PubMed DOI I
Wei,Y., Li,J., Chen,Z., Wang,F., Huang,W., Hong,Z. and Lin,J. Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods Eur J Med Chem (2015) 101, 409-418. PubMed Europe PubMed DOI I
Windsor,I.W. and Raines,R.T. Fluorogenic assay for inhibitors of HIV-1 protease with sub-picomolar affinity Sci Rep (2015) 5, 11286-11286. PubMed Europe PubMed DOI PMC EPMC A I
Yang,Z.H., Bai,X.G., Zhou,L., Wang,J.X., Liu,H.T. and Wang,Y.C. Synthesis and biological evaluation of novel HIV-1 protease inhibitors using tertiary amine as P2-ligands Bioorg Med Chem Lett (2015) 25, 1880-1883. PubMed Europe PubMed DOI I
Yu,Y., Wang,J., Shao,Q., Shi,J. and Zhu,W. Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by amprenavir and darunavir Sci Rep (2015) 5, 10517-10517. PubMed Europe PubMed DOI PMC EPMC I
Zhou,H., Li,S., Badger,J., Nalivaika,E., Cai,Y., Foulkes-Murzycki,J., Schiffer,C. and Makowski,L. Modulation of HIV protease flexibility by the T80N mutation Proteins (2015) 83, 1929-1939. PubMed Europe PubMed DOI

2014

New FRET probes for protease inhibitor discovery Biotechnol Bioeng (2014) 111, vi-vi. DOI A
Ahmed,S.M., Maguire,G.E., Kruger,H.G. and Govender,T. The impact of active site mutations of South African HIV PR on drug resistance: insight from molecular dynamics simulations, binding free energy and per-residue footprints Chem Biol Drug Des (2014) 83, 472-481. PubMed Europe PubMed DOI I
Antunes,D.A., Rigo,M.M., Sinigaglia,M., de Medeiros,R.M., Junqueira,D.M., Almeida,S.E. and Vieira,G.F. New insights into the in silico prediction of HIV protease resistance to nelfinavir PLoS ONE (2014) 9, e87520-e87520. PubMed Europe PubMed DOI PMC EPMC I
Benedetti,F., Berti,F., Campaner,P., Fanfoni,L., Demitri,N., Olajuyigbe,F.M., De March,M. and Geremia,S. Impact of stereochemistry on ligand binding: X-ray crystallographic analysis of an epoxide-based HIV protease inhibitor ACS Med Chem Lett (2014) 5, 968-972. PubMed Europe PubMed DOI PMC EPMC I
Berti,F., Frecer,V. and Miertus,S. Inhibitors of HIV-Protease from computational design. A history of theory and synthesis still to be fully appreciated Curr Pharm Des (2014) 20, 3398-3411. PubMed Europe PubMed DOI I
Bonini,C., Chiummiento,L., Di Blasio,N., Funicello,M., Lupattelli,P., Tramutola,F., Berti,F., Ostric,A., Miertus,S., Frecer,V. and Kong,D.X. Synthesis and biological evaluation of new simple indolic non peptidic HIV protease inhibitors: the effect of different substitution patterns Bioorg Med Chem (2014) 22, 4792-4802. PubMed Europe PubMed DOI I
Cai,Y., Myint,W., Paulsen,J.L., Schiffer,C.A., Ishima,R. and Kurt Yilmaz,N. Drug resistance mutations alter dynamics of inhibitor-bound HIV-1 protease J Chem Theory Comput (2014) 10, 3438-3448. PubMed Europe PubMed DOI PMC EPMC I
Caldarini,M., Sonar,P., Valpapuram,I., Tavella,D., Volonte,C., Pandini,V., Vanoni,M.A., Aliverti,A., Broglia,R.A., Tiana,G. and Cecconi,C. The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations Biophys Chem (2014) 195, 32-42. PubMed Europe PubMed DOI
Calugi,C., Guarna,A. and Trabocchi,A. Identification of constrained peptidomimetic chemotypes as HIV protease inhibitors Eur J Med Chem (2014) 84, 444-453. PubMed Europe PubMed DOI I
Capel,E., Parera,M. and Martinez,M.A. Epistasis as a determinant of the HIV-1 protease's robustness to mutation PLoS ONE (2014) 9, e116301-e116301. PubMed Europe PubMed DOI
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Costa,M.G., Benetti-Barbosa,T.G., Desdouits,N., Blondel,A., Bisch,P.M., Pascutti,P.G. and Batista,P.R. Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics BMC Genomics (2014) 15 Suppl 7, S5-S5. PubMed Europe PubMed DOI PMC EPMC
De Rosa,M., Unge,J., Motwani,H.V., Rosenquist,A., Vrang,L., Wallberg,H. and Larhed,M. Synthesis of P1'-functionalized macrocyclic transition-state mimicking HIV-1 protease inhibitors encompassing a tertiary alcohol J Med Chem (2014) 57, 6444-6457. PubMed Europe PubMed DOI I
Fanelli,R., Ressurreicao,A.S., Dufau,L., Soulier,J.-L., Vidu,A., Tonali,N., Bernadat,G., Reboud-Ravaux,M. and Ongeri,S. Introduction of polar groups on the naphthalene scaffold of molecular tongs inhibiting wild-type and mutated HIV-1 protease dimerization MedChemComm (2014) 5, 719-727. DOI I
Fuwa,H., Muto,T., Sekine,K. and Sasaki,M. Total synthesis and structure revision of didemnaketal B Chemistry (2014) 20, 1848-1860. PubMed Europe PubMed DOI I
Grantz Saskova,K., Kozisek,M., Stray,K., de Jong,D., Rezacova,P., Brynda,J., van Maarseveen,N.M., Nijhuis,M., Cihlar,T. and Konvalinka,J. GS-8374, a prototype phosphonate-containing inhibitor of HIV-1 protease, effectively inhibits protease mutants with amino acid insertions J Virol (2014) 88, 3586-3590. PubMed Europe PubMed DOI I
Hayashi,H., Takamune,N., Nirasawa,T., Aoki,M., Morishita,Y., Das,D., Koh,Y., Ghosh,A.K., Misumi,S. and Mitsuya,H. Dimerization of HIV-1 protease occurs through two steps relating to the mechanism of protease dimerization inhibition by darunavir Proc Natl Acad Sci U S A (2014) 111, 12234-12239. PubMed Europe PubMed DOI I
Jensen,J.H., Willemoes,M., Winther,J.R. and De Vico,L. In silico prediction of mutant HIV-1 proteases cleaving a target sequence PLoS ONE (2014) 9, e95833-e95833. PubMed Europe PubMed DOI PMC EPMC
Khadra,K.A., Mizyed,S., Marji,D., Haddad,S.F., Ashram,M. and Foudeh,A. Synthesis of novel p-tert-butylcalix[4]arene Schiff bases and their complexes with C60, potential HIV-protease inhibitors Spectrochim Acta A Mol Biomol Spectrosc (2014) 136, 1869-1874. PubMed Europe PubMed DOI I
Kimura,S., Caldarini,M., Broglia,R.A., Dokholyan,N.V. and Tiana,G. The maturation of HIV-1 protease precursor studied by discrete molecular dynamics Proteins (2014) 82, 633-639. PubMed Europe PubMed DOI
Kolli,M., Ozen,A., Kurt-Yilmaz,N. and Schiffer,C.A. HIV-1 protease-substrate coevolution in nelfinavir resistance J Virol (2014) 88, 7145-7154. PubMed Europe PubMed DOI I
Kozisek,M., Lepsik,M., Grantz Saskova,K., Brynda,J., Konvalinka,J. and Rezacova,P. Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases FEBS J (2014) 281, 1834-1847. PubMed Europe PubMed DOI I
Kunze,J., Todoroff,N., Schneider,P., Rodrigues,T., Geppert,T., Reisen,F., Schreuder,H., Saas,J., Hessler,G., Baringhaus,K.H. and Schneider,G. Targeting dynamic pockets of HIV-1 protease by structure-based computational screening for allosteric inhibitors J Chem Inf Model (2014) 54, 987-991. PubMed Europe PubMed DOI I
Kutalkova,E., Hrncirik,J. and Ingr,M. Pressure induced structural changes and dimer destabilization of HIV-1 protease studied by molecular dynamics simulations Phys Chem Chem Phys (2014) 16, 25906-25915. PubMed Europe PubMed DOI
Levita,J., Chao,K.H. and Mutakin Interactions of ganoderiol-F with aspartic proteases of HIV and plasmepsin for anti-HIV and anti-malaria discovery Int J Pharmcy Pharm Sci (2014) 6, 561-566. I
Li,D., Zhang,Y., Zhao,R.N., Fan,S. and Han,J.G. Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation J Mol Model (2014) 20, 2122-2122. PubMed Europe PubMed DOI I
Mata-Munguia,C., Escoto-Delgadillo,M., Torres-Mendoza,B., Flores-Soto,M., Vazquez-Torres,M., Galvez-Gastelum,F., Viniegra-Osorio,A., Castillero-Manzano,M. and Vazquez-Valls,E. Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis BMC Bioinformatics (2014) 15, 72-72. PubMed Europe PubMed DOI
Mattei,S., Anders,M., Konvalinka,J., Krausslich,H.G., Briggs,J.A. and Muller,B. Induced maturation of human immunodeficiency virus J Virol (2014) 88, 13722-13731. PubMed Europe PubMed DOI
McGee,T.D., Jr., Edwards,J. and Roitberg,A.E. pH-REMD simulations indicate that the catalytic aspartates of HIV-1 protease exist primarily in a monoprotonated state J Phys Chem B (2014) 118, 12577-12585. PubMed Europe PubMed DOI
Meher,B.R., Kumar,M.V. and Bandyopadhyay,P. Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from molecular dynamics J Biomol Struct Dyn (2014) 32, 899-915. PubMed Europe PubMed DOI
Mendonca,L.M., Poeys,S.C., Abreu,C.M., Tanuri,A. and Costa,L.J. HIV-1 Nef inhibits protease activity and its absence alters protein content of mature viral particles PLoS ONE (2014) 9, e95352-e95352. PubMed Europe PubMed DOI PMC EPMC
Naicker,P., Stoychev,S., Dirr,H.W. and Sayed,Y. Amide hydrogen exchange in HIV-1 subtype B and C proteases - insights into reduced drug susceptibility and dimer stability FEBS J (2014) 281, 5395-5410. PubMed Europe PubMed DOI
Ozen,A., Lin,K.H., Kurt Yilmaz,N. and Schiffer,C.A. Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease Proc Natl Acad Sci U S A (2014) 111, 15993-15998. PubMed Europe PubMed DOI S
Pang,X., Liu,Z. and Zhai,G. Advances in non-peptidomimetic HIV protease inhibitors Curr Med Chem (2014) 21, 1997-2011. PubMed Europe PubMed DOI V I
Patel,R.V. and Park,S.W. Journey describing the discoveries of anti-HIV triterpene acid families targeting HIV-entry/fusion, protease functioning and maturation stages Curr Top Med Chem (2014) 14, 1940-1966. PubMed Europe PubMed I
Poveda,E. Multi-step inhibition against HIV lifecycle-underlying the "magic" of protease inhibitors AIDS Rev (2014) 16, 52-52. PubMed Europe PubMed I
Qi,F., Fudo,S., Neya,S. and Hoshino,T. A cluster analysis on the structural diversity of protein crystals, exemplified by human immunodeficiency virus type 1 protease Chem Pharm Bull (Tokyo) (2014) 62, 568-577. PubMed Europe PubMed DOI S
Qiu,X., Zhao,G.D., Tang,L.Q. and Liu,Z.P. Design and synthesis of highly potent HIV-1 protease inhibitors with novel isosorbide-derived P2 ligands Bioorg Med Chem Lett (2014) 24, 2465-2468. PubMed Europe PubMed DOI I
Ragland,D.A., Nalivaika,E.A., Nalam,M.N., Prachanronarong,K.L., Cao,H., Bandaranayake,R.M., Cai,Y., Kurt-Yilmaz,N. and Schiffer,C.A. Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease J Am Chem Soc (2014) 136, 11956-11963. PubMed Europe PubMed DOI I
Saleh,N.A. The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors Spectrochim Acta A Mol Biomol Spectrosc (2014) 136, 1523-1529. PubMed Europe PubMed DOI I
Schimer,J. and Konvalinka,J. Unorthodox inhibitors of HIV protease: looking beyond active-site-directed peptidomimetics Curr Pharm Des (2014) 20, 3389-3397. PubMed Europe PubMed DOI I
Shing,C.-Y., Whiteley,C.G. and Lee,D.-J. HIV protease: multiple fold inhibition by silver nanoparticles - spectrofluorimetric, thermodynamic and kinetic analysis J Taiwan Inst Chem Eng (2014) 45, 1140-1148. DOI I
Tiefenbrunn,T., Forli,S., Happer,M., Gonzalez,A., Tsai,Y., Soltis,M., Elder,J.H., Olson,A.J. and Stout,C.D. Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease Chem Biol Drug Des (2014) 83, 141-148. PubMed Europe PubMed DOI I
Tingjun,H., Wei,Z., Jian,W. and Wei,W. Predicting drug resistance of the HIV-1 protease using molecular interaction energy components Proteins Struct Funct Bioinformatics (2014) 82, 1099-1099. DOI I
Ung,P.M., Dunbar,J.B., Jr., Gestwicki,J.E. and Carlson,H.A. An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases J Med Chem (2014) 57, 6468-6478. PubMed Europe PubMed DOI I
Wright,D.W., Hall,B.A., Kenway,O.A., Jha,S. and Coveney,P.V. Computing clinically relevant binding free energies of HIV-1 protease inhibitors J Chem Theory Comput (2014) 10, 1228-1241. PubMed Europe PubMed DOI PMC EPMC I
Yang,M., Jiang,X. and Jiang,N. Protonation state and free energy calculation of HIV-1 protease-inhibitor complex based on electrostatic polarisation effect Mol Phys (2014) 112, 1659-1669. DOI I
Yang,Z.-H., Bai,X.-G., Wang,J.-X. and Wang,Y.-C. Recent advance in research and development of HIV-1 protease inhibitors Chin J New Drugs (2014) 23, 2246-2254. I
Yedidi,R.S., Proteasa,G., Martin,P.D., Liu,Z., Vickrey,J.F., Kovari,I.A. and Kovari,L.C. A multi-drug resistant HIV-1 protease is resistant to the dimerization inhibitory activity of TLF-PafF J Mol Graph Model (2014) 53, 105-111. PubMed Europe PubMed DOI I
Yedidi,R.S., Liu,Z., Kovari,I.A., Woster,P.M. and Kovari,L.C. P1 and P1' para-fluoro phenyl groups show enhanced binding and favorable predicted pharmacological properties: structure-based virtual screening of extended lopinavir analogs against multi-drug resistant HIV-1 protease J Mol Graph Model (2014) 47, 18-24. PubMed Europe PubMed DOI I
Yedidi,R.S., Garimella,H., Aoki,M., Aoki-Ogata,H., Desai,D.V., Chang,S.B., Davis,D.A., Fyvie,W.S., Kaufman,J.D., Smith,D.W., Das,D., Wingfield,P.T., Maeda,K., Ghosh,A.K. and Mitsuya,H. A conserved hydrogen-bonding network of P2 bis-tetrahydrofuran-containing HIV-1 protease inhibitors (PIs) with a protease active-site amino acid backbone aids in their activity against PI-resistant HIV Antimicrob Agents Chemother (2014) 58, 3679-3688. PubMed Europe PubMed DOI I
Yu,X., Weber,I.T. and Harrison,R.W. Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure BMC Genomics (2014) 15 Suppl 5, S1-S1. PubMed Europe PubMed DOI PMC EPMC I
Zhang,Y., Chang,Y.C., Louis,J.M., Wang,Y.F., Harrison,R.W. and Weber,I.T. Structures of Darunavir-Resistant HIV-1 Protease Mutant Reveal Atypical Binding of Darunavir to Wide Open Flaps ACS Chem Biol (2014) 9, 1351-1358. PubMed Europe PubMed DOI S I

2013

Agniswamy,J., Shen,C.H., Wang,Y.F., Ghosh,A.K., Rao,K.V., Xu,C.X., Sayer,J.M., Louis,J.M. and Weber,I.T. Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran J Med Chem (2013) 56, 4017-4027. PubMed Europe PubMed DOI S I
Amano,M., Tojo,Y., Salcedo-Gomez,P.M., Campbell,J.R., Das,D., Aoki,M., Xu,C.X., Rao,K.V., Ghosh,A.K. and Mitsuya,H. GRL-0519, a novel oxatricyclic ligand-containing nonpeptidic HIV-1 protease inhibitor (PI), potently suppresses replication of a wide spectrum of multi-PI-resistant HIV-1 variants in vitro Antimicrob Agents Chemother (2013) 57, 2036-2046. PubMed Europe PubMed DOI I
Asahchop,E.L., Oliveira,M., Quashie,P.K., Moisi,D., Martinez-Cajas,J.L., Brenner,B.G., Tremblay,C.L. and Wainberg,M.A. In vitro and structural evaluation of PL-100 as a potential second-generation HIV-1 protease inhibitor J Antimicrob Chemother (2013) 68, 105-112. PubMed Europe PubMed DOI I
Borchani,H., Bielza,C., Toro,C. and Larranaga,P. Predicting human immunodeficiency virus inhibitors using multi-dimensional Bayesian network classifiers Artif Intell Med (2013) 57, 219-229. PubMed Europe PubMed DOI I
Calugi,C., Guarna,A. and Trabocchi,A. Heterocyclic HIV-protease inhibitors Curr Med Chem (2013) 20, 3693-3710. PubMed Europe PubMed DOI I
Calugi,C., Guarna,A. and Trabocchi,A. Insight into the structural similarity between HIV protease and secreted aspartic protease-2 and binding mode analysis of HIV-Candida albicans inhibitors J Enzyme Inhib Med Chem (2013) 28, 936-943. PubMed Europe PubMed DOI
Charpentier,C., Lambert-Niclot,S., Alteri,C., Storto,A., Flandre,P., Svicher,V., Perno,C.F., Brun-Vezinet,F., Calvez,V., Marcelin,A.G., Ceccherini-Silberstein,F. and Descamps,D. Description of the L76V resistance protease mutation in HIV-1 B and "non-B" subtypes PLoS ONE (2013) 8, e54381-e54381. PubMed Europe PubMed DOI PMC EPMC
Dayer,M.R. and Dayer,M.S. Whiskers-less HIV-protease: a possible way for HIV-1 deactivation J Biomed Sci (2013) 20, 67-67. PubMed Europe PubMed DOI I
de Vera,I.M., Smith,A.N., Dancel,M.C., Huang,X., Dunn,B.M. and Fanucci,G.E. Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease Biochemistry (2013) 52, 3278-3288. PubMed Europe PubMed DOI
Esseghaier,C., Ng,A. and Zourob,M. A novel and rapid assay for HIV-1 protease detection using magnetic bead mediation Biosens Bioelectron (2013) 41, 335-341. PubMed Europe PubMed DOI A
Foulkes-Murzycki,J.E., Rosi,C., Kurt Yilmaz,N., Shafer,R.W. and Schiffer,C.A. Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease ACS Chem Biol (2013) 8, 513-518. PubMed Europe PubMed DOI
Ghosh,A.K. and Chapsal,B.D. Design of the anti-HIV protease inhibitor darunavir Introd to Bio and Small Molecule Drug Res and Develop (2013) 2013, 355-384. DOI I
Ghosh,A.K., Parham,G.L., Martyr,C.D., Nyalapatla,P.R., Osswald,H.L., Agniswamy,J., Wang,Y.F., Amano,M., Weber,I.T. and Mitsuya,H. Highly potent HIV-1 protease inhibitors with novel tricyclic P2 ligands: design, synthesis, and protein-ligand X-ray studies J Med Chem (2013) 56, 6792-6802. PubMed Europe PubMed DOI I
Huang,L. and Chen,C. Understanding HIV-1 protease autoprocessing for novel therapeutic development Future Med Chem (2013) 5, 1215-1229. PubMed Europe PubMed DOI
Huang,X., de Vera,I.M., Veloro,A.M., Rocca,J.R., Simmerling,C., Dunn,B.M. and Fanucci,G.E. Backbone 1H, 13C, and 15N chemical shift assignment for HIV-1 protease subtypes and multi-drug resistant variant MDR 769 Biomol NMR Assign (2013) 7, 199-202. PubMed Europe PubMed DOI S
Jones,S.A., Neilsen,P.M., Siew,L., Callen,D.F., Goldfarb,N.E., Dunn,B.M. and Abell,A.D. A template-based approach to inhibitors of calpain 2, 20S proteasome, and HIV-1 protease ChemMedChem (2013) 8, 1918-1921. PubMed Europe PubMed DOI I
Joshi,A., Veron,J.B., Unge,J., Rosenquist,A., Wallberg,H., Samuelsson,B., Hallberg,A. and Larhed,M. Design and synthesis of P1-P3 macrocyclic tertiary-alcohol-comprising HIV-1 protease inhibitors J Med Chem (2013) 56, 8999-9007. PubMed Europe PubMed DOI I
Kar,P., Lipowsky,R. and Knecht,V. Importance of Polar Solvation and Configurational Entropy for Design of Antiretroviral Drugs Targeting HIV-1 Protease J Phys Chem B (2013) 117, 5793-5805. PubMed Europe PubMed DOI I
Koh,Y. [Study of HIV protease dimerization (PD) and identification of novel PD inhibitors (PDIs)] Jpn J Antibiot (2013) 66, 45-53. PubMed Europe PubMed I
Lee,S.K., Cheng,N., Hull-Ryde,E., Potempa,M., Schiffer,C.A., Janzen,W. and Swanstrom,R. A sensitive assay using a native protein substrate for screening HIV-1 maturation inhibitors targeting the protease cleavage site between the matrix and capsid Biochemistry (2013) 52, 4929-4940. PubMed Europe PubMed DOI A I
Liu,Z., Wang,Y., Yedidi,R.S., Dewdney,T.G., Reiter,S.J., Brunzelle,J.S., Kovari,I.A. and Kovari,L.C. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes Biochem Biophys Res Commun (2013) 430, 1022-1027. PubMed Europe PubMed DOI S
Liu,Z., Yedidi,R.S., Wang,Y., Dewdney,T.G., Reiter,S.J., Brunzelle,J.S., Kovari,I.A. and Kovari,L.C. Insights into the mechanism of drug resistance: X-ray structure analysis of multi-drug resistant HIV-1 protease ritonavir complex Biochem Biophys Res Commun (2013) 431, 232-238. PubMed Europe PubMed DOI S I
Liu,Z., Yedidi,R.S., Wang,Y., Dewdney,T.G., Reiter,S.J., Brunzelle,J.S., Kovari,I.A. and Kovari,L.C. Crystallographic study of multi-drug resistant HIV-1 protease lopinavir complex: Mechanism of drug recognition and resistance Biochem Biophys Res Commun (2013) 437, 199-204. PubMed Europe PubMed DOI S I
Louis,J.M., Tozser,J., Roche,J., Matuz,K., Aniana,A. and Sayer,J.M. Enhanced stability of monomer fold correlates with extreme drug resistance of HIV-1 protease Biochemistry (2013) 52, 7678-7688. PubMed Europe PubMed DOI I
Mittal,S., Bandaranayake,R.M., King,N.M., Prabu-Jeyabalan,M., Nalam,M.N., Nalivaika,E.A., Kurt Yilmaz,N. and Schiffer,C.A. Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50 J Virol (2013) 87, 4176-4184. PubMed Europe PubMed DOI I
Naicker,P., Achilonu,I., Fanucchi,S., Fernandes,M., Ibrahim,M.A., Dirr,H.W., Soliman,M.E. and Sayed,Y. Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance J Biomol Struct Dyn (2013) 31, 1370-1380. PubMed Europe PubMed DOI S
Nalam,M.N., Ali,A., Reddy,G.S., Cao,H., Anjum,S.G., Altman,M.D., Yilmaz,N.K., Tidor,B., Rana,T.M. and Schiffer,C.A. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance Chem Biol (2013) 20, 1116-1124. PubMed Europe PubMed DOI I
Ni,Z., Chen,H., Qi,X. and Jin,R. Why is substrate peptide binding unsusceptible to multidrug-resistant mutations in HIV-1 protease? A structural and energetic analysis Int J Pept Res Ther (2013) 20, 43-51. DOI I
Niu,B., Yuan,X.C., Roeper,P., Su,Q., Peng,C.R., Yin,J.Y., Ding,J., Li,H. and Lu,W.C. HIV-1 protease cleavage site prediction based on two-stage feature selection method Protein Pept Lett (2013) 20, 290-298. PubMed Europe PubMed
Oehme,D.P., Brownlee,R.T. and Wilson,D.J. Can cyclic HIV protease inhibitors bind in a non-preferred form? An ab initio, DFT and MM-PB(GB)SA study J Mol Model (2013) 19, 1125-1142. PubMed Europe PubMed DOI I
Ozturk,O., Aksac,A., Elsheikh,A., Ozyer,T. and Alhajj,R. A consistency-based feature selection method allied with linear SVMs for HIV-1 protease cleavage site prediction PLoS ONE (2013) 8, e63145-e63145. PubMed Europe PubMed DOI PMC EPMC
Pokorna,J., Heyda,J. and Konvalinka,J. Ion specific effects of alkali cations on the catalytic activity of HIV-1 protease Faraday Discuss (2013) 160, 359-370. PubMed Europe PubMed DOI
Rabi,S.A., Laird,G.M., Durand,C.M., Laskey,S., Shan,L., Bailey,J.R., Chioma,S., Moore,R.D. and Siliciano,R.F. Multi-step inhibition explains HIV-1 protease inhibitor pharmacodynamics and resistance J Clin Invest (2013) 123, 3848-3860. PubMed Europe PubMed DOI I
Rout,M.K., Reddy,J.G., Phillips,M. and Hosur,R.V. Single point mutation induced alterations in the equilibrium structural transitions on the folding landscape of HIV-1 protease J Biomol Struct Dyn (2013) 31, 684-693. PubMed Europe PubMed DOI
Salcedo Gomez,P.M., Amano,M., Yashchuk,S., Mizuno,A., Das,D., Ghosh,A.K. and Mitsuya,H. GRL-04810 and GRL-05010, difluoride-containing nonpeptidic HIV-1 protease inhibitors (PIs) that inhibit the replication of multi-PI-resistant HIV-1 in vitro and possess favorable lipophilicity that may allow blood-brain barrier penetration Antimicrob Agents Chemother (2013) 57, 6110-6121. PubMed Europe PubMed DOI I
Tiefenbrunn,T., Forli,S., Baksh,M.M., Chang,M.W., Happer,M., Lin,Y.C., Perryman,A.L., Rhee,J.K., Torbett,B.E., Olson,A.J., Elder,J.H., Finn,M.G. and Stout,C.D. Small molecule regulation of protein conformation by binding in the flap of HIV protease ACS Chem Biol (2013) 8, 1223-1231. PubMed Europe PubMed DOI
Weber,I.T., Waltman,M.J., Mustyakimov,M., Blakeley,M.P., Keen,D.A., Ghosh,A.K., Langan,P. and Kovalevsky,A.Y. Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir: insights for drug design J Med Chem (2013) 56, 5631-5635. PubMed Europe PubMed DOI S I
Weikl,T.R. and Hemmateenejad,B. How conformational changes can affect catalysis, inhibition and drug resistance of enzymes with induced-fit binding mechanism such as the HIV-1 protease Biochim Biophys Acta (2013) 1834, 867-873. PubMed Europe PubMed DOI
Yedidi,R.S., Muhuhi,J.M., Liu,Z., Bencze,K.Z., Koupparis,K., O'Connor,C.E., Kovari,I.A., Spaller,M.R. and Kovari,L.C. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease Biochem Biophys Res Commun (2013) 438, 703-708. PubMed Europe PubMed DOI I
Yedidi,R.S., Maeda,K., Fyvie,W.S., Steffey,M., Davis,D.A., Palmer,I., Aoki,M., Kaufman,J.D., Stahl,S.J., Garimella,H., Das,D., Wingfield,P.T., Ghosh,A.K. and Mitsuya,H. P2' benzene carboxylic acid moiety is associated with decrease in cellular uptake: evaluation of novel nonpeptidic HIV-1 protease inhibitors containing P2 bis-tetrahydrofuran moiety Antimicrob Agents Chemother (2013) 57, 4920-4927. PubMed Europe PubMed DOI I
Zhang,H., Wang,Y.F., Shen,C.H., Agniswamy,J., Rao,K.V., Xu,C.X., Ghosh,A.K., Harrison,R.W. and Weber,I.T. Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease J Med Chem (2013) 56, 1074-1083. PubMed Europe PubMed DOI I

2012

Adamson,C.S. Protease-mediated maturation of HIV: inhibitors of protease and the maturation process Mol Biol Int (2012) 2012, 604261-604261. PubMed Europe PubMed DOI PMC EPMC I
Agniswamy,J., Sayer,J.M., Weber,I.T. and Louis,J.M. Terminal Interface Conformations Modulate Dimer Stability Prior to Amino Terminal Autoprocessing of HIV-1 Protease Biochemistry (2012) 51, 1041-1050. PubMed Europe PubMed DOI I
Agniswamy,J., Shen,C.H., Aniana,A., Sayer,J.M., Louis,J.M. and Weber,I.T. HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements Biochemistry (2012) 51, 2819-2828. PubMed Europe PubMed DOI I
Alvizo,O., Mittal,S., Mayo,S.L. and Schiffer,C.A. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease Protein Sci (2012) 21, 1029-1041. PubMed Europe PubMed DOI P
Benedetti,F., Berti,F., Budal,S., Campaner,P., Dinon,F., Tossi,A., Argirova,R., Genova,P., Atanassov,V. and Hinkov,A. Synthesis and biological activity of potent HIV-1 protease inhibitors based on Phe-Pro dihydroxyethylene isosteres J Med Chem (2012) 55, 3900-3910. PubMed Europe PubMed DOI I
Buzon,M.J., Erkizia,I., Pou,C., Minuesa,G., Puertas,M.C., Esteve,A., Castello,A., Santos,J.R., Prado,J.G., Izquierdo-Useros,N., Pattery,T., Van Houtte,M., Carrasco,L., Clotet,B., Ruiz,L. and Martinez-Picado,J. A non-infectious cell-based phenotypic assay for the assessment of HIV-1 susceptibility to protease inhibitors J Antimicrob Chemother (2012) 67, 32-38. PubMed Europe PubMed DOI I
Cai,Y. and Schiffer,C. Decomposing the energetic impact of drug-resistant mutations: the example of HIV-1 protease-DRV binding Methods Mol Biol (2012) 819, 551-560. PubMed Europe PubMed DOI I
Chang,Y.C., Yu,X., Zhang,Y., Tie,Y., Wang,Y.F., Yashchuk,S., Ghosh,A.K., Harrison,R.W. and Weber,I.T. Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring J Med Chem (2012) 55, 3387-3397. PubMed Europe PubMed DOI I
Chiummiento,L., Funicello,M., Lupattelli,P., Tramutola,F., Berti,F. and Marino-Merlo,F. Synthesis and biological evaluation of novel small non-peptidic HIV-1 PIs: the benzothiophene ring as an effective moiety Bioorg Med Chem Lett (2012) 22, 2948-2950. PubMed Europe PubMed DOI I
Davis,D.A., Soule,E.E., Davidoff,K.S., Daniels,S.I., Naiman,N.E. and Yarchoan,R. Activity of human immunodeficiency virus type 1 protease inhibitors against the initial autocleavage in Gag-Pol polyprotein processing Antimicrob Agents Chemother (2012) 56, 3620-3628. PubMed Europe PubMed DOI I
Dominguez,J.L., Gossas,T., Carmen Villaverde,M., Helena Danielson,U. and Sussman,F. Experimental and 'in silico' analysis of the effect of pH on HIV-1 protease inhibitor affinity: implications for the charge state of the protein ionogenic groups Bioorg Med Chem (2012) 20, 4838-4847. PubMed Europe PubMed DOI I
Dufau,L., Marques Ressurreicao,A.S., Fanelli,R., Kihal,N., Vidu,A., Milcent,T., Soulier,J.L., Rodrigo,J., Desvergne,A., Leblanc,K., Bernadat,G., Crousse,B., Reboud-Ravaux,M. and Ongeri,S. Carbonylhydrazide-based molecular tongs inhibit wild-type and mutated HIV-1 protease dimerization J Med Chem (2012) 55, 6762-6775. PubMed Europe PubMed DOI I
Eissenstat,M., Guerassina,T., Gulnik,S., Afonina,E., Silva,A.M., Ludtke,D., Yokoe,H., Yu,B. and Erickson,J. Enamino-oxindole HIV protease inhibitors Bioorg Med Chem Lett (2012) 22, 5078-5083. PubMed Europe PubMed DOI I
Ershov,P.V., Gnedenko,O.V., Molnar,A.A., Lisitsa,A.V., Ivanov,A.S. and Archakov,A.I. Thermodynamic analysis of dimerization inhibitors binding to HIV protease monomers Biomeditsinskaya Khim (2012) 58, 43-49. I
Esseghaier,C., Ng,A. and Zourob,M. A novel assay for rapid HIV-1 protease detection using optical sensors and magnetic carriers Proc SPIE Int Soc Opt Eng (2012) 8412, Article-Article. A
Flausino,O.A., Dufau,L., Regasini,L.O., Petronio,M.S., Silva,D.H., Rose,T., Bolzani,V.S. and Reboud-Ravaux,M. Alkyl hydroxybenzoic acid derivatives that inhibit HIV-1 protease dimerization Curr Med Chem (2012) 19, 4534-4540. PubMed Europe PubMed DOI I
Ghosh,A.K., Chapsal,B.D., Steffey,M., Agniswamy,J., Wang,Y.F., Amano,M., Weber,I.T. and Mitsuya,H. Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors Bioorg Med Chem Lett (2012) 22, 2308-2311. PubMed Europe PubMed DOI S I
Goldfarb,N.E. and Dunn,B.M. Human immunodeficiency virus 1 retropepsin [ISSN:978-0-12-407744-7] (2012) 3, 190-199. DOI
Haidara,A., Chamberland,A., Sylla,M., Aboubacrine,S.A., Cisse,M., Traore,H.A., Maiga,M.Y., Tounkara,A., Nguyen,V.K. and Tremblay,C.L. Drug resistance pathways and impact of protease mutation L10I/V in HIV-1 non-B subtypes J Antivirals Antiretrovirals (2012) 4, 43-50. DOI I
Hall,B.A., Wright,D.W., Jha,S. and Coveney,P.V. Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity Biochemistry (2012) 51, 6487-6489. PubMed Europe PubMed DOI I
Henderson,G.J., Lee,S.K., Irlbeck,D.M., Harris,J., Kline,M., Pollom,E., Parkin,N. and Swanstrom,R. Interplay between single resistance-associated mutations in the HIV-1 protease and viral infectivity, protease activity, and inhibitor sensitivity Antimicrob Agents Chemother (2012) 56, 623-633. PubMed Europe PubMed DOI
Honarparvar,B., Makatini,M.M., Pawar,S.A., Petzold,K., Soliman,M.E., Arvidsson,P.I., Sayed,Y., Govender,T., Maguire,G.E. and Kruger,H.G. Pentacycloundecane-diol-based HIV-1 protease inhibitors: biological screening, 2D NMR, and molecular simulation studies ChemMedChem (2012) 7, 1009-1019. PubMed Europe PubMed DOI I
Huang,D. and Caflisch,A. How does darunavir prevent HIV-1 protease dimerization? J Chem Theory Comput (2012) 8, 1786-1794. PubMed Europe PubMed DOI I
Huang,X., de Vera,I.M., Veloro,A.M., Blackburn,M.E., Kear,J.L., Carter,J.D., Rocca,J.R., Simmerling,C., Dunn,B.M. and Fanucci,G.E. Inhibitor-induced conformational shifts and ligand-exchange dynamics for HIV-1 protease measured by pulsed EPR and NMR spectroscopy J Phys Chem B (2012) 116, 14235-14244. PubMed Europe PubMed DOI I
Impens,F., Timmerman,E., Staes,A., Moens,K., Arien,K.K., Verhasselt,B., Vandekerckhove,J. and Gevaert,K. A catalogue of putative HIV-1 protease host cell substrates Biol Chem (2012) 393, 915-931. PubMed Europe PubMed DOI P
Kar,P. and Knecht,V. Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir J Comput Aided Mol Des (2012) 26, 215-232. PubMed Europe PubMed DOI I
Karpoormath,R., Sayed,Y., Govender,P., Govender,T., Kruger,H.G., Soliman,M.E. and Maguire,G.E. Pentacycloundecane derived hydroxy acid peptides: a new class of irreversible non-scissile ether bridged type isoster as potential HIV-1 wild type C-SA protease inhibitors Bioorg Chem (2012) 40, 19-29. PubMed Europe PubMed DOI I
Kimura,S., Broglia,R.A. and Tiana,G. Thermodynamics of strongly allosteric inhibition: a model study of HIV-1 protease Eur Biophys J (2012) 41, 991-1001. PubMed Europe PubMed DOI I
King,N.M., Prabu-Jeyabalan,M., Bandaranayake,R.M., Nalam,M.N., Nalivaika,E.A., Ozen,A., Haliloglu,T., Yilmaz,N.K. and Schiffer,C.A. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease ACS Chem Biol (2012) 7, 1536-1546. PubMed Europe PubMed DOI PMC EPMC
Kitidee,K., Nangola,S., Hadpech,S., Laopajon,W., Kasinrerk,W. and Tayapiwatana,C. A drug discovery platform: a simplified immunoassay for analyzing HIV protease activity J Virol Methods (2012) 186, 21-29. PubMed Europe PubMed DOI I
Kozisek,M., Henke,S., Saskova,K.G., Jacobs,G.B., Schuch,A., Buchholz,B., Muller,V., Krausslich,H.G., Rezacova,P., Konvalinka,J. and Bodem,J. Mutations in HIV-1 gag and pol compensate for the loss of viral fitness caused by a highly mutated protease Antimicrob Agents Chemother (2012) 56, 4320-4330. PubMed Europe PubMed DOI
Lee,S.K., Potempa,M., Kolli,M., Ozen,A., Schiffer,C.A. and Swanstrom,R. Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease J Biol Chem (2012) 287, 13279-13290. PubMed Europe PubMed DOI P
Lemmon,G., Kaufmann,K. and Meiler,J. Prediction of HIV-1 protease/inhibitor affinity using RosettaLigand Chem Biol Drug Des (2012) 79, 888-896. PubMed Europe PubMed DOI I
Li,D., Han,J.G., Chen,H., Li,L., Zhao,R.N., Liu,G. and Duan,Y. Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations J Mol Model (2012) 18, 1841-1854. PubMed Europe PubMed DOI I
Li,D., Liu,M.S., Ji,B., Hwang,K.C. and Huang,Y. Identifying the molecular mechanics and binding dynamics characteristics of potent inhibitors to HIV-1 protease Chem Biol Drug Des (2012) 80, 440-454. PubMed Europe PubMed DOI I
Liu,X., Gan,M., Dong,B., Zhang,T., Li,Y., Zhang,Y., Fan,X., Wu,Y., Bai,S., Chen,M., Yu,L., Tao,P., Jiang,W. and Si,S. 4862F, a new inhibitor of HIV-1 protease, from the culture of Streptomyces I03A-04862 Molecules (2012) 18, 236-243. PubMed Europe PubMed DOI I
Matuz,K., Motyan,J., Li,M., Wlodawer,A. and Tozser,J. Inhibition of XMRV and HIV-1 proteases by pepstatin A and acetyl-pepstatin FEBS J (2012) 279, 3276-3286. PubMed Europe PubMed DOI I
Meher,B.R. and Wang,Y. Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies J Phys Chem B (2012) 116, 1884-1900. PubMed Europe PubMed DOI I
Meher,B.R., Satish Kumar,M.V., Sharma,S. and Bandyopadhyay,P. Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple AMBER force fields J Bioinform Comput Biol (2012) 10, 1250018-1250018. PubMed Europe PubMed DOI
Mittal,S., Cai,Y., Nalam,M.N., Bolon,D.N. and Schiffer,C.A. Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease J Am Chem Soc (2012) 134, 4163-4168. PubMed Europe PubMed DOI
Oehme,D.P., Brownlee,R.T. and Wilson,D.J. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease J Comput Chem (2012) 33, 2566-2580. PubMed Europe PubMed DOI
Palma,A.C., Covens,K., Snoeck,J., Vandamme,A.M., Camacho,R.J. and Van Laethem,K. HIV-1 protease mutation 82M contributes to phenotypic resistance to protease inhibitors in subtype G J Antimicrob Chemother (2012) 67, 1075-1079. PubMed Europe PubMed DOI M
Pan,Y.Y., Wang,S.M., Huang,K.J., Chiang,C.C. and Wang,C.T. Placement of leucine zipper motifs at the carboxyl terminus of HIV-1 protease significantly reduces virion production PLoS ONE (2012) 7, e32845-e32845. PubMed Europe PubMed DOI PMC EPMC
Pawar,S.A., Jabgunde,A.M., Govender,P., Maguire,G.E., Kruger,H.G., Parboosing,R., Soliman,M.E., Sayed,Y., Dhavale,D.D. and Govender,T. Synthesis and molecular modelling studies of novel carbapeptide analogs for inhibition of HIV-1 protease Eur J Med Chem (2012) 53, 13-21. PubMed Europe PubMed DOI I
Sadiq,S.K., Noe,F. and De Fabritiis,G. Kinetic characterization of the critical step in HIV-1 protease maturation Proc Natl Acad Sci U S A (2012) 109, 20449-20454. PubMed Europe PubMed DOI
Santos,J.R., Llibre,J.M., Imaz,A., Domingo,P., Iribarren,J.A., Marino,A., Miralles,C., Galindo,M.J., Ornelas,A., Moreno,S., Schapiro,J.M. and Clotet,B. Mutations in the protease gene associated with virological failure to lopinavir/ritonavir-containing regimens J Antimicrob Chemother (2012) 67, 1462-1469. PubMed Europe PubMed DOI I
Saranya,N. and Selvaraj,S. QSAR studies on HIV-1 protease inhibitors using non-linearly transformed descriptors Curr Comput Aided Drug Des (2012) 8, 10-49. PubMed Europe PubMed DOI I
Schimer,J., Cigler,P., Vesely,J., Grantz Saskova,K., Lepsik,M., Brynda,J., Rezacova,P., Kozisek,M., Cisarova,I., Oberwinkler,H., Kraeusslich,H.G. and Konvalinka,J. Structure-aided design of novel inhibitors of HIV protease based on a benzodiazepine scaffold J Med Chem (2012) 55, 10130-10135. PubMed Europe PubMed DOI I
Shen,C.H., Tie,Y., Yu,X., Wang,Y.F., Kovalevsky,A.Y., Harrison,R.W. and Weber,I.T. Capturing the reaction pathway in near-atomic-resolution crystal structures of HIV-1 protease Biochemistry (2012) 51, 7726-7732. PubMed Europe PubMed DOI S
Tang,M.W., Liu,T.F. and Shafer,R.W. The HIVdb system for HIV-1 genotypic resistance interpretation Intervirology (2012) 55, 98-101. PubMed Europe PubMed DOI
Torbeev,V.Y. and Kent,S.B. Ionization state of the catalytic dyad Asp25/25' in the HIV-1 protease: NMR studies of site-specifically 13C labelled HIV-1 protease prepared by total chemical synthesis Org Biomol Chem (2012) 10, 5887-5891. PubMed Europe PubMed DOI
Wu,X., Ohrngren,P., Joshi,A.A., Trejos,A., Persson,M., Arvela,R.K., Wallberg,H., Vrang,L., Rosenquist,A., Samuelsson,B.B., Unge,J. and Larhed,M. Synthesis, X-ray analysis, and biological evaluation of a new class of stereopure lactam-based HIV-1 protease inhibitors J Med Chem (2012) 55, 2724-2736. PubMed Europe PubMed DOI I
Yadav,D., Paliwal,S., Yadav,R., Pal,M. and Pandey,A. Identification of novel HIV 1-protease inhibitors: application of ligand and structure based pharmacophore mapping and virtual screening PLoS ONE (2012) 7, e48942-e48942. PubMed Europe PubMed DOI PMC EPMC I
Yan,J., Huang,N., Li,S., Yang,L.M., Xing,W., Zheng,Y.T. and Hu,Y. Synthesis and biological evaluation of novel amprenavir-based P1-substituted bi-aryl derivatives as ultra-potent HIV-1 protease inhibitors Bioorg Med Chem Lett (2012) 22, 1976-1979. PubMed Europe PubMed DOI I
Yang,H., Nkeze,J. and Zhao,R.Y. Effects of HIV-1 protease on cellular functions and their potential applications in antiretroviral therapy Cell Biosci (2012) 2, 32-32. PubMed Europe PubMed DOI I
Yedidi,R.S., Liu,Z., Wang,Y., Brunzelle,J.S., Kovari,I.A., Woster,P.M., Kovari,L.C. and Gupta,D. Crystal structures of multidrug-resistant HIV-1 protease in complex with two potent anti-malarial compounds Biochem Biophys Res Commun (2012) 421, 413-417. PubMed Europe PubMed DOI S I
Ziolkowska,N.E., Bujacz,A., Randad,R.S., Erickson,J.W., Skalova,T., Hasek,J. and Bujacz,G. New active HIV-1 protease inhibitors derived from 3-hexanol: conformation study of the free inhibitors in crystalline state and in complex with the enzyme Chem Biol Drug Des (2012) 79, 798-809. PubMed Europe PubMed DOI I

2011

Batista,P.R., Pandey,G., Pascutti,P.G., Bisch,P.M., Perahia,D. and Robert,C.H. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening J Chem Theory Comput (2011) 7, 2348-2352. PubMed Europe PubMed DOI
Biswas,P., Cella,L.N., Kang,S.H., Mulchandani,A., Yates,M.V. and Chen,W. A quantum-dot based protein module for in vivo monitoring of protease activity through fluorescence resonance energy transfer Chem Commun (Camb) (2011) 47, 5259-5261. PubMed Europe PubMed DOI A
Blum,A., Bottcher,J., Dorr,S., Heine,A., Klebe,G. and Diederich,W.E. Two solutions for the same problem: multiple binding modes of pyrrolidine-based HIV-1 protease inhibitors J Mol Biol (2011) 410, 745-755. PubMed Europe PubMed DOI S I
Borkar,A.N., Rout,M.K. and Hosur,R.V. Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study PLoS ONE (2011) 6, e19830-e19830. PubMed Europe PubMed DOI PMC EPMC
Breuer,S., Sepulveda,H., Chen,Y., Trotter,J. and Torbett,B.E. A cleavage enzyme-cytometric bead array provides biochemical profiling of resistance mutations in HIV-1 gag and protease Biochemistry (2011) 50, 4371-4381. PubMed Europe PubMed DOI A
Callebaut,C., Stray,K., Tsai,L., Williams,M., Yang,Z.Y., Cannizzaro,C., Leavitt,S.A., Liu,X., Wang,K., Murray,B.P., Mulato,A., Hatada,M., Priskich,T., Parkin,N., Swaminathan,S., Lee,W., He,G.X., Xu,L. and Cihlar,T. In vitro characterization of GS-8374, a novel phosphonate-containing inhibitor of HIV-1 protease with a favorable resistance profile Antimicrob Agents Chemother (2011) 55, 1366-1376. PubMed Europe PubMed DOI I
Chang,M.W. and Torbett,B.E. Accessory mutations maintain stability in drug-resistant HIV-1 protease J Mol Biol (2011) 410, 756-760. PubMed Europe PubMed DOI PMC EPMC I
Degoey,D.A., Grampovnik,D.J., Chen,H.J., Flosi,W.J., Klein,L.L., Dekhtyar,T., Stoll,V., Mamo,M., Molla,A. and Kempf,D.J. P1-Substituted symmetry-based human immunodeficiency virus protease inhibitors with potent antiviral activity against drug-resistant viruses J Med Chem (2011) 54, 7094-7104. PubMed Europe PubMed DOI I
Deng,N.J., Zheng,W., Gallicchio,E. and Levy,R.M. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations J Am Chem Soc (2011) 133, 9387-9394. PubMed Europe PubMed DOI
Dierynck,I., Van Marck,H., Van Ginderen,M., Jonckers,T.H., Nalam,M.N., Schiffer,C.A., Raoof,A., Kraus,G. and Picchio,G. TMC310911, a novel human immunodeficiency virus type 1 protease inhibitor, shows in vitro an improved resistance profile and higher genetic barrier to resistance compared with current protease inhibitors Antimicrob Agents Chemother (2011) 55, 5723-5731. PubMed Europe PubMed DOI I
Elgadi,M.M. and Piliero,P.J. Boosted tipranavir versus darunavir in treatment-experienced patients: observational data from the randomized POTENT trial Drugs R D (2011) 11, 295-302. PubMed Europe PubMed DOI I
Ferreira,L.G., Leitao,A., Montanari,C.A. and Andricopulo,A.D. Comparative molecular field analysis of a series of inhibitors of HIV-1 protease Med Chem (2011) 7, 71-79. PubMed Europe PubMed I
Flor-Parra,F., Perez-Pulido,A.J., Pachon,J. and Perez-Romero,P. The HIV type 1 protease L10I minor mutation decreases replication capacity and confers resistance to protease inhibitors AIDS Res Hum Retroviruses (2011) 27, 65-70. PubMed Europe PubMed DOI
Ganguly,A.K., Alluri,S.S., Caroccia,D., Biswas,D., Wang,C.H., Kang,E., Zhang,Y., McPhail,A.T., Carroll,S.S., Burlein,C., Munshi,V., Orth,P. and Strickland,C. Design, synthesis, and X-ray crystallographic analysis of a novel class of HIV-1 protease inhibitors J Med Chem (2011) 54, 7176-7183. PubMed Europe PubMed DOI S I
Gao,B.L., Zhang,C.M., Yin,Y.Z., Tang,L.Q. and Liu,Z.P. Design and synthesis of potent HIV-1 protease inhibitors incorporating hydroxyprolinamides as novel P2 ligands Bioorg Med Chem Lett (2011) 21, 3730-3733. PubMed Europe PubMed DOI I
Ghosh,A.K., Chapsal,B.D., Baldridge,A., Steffey,M.P., Walters,D.E., Koh,Y., Amano,M. and Mitsuya,H. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation J Med Chem (2011) 54, 622-634. PubMed Europe PubMed DOI I
Ghosh,A.K., Martyr,C.D., Steffey,M., Wang,Y.F., Agniswamy,J., Amano,M., Weber,I.T. and Mitsuya,H. Design of substituted bis-tetrahydrofuran (bis-THF)-derived potent HIV-1 protease inhibitors, protein-ligand X-ray structure, and convenient syntheses of bis-THF and substituted bis-THF ligands ACS Med Chem Lett (2011) 2, 298-302. PubMed Europe PubMed DOI S I
Ghosh,A.K. and Anderson,D.D. Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors Future Med Chem (2011) 3, 1181-1197. PubMed Europe PubMed DOI I
Ghosh,A.K., Chapsal,B.D., Parham,G.L., Steffey,M., Agniswamy,J., Wang,Y.F., Amano,M., Weber,I.T. and Mitsuya,H. Design of HIV-1 protease inhibitors with C3-substituted hexahydrocyclopentafuranyl urethanes as P2-ligands: synthesis, biological evaluation, and protein-ligand X-ray crystal structure J Med Chem (2011) 54, 5890-5901. PubMed Europe PubMed DOI S I
Grotto,R.M., Corvino,S.M., Munhoz,L., Ghedini,C.G. and Pardini,M.I. A first case of protease codon 35 amino acid insertion in a HIV-1 subtype B sequence detected in the Bauru region, state of Sao Paulo, Brazil: case report Rev Soc Bras Med Trop (2011) 44, 392-394. PubMed Europe PubMed M
Hallengard,D., Haller,B.K., Petersson,S., Boberg,A., Maltais,A.K., Isaguliants,M., Wahren,B. and Brave,A. Increased expression and immunogenicity of HIV-1 protease following inactivation of the enzymatic activity Vaccine (2011) 29, 839-848. PubMed Europe PubMed DOI
Heal,J.W., Wells,S.A., Jimenez-Roldan,E., Freedman,R.F. and Romer,R.A. Rigidity analysis of HIV-1 protease J Phys Conf Ser (2011) 286, 012006-012006. DOI
Huang,L., Li,Y. and Chen,C. Flexible catalytic site conformations implicated in modulation of HIV-1 protease autoprocessing reactions Retrovirology (2011) 8, 79-79. PubMed Europe PubMed DOI
Ide,K., Aoki,M., Amano,M., Koh,Y., Yedidi,R.S., Das,D., Leschenko,S., Chapsal,B., Ghosh,A.K. and Mitsuya,H. Novel HIV-1 protease inhibitors (PIs) containing a bicyclic P2 functional moiety, tetrahydropyrano-tetrahydrofuran, that are potent against multi-PI-resistant HIV-1 variants Antimicrob Agents Chemother (2011) 55, 1717-1727. PubMed Europe PubMed DOI I
Jin,S., Ellis,E., Veetil,J.V., Yao,H. and Ye,K. Visualization of human immunodeficiency virus protease inhibition using a novel Forster resonance energy transfer molecular probe Biotechnol Prog (2011) 27, 1107-1114. PubMed Europe PubMed DOI A
Karthik,S. and Senapati,S. Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle Proteins (2011) 79, 1830-1840. PubMed Europe PubMed DOI
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Kuznetsov,N.A., Kozyr,A.V., Dronina,M.A., Smirnov,I.V., Kaliberda,E.N., Mikhailova,A.G., Rumsh,L.D., Fedorova,O.S., Gabibov,A.G. and Kolesnikov,A.V. Pre-steady-state kinetics of interaction of wild-type and multiple drug-resistant HIV protease with first and second generation inhibitory drugs Dokl Biochem Biophys (2011) 440, 239-243. PubMed Europe PubMed DOI I
Lexa,K.W. and Carlson,H.A. Binding to the open conformation of HIV-1 protease Proteins (2011) 79, 2282-2290. PubMed Europe PubMed DOI S
Li,D., Ji,B., Hwang,K.C. and Huang,Y. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket PLoS ONE (2011) 6, e19268-e19268. PubMed Europe PubMed DOI PMC EPMC I
Liu,X., Dai,Q., Li,L. and Xiu,Z. Resistant mechanism against nelfinavir of subtype C human immunodeficiency virus type 1 proteases J Mol Struct (2011) 986, 30-38. DOI I
Liu,Z., Wang,Y., Brunzelle,J., Kovari,I.A. and Kovari,L.C. Nine crystal structures determine the substrate envelope of the MDR HIV-1 protease Protein J (2011) 30, 173-183. PubMed Europe PubMed DOI S I
Louis,J.M., Zhang,Y., Sayer,J.M., Wang,Y.F., Harrison,R.W. and Weber,I.T. The L76V drug resistance mutation decreases the dimer stability and rate of autoprocessing of HIV-1 protease by reducing internal hydrophobic contacts Biochemistry (2011) 50, 4786-4795. PubMed Europe PubMed DOI S
Magiorkinis,E., Paraskevis,D., Detsika,M.G., Lu,L., Magiorkinis,G., Lazanas,M., Imbrechts,S., Van Laethem,K., Vandamme,A.M., Pilot-Matias,T., Molla,A., Camacho,R.J. and Hatzakis,A. Appearance of a single amino acid insertion at position 33 in HIV type 1 protease under a lopinavir-containing regimen, associated with reduced protease inhibitor susceptibility AIDS Res Hum Retroviruses (2011) 27, 1223-1229. PubMed Europe PubMed DOI M I
Makatini,M.M., Petzold,K., Sriharsha,S.N., Ndlovu,N., Soliman,M.E., Honarparvar,B., Parboosing,R., Naidoo,A., Arvidsson,P.I., Sayed,Y., Govender,P., Maguire,G.E., Kruger,H.G. and Govender,T. Synthesis and structural studies of pentacycloundecane-based HIV-1 PR inhibitors: a hybrid 2D NMR and docking/QM/MM/MD approach Eur J Med Chem (2011) 46, 3976-3985. PubMed Europe PubMed DOI I
Mao,Y. Dynamical basis for drug resistance of HIV-1 protease BMC Struct Biol (2011) 11, 31-31. PubMed Europe PubMed DOI I
Neogi,U., Sahoo,P.N., Kumar,R., De Costa,A. and Shet,A. Characterization of HIV type 1 subtype C protease gene: selection of L63P mutation in protease inhibitor-naive Indian patients AIDS Res Hum Retroviruses (2011) 27, 1249-1253. PubMed Europe PubMed DOI
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Ohrngren,P., Wu,X., Persson,M., Ekegren,J.K., Wallberg,H., Vrang,L., Rosenquist,A., Samuelsson,B., Unge,T. and Larhed,M. HIV-1 protease inhibitors with a tertiary alcohol containing transition-state mimic and various P2 and P1' substituents MedChemComm (2011) 2, 701-709. DOI I
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Ravichandran,V., Mourya,V.K. and Agrawal,R.K. Prediction of HIV-1 protease inhibitory activity of 4-hydroxy-5,6-dihydropyran-2-ones: QSAR study J Enzyme Inhib Med Chem (2011) 26, 288-294. PubMed Europe PubMed DOI I
Rucker,P., Horn,A.H.C., Meiselbach,H. and Sticht,H. A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network J Mol Model (2011) 17, 2693-2705. PubMed Europe PubMed DOI
Santos,A.F. and Soares,M.A. The impact of the nelfinavir resistance-conferring mutation D30N on the susceptibility of HIV-1 subtype B to other protease inhibitors Mem Inst Oswaldo Cruz (2011) 106, 177-181. PubMed Europe PubMed M I
Singh,M.K., Streu,K., McCrone,A.J. and Dominy,B.N. The evolution of catalytic function in the HIV-1 protease J Mol Biol (2011) 408, 792-805. PubMed Europe PubMed DOI
Torbeev,V.Y., Myong,S.A., Ha,T. and Kent,S.B.H. Single-molecule studies of HIV-1 protease catalysis enabled by chemical protein synthesis Isr J Chem (2011) 51, 960-967. DOI
Torbeev,V.Y., Raghuraman,H., Hamelberg,D., Tonelli,M., Westler,W.M., Perozo,E. and Kent,S.B. Protein conformational dynamics in the mechanism of HIV-1 protease catalysis Proc Natl Acad Sci U S A (2011) 108, 20982-20987. PubMed Europe PubMed DOI
Tzoupis,H., Leonis,G., Durdagi,S., Mouchlis,V., Mavromoustakos,T. and Papadopoulos,M.G. Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations J Comput Aided Mol Des (2011) 25, 959-976. PubMed Europe PubMed DOI I
Ungwitayatorn,J., Wiwat,C., Samee,W., Nunthanavanit,P. and Phosrithong,N. Synthesis, in vitro evaluation, and docking studies of novel chromone derivatives as HIV-1 protease inhibitor J Mol Struct (2011) 100, 152-161. DOI I
Volonte,F., Piubelli,L. and Pollegioni,L. Optimizing HIV-1 protease production in Escherichia coli as fusion protein Microb Cell Fact (2011) 10, 53-53. PubMed Europe PubMed DOI E
Wang,Y., Liu,Z., Brunzelle,J.S., Kovari,I.A., Dewdney,T.G., Reiter,S.J. and Kovari,L.C. The higher barrier of darunavir and tipranavir resistance for HIV-1 protease Biochem Biophys Res Commun (2011) 412, 737-742. PubMed Europe PubMed DOI I
Weber,I.T. and Wang,Y. HIV-1 protease: role in viral replication, protein-ligand x-ray crystal structures and inhibitor design Aspartic Acid Proteases as Therapeutic Targets (2011) 45, 107-137. DOI
Wright,D.W. and Coveney,P.V. Resolution of discordant HIV-1 protease resistance rankings using molecular dynamics simulations J Chem Inf Model (2011) 51, 2636-2649. PubMed Europe PubMed DOI I
Yedidi,R.S., Proteasa,G., Martinez,J.L., Vickrey,J.F., Martin,P.D., Wawrzak,Z., Liu,Z., Kovari,I.A. and Kovari,L.C. Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants Acta Crystallogr D Biol Crystallogr (2011) 67, 524-532. PubMed Europe PubMed DOI S

2010

Adrian Meredith,J., Wallberg,H., Vrang,L., Oscarson,S., Parkes,K., Hallberg,A. and Samuelsson,B. Design and synthesis of novel P2 substituents in diol-based HIV protease inhibitors Eur J Med Chem (2010) 45, 160-170. PubMed Europe PubMed DOI I
Ali,A., Bandaranayake,R.M., Cai,Y., King,N.M., Kolli,M., Mittal,S., Murzycki,J.F., Nalam,M.N.L., Nalivaika,E.A., Ozen,A., Prabu-Jeyabalan,M.M., Thayer,K. and Schiffer,C.A. Molecular basis for drug resistance in HIV-1 protease Viruses (2010) 2, 2509-2535. PubMed Europe PubMed DOI I
Ali,A., Reddy,G.S., Nalam,M.N., Anjum,S.G., Cao,H., Schiffer,C.A. and Rana,T.M. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones J Med Chem (2010) 53, 7699-7708. PubMed Europe PubMed DOI I
Bonini,C., Chiummiento,L., De Bonis,M., Di Blasio,N., Funicello,M., Lupattelli,P., Pandolfo,R., Tramutola,F. and Berti,F. Synthesis of new thienyl ring containing HIV-1 protease inhibitors: promising preliminary pharmacological evaluation against recombinant HIV-1 proteases J Med Chem (2010) 53, 1451-1457. PubMed Europe PubMed DOI I
Bonomi,M., Barducci,A., Gervasio,F.L. and Parrinello,M. Multiple routes and milestones in the folding of HIV-1 protease monomer PLoS ONE (2010) 5, e13208-e13208. PubMed Europe PubMed DOI PMC EPMC
Chang,M.W., Giffin,M.J., Muller,R., Savage,J., Lin,Y.C., Hong,S., Jin,W., Whitby,L.R., Elder,J.H., Boger,D.L. and Torbett,B.E. Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries Biochem J (2010) 429, 527-532. PubMed Europe PubMed DOI I
Chen,J., Zhang,S., Liu,X. and Zhang,Q. Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation J Mol Model (2010) 16, 459-468. PubMed Europe PubMed DOI I
Choi,Y., Lee,J., Kim,K., Kim,H., Sommer,P. and Song,R. Fluorogenic assay and live cell imaging of HIV-1 protease activity using acid-stable quantum dot-peptide complex Chem Commun (Camb) (2010) 46, 9146-9148. PubMed Europe PubMed DOI A L
Coburger,C., Lage,H., Molnar,J., Langner,A. and Hilgeroth,A. Multidrug resistance reversal properties and cytotoxic evaluation of representatives of a novel class of HIV-1 protease inhibitors J Pharm Pharmacol (2010) 62, 1704-1710. PubMed Europe PubMed DOI I
Das,A., Mahale,S., Prashar,V., Bihani,S., Ferrer,J.L. and Hosur,M.V. X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate J Am Chem Soc (2010) 132, 6366-6373. PubMed Europe PubMed DOI S I
Dirauf,P., Meiselbach,H. and Sticht,H. Effects of the V82A and I54V mutations on the dynamics and ligand binding properties of HIV-1 protease J Mol Model (2010) 16, 1577-1583. PubMed Europe PubMed DOI I
Friedman,R. and Caflisch,A. On the orientation of the catalytic dyad in aspartic proteases Proteins (2010) 78, 1575-1582. PubMed Europe PubMed DOI S
Ghosh,A.K., Gemma,S., Simoni,E., Baldridge,A., Walters,D.E., Ide,K., Tojo,Y., Koh,Y., Amano,M. and Mitsuya,H. Synthesis and biological evaluation of novel allophenylnorstatine-based HIV-1 protease inhibitors incorporating high affinity P2-ligands Bioorg Med Chem Lett (2010) 20, 1241-1246. PubMed Europe PubMed DOI I
Ghosh,A.K., Xu,C.X., Rao,K.V., Baldridge,A., Agniswamy,J., Wang,Y.F., Weber,I.T., Aoki,M., Miguel,S.G., Amano,M. and Mitsuya,H. Probing multidrug-resistance and protein-ligand interactions with oxatricyclic designed ligands in HIV-1 protease inhibitors ChemMedChem (2010) 5, 1850-1854. PubMed Europe PubMed DOI PMC EPMC I
Hamacher,K. Temperature dependence of fluctuations in HIV1-protease Eur Biophys J (2010) 39, 1051-1056. PubMed Europe PubMed DOI
Hao,G.F., Yang,G.F. and Zhan,C.G. Computational mutation scanning and drug resistance mechanisms of HIV-1 protease inhibitors J Phys Chem B (2010) 114, 9663-9676. PubMed Europe PubMed DOI I
He,M., Yang,N., Sun,C., Yao,X. and Yang,M. Modification and biological evaluation of novel 4-hydroxy-pyrone derivatives as non-peptidic HIV-1 protease inhibitors Med Chem Res (2010) 20, 200-209. DOI I
He,M., Zhang,H., Yao,X., Eckart,M., Zuo,E. and Yang,M. Design, biologic evaluation, and SAR of novel pseudo-peptide incorporating benzheterocycles as HIV-1 protease inhibitors Chem Biol Drug Des (2010) 76, 174-180. PubMed Europe PubMed DOI I
Hilton,B.J. and Wolkowicz,R. An assay to monitor HIV-1 protease activity for the identification of novel inhibitors in T-cells PLoS ONE (2010) 5, e10940-e10940. PubMed Europe PubMed DOI PMC EPMC A
Hu,G.D., Zhu,T., Zhang,S.L., Wang,D. and Zhang,Q.G. Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations Eur J Med Chem (2010) 45, 227-235. PubMed Europe PubMed DOI I
Huang,L., Hall,A. and Chen,C. Cysteine 95 and other residues influence the regulatory effects of histidine 69 mutations on human immunodeficiency virus type 1 protease autoprocessing Retrovirology (2010) 7, 24-24. PubMed Europe PubMed DOI
Ishima,R., Gong,Q., Tie,Y., Weber,I.T. and Louis,J.M. Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV-1 protease Proteins (2010) 78, 1015-1025. PubMed Europe PubMed DOI S
Johnson,V.A., Brun-Vezinet,F., Clotet,B., Gunthard,H.F., Kuritzkes,D.R., Pillay,D., Schapiro,J.M. and Richman,D.D. Update of the drug resistance mutations in HIV-1: December 2010 Top HIV Med (2010) 18, 156-163. PubMed Europe PubMed
Jones,K.L., Holloway,M.K., Su,H.P., Carroll,S.S., Burlein,C., Touch,S., Distefano,D.J., Sanchez,R.I., Williams,T.M., Vacca,J.P. and Coburn,C.A. Epsilon substituted lysinol derivatives as HIV-1 protease inhibitors Bioorg Med Chem Lett (2010) 20, 4065-4068. PubMed Europe PubMed DOI I
Khedkar,V.M., Ambre,P.K., Verma,J., Shaikh,M.S., Pissurlenkar,R.R.S. and Coutinho,E.C. Molecular docking and 3D-QSAR studies of HIV-1 protease inhibitors J Mol Model (2010) 16, 1251-1268. PubMed Europe PubMed DOI I
Kim,K.S., Jin,D.B., Ahn,S.S., Park,K.S., Seo,S.H., Suh,Y.S. and Sung,Y.C. HIV-1 protease has a genetic T-cell adjuvant effect which is negatively regulated by proteolytic activity J Virol (2010) 84, 7743-7749. PubMed Europe PubMed DOI
Knops,E., Kemper,I., Schulter,E., Pfister,H., Kaiser,R. and Verheyen,J. The evolution of protease mutation 76V is associated with protease mutation 46I and gag mutation 431V AIDS (2010) 24, 779-781. PubMed Europe PubMed DOI
Lee,S.G. and Chmielewski,J. Cross-linked peptoid-based dimerization inhibitors of HIV-1 protease Chembiochem (2010) 11, 1513-1516. PubMed Europe PubMed DOI I
Lentini,A., Tabolacci,C., Melino,S., Provenzano,B. and Beninati,S. Post-translational modification of glutamine and lysine residues of HIV-1 aspartyl protease by transglutaminase increases its catalytic activity Biochem Biophys Res Commun (2010) 393, 546-550. PubMed Europe PubMed DOI
Li,D., Ji,B., Hwang,K. and Huang,Y. Crucial roles of the subnanosecond local dynamics of the flap tips in the global conformational changes of HIV-1 protease J Phys Chem B (2010) 114, 3060-3069. PubMed Europe PubMed DOI
Li,X., Hu,H. and Shu,L. Predicting human immunodeficiency virus protease cleavage sites in nonlinear projection space Mol Cell Biochem (2010) 339, 127-133. PubMed Europe PubMed DOI
Lin,Y.C., Huang,Y.M. and Leu,J.J.Y. A new logic correlation rule for HIV-1 protease mutation Expert Syst Appl (2010) 38, 5448-5455. DOI I
Lisovsky,I., Schader,S.M., Martinez-Cajas,J.L., Oliveira,M., Moisi,D. and Wainberg,M.A. HIV-1 protease codon 36 polymorphisms and differential development of resistance to nelfinavir, lopinavir, and atazanavir in different HIV-1 subtypes Antimicrob Agents Chemother (2010) 54, 2878-2885. PubMed Europe PubMed DOI I
Lu,D., Sham,Y.Y. and Vince,R. Design, asymmetric synthesis, and evaluation of pseudosymmetric sulfoximine inhibitors against HIV-1 protease Bioorg Med Chem (2010) 18, 2037-2048. PubMed Europe PubMed DOI I
Lu,T., Chen,Y. and Li,X.Y. An insight into the opening path to semi-open conformation of HIV-1 protease by molecular dynamics simulation AIDS (2010) 24, 1121-1125. PubMed Europe PubMed DOI
Mahalingam,A.K., Axelsson,L., Ekegren,J.K., Wannberg,J., Kihlstrom,J., Unge,T., Wallberg,H., Samuelsson,B., Larhed,M. and Hallberg,A. HIV-1 protease inhibitors with a transition-state mimic comprising a tertiary alcohol: improved antiviral activity in cells J Med Chem (2010) 53, 607-615. PubMed Europe PubMed DOI I
Mahmoud,K.A. and Luong,J.H.T. A sensitive electrochemical assay for early detection of HIV-1 protease using ferrocenepeptide conjugate/AU nanoparticle/single walled carbon nanotube modified electrode Anal Lett (2010) 43, 1680-1687. DOI A
Manosuthi,W., Butler,D.M., Perez-Santiago,J., Poon,A.F., Pillai,S.K., Mehta,S.R., Pacold,M.E., Richman,D.D., Pond,S.K. and Smith,D.M. Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure AIDS (2010) 24, 411-416. PubMed Europe PubMed DOI
Miller,M. The early years of retroviral protease crystal structures Biopolymers (2010) 94, 521-529. PubMed Europe PubMed DOI V S I
Nalam,M.N., Ali,A., Altman,M.D., Reddy,G.S., Chellappan,S., Kairys,V., Ozen,A., Cao,H., Gilson,M.K., Tidor,B., Rana,T.M. and Schiffer,C.A. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance J Virol (2010) 84, 5368-5378. PubMed Europe PubMed DOI I
Perez,M.A., Fernandes,P.A. and Ramos,M.J. Substrate recognition in HIV-1 protease: a computational study J Phys Chem B (2010) 114, 2525-2532. PubMed Europe PubMed DOI
Perryman,A.L., Zhang,Q., Soutter,H.H., Rosenfeld,R., McRee,D.E., Olson,A.J., Elder,J.E. and David Stout,C. Fragment-based screen against HIV protease Chem Biol Drug Des (2010) 75, 257-268. PubMed Europe PubMed DOI S I
Prashar,V., Bihani,S.C., Das,A., Rao,D.R. and Hosur,M.V. Insights into the mechanism of drug resistance: X-ray structure analysis of G48V/C95F tethered HIV-1 protease dimer/saquinavir complex Biochem Biophys Res Commun (2010) 396, 1018-1023. PubMed Europe PubMed DOI I
Reddy,A.S., Kumar,S. and Garg,R. Hybrid-genetic algorithm based descriptor optimization and QSAR models for predicting the biological activity of Tipranavir analogs for HIV protease inhibition J Mol Graph Model (2010) 28, 852-862. PubMed Europe PubMed DOI I
Robbins,A.H., Coman,R.M., Bracho-Sanchez,E., Fernandez,M.A., Gilliland,C.T., Li,M., Agbandje-McKenna,M., Wlodawer,A., Dunn,B.M. and McKenna,R. Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes Acta Crystallogr D Biol Crystallogr (2010) 66, 233-242. PubMed Europe PubMed DOI PMC EPMC S
Sayer,J.M., Agniswamy,J., Weber,I.T. and Louis,J.M. Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: relevance to drug resistance Protein Sci (2010) 19, 2055-2072. PubMed Europe PubMed DOI S
Shen,C.H., Wang,Y.F., Kovalevsky,A.Y., Harrison,R.W. and Weber,I.T. Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters FEBS J (2010) 277, 3699-3714. PubMed Europe PubMed DOI PMC EPMC I
Singh,S., Singh,S. and Shukla,P. Modeling of novel HIV-1 protease inhibitors incorporating N-aryl-oxazolidinone-5-carboxamides as P2 ligands using quantum chemical and topological finger print descriptors Med Chem Res (2010) 20, 1556-1565. DOI I
Soares,R.O., Batista,P.R., Costa,M.G., Dardenne,L.E., Pascutti,P.G. and Soares,M.A. Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations J Mol Graph Model (2010) 29, 137-147. PubMed Europe PubMed DOI I
Steuber,H. and Hilgenfeld,R. Recent advances in targeting viral proteases for the discovery of novel antivirals Curr Top Med Chem (2010) 10, 323-345. PubMed Europe PubMed DOI V
Tojo,Y., Koh,Y., Amano,M., Aoki,M., Das,D., Kulkarni,S., Anderson,D.D., Ghosh,A.K. and Mitsuya,H. Novel protease inhibitors (PIs) containing macrocyclic components and 3(R),3a(S),6a(R)-bis-tetrahydrofuranylurethane that are potent against multi-PI-resistant HIV-1 variants in vitro Antimicrob Agents Chemother (2010) 54, 3460-3470. PubMed Europe PubMed DOI I
Vidu,A., Dufau,L., Bannwarth,L., Soulier,J.L., Sicsic,S., Piarulli,U., Reboud-Ravaux,M. and Ongeri,S. Toward the first nonpeptidic molecular tong inhibitor of wild-type and mutated HIV-1 protease dimerization ChemMedChem (2010) 5, 1899-1906. PubMed Europe PubMed DOI I
Waheed,A.A., Ablan,S.D., Sowder,R.C., Roser,J.D., Schaffner,C.P., Chertova,E. and Freed,E.O. Effect of mutations in the human immunodeficiency virus type 1 protease on cleavage of the GP41 cytoplasmic tail J Virol (2010) 84, 3121-3126. PubMed Europe PubMed DOI
Young,T.P., Parkin,N.T., Stawiski,E., Pilot-Matias,T., Trinh,R., Kempf,D.J. and Norton,M. Prevalence, mutation patterns, and effects on protease inhibitor susceptibility of the L76V mutation in HIV-1 protease Antimicrob Agents Chemother (2010) 54, 4903-4906. PubMed Europe PubMed DOI M
Yu,Z., Kabashima,T., Tang,C., Shibata,T., Kitazato,K., Kobayashi,N., Lee,M.K. and Kai,M. Selective and facile assay of human immunodeficiency virus protease activity by a novel fluorogenic reaction Anal Biochem (2010) 397, 197-201. PubMed Europe PubMed DOI A

2009

Adachi,M., Ohhara,T., Kurihara,K., Tamada,T., Honjo,E., Okazaki,N., Arai,S., Shoyama,Y., Kimura,K., Matsumura,H., Sugiyama,S., Adachi,H., Takano,K., Mori,Y., Hidaka,K., Kimura,T., Hayashi,Y., Kiso,Y. and Kuroki,R. Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography Proc Natl Acad Sci U S A (2009) 106, 4641-4646. PubMed Europe PubMed DOI PMC EPMC S I
Alcaro,S., Artese,A., Ceccherini-Silberstein,F., Ortuso,F., Perno,C.F., Sing,T. and Svicher,V. Molecular dynamics and free energy studies on the wild-type and mutated HIV-1 protease complexed with four approved drugs: mechanism of binding and drug resistance J Chem Inf Model (2009) 49, 1751-1761. PubMed Europe PubMed DOI I
Bihani,S., Das,A., Prashar,V., Ferrer,J.L. and Hosur,M.V. X-ray structure of HIV-1 protease in situ product complex Proteins (2009) 74, 594-602. PubMed Europe PubMed DOI S
Bihani,S.C., Das,A., Prashar,V., Ferrer,J.L. and Hosur,M.V. Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S Biochem Biophys Res Commun (2009) 389, 295-300. PubMed Europe PubMed DOI S I
Blackburn,M.E., Veloro,A.M. and Fanucci,G.E. Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy Biochemistry (2009) 48, 8765-8767. PubMed Europe PubMed DOI
Boda,D., Valisko,M., Henderson,D., Gillespie,D., Eisenberg,B. and Gilson,M.K. Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory Biophys J (2009) 96, 1293-1306. PubMed Europe PubMed DOI PMC EPMC
Bowman,M.J. and Chmielewski,J. Sidechain-linked inhibitors of HIV-1 protease dimerization Bioorg Med Chem (2009) 17, 967-976. PubMed Europe PubMed DOI I
Chaudhury,S. and Gray,J.J. Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance Structure (2009) 17, 1636-1648. PubMed Europe PubMed DOI
Chen,J., Yang,M., Hu,G., Shi,S., Yi,C. and Zhang,Q. Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations J Mol Model (2009) 15, 1245-1252. PubMed Europe PubMed DOI I
Chen,J.Z., Yang,M.Y., Yi,C.H., Shi,S.H. and Zhang,Q.G. Molecular dynamics simulation and free energy calculations of symmetric fluoro-substituted diol-based HIV-1 protease inhibitors Theochem (2009) 899, 1-8. DOI I
Chiummiento,L., Funicello,M., Lupattelli,P., Tramutola,F. and Campaner,P. New indolic non-peptidic HIV protease inhibitors from (S)-glycidol: synthesis and preliminary biological activity Tetrahedron (2009) 65, 5984-5989. DOI I
Degoey,D.A., Grampovnik,D.J., Flentge,C.A., Flosi,W.J., Chen,H.J., Yeung,C.M., Randolph,J.T., Klein,L.L., Dekhtyar,T., Colletti,L., Marsh,K.C., Stoll,V., Mamo,M., Morfitt,D.C., Nguyen,B., Schmidt,J.M., Swanson,S.J., Mo,H., Kati,W.M., Molla,A. and Kempf,D.J. 2-Pyridyl P1'-substituted symmetry-based human immunodeficiency virus protease inhibitors (A-792611 and A-790742) with potential for convenient dosing and reduced side effects J Med Chem (2009) 52, 2571-2586. PubMed Europe PubMed DOI I
Fong,P., McNamara,J.P., Hillier,I.H. and Bryce,R.A. Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease J Chem Inf Model (2009) 49, 913-924. PubMed Europe PubMed DOI I
Galiano,L., Blackburn,M.E., Veloro,A.M., Bonora,M. and Fanucci,G.E. Solute effects on spin labels at an aqueous-exposed site in the flap region of HIV-1 protease J Phys Chem B (2009) 113, 1673-1680. PubMed Europe PubMed DOI
Galiano,L., Ding,F., Veloro,A.M., Blackburn,M.E., Simmerling,C. and Fanucci,G.E. Drug pressure selected mutations in HIV-1 protease alter flap conformations J Am Chem Soc (2009) 131, 430-431. PubMed Europe PubMed DOI PMC EPMC
Ghosh,A.K., Leshchenko-Yashchuk,S., Anderson,D.D., Baldridge,A., Noetzel,M., Miller,H.B., Tie,Y., Wang,Y.F., Koh,Y., Weber,I.T. and Mitsuya,H. Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies J Med Chem (2009) 52, 3902-3914. PubMed Europe PubMed DOI PMC EPMC I
Ghosh,A.K., Kulkarni,S., Anderson,D.D., Hong,L., Baldridge,A., Wang,Y.F., Chumanevich,A.A., Kovalevsky,A.Y., Tojo,Y., Amano,M., Koh,Y., Tang,J., Weber,I.T. and Mitsuya,H. Design, synthesis, protein-ligand X-ray structure, and biological evaluation of a series of novel macrocyclic human immunodeficiency virus-1 protease inhibitors to combat drug resistance J Med Chem (2009) 52, 7689-7705. PubMed Europe PubMed DOI I
Hernandez,N., Kiralj,R., Ferreira,M.M.C. and Talavera,I. Critical comparative analysis, validation and interpretation of SVM and PLS regression models in a QSAR study on HIV-1 protease inhibitors Chemometr Intelligent Lab Syst (2009) 98, 65-77. DOI I
Heyda,J., Pokorna,J., Vrbka,L., Vacha,R., Jagoda-Cwiklik,B., Konvalinka,J., Jungwirth,P. and Vondrasek,J. Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease Phys Chem Chem Phys (2009) 11, 7599-7604. PubMed Europe PubMed DOI
Hidaka,K., Kimura,T., Abdel-Rahman,H.M., Nguyen,J.T., McDaniel,K.F., Kohlbrenner,W.E., Molla,A., Adachi,M., Tamada,T., Kuroki,R., Katsuki,N., Tanaka,Y., Matsumoto,H., Wang,J., Hayashi,Y., Kempf,D.J. and Kiso,Y. Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2' pocket J Med Chem (2009) 52, 7604-7617. PubMed Europe PubMed DOI I
Jochim,A.L., Miller,S.E., Angelo,N.G. and Arora,P.S. Evaluation of triazolamers as active site inhibitors of HIV-1 protease Bioorg Med Chem Lett (2009) 19, 6023-6026. PubMed Europe PubMed DOI I
Johnson,V.A., Brun-Vezinet,F., Clotet,B., Gunthard,H.F., Kuritzkes,D.R., Pillay,D., Schapiro,J.M. and Richman,D.D. Update of the drug resistance mutations in HIV-1: December 2009 Top HIV Med (2009) 17, 138-145. PubMed Europe PubMed
Kogo,H., Takeuchi,K., Inoue,H., Kihara,H., Kojima,M. and Takahashi,K. Urea-dependent unfolding of HIV-1 protease studied by circular dichroism and small-angle X-ray scattering Biochim Biophys Acta (2009) 1794, 70-74. PubMed Europe PubMed DOI
Koh,Y., Das,D., Leschenko,S., Nakata,H., Ogata-Aoki,H., Amano,M., Nakayama,M., Ghosh,A.K. and Mitsuya,H. GRL-02031, a novel nonpeptidic protease inhibitor (PI) containing a stereochemically defined fused cyclopentanyltetrahydrofuran potent against multi-PI-resistant human immunodeficiency virus type 1 in vitro Antimicrobial Agents Chemother (2009) 53, 997-1006. PubMed Europe PubMed DOI PMC EPMC I
Kolli,M., Stawiski,E., Chappey,C. and Schiffer,C.A. Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance J Virol (2009) 83, 11027-11042. PubMed Europe PubMed DOI PMC EPMC
Kontijevskis,A., Petrovska,R., Yahorava,S., Komorowski,J. and Wikberg,J.E. Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates Bioorg Med Chem (2009) 17, 5229-5237. PubMed Europe PubMed DOI V I
Krauchenco,S., Martins,N.H., Sanches,M. and Polikarpov,I. Effectiveness of commercial inhibitors against subtype F HIV-1 protease J Enzyme Inhib Med Chem (2009) 24, 638-645. PubMed Europe PubMed DOI I
Lexa,K.W., Damm,K.L., Quintero,J.J., Gestwicki,J.E. and Carlson,H.A. Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease Proteins (2009) 74, 872-880. PubMed Europe PubMed DOI PMC EPMC S
Liu,X., Xiu,Z. and Hao,C. Drug-resistant molecular mechanism of CRF01_AE HIV-1 protease due to V82F mutation J Comput Aided Mol Des (2009) 23, 261-272. PubMed Europe PubMed DOI I
Niu,B., Lu,L., Liu,L., Gu,T.H., Feng,K.Y., Lu,W.C. and Cai,Y.D. HIV-1 protease cleavage site prediction based on amino acid property J Comput Chem (2009) 30, 33-39. PubMed Europe PubMed DOI
Noel,A.F., Bilsel,O., Kundu,A., Wu,Y., Zitzewitz,J.A. and Matthews,C.R. The folding free-energy surface of HIV-1 protease: insights into the thermodynamic basis for resistance to inhibitors J Mol Biol (2009) 387, 1002-1016. PubMed Europe PubMed DOI PMC EPMC I
Ocul,H. Variable context Markov chains for HIV protease cleavage site prediction Biosystems (2009) 96, 246-250. PubMed Europe PubMed DOI
Pandey,R.B. and Farmer,B.L. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation J Chem Phys (2009) 130, 044906-044906. PubMed Europe PubMed DOI
Prashar,V., Bihani,S., Das,A., Ferrer,J.L. and Hosur,M. Catalytic water co-existing with a product peptide in the active site of HIV-1 protease revealed by X-ray structure analysis PLoS ONE (2009) 4, e7860-e7860. PubMed Europe PubMed DOI PMC EPMC
Purohit,R. and Sethumadhavan,R. Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease Interdiscip Sci (2009) 1, 320-328. PubMed Europe PubMed DOI I
Ravichandran,V., Jain,A.K., Mourya,V.K. and Agrawal,R.K. Prediction of HIV-1 protease inhibitory activity of (4-hydroxy-6-phenyl-2-oxo-2h-pyran-3-yl) thiomethanes: QSAR study Curr Trends Biotechnol Pharm (2009) 3, 149-154. I
Rezacova,P., Pokorna,J., Brynda,J., Kozisek,M., Cigler,P., Lepsik,M., Fanfrlik,J., Rezac,J., Grantz Saskova,K., Sieglova,I., Plesek,J., Sicha,V., Gruner,B., Oberwinkler,H., Sedlacek',J., Krausslich,H.G., Hobza,P., Kral,V. and Konvalinka,J. Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes J Med Chem (2009) 52, 7132-7141. PubMed Europe PubMed DOI I
Rognvaldsson,T., Etchells,T.A., You,L., Garwicz,D., Jarman,I. and Lisboa,P.J. How to find simple and accurate rules for viral protease cleavage specificities BMC Bioinformatics (2009) 10, 149-149. PubMed Europe PubMed DOI PMC EPMC P
Saskova,K.G., Kozisek,M., Rezacova,P., Brynda,J., Yashina,T., Kagan,R.M. and Konvalinka,J. Molecular characterization of clinical isolates of human immunodeficiency virus resistant to the protease inhibitor darunavir J Virol (2009) 83, 8810-8818. PubMed Europe PubMed DOI PMC EPMC I
Sayer,J.M. and Louis,J.M. Interactions of different inhibitors with active-site aspartyl residues of HIV-1 protease and possible relevance to pepsin Proteins (2009) 75, 556-568. PubMed Europe PubMed DOI PMC EPMC I
Soares,E.A., Santos,A.F., Gonzalez,L.M., Lalonde,M.S., Tebit,D.M., Tanuri,A., Arts,E.J. and Soares,M.A. Mutation T74S in HIV-1 subtype B and C proteases resensitizes them to ritonavir and indinavir and confers fitness advantage J Antimicrob Chemother (2009) 64, 938-944. PubMed Europe PubMed DOI
Takkis,K. and Sild,S. QSAR modeling of HIV-1 protease inhibition on six- and seven-membered cyclic ureas QSAR Comb Sci (2009) 28, 52-58. DOI I
Tiana,G. and Broglia,R.A. The molecular evolution of HIV-1 protease simulated at atomic detail Proteins (2009) 76, 895-910. PubMed Europe PubMed DOI
Torbeev,V.Y., Raghuraman,H., Mandal,K., Senapati,S., Perozo,E. and Kent,S.B. Dynamics of "flap" structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy J Am Chem Soc (2009) 131, 884-885. PubMed Europe PubMed DOI I
Van Marck,H., Dierynck,I., Kraus,G., Hallenberger,S., Pattery,T., Muyldermans,G., Geeraert,L., Borozdina,L., Bonesteel,R., Aston,C., Shaw,E., Chen,Q., Martinez,C., Koka,V., Lee,J., Chi,E., de Bethune,M.P. and Hertogs,K. The impact of individual human immunodeficiency virus type 1 protease mutations on drug susceptibility is highly influenced by complex interactions with the background protease sequence J Virol (2009) 83, 9512-9520. PubMed Europe PubMed DOI PMC EPMC M
Verkhivker,G.M. Coarse-grained modeling of the HIV-1 protease binding mechanisms: II. Folding inhibition Lect Notes Comput Sci (2009) 5488 LNBI, 13-24. DOI
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2008

Altman,M.D., Nalivaika,E.A., Prabu-Jeyabalan,M., Schiffer,C.A. and Tidor,B. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease Proteins (2008) 70, 678-694. PubMed Europe PubMed DOI
Altman,M.D., Ali,A., Reddy,G.S., Nalam,M.N., Anjum,S.G., Cao,H., Chellappan,S., Kairys,V., Fernandes,M.X., Gilson,M.K., Schiffer,C.A., Rana,T.M. and Tidor,B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants J Am Chem Soc (2008) 130, 6099-6113. PubMed Europe PubMed DOI I
Bandaranayake,R.M., Prabu-Jeyabalan,M., Kakizawa,J., Sugiura,W. and Schiffer,C.A. Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6 J Virol (2008) 82, 6762-6766. PubMed Europe PubMed DOI PMC EPMC S
Blum,A., Bottcher,J., Heine,A., Klebe,G. and Diederich,W.E. Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold J Med Chem (2008) 51, 2078-2087. PubMed Europe PubMed DOI T I
Bottcher,J., Blum,A., Dorr,S., Heine,A., Diederich,W.E. and Klebe,G. Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors ChemMedChem (2008) 3, 1337-1344. PubMed Europe PubMed DOI S I
Bottcher,J., Blum,A., Heine,A., Diederich,W.E. and Klebe,G. Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease J Mol Biol (2008) 383, 347-357. PubMed Europe PubMed DOI T I
Broglia,R., Levy,Y. and Tiana,G. HIV-1 protease folding and the design of drugs which do not create resistance Curr Opin Struct Biol (2008) 18, 60-66. PubMed Europe PubMed DOI I
Carnevale,V., Raugei,S., Piana,S. and Carloni,P. On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study Comput Phys Commun (2008) 179, 120-123. DOI
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Coman,R.M., Robbins,A.H., Fernandez,M.A., Gilliland,C.T., Sochet,A.A., Goodenow,M.M., McKenna,R. and Dunn,B.M. The contribution of naturally occurring polymorphisms in altering the biochemical and structural characteristics of HIV-1 subtype C protease Biochemistry (2008) 47, 731-743. PubMed Europe PubMed DOI
Coman,R.M., Robbins,A.H., Goodenow,M.M., Dunn,B.M. and McKenna,R. High-resolution structure of unbound human immunodeficiency virus 1 subtype C protease: implications of flap dynamics and drug resistance Acta Crystallogr D Biol Crystallogr (2008) D64, 754-763. PubMed Europe PubMed DOI S
Damm,K.L., Ung,P.M., Quintero,J.J., Gestwicki,J.E. and Carlson,H.A. A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket Biopolymers (2008) 89, 643-652. PubMed Europe PubMed DOI I
Dandache,S., Coburn,C.A., Oliveira,M., Allison,T.J., Holloway,M.K., Wu,J.J., Stranix,B.R., Panchal,C., Wainberg,M.A. and Vacca,J.P. PL-100, a novel HIV-1 protease inhibitor displaying a high genetic barrier to resistance: an in vitro selection study J Med Virol (2008) 80, 2053-2063. PubMed Europe PubMed DOI I
Dekhtyar,T., Ng,T.I., Lu,L., Masse,S., Degoey,D.A., Flosi,W.J., Grampovnik,D.J., Klein,L.L., Kempf,D.J. and Molla,A. Characterization of a novel human immunodeficiency virus type 1 protease inhibitor, A-790742 Antimicrob Agents Chemother (2008) 52, 1337-1344. PubMed Europe PubMed DOI PMC EPMC I
Ding,F., Layten,M. and Simmerling,C. Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments J Am Chem Soc (2008) 130, 7184-7185. PubMed Europe PubMed DOI S
Eizert,H., Bander,P., Bagossi,P., Sperka,T., Miklossy,G., Boross,P., Weber,I.T. and Tozser,J. Amino acid preferences of retroviral proteases for amino-terminal positions in a type 1 cleavage site J Virol (2008) 82, 10111-10117. PubMed Europe PubMed DOI PMC EPMC P
Frecer,V., Berti,F., Benedetti,F. and Miertus,S. Design of peptidomimetic inhibitors of aspartic protease of HIV-1 containing -PhePsiPro- core and displaying favourable ADME-related properties J Mol Graph Model (2008) 27, 376-387. PubMed Europe PubMed DOI I
Garg,R. and Bhhatarai,B. Possible allosteric interactions of monoindazole-substituted P2 cyclic urea analogues with wild-type and mutant HIV-1 protease J Comput Aided Mol Des (2008) 22, 737-745. PubMed Europe PubMed DOI I
Ghosh,A.K., Chapsal,B.D., Weber,I.T. and Mitsuya,H. Design of HIV protease inhibitors targeting protein backbone: an effective strategy for combating drug resistance Acc Chem Res (2008) 41, 78-86. PubMed Europe PubMed DOI I
Ghosh,A.K., Gemma,S., Baldridge,A., Wang,Y.F., Kovalevsky,A.Y., Koh,Y., Weber,I.T. and Mitsuya,H. Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: design, synthesis, biological evaluation, and protein-ligand X-ray studies J Med Chem (2008) 51, 6021-6033. PubMed Europe PubMed DOI I
Ghosh,A.K., Gemma,S., Takayama,J., Baldridge,A., Leshchenko-Yashchuk,S., Miller,H.B., Wang,Y.F., Kovalevsky,A.Y., Koh,Y., Weber,I.T. and Mitsuya,H. Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies Org Biomol Chem (2008) 6, 3703-3713. PubMed Europe PubMed DOI I
Ghosh,A.K., Chapsal,B.D., Baldridge,A., Ide,K., Koh,Y. and Mitsuya,H. Design and synthesis of stereochemically defined novel spirocyclic P2-ligands for HIV-1 protease inhibitors Org Lett (2008) 10, 5135-5138. PubMed Europe PubMed DOI PMC EPMC I
Giffin,M.J., Heaslet,H., Brik,A., Lin,Y.C., Cauvi,G., Wong,C.H., McRee,D.E., Elder,J.H., Stout,C.D. and Torbett,B.E. A copper(I)-catalyzed 1,2,3-triazole azide-alkyne click compound is a potent inhibitor of a multidrug-resistant HIV-1 protease variant J Med Chem (2008) 51, 6263-6270. PubMed Europe PubMed DOI PMC EPMC I
Gonzalez,L.M., Santos,A.F., Abecasis,A.B., Van Laethem,K., Soares,E.A., Deforche,K., Tanuri,A., Camacho,R., Vandamme,A.M. and Soares,M.A. Impact of HIV-1 protease mutations A71V/T and T74S on M89I/V-mediated protease inhibitor resistance in subtype G isolates J Antimicrob Chemother (2008) 61, 1201-1204. PubMed Europe PubMed DOI
Gulnik,S.V. and Eissenstat,M. Approaches to the design of HIV protease inhibitors with improved resistance profiles Curr Opin HIV AIDS (2008) 3, 633-641. PubMed Europe PubMed DOI V I
Hamacher,K. Relating sequence evolution of HIV1-protease to its underlying molecular mechanics Gene (2008) 422, 30-36. PubMed Europe PubMed DOI
Hosur,M.V. and Prashar,V. HIV-1 protease crystallography at BARC J Indian Inst Sci (2008) 88, 95-105. S
Ishima,R. and Louis,J.M. A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps Proteins (2008) 70, 1408-1415. PubMed Europe PubMed DOI S
Johnson,V.A., Brun-Vezinet,F., Clotet,B., Gunthard,H.F., Kuritzkes,D.R., Pillay,D., Schapiro,J.M. and Richman,D.D. Update of the drug resistance mutations in HIV-1: Spring 2008 Top HIV Med (2008) 16, 62-68. PubMed Europe PubMed
Kim,R. and Baxter,J.D. Protease inhibitor resistance update: where are we now? AIDS Patient Care STDS (2008) 22, 267-277. PubMed Europe PubMed DOI I
Kona,J. Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease Org Biomol Chem (2008) 6, 359-365. PubMed Europe PubMed DOI I
Kovalevsky,A.Y., Ghosh,A.K. and Weber,I.T. Solution Kinetics Measurements Suggest HIV-1 Protease Has Two Binding Sites for Darunavir and Amprenavir J Med Chem (2008) 51, 6599-6603. PubMed Europe PubMed DOI PMC EPMC I
Kozisek,M., Cigler,P., Lepsik,M., Fanfrlik,J., Rezacova,P., Brynda,J., Pokorna,J., Plesek,J., Gruner,B., Grantz Saskova,K., Vaclavikova,J., Kral,V. and Konvalinka,J. Inorganic polyhedral metallacarborane inhibitors of HIV protease: a new approach to overcoming antiviral resistance J Med Chem (2008) 51, 4839-4843. PubMed Europe PubMed DOI I
Kozisek,M., Saskova,K.G., Rezacova,P., Brynda,J., van Maarseveen,N.M., de Jong,D., Boucher,C.A., Kagan,R.M., Nijhuis,M. and Konvalinka,J. Ninety-nine is not enough: molecular characterization of inhibitor-resistant human immunodeficiency virus type 1 protease mutants with insertions in the flap region J Virol (2008) 82, 5869-5878. PubMed Europe PubMed DOI PMC EPMC
Kumar,S., Garg,R., Alla,S.R., Zhang,X. and Jalahalli,V.K. 3D-shape analysis of the HIV-1 protease ligand binding site [ISSN:ISBN 978-1-4244-1778-0] (2008) 2008, 151-158. DOI S
Lambert-Niclot,S., Flandre,P., Canestri,A., Peytavin,G., Blanc,C., Agher,R., Soulie,C., Wirden,M., Katlama,C., Calvez,V. and Marcelin,A.G. Factors associated with the selection of mutations conferring resistance to protease inhibitors (PIs) in PI-experienced patients displaying treatment failure on darunavir Antimicrob Agents Chemother (2008) 52, 491-496. PubMed Europe PubMed DOI PMC EPMC I
Liu,F., Kovalevsky,A.Y., Tie,Y., Ghosh,A.K., Harrison,R.W. and Weber,I.T. Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir J Mol Biol (2008) 381, 102-115. PubMed Europe PubMed DOI PMC EPMC S I
Margerison,E.S., Maguire,M., Pillay,D., Cane,P. and Elston,R.C. The HIV-1 protease substitution K55R: a protease-inhibitor-associated substitution involved in restoring viral replication J Antimicrob Chemother (2008) 61, 786-791. PubMed Europe PubMed DOI
Matsumura,H., Adachi,M., Sugiyama,S., Okada,S., Yamakami,M., Tamada,T., Hidaka,K., Hayashi,Y., Kimura,T., Kiso,Y., Kitatani,T., Maki,S., Yoshikawa,H.Y., Adachi,H., Takano,K., Murakami,S., Inoue,T., Kuroki,R. and Mori,Y. Crystallization and preliminary neutron diffraction studies of HIV-1 protease cocrystallized with inhibitor KNI-272 Acta Crystallograph Sect F Struct Biol Cryst Commun (2008) 64, 1003-1006. PubMed Europe PubMed DOI PMC EPMC I
Mihara,H., Sohtome,Y., Matsunaga,S. and Shibasaki,M. Chiral-catalyst-based convergent synthesis of HIV protease inhibitor GRL-06579A Chem Asian J (2008) 3, 359-366. PubMed Europe PubMed DOI I
Miklossy,G., Tozser,J., Kadas,J., Ishima,R., Louis,J.M. and Bagossi,P. Novel macromolecular inhibitors of human immunodeficiency virus-1 protease Protein Eng Des Sel (2008) 21, 453-461. PubMed Europe PubMed DOI I
Mimoto,T., Nojima,S., Terashima,K., Takaku,H., Shintani,M. and Hayashi,H. Structure-activity relationships of novel HIV-1 protease inhibitors containing the 3-amino-2-chlorobenzoyl-allophenylnorstatine structure Bioorg Med Chem (2008) 16, 1299-1308. PubMed Europe PubMed DOI I
Mosebi,S., Morris,L., Dirr,H.W. and Sayed,Y. Active-site mutations in the South african human immunodeficiency virus type 1 subtype C protease have a significant impact on clinical inhibitor binding: kinetic and thermodynamic study J Virol (2008) 82, 11476-11479. PubMed Europe PubMed DOI PMC EPMC I
Nakatani,S., Hidaka,K., Ami,E., Nakahara,K., Sato,A., Nguyen,J.T., Hamada,Y., Hori,Y., Ohnishi,N., Nagai,A., Kimura,T., Hayashi,Y. and Kiso,Y. Combination of non-natural d-amino acid derivatives and allophenylnorstatine-dimethylthioproline scaffold in HIV protease inhibitors have high efficacy in mutant HIV J Med Chem (2008) 51, 2992-3004. PubMed Europe PubMed DOI I
Nalam,M.N. and Schiffer,C.A. New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors Curr Opin HIV AIDS (2008) 3, 642-646. PubMed Europe PubMed DOI PMC EPMC V I
Narendra Babu,S.N. and Rangappa,K.S. Design, synthesis and structure-activity study of shorter hexa peptide analogues as HIV-1 protease inhibitors Bioorg Med Chem (2008) 16, 874-880. PubMed Europe PubMed DOI I
Nie,Z., Bren,G.D., Rizza,S.A. and Badley,A.D. HIV Protease cleavage of procaspase 8 is necessary for death of HIV-infected cells Open Virol J (2008) 2, 1-7. PubMed Europe PubMed DOI PMC EPMC
Nijhuis,M., van Maarseveen,N.M., Verheyen,J. and Boucher,C.A. Novel mechanisms of HIV protease inhibitor resistance Curr Opin HIV AIDS (2008) 3, 627-632. PubMed Europe PubMed DOI I
Nunthanavanit,P., Anthony,N.G., Johnston,B.F., Mackay,S.P. and Ungwitayatorn,J. 3D-QSAR Studies on chromone derivatives as HIV-1 protease inhibitors: application of molecular field analysis Arch Pharm (Weinheim) (2008) 341, 357-364. PubMed Europe PubMed DOI I
Poveda,E. New resistance score for tipranavir AIDS Rev (2008) 10, 127-127. PubMed Europe PubMed I
Purohit,R., Rajasekaran,R., Sudandiradoss,C., George Priya Doss,C., Ramanathan,K. and Rao,S. Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants Int J Biol Macromol (2008) 42, 386-391. PubMed Europe PubMed DOI I
Raza,A., Sham,Y.Y. and Vince,R. Design and synthesis of sulfoximine based inhibitors for HIV-1 protease Bioorg Med Chem Lett (2008) 18, 5406-5410. PubMed Europe PubMed DOI I
Saskova,K.G., Kozisek,M., Lepsik,M., Brynda,J., Rezacova,P., Vaclavikova,J., Kagan,R.M., Machala,L. and Konvalinka,J. Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir Protein Sci (2008) 17, 1555-1564. PubMed Europe PubMed DOI PMC EPMC S I
Sayer,J.M., Liu,F., Ishima,R., Weber,I.T. and Louis,J.M. Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease J Biol Chem (2008) 283, 13459-13470. PubMed Europe PubMed DOI PMC EPMC
Schlick,P. and Skern,T. Investigating human immunodeficiency virus-1 proteinase specificity at positions P4 to P2 using a bacterial screening system Anal Biochem (2008) 377, 162-169. PubMed Europe PubMed DOI P
Sherman,W. and Tidor,B. Novel method for probing the specificity binding profile of ligands: applications to HIV protease Chem Biol Drug Des (2008) 71, 387-407. PubMed Europe PubMed DOI
Singh,G. and Senapati,S. Molecular dynamics simulations of ligand-induced flap closing in HIV-1 protease approach X-ray resolution: establishing the role of bound water in the flap closing mechanism Biochemistry (2008) 47, 10657-10664. PubMed Europe PubMed DOI S
Sista,P., Wasikowski,B., Lecocq,P., Pattery,T. and Bacheler,L. The HIV-1 protease resistance mutation I50L is associated with resistance to atazanavir and susceptibility to other protease inhibitors in multiple mutational contexts J Clin Virol (2008) 42, 405-408. PubMed Europe PubMed DOI
Stoica,I., Sadiq,S.K. and Coveney,P.V. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases J Am Chem Soc (2008) 130, 2639-2648. PubMed Europe PubMed DOI I
Suresh,C.H., Vargheese,A.M., Vijayalakshmi,K.P., Mohan,N. and Koga,N. Role of structural water molecule in HIV protease-inhibitor complexes: a QM/MM study J Comput Chem (2008) 29, 1840-1849. PubMed Europe PubMed DOI I
Tang,C., Louis,J.M., Aniana,A., Suh,J.Y. and Clore,G.M. Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease Nature (2008) 455, 693-696. PubMed Europe PubMed DOI
Torbeev,V.Y., Mandal,K., Terechko,V.A. and Kent,S.B. Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site Bioorg Med Chem Lett (2008) 18, 4554-4557. PubMed Europe PubMed DOI S I
Tyndall,J.D., Pattenden,L.K., Reid,R.C., Hu,S.H., Alewood,D., Alewood,P.F., Walsh,T., Fairlie,D.P. and Martin,J.L. Crystal structures of highly constrained substrate and hydrolysis products bound to HIV-1 protease. Implications for the catalytic mechanism Biochemistry (2008) 47, 3736-3744. PubMed Europe PubMed DOI S
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2007

Amano,M., Koh,Y., Das,D., Li,J., Leschenko,S., Wang,Y.F., Boross,P.I., Weber,I.T., Ghosh,A.K. and Mitsuya,H. A novel bis-tetrahydrofuranylurethane-containing nonpeptidic protease inhibitor (PI), GRL-98065, is potent against multiple-PI-resistant human immunodeficiency virus in vitro Antimicrob Agents Chemother (2007) 51, 2143-2155. PubMed Europe PubMed DOI PMC EPMC I
Bannwarth,L. and Reboud-Ravaux,M. An alternative strategy for inhibiting multidrug-resistant mutants of the dimeric HIV-1 protease by targeting the subunit interface Biochem Soc Trans (2007) 35, 551-554. PubMed Europe PubMed DOI I
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Chang,C.E., Trylska,J., Tozzini,V. and McCammon,J.A. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations Chem Biol Drug Des (2007) 69, 5-13. PubMed Europe PubMed DOI I
Chellappan,S., Kairys,V., Fernandes,M.X., Schiffer,C. and Gilson,M.K. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease Proteins (2007) 68, 561-567. PubMed Europe PubMed DOI
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Coman,R.M., Robbins,A., Goodenow,M.M., McKenna,R. and Dunn,B.M. Expression, purification and preliminary X-ray crystallographic studies of the human immunodeficiency virus 1 subtype C protease Acta Crystallograph Sect F Struct Biol Cryst Commun (2007) 63, 320-323. PubMed Europe PubMed DOI PMC EPMC S
Czodrowski,P., Sotriffer,C.A. and Klebe,G. Atypical protonation states in the active site of HIV-1 protease: a computational study J Chem Inf Model (2007) 47, 1590-1598. PubMed Europe PubMed DOI
Dandache,S., Sevigny,G., Yelle,J., Stranix,B.R., Parkin,N., Schapiro,J.M., Wainberg,M.A. and Wu,J.J. In vitro antiviral activity and cross-resistance profile of PL-100, a novel protease inhibitor of human immunodeficiency virus type 1 Antimicrob Agents Chemother (2007) 51, 4036-4043. PubMed Europe PubMed DOI PMC EPMC I
Das,A., Rao,D.R. and Hosur,M.V. X-Ray structure of HIV-1 protease tethered dimer complexed to Ritonavir Protein Pept Lett (2007) 14, 565-568. PubMed Europe PubMed S
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Duan,L.L., Tong,Y., Mei,Y., Zhang,Q.G. and Zhang,J.Z. Quantum study of HIV-1 protease-bridge water interaction J Chem Phys (2007) 127, 145101-145101. PubMed Europe PubMed DOI
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Frutos,S., Tulla-Puche,J., Albericio,F. and Giralt,E. Chemical synthesis of 19F-labeled HIV-1 protease using Fmoc-chemistry and chemmatrix resin Int J Pept Res Ther (2007) 13, 221-227. DOI
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Hou,T. and Yu,R. Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with Amprenavir and two Amprenavir-related inhibitors: mechanism for binding and drug resistance J Med Chem (2007) 50, 1177-1188. PubMed Europe PubMed DOI I
Ishima,R., Torchia,D.A. and Louis,J.M. Mutational and structural studies aimed at characterizing the monomer of HIV-1 protease and its precursor J Biol Chem (2007) 282, 17190-17199. PubMed Europe PubMed DOI
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Johnson,V.A., Brun-Vezinet,F., Clotet,B., Gunthard,H.F., Kuritzkes,D.R., Pillay,D., Schapiro,J.M. and Richman,D.D. Update of the drug resistance mutations in HIV-1: 2007 Top HIV Med (2007) 15, 119-125. PubMed Europe PubMed
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Kontijevskis,A., Prusis,P., Petrovska,R., Yahorava,S., Mutulis,F., Mutule,I., Komorowski,J. and Wikberg,J.E. A look inside HIV resistance through retroviral protease interaction maps PLoS Comput Biol (2007) 3, e48-e48. PubMed Europe PubMed DOI PMC EPMC P
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Kozisek,M., Bray,J., Rezacova,P., Saskova,K., Brynda,J., Pokorna,J., Mammano,F., Rulisek,L. and Konvalinka,J. Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants J Mol Biol (2007) 374, 1005-1016. PubMed Europe PubMed DOI S I
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Lauria,A., Ippolito,M. and Almerico,A.M. Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant J Mol Model (2007) 13, 1151-1156. PubMed Europe PubMed DOI
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Louis,J.M., Ishima,R., Torchia,D.A. and Weber,I.T. HIV-1 protease: structure, dynamics, and inhibition Adv Pharmacol (2007) 55, 261-298. PubMed Europe PubMed DOI V
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Mastrolorenzo,A., Rusconi,S., Scozzafava,A., Barbaro,G. and Supuran,C.T. Inhibitors of HIV-1 protease: current state of the art 10 years after their introduction. From antiretroviral drugs to antifungal, antibacterial and antitumor agents based on aspartic protease inhibitors Curr Med Chem (2007) 14, 2734-2748. PubMed Europe PubMed DOI V I
Mo,H., Parkin,N., Stewart,K.D., Lu,L., Dekhtyar,T., Kempf,D.J. and Molla,A. Identification and structural characterization of I84C and I84A mutations that are associated with high-level resistance to human immunodeficiency virus protease inhibitors and impair viral replication Antimicrob Agents Chemother (2007) 51, 732-735. PubMed Europe PubMed DOI PMC EPMC
Muzammil,S., Armstrong,A.A., Kang,L.W., Jakalian,A., Bonneau,P.R., Schmelmer,V., Amzel,L.M. and Freire,E. Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations J Virol (2007) 81, 5144-5154. PubMed Europe PubMed DOI PMC EPMC I
Nalam,M.N., Peeters,A., Jonckers,T.H., Dierynck,I. and Schiffer,C.A. Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease J Virol (2007) 81, 9512-9518. PubMed Europe PubMed DOI PMC EPMC S I
Nie,Z., Bren,G.D., Vlahakis,S.R., Schimnich,A.A., Brenchley,J.M., Trushin,S.A., Warren,S., Schnepple,D.J., Kovacs,C.M., Loutfy,M.R., Douek,D.C. and Badley,A.D. Human immunodeficiency virus type 1 protease cleaves procaspase 8 in vivo J Virol (2007) 81, 6947-6956. PubMed Europe PubMed DOI PMC EPMC
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Ode,H., Matsuyama,S., Hata,M., Neya,S., Kakizawa,J., Sugiura,W. and Hoshino,T. Computational characterization of structural role of the non-active site mutation M36I of human immunodeficiency virus type 1 protease J Mol Biol (2007) 370, 598-607. PubMed Europe PubMed DOI
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Poon,A.F., Kosakovsky Pond,S.L., Richman,D.D. and Frost,S.D. Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients J Virol (2007) 81, 13598-13607. PubMed Europe PubMed DOI PMC EPMC
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Reddy,G.S., Ali,A., Nalam,M.N., Anjum,S.G., Cao,H., Nathans,R.S., Schiffer,C.A. and Rana,T.M. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres J Med Chem (2007) 50, 4316-4328. PubMed Europe PubMed DOI I
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2006

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Bandyopadhyay,P. and Meher,B.R. Drug resistance of HIV-1 protease against JE-2147: I47V mutation investigated by molecular dynamics simulation Chem Biol Drug Des (2006) 67, 155-161. PubMed Europe PubMed DOI I
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[YEAR:28-12-2006]Whiting,M., Tripp,J.C., Lin,Y.C., Lindstrom,W., Olson,A.J., Elder,J.H., Sharpless,K.B. and Fokin,V.V. Rapid discovery and structure-activity profiling of novel inhibitors of human immunodeficiency virus type 1 protease enabled by the copper(i)-catalyzed synthesis of 1,2,3-triazoles and their further functionalization J Med Chem (28-12-2006) 49, 7697-7710. PubMed Europe PubMed DOI I
Whiting,M., Muldoon,J., Lin,Y.C., Silverman,S.M., Lindstrom,W., Olson,A.J., Kolb,H.C., Finn,M.G., Sharpless,K.B., Elder,J.H. and Fokin,V.V. Inhibitors of HIV-1 protease by using in situ click chemistry Angew Chem Int Ed Engl (2006) 45, 1435-1439. PubMed Europe PubMed DOI I
You,L. Detection of cleavage sites for HIV-1 protease in native proteins Comput Syst Bioinformatics Conf (2006) 2006, 249-256. PubMed Europe PubMed P
You,L., Garwicz,D. and Rognvaldsson,T. Erratum: Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease (Journal of Virology (2005) 79, 19 (12477-12486)) J Virol (2006) 80, 4205- PubMed Europe PubMed DOI PMC EPMC

2005

[YEAR:1-2-2005]Ax,A., Schaal,W., Vrang,L., Samuelsson,B., Hallberg,A. and Karlen,A. Cyclic sulfamide HIV-1 protease inhibitors, with sidechains spanning from P2/P2' to P1/P1' Bioorg Med Chem (1-2-2005) 13, 755-764. PubMed Europe PubMed DOI I
Bagossi,P., Sperka,T., Feher,A., Kadas,J., Zahuczky,G., Miklossy,G., Boross,P. and Tozser,J. Amino acid preferences for a critical substrate binding subsite of retroviral proteases in type 1 cleavage sites J Virol (2005) 79, 4213-4218. PubMed Europe PubMed DOI PMC EPMC P
[YEAR:1-3-2005]Bouzide,A., Sauve,G. and Yelle,J. Lysine derivatives as potent HIV protease inhibitors. Discovery, synthesis and structure-activity relationship studies Bioorg Med Chem Lett (1-3-2005) 15, 1509-1513. PubMed Europe PubMed DOI I
Bowman,M.J., Byrne,S. and Chmielewski,J. Switching between allosteric and dimerization inhibition of HIV-1 protease Chem Biol (2005) 12, 439-444. PubMed Europe PubMed DOI I
Broglia,R.A., Tiana,G., Sutto,L., Provasi,D. and Simona,F. Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers Protein Sci (2005) 14, 2668-2681. PubMed Europe PubMed DOI PMC EPMC I
[YEAR:1-6-2005]Calazans,A., Brindeiro,R., Brindeiro,P., Verli,H., Arruda,M.B., Gonzalez,L.M., Guimaraes,J.A., Diaz,R.S., Antunes,O.A. and Tanuri,A. Low accumulation of L90M in protease from subtype FHIV-1 with resistance to protease inhibitors is caused by the L89M polymorphism J Infect Dis (1-6-2005) 191, 1961-1970. PubMed Europe PubMed DOI
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[YEAR:25-10-2005]Cigler,P., Kozisek,M., Rezacova,P., Brynda,J., Otwinowski,Z., Pokorna,J., Plesek,J., Gruner,B., Doleckova-Maresova,L., Masa,M., Sedlacek,J., Bodem,J., Krausslich,H.G., Kral,V. and Konvalinka,J. From nonpeptide toward noncarbon protease inhibitors: metallacarboranes as specific and potent inhibitors of HIV protease Proc Natl Acad Sci U S A (25-10-2005) 102, 15394-15399. PubMed Europe PubMed DOI PMC EPMC I
De Meyer,S., Azijn,H., Surleraux,D., Jochmans,D., Tahri,A., Pauwels,R., Wigerinck,P. and de Bethune,M.P. TMC114, a novel human immunodeficiency virus type 1 protease inhibitor active against protease inhibitor-resistant viruses, including a broad range of clinical isolates Antimicrob Agents Chemother (2005) 49, 2314-2321. PubMed Europe PubMed DOI PMC EPMC I
[YEAR:15-12-2005]Ekegren,J.K., Unge,T., Safa,M.Z., Wallberg,H., Samuelsson,B. and Hallberg,A. A new class of HIV-1 protease inhibitors containing a tertiary alcohol in the transition-state mimicking scaffold J Med Chem (15-12-2005) 48, 8098-8102. PubMed Europe PubMed DOI I
Ellis,J.M. and Ross,J. A novel nonpeptidic protease inhibitor Formulary (2005) 40 I
Fuster,D. and Clotet,B. Review of atazanavir: a novel HIV protease inhibitor Expert Opin Pharmacother (2005) 6, 1565-1572. PubMed Europe PubMed DOI I
[YEAR:19-5-2005]Ghosh,A.K., Swanson,L.M., Cho,H., Leshchenko,S., Hussain,K.A., Kay,S., Walters,D.E., Koh,Y. and Mitsuya,H. Structure-based design: synthesis and biological evaluation of a series of novel cycloamide-derived HIV-1 protease inhibitors J Med Chem (19-5-2005) 48, 3576-3585. PubMed Europe PubMed DOI I
Hoffmann,D., Buchberger,B. and Nemetz,C. In vitro synthesis of enzymatically active HIV-1 protease for rapid phenotypic resistance profiling J Clin Virol (2005) 32, 294-299. PubMed Europe PubMed DOI E
[YEAR:24-3-2005]Hwang,Y.S. and Chmielewski,J. Development of low molecular weight HIV-1 protease dimerization inhibitors J Med Chem (24-3-2005) 48, 2239-2242. PubMed Europe PubMed DOI I
Johnson,V.A., Brun-Vezinet,F., Clotet,B., Conway,B., Kuritzkes,D.R., Pillay,D., Schapiro,J.M., Telenti,A. and Richman,D.D. Update of the drug resistance mutations in HIV-1: Fall 2005 Top HIV Med (2005) 13, 125-131. PubMed Europe PubMed
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Kandula,V.R., Khanlou,H. and Farthing,C. Tipranavir: a novel second-generation nonpeptidic protease inhibitor Expert Rev Anti Infect Ther (2005) 3, 9-21. PubMed Europe PubMed DOI I
Kaplan,S.S. and Hicks,C.B. Lopinavir/ritonavir in the treatment of human immunodeficiency virus infection Expert Opin Pharmacother (2005) 6, 1573-1585. PubMed Europe PubMed DOI I
[YEAR:23-11-2005]Kovalskyy,D., Dubyna,V., Mark,A.E. and Kornelyuk,A. A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: the role of Na+ ions in stabilizing the active site Proteins (23-11-2005) 58, 450-458. PubMed Europe PubMed DOI
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[YEAR:1-12-2005]Lu,Z., Bohn,J., Rano,T., Rutkowski,C.A., Simcoe,A.L., Olsen,D.B., Schleif,W.A., Carella,A., Gabryelski,L., Jin,L., Lin,J.H., Emini,E., Chapman,K. and Tata,J.R. Orally bioavailable highly potent HIV protease inhibitors against PI-resistant virus Bioorg Med Chem Lett (1-12-2005) 15, 5311-5314. PubMed Europe PubMed DOI I
Martin,P., Vickrey,J.F., Proteasa,G., Jimenez,Y.L., Wawrzak,Z., Winters,M.A., Merigan,T.C. and Kovari,L.C. "Wide-open" 1.3 A structure of a multidrug-resistant HIV-1 protease as a drug target Structure (2005) 13, 1887-1895. PubMed Europe PubMed DOI S
[YEAR:1-11-2005]Meagher,K.L. and Carlson,H.A. Solvation influences flap collapse in HIV-1 protease Proteins (1-11-2005) 58, 119-125. PubMed Europe PubMed DOI
Ohtaka,H. and Freire,E. Adaptive inhibitors of the HIV-1 protease Prog Biophys Mol Biol (2005) 88, 193-208. PubMed Europe PubMed DOI I
[YEAR:1-11-2005]Pettit,S.C., Lindquist,J.N., Kaplan,A.H. and Swanstrom,R. Processing sites in the human immunodeficiency virus type 1 (HIV-1) Gag-Pro-Pol precursor are cleaved by the viral protease at different rates Retrovirology (1-11-2005) 2, 66-66. PubMed Europe PubMed DOI PMC EPMC
[YEAR:28-4-2005]Prasanna,M.D., Vondrasek,J., Wlodawer,A. and Bhat,T.N. Application of InChI to curate, index, and query 3-D structures Proteins (28-4-2005) 60, 1-4. PubMed Europe PubMed DOI
[YEAR:3-1-2005]Sherrill,R.G., Andrews,C.W., Bock,W.J., Davis-Ward,R.G., Furfine,E.S., Hazen,R.J., Rutkowske,R.D., Spaltenstein,A. and Wright,L.L. Optimization of pyrrolidinone based HIV protease inhibitors Bioorg Med Chem Lett (3-1-2005) 15, 81-84. PubMed Europe PubMed DOI I
[YEAR:20-6-2005]Sherrill,R.G., Furfine,E.S., Hazen,R.J., Miller,J.F., Reynolds,D.J., Sammond,D.M., Spaltenstein,A., Wheelan,P. and Wright,L.L. Synthesis and antiviral activities of novel N-alkoxy-arylsulfonamide-based HIV protease inhibitors Bioorg Med Chem Lett (20-6-2005) 15, 3560-3564. PubMed Europe PubMed DOI I
Spaltenstein,A., Kazmierski,W.M., Miller,J.F. and Samano,V. Discovery of next generation inhibitors of HIV protease Curr Top Med Chem (2005) 5, 1589-1607. PubMed Europe PubMed DOI V I
Specker,E., Bottcher,J., Lilie,H., Heine,A., Schoop,A., Muller,G., Griebenow,N. and Klebe,G. An old target revisited: two new privileged skeletons and an unexpected binding mode for HIV-protease inhibitors Angew Chem Int Ed Engl (2005) 44, 3140-3144. PubMed Europe PubMed DOI I
[YEAR:20-10-2005]Specker,E., Bottcher,J., Heine,A., Sotriffer,C.A., Lilie,H., Schoop,A., Muller,G., Griebenow,N. and Klebe,G. Hydroxyethylene sulfones as a new scaffold to address aspartic proteases: design, synthesis, and structural characterization J Med Chem (20-10-2005) 48, 6607-6619. PubMed Europe PubMed DOI S I
[YEAR:24-3-2005]Surleraux,D.L., Tahri,A., Verschueren,W.G., Pille,G.M., de Kock,H.A., Jonckers,T.H., Peeters,A., De Meyer,S., Azijn,H., Pauwels,R., de Bethune,M.P., King,N.M., Prabu-Jeyabalan,M., Schiffer,C.A. and Wigerinck,P.B. Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor J Med Chem (24-3-2005) 48, 1813-1822. PubMed Europe PubMed DOI I
[YEAR:24-3-2005]Surleraux,D.L., de Kock,H.A., Verschueren,W.G., Pille,G.M., Maes,L.J., Peeters,A., Vendeville,S., De Meyer,S., Azijn,H., Pauwels,R., de Bethune,M.P., King,N.M., Prabu-Jeyabalan,M., Schiffer,C.A. and Wigerinck,P.B. Design of HIV-1 protease inhibitors active on multidrug-resistant virus J Med Chem (24-3-2005) 48, 1965-1973. PubMed Europe PubMed DOI I
Svedhem,V., Lindkvist,A., Bergroth,T., Knut,L. and Sonnerborg,A. Diverse pattern of protease inhibitor resistance mutations in HIV-1 infected patients failing nelfinavir J Med Virol (2005) 76, 447-451. PubMed Europe PubMed DOI I
Svicher,V., Ceccherini-Silberstein,F., Erba,F., Santoro,M., Gori,C., Bellocchi,M.C., Giannella,S., Trotta,M.P., Monforte,A., Antinori,A. and Perno,C.F. Novel human immunodeficiency virus type 1 protease mutations potentially involved in resistance to protease inhibitors Antimicrob Agents Chemother (2005) 49, 2015-2025. PubMed Europe PubMed DOI PMC EPMC I
Tie,Y., Boross,P.I., Wang,Y.F., Gaddis,L., Liu,F., Chen,X., Tozser,J., Harrison,R.W. and Weber,I.T. Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs FEBS J (2005) 272, 5265-5277. PubMed Europe PubMed DOI PMC EPMC S I
Ventoso,I., Navarro,J., Munoz,M.A. and Carrasco,L. Involvement of HIV-1 protease in virus-induced cell killing Antiviral Res (2005) 66, 47-55. PubMed Europe PubMed DOI
Weinheimer,S., Discotto,L., Friborg,J., Yang,H. and Colonno,R. Atazanavir signature I50L resistance substitution accounts for unique phenotype of increased susceptibility to other protease inhibitors in a variety of human immunodeficiency virus type 1 genetic backbones Antimicrob Agents Chemother (2005) 49, 3816-3824. PubMed Europe PubMed DOI PMC EPMC I
Winters,M.A., Kagan,R.M., Heseltine,P.N. and Merigan,T.C. New two-amino acid insertion near codon 70 of the HIV type 1 protease gene AIDS Res Hum Retroviruses (2005) 21, 311-313. PubMed Europe PubMed DOI M
Winters,M.A. and Merigan,T.C. Insertions in the human immunodeficiency virus type 1 protease and reverse transcriptase genes: clinical impact and molecular mechanisms Antimicrob Agents Chemother (2005) 49, 2575-2582. PubMed Europe PubMed DOI PMC EPMC
Yanchunas,J., Jr., Langley,D.R., Tao,L., Rose,R.E., Friborg,J., Colonno,R.J. and Doyle,M.L. Molecular basis for increased susceptibility of isolates with atazanavir resistance-conferring substitution I50L to other protease inhibitors Antimicrob Agents Chemother (2005) 49, 3825-3832. PubMed Europe PubMed DOI PMC EPMC I
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You,L., Garwicz,D. and Rognvaldsson,T. Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease J Virol (2005) 79, 12477-12486. PubMed Europe PubMed DOI PMC EPMC P
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2004

Abdel-Rahman,H.M., el-Koussi,N.A., Alkaramany,G.S., Youssef,A.F. and Kiso,Y. A novel dipeptide-based HIV protease inhibitor containing allophenylnorstatine Arch Pharm (Weinheim) (2004) 337, 587-598. PubMed Europe PubMed DOI I
Abdel-Rahman,H.M., Kimura,T., Hidaka,K., Kiso,A., Nezami,A., Freire,E., Hayashi,Y. and Kiso,Y. Design of inhibitors against HIV, HTLV-I, and Plasmodium falciparum aspartic proteases Biol Chem (2004) 385, 1035-1039. PubMed Europe PubMed DOI
Bagossi,P., Kadas,J., Miklossy,G., Boross,P., Weber,I.T. and Tozser,J. Development of a microtiter plate fluorescent assay for inhibition studies on the HTLV-1 and HIV-1 proteinases J Virol Methods (2004) 119, 87-93. PubMed Europe PubMed DOI A I
Boyle,B.A., Elion,R.A., Moyle,G.J. and Cohen,C.J. Considerations in selecting protease inhibitor therapy AIDS Rev (2004) 6, 218-225. PubMed Europe PubMed
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Brynda,J., Rezacova,P., Fabry,M., Horejsi,M., Stouracova,R., Soucek,M., Hradilek,M., Konvalinka,J. and Sedlacek,J. Inhibitor binding at the protein interface in crystals of a HIV-1 protease complex Acta Crystallogr D Biol Crystallogr (2004) 60, 1943-1948. PubMed Europe PubMed DOI S I
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de Mendoza,C. and Soriano,V. Resistance to HIV protease inhibitors: mechanisms and clinical consequences Curr Drug Metab (2004) 5, 321-328. PubMed Europe PubMed DOI I
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Gonzalez,L.M., Brindeiro,R.M., Aguiar,R.S., Pereira,H.S., Abreu,C.M., Soares,M.A. and Tanuri,A. Impact of nelfinavir resistance mutations on in vitro phenotype, fitness, and replication capacity of human immunodeficiency virus type 1 with subtype B and C proteases Antimicrob Agents Chemother (2004) 48, 3552-3555. PubMed Europe PubMed DOI PMC EPMC I
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[YEAR:16-11-2004]Hanlon,M.H., Porter,D.J., Furfine,E.S., Spaltenstein,A., Carter,H.L., Danger,D., Shu,A.Y., Kaldor,I.W., Miller,J.F. and Samano,V.A. Inhibition of wild-type and mutant human immunodeficiency virus type 1 proteases by GW0385 and other arylsulfonamides Biochemistry (16-11-2004) 43, 14500-14507. PubMed Europe PubMed DOI I
[YEAR:15-11-2004]Kazmierski,W.M., Furfine,E., Gray-Nunez,Y., Spaltenstein,A. and Wright,L. Potent inhibitors of the HIV-1 protease incorporating cyclic urea P1-P2 scaffold Bioorg Med Chem Lett (15-11-2004) 14, 5685-5687. PubMed Europe PubMed DOI I
[YEAR:15-11-2004]Kazmierski,W.M., Andrews,W., Furfine,E., Spaltenstein,A. and Wright,L. Discovery of potent pyrrolidone-based HIV-1 protease inhibitors with enhanced drug-like properties Bioorg Med Chem Lett (15-11-2004) 14, 5689-5692. PubMed Europe PubMed DOI I
[YEAR:20-9-2004]Kim,R.M., Rouse,E.A., Chapman,K.T., Schleif,W.A., Olsen,D.B., Stahlhut,M., Rutkowski,C.A., Emini,E.A. and Tata,J.R. P1' oxadiazole protease inhibitors with excellent activity against native and protease inhibitor-resistant HIV-1 Bioorg Med Chem Lett (20-9-2004) 14, 4651-4654. PubMed Europe PubMed DOI I
King,N.M., Prabu-Jeyabalan,M., Nalivaika,E.A., Wigerinck,P., de Bethune,M.P. and Schiffer,C.A. Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor J Virol (2004) 78, 12012-12021. PubMed Europe PubMed DOI PMC EPMC S I
Kovalskyy,D.B., Dubina,V.M. and Kornelyuk,A.I. Molecular dynamics simulation study of effect of the conservative Leu10-->Ile mutation on intramolecular mobility of HIV-1 protease Biopolym Cell (2004) 20, 321-324. DOI
Kumar,S. and Seth,P. Immunogenicity of recombinant modified vaccinia Ankara viruses (rMVA) expressing HIV-1 Indian subtype C gag-protease and env-gp120 genes in mice Viral Immunol (2004) 17, 574-579. PubMed Europe PubMed DOI
Leigh Brown,A.J., Frost,S.D., Good,B., Daar,E.S., Simon,V., Markowitz,M., Collier,A.C., Connick,E., Conway,B., Margolick,J.B., Routy,J.P., Corbeil,J., Hellmann,N.S., Richman,D.D. and Little,S.J. Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection J Virol (2004) 78, 2242-2246. PubMed Europe PubMed DOI PMC EPMC I
Lindberg,J., Pyring,D., Lowgren,S., Rosenquist,A., Zuccarello,G., Kvarnstrom,I., Zhang,H., Vrang,L., Classon,B., Hallberg,A., Samuelsson,B. and Unge,T. Symmetric fluoro-substituted diol-based HIV protease inhibitors. Ortho-fluorinated and meta-fluorinated P1/P1'-benzyloxy side groups significantly improve the antiviral activity and preserve binding efficacy Eur J Biochem (2004) 271, 4594-4602. PubMed Europe PubMed DOI I
Logsdon,B.C., Vickrey,J.F., Martin,P., Proteasa,G., Koepke,J.I., Terlecky,S.R., Wawrzak,Z., Winters,M.A., Merigan,T.C. and Kovari,L.C. Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity J Virol (2004) 78, 3123-3132. PubMed Europe PubMed DOI PMC EPMC S I
Mahalingam,B., Wang,Y.F., Boross,P.I., Tozser,J., Louis,J.M., Harrison,R.W. and Weber,I.T. Crystal structures of HIV protease V82A and L90M mutants reveal changes in the indinavir-binding site Eur J Biochem (2004) 271, 1516-1524. PubMed Europe PubMed DOI S I
[YEAR:2-12-2004]Merabet,N., Dumond,J., Collinet,B., Van Baelinghem,L., Boggetto,N., Ongeri,S., Ressad,F., Reboud-Ravaux,M. and Sicsic,S. New constrained "molecular tongs" designed to dissociate HIV-1 protease dimer J Med Chem (2-12-2004) 47, 6392-6400. PubMed Europe PubMed DOI I
[YEAR:23-2-2004]Miller,J.F., Furfine,E.S., Hanlon,M.H., Hazen,R.J., Ray,J.A., Robinson,L., Samano,V. and Spaltenstein,A. Novel arylsulfonamides possessing sub-picomolar HIV protease activities and potent anti-HIV activity against wild-type and drug-resistant viral strains Bioorg Med Chem Lett (23-2-2004) 14, 959-963. PubMed Europe PubMed DOI I
[YEAR:2-1-2004]Mimoto,T., Terashima,K., Nojima,S., Takaku,H., Nakayama,M., Shintani,M., Yamaoka,T. and Hayashi,H. Structure-activity and structure-metabolism relationships of HIV protease inhibitors containing the 3-hydroxy-2-methylbenzoyl-allophenylnorstatine structure Bioorg Med Chem (2-1-2004) 12, 281-293. PubMed Europe PubMed DOI I
[YEAR:1-7-2004]Musial,B.L., Chojnacki,J.K. and Coleman,C.I. Atazanavir: a new protease inhibitor to treat HIV infection Am J Health Syst Pharm (1-7-2004) 61, 1365-1374. PubMed Europe PubMed I
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Petrokova,H., Duskova,J., Dohnalek,J., Skalova,T., Vondrackova-Buchtelova,E., Soucek,M., Konvalinka,J., Brynda,J., Fabry,M., Sedlacek,J. and Hasek,J. Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors Eur J Biochem (2004) 271, 4451-4461. PubMed Europe PubMed DOI I
Pettit,S.C., Everitt,L.E., Choudhury,S., Dunn,B.M. and Kaplan,A.H. Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism J Virol (2004) 78, 8477-8485. PubMed Europe PubMed DOI PMC EPMC
Piliero,P.J. Atazanavir: a novel once-daily protease inhibitor Drugs Today (Barc) (2004) 40, 901-912. PubMed Europe PubMed DOI I
Prabu-Jeyabalan,M., Nalivaika,E.A., King,N.M. and Schiffer,C.A. Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease J Virol (2004) 78, 12446-12454. PubMed Europe PubMed DOI PMC EPMC
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Sanches,M., Helena Martins,N., Calazans,A., de Moraes Brindeiro,R., Tanuri,A., Antunes,O.A. and Polikarpov,I. Crystallization of a non-B and a B mutant HIV protease Acta Crystallogr D Biol Crystallogr (2004) 60, 1625-1627. PubMed Europe PubMed DOI M S I
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Trylska,J., Grochowski,P. and McCammon,J.A. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease Protein Sci (2004) 13, 513-528. PubMed Europe PubMed DOI PMC EPMC
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2003

Alvarez,E., Menendez-Arias,L. and Carrasco,L. The eukaryotic translation initiation factor 4GI is cleaved by different retroviral proteases J Virol (2003) 77, 12392-12400. PubMed Europe PubMed DOI PMC EPMC
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Dautin,N., Karimova,G. and Ladant,D. Human immunodeficiency virus (HIV) type 1 transframe protein can restore activity to a dimerization-deficient HIV protease variant J Virol (2003) 77, 8216-8226. PubMed Europe PubMed DOI PMC EPMC
Davis,D.A., Brown,C.A., Newcomb,F.M., Boja,E.S., Fales,H.M., Kaufman,J., Stahl,S.J., Wingfield,P. and Yarchoan,R. Reversible oxidative modification as a mechanism for regulating retroviral protease dimerization and activation J Virol (2003) 77, 3319-3325. PubMed Europe PubMed DOI PMC EPMC
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Karlsson,A.C., Deeks,S.G., Barbour,J.D., Heiken,B.D., Younger,S.R., Hoh,R., Lane,M., Sallberg,M., Ortiz,G.M., Demarest,J.F., Liegler,T., Grant,R.M., Martin,J.N. and Nixon,D.F. Dual pressure from antiretroviral therapy and cell-mediated immune response on the human immunodeficiency virus type 1 protease gene J Virol (2003) 77, 6743-6752. PubMed Europe PubMed DOI PMC EPMC
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Mehandru,S. and Markowitz,M. Tipranavir: a novel non-peptidic protease inhibitor for the treatment of HIV infection Expert Opin Investig Drugs (2003) 12, 1821-1828. PubMed Europe PubMed DOI I
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Prabu-Jeyabalan,M., Nalivaika,E.A., King,N.M. and Schiffer,C.A. Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy J Virol (2003) 77, 1306-1315. PubMed Europe PubMed DOI PMC EPMC I
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Schaller,M., Bein,M., Korting,H.C., Baur,S., Hamm,G., Monod,M., Beinhauer,S. and Hube,B. The secreted aspartyl proteinases Sap1 and Sap2 cause tissue damage in an in vitro model of vaginal candidiasis based on reconstituted human vaginal epithelium Infect Immun (2003) 71, 3227-3234. PubMed Europe PubMed DOI PMC EPMC I
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Skalova,T., Hasek,J., Dohnalek,J., Petrokova,H., Buchtelova,E., Duskova,J., Soucek,M., Majer,P., Uhlikova,T. and Konvalinka,J. An ethylenamine inhibitor binds tightly to both wild type and mutant HIV-1 proteases. Structure and energy study J Med Chem (2003) 46, 1636-1644. PubMed Europe PubMed DOI S I
Smith,A.B., III, Cantin,L.D., Pasternak,A., Guise-Zawacki,L., Yao,W., Charnley,A.K., Barbosa,J., Sprengeler,P.A., Hirschmann,R., Munshi,S., Olsen,D.B., Schleif,W.A. and Kuo,L.C. Design, synthesis, and biological evaluation of monopyrrolinone-based HIV-1 protease inhibitors J Med Chem (2003) 46, 1831-1844. PubMed Europe PubMed DOI S I
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2002

Badalassi,F., Nguyen,H.K., Crotti,P. and Reymond,J.L. A selective HIV-protease assay based on a chromogenic amino acid Helv Chim Acta (2002) 85, 3090-3098. A
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2001

Beck,Z.Q., Lin,Y.C. and Elder,J.H. Molecular basis for the relative substrate specificity of human immunodeficiency virus type 1 and feline immunodeficiency virus proteases J Virol (2001) 75, 9458-9469. PubMed Europe PubMed DOI PMC EPMC
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2000

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1999

Dunn,B.M., Pennington,M.W., Frase,D.C. and Nash,K. Comparison of inhibitor binding to feline and human immunodeficiency virus proteases: structure-based drug design and the resistance problem Biopolymers (1999) 51, 69-77. PubMed Europe PubMed DOI I
Kashparov,I.V., Popov,M.E., Rumsh,L.D. and Popov,E.M. [Mechanism of action of aspartyl proteinases. VI. Noncovalent enzyme-inhibitory and enzyme-substrate complexes of the aspartyl proteinase rhizopus pepsin] Bioorg Khim (1999) 25, 747-762. PubMed Europe PubMed
Kashparov,I.V., Popov,M.E., Rumsh,L.D. and Popov,E.M. [Mechanism of action of aspartic proteinases. V. Conformational characteristics of fragments of substrate-binding sites in rhizopuspepsin and HIV-1 proteinase] Bioorg Khim (1999) 25, 597-602. PubMed Europe PubMed
Kiso,Y., Matsumoto,H., Mizumoto,S., Kimura,T., Fujiwara,Y. and Akaji,K. Small dipeptide-based HIV protease inhibitors containing the hydroxymethylcarbonyl isostere as an ideal transition-state mimic Biopolymers (1999) 51, 59-68. PubMed Europe PubMed DOI I
Mahalingam,B., Louis,J.M., Reed,C.C., Adomat,J.M., Krouse,J., Wang,Y.F., Harrison,R.W. and Weber,I.T. Structural and kinetic analysis of drug resistant mutants of HIV-1 protease Eur J Biochem (1999) 263, 238-245. PubMed Europe PubMed DOI S
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Martinez-Picado,J., Savara,A.V., Sutton,L. and D'Aquila,R.T. Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1 J Virol (1999) 73, 3744-3752. PubMed Europe PubMed PMC EPMC
Nijhuis,M., Schuurman,R., de Jong,D., Erickson,J., Gustchina,E., Albert,J., Schipper,P., Gulnik,S. and Boucher,C.A. Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy AIDS (1999) 13, 2349-2359. PubMed Europe PubMed DOI
[YEAR:5-3-1999]Ringhofer,S., Kallen,J., Dutzler,R., Billich,A., Visser,A.J., Scholz,D., Steinhauser,O., Schreiber,H., Auer,M. and Kungl,A.J. X-ray structure and conformational dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: agreement of time-resolved spectroscopy and molecular dynamics simulations J Mol Biol (5-3-1999) 286, 1147-1159. PubMed Europe PubMed DOI I
Thaisrivongs,S. and Strohbach,J.W. Structure-based discovery of Tipranavir disodium (PNU-140690E): a potent, orally bioavailable, nonpeptidic HIV protease inhibitor Biopolymers (1999) 51, 51-58. PubMed Europe PubMed DOI I
[YEAR:1-8-1999]Todd,M.J. and Freire,E. The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease Proteins (1-8-1999) 36, 147-156. PubMed Europe PubMed DOI I
[YEAR:20-7-1999]Yoshimura,K., Kato,R., Yusa,K., Kavlick,M.F., Maroun,V., Nguyen,A., Mimoto,T., Ueno,T., Shintani,M., Falloon,J., Masur,H., Hayashi,H., Erickson,J. and Mitsuya,H. JE-2147: a dipeptide protease inhibitor (PI) that potently inhibits multi-PI-resistant HIV-1 Proc Natl Acad Sci U S A (20-7-1999) 96, 8675-8680. PubMed Europe PubMed DOI PMC EPMC S I

1998

Ala,P.J., Huston,E.E., Klabe,R.M., Jadhav,P.K., Lam,P.Y. and Chang,C.H. Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities Biochemistry (1998) 37, 15042-15049. PubMed Europe PubMed DOI S I
Ala,P.J., DeLoskey,R.J., Huston,E.E., Jadhav,P.K., Lam,P.Y., Eyermann,C.J., Hodge,C.N., Schadt,M.C., Lewandowski,F.A., Weber,P.C., McCabe,D.D., Duke,J.L. and Chang,C.H. Molecular recognition of cyclic urea HIV-1 protease inhibitors J Biol Chem (1998) 273, 12325-12331. PubMed Europe PubMed DOI S I
Bagossi,P., Cheng,Y.S., Oroszlan,S. and Tozser,J. Comparison of the specificity of homo- and heterodimeric linked HIV-1 and HIV-2 proteinase dimers Protein Eng (1998) 11, 439-445. PubMed Europe PubMed
Bold,G., Fassler,A., Capraro,H.G., Cozens,R., Klimkait,T., Lazdins,J., Mestan,J., Poncioni,B., Rosel,J., Stover,D., Tintelnot-Blomley,M., Acemoglu,F., Beck,W., Boss,E., Eschbach,M., Hurlimann,T., Masso,E., Roussel,S., Ucci-Stoll,K., Wyss,D. and Lang,M. New aza-dipeptide analogues as potent and orally absorbed HIV-1 protease inhibitors: candidates for clinical development J Med Chem (1998) 41, 3387-3401. PubMed Europe PubMed DOI I
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Ghosh,A.K., Kincaid,J.F., Cho,W., Walters,D.E., Krishnan,K., Hussain,K.A., Koo,Y., Cho,H., Rudall,C., Holland,L. and Buthod,J. Potent HIV protease inhibitors incorporating high-affinity P2-ligands and (R)-(hydroxyethylamino)sulfonamide isostere Bioorg Med Chem Lett (1998) 8, 687-690. PubMed Europe PubMed DOI I
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Kervinen,J., Lubkowski,J., Zdanov,A., Bhatt,D., Dunn,B.M., Hui,K.Y., Powell,D.J., Kay,J., Wlodawer,A. and Gustchina,A. Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV Protein Sci (1998) 7, 2314-2323. PubMed Europe PubMed DOI PMC EPMC S I
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Sham,H.L., Kempf,D.J., Molla,A., Marsh,K.C., Kumar,G.N., Chen,C.M., Kati,W., Stewart,K., Lal,R., Hsu,A., Betebenner,D., Korneyeva,M., Vasavanonda,S., McDonald,E., Saldivar,A., Wideburg,N., Chen,X., Niu,P., Park,C., Jayanti,V., Grabowski,B., Granneman,G.R., Sun,E., Japour,A.J., Leonard,J.M., Plattner,J.J. and Norbeck,D.W. ABT-378, a highly potent inhibitor of the human immunodeficiency virus protease Antimicrob Agents Chemother (1998) 42, 3218-3224. PubMed Europe PubMed PMC EPMC I
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Wlodawer,A. and Vondrasek,J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design Annu Rev Biophys Biomol Struct (1998) 27, 249-284. PubMed Europe PubMed DOI V I
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1997

[YEAR:18-2-1997]Ala,P.J., Huston,E.E., Klabe,R.M., McCabe,D.D., Duke,J.L., Rizzo,C.J., Korant,B.D., DeLoskey,R.J., Lam,P.Y., Hodge,C.N. and Chang,C.H. Molecular basis of HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with cyclic urea inhibitors Biochemistry (18-2-1997) 36, 1573-1580. PubMed Europe PubMed DOI S I
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Bardi,J.S., Luque,I. and Freire,E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors Biochemistry (1997) 36, 6588-6596. PubMed Europe PubMed DOI I
Bukovsky,A.A., Dorfman,T., Weimann,A. and Gottlinger,H.G. Nef association with human immunodeficiency virus type 1 virions and cleavage by the viral protease J Virol (1997) 71, 1013-1018. PubMed Europe PubMed PMC EPMC I
Cornelissen,M., van den Burg,R., Zorgdrager,F., Lukashov,V. and Goudsmit,J. pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D J Virol (1997) 71, 6348-6358. PubMed Europe PubMed PMC EPMC I
Fournout,S., Roquet,F., Salhi,S.L., Seyer,R., Valverde,V., Masson,J.M., Jouin,P., Pau,B., Nicolas,M. and Hanin,V. Development and standardization of an immuno-quantified solid phase assay for HIV-1 aspartyl protease activity and its application to the evaluation of inhibitors Anal Chem (1997) 69, 1746-1752. PubMed Europe PubMed A
Geller,M., Miller,M., Swanson,S.M. and Maizel,J. Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region Proteins (1997) 27, 195-203. PubMed Europe PubMed DOI S I
Hong,L., Zhang,X.J., Foundling,S., Hartsuck,J.A. and Tang,J. Structure of a G48H mutant of HIV-1 protease explains how glycine-48 replacements produce mutants resistant to inhibitor drugs FEBS Lett (1997) 420, 11-16. PubMed Europe PubMed DOI S
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Janetka,J.W., Raman,P., Satyshur,K., Flentke,G.R. and Rich,D.H. Novel cyclic biphenyl ether peptide beta-strand mimetics and HIV-protease inhibitors J Am Chem Soc (1997) 119, 441-442. DOI I
Kaldor,S.W., Kalish,V.J., Davies,J.F., Shetty,B.V., Fritz,J.E., Appelt,K., Burgess,J.A., Campanale,K.M., Chirgadze,N.Y., Clawson,D.K., Dressman,B.A., Hatch,S.D., Khalil,D.A., Kosa,M.B., Lubbehusen,P.P., Muesing,M.A., Patick,A.K., Reich,S.H., Su,K.S. and Tatlock,J.H. Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease J Med Chem (1997) 40, 3979-3985. PubMed Europe PubMed DOI I
Kempf,D.J., Molla,A., Marsh,K.C., Park,C., Rodrigues,A.D., Korneyeva,M., Vasavanonda,S., McDonald,E., Flentge,C.A., Muchmore,S., Wideburg,N.E., Saldivar,A., Cooper,A., Kati,W.M., Stewart,K.D. and Norbeck,D.W. Lack of stereospecificity in the binding of the P2 amino acid of ritonavir to HIV protease Bioorg Med Chem Lett (1997) 7, 699-704. S I
Lange-Savage,G., Berchtold,H., Liesum,A., Budt,K.H., Peyman,A., Knolle,J., Sedlacek,J., Fabry,M. and Hilgenfeld,R. Structure of HOE/BAY 793 complexed to human immunodeficiency virus (HIV-1) protease in two different crystal forms - structure/function relationship and influence of crystal packing Eur J Biochem (1997) 248, 313-322. PubMed Europe PubMed S I
Miller,M., Geller,M., Gribskov,M. and Kent,S.B. Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: Crystallographic refinement of 2 A data Proteins (1997) 27, 184-194. PubMed Europe PubMed DOI S I
Misumi,S., Kudo,A., Azuma,R., Tomonaga,M., Furuishi,K. and Shoji,S. The p2gag peptide, AEAMSQVTNTATIM, processed from HIV-1 pr55gag was found to be a suicide inhibitor of HIV-1 protease Biochem Biophys Res Commun (1997) 241, 275-280. PubMed Europe PubMed DOI I
Okimoto,N., Makiyama,M., Hata,M. and Tsuda,M. Gag protein hydrolysis mechanism by HIV-1 protease - investigation by semiempirical molecular orbital method Nippon Kagaku Kaishi Chem Soc Japan Chem Indus Chem J (1997) 1997, 260-266.
Peyman,A., Budt,K.H., Stowasser,B., Hansen,J., Jian-Qi,L., Knolle,J., Meichsner,C., Paessens,A., Ruppert,D., Spanig,J. and Winkler,I. Structure-activity relationships in a series of C2-symmetric HIV-protease inhibitors Pharmacochem Libr (1997) 28, 397-408. DOI I
Skulnick,H.I., Johnson,P.D., Aristoff,P.A., Morris,J.K., Lovasz,K.D., Howe,W.J., Watenpaugh,K.D., Janakiraman,M.N., Anderson,D.J., Reischer,R.J., Schwartz,T.M., Banitt,L.S., Tomich,P.K., Lynn,J.C., Horng,M.M., Chong,K.T., Hinshaw,R.R., Dolak,L.A., Seest,E.P., Schwende,F.J., Rush,B.D., Howard,G.M., Toth,L.N., Wilkinson,K.R. and Romines,K.R. Structure-based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyramones J Med Chem (1997) 40, 1149-1164. PubMed Europe PubMed DOI S I
Stebbins,J. and Debouck,C. A microtiter colorimetric assay for the HIV-1 protease Anal Biochem (1997) 248, 246-250. PubMed Europe PubMed DOI A
Tozser,J. Specificity of retroviral proteinases based on substrates containing tyrosine and proline at the site of cleavage Pathol Oncol.Res (1997) 3, 142-146. PubMed Europe PubMed P
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Vance,J.E., LeBlanc,D.A., Wingfield,P. and London,R.E. Conformational selectivity of HIV-1 protease cleavage of X-Pro peptide bonds and its implications J Biol Chem (1997) 272, 15603-15606. PubMed Europe PubMed DOI P
Vondrasek,J., van Buskirk,C.P. and Wlodawer,A. Database of three-dimensional structures of HIV proteinases Nat Struct Biol (1997) 4, 8-8. PubMed Europe PubMed DOI S
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Wilson,S.I., Phylip,L.H., Mills,J.S., Gulnik,S.V., Erickson,J.W., Dunn,B.M. and Kay,J. Escape mutants of HIV-1 proteinase: enzymic efficiency and susceptibility to inhibition Biochim Biophys Acta (1997) 1339, 113-125. PubMed Europe PubMed DOI I

1996

Abbenante,G., Bergman,D.A., Brinkworth,R.I., March,D.R., Reid,R.C., Hunt,P.A., James,I.W., Dancer,R.J., Garnham,B., Stoermer,M.L. and Fairlie,D.P. Structure-activity relationships for macrocyclic peptidomimetic inhibitors of HIV-1 protease Bioorg Med Chem Lett (1996) 6, 2531-2536. I
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Hong,L., Treharne,A., Hartsuck,J.A., Foundling,S. and Tang,J. Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases Biochemistry (1996) 35, 10627-10633. PubMed Europe PubMed DOI S I
Hoog,S.S., Towler,E.M., Zhao,B., Doyle,M.L., Debouck,C. and Abdel-Meguid,S.S. Human immunodeficiency virus protease ligand specificity conferred by residues outside of the active site cavity Biochemistry (1996) 35, 10279-10286. PubMed Europe PubMed DOI S
Kervinen,J., Thanki,N., Zdanov,A., Tino,J., Barrish,J., Lin,P.F., Colonno,R., Riccardi,K., Samanta,H. and Wlodawer,A. Structural analysis of the native and drug-resistant HIV-1 proteinases complexed with an aminodiol inhibitor Protein Pept Lett (1996) 3, 399-406. S I
Kozal,M.J., Shah,N., Shen,N., Yang,R., Fucini,R., Merigan,T.C., Richman,D.D., Morris,D., Hubbell,E., Chee,M. and Gingeras,T.R. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays Nat Med (1996) 2, 753-759. PubMed Europe PubMed DOI M
March,D.R., Abbenante,G., Bergman,D.A., Brinkworth,R.I., Wickramasinghe,W., Begun,J., Martin,J.L. and Fairlie,D.P. Substrate-based cyclic peptidomimetics of Phe-Ile-Val that inhibit HIV-1 protease using a novel enzyme-binding mode J Am Chem Soc (1996) 118, 3375-3379. DOI S I
Maschera,B., Darby,G., Palu,G., Wright,L.L., Tisdale,M., Myers,R., Blair,E.D. and Furfine,E.S. Human immunodeficiency virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex J Biol Chem (1996) 271, 33231-33235. PubMed Europe PubMed DOI I
Molla,A., Korneyeva,M., Gao,Q., Vasavanonda,S., Schipper,P.J., Mo,H.M., Markowitz,M., Chernyavskiy,T., Niu,P., Lyons,N., Hsu,A., Granneman,G.R., Ho,D.D., Boucher,C.A., Leonard,J.M., Norbeck,D.W. and Kempf,D.J. Ordered accumulation of mutations in HIV protease confers resistance to ritonavir Nat Med (1996) 2, 760-766. PubMed Europe PubMed DOI I
Ott,D.E., Coren,L.V., Kane,B.P., Busch,L.K., Johnson,D.G., Sowder,R.C., Chertova,E.N., Arthur,L.O. and Henderson,L.E. Cytoskeletal proteins inside human immunodeficiency virus type 1 virions J Virol (1996) 70, 7734-7743. PubMed Europe PubMed PMC EPMC
Rose,R.B., Craik,C.S., Douglas,N.L. and Stroud,R.M. Three-dimensional structures of HIV-1 and SIV protease product complexes Biochemistry (1996) 35, 12933-12944. PubMed Europe PubMed DOI
Rutenber,E.E., McPhee,F., Kaplan,A.P., Gallion,S.L., Hogan,J.C., Jr., Craik,C.S. and Stroud,R.M. A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere Bioorg Med Chem (1996) 4, 1545-1558. PubMed Europe PubMed DOI S I
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Sham,H.L., Zhao,C., Stewart,K.D., Betebenner,D.A., Lin,S., Park,C.H., Kong,X.P., Rosenbrook,W., Jr., Herrin,T., Madigan,D., Vasavanonda,S., Lyons,N., Molla,A., Saldivar,A., Marsh,K.C., McDonald,E., Wideburg,N.E., Denissen,J.F., Robins,T., Kempf,D.J., Plattner,J.J. and Norbeck,D.W. A novel, picomolar inhibitor of human immunodeficiency virus type 1 protease J Med Chem (1996) 39, 392-397. PubMed Europe PubMed DOI S I
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Smith,R., Brereton,I.M., Chai,R.Y. and Kent,S.B. Ionization states of the catalytic residues in HIV-1 protease Nat Struct Biol (1996) 3, 946-950. PubMed Europe PubMed DOI I
Stebbins,J., Deckman,I.C., Richardson,S.B. and Debouck,C. A heterologous substrate assay for the HIV-1 protease engineered in Escherichia coli Anal Biochem (1996) 242, 90-94. PubMed Europe PubMed DOI A
Thaisrivongs,S., Skulnick,H.I., Turner,S.R., Strohbach,J.W., Tommasi,R.A., Johnson,P.D., Aristoff,P.A., Judge,T.M., Gammill,R.B., Morris,J.K., Romines,K.R., Chrusciel,R.A., Hinshaw,R.R., Chong,K.T., Tarpley,W.G., Poppe,S.M., Slade,D.E., Lynn,J.C., Horng,M.M., Tomich,P.K., Seest,E.P., Dolak,L.A., Howe,W.J., Howard,G.M. and Watenpaugh,K.D. Structure-based design of HIV protease inhibitors: sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors J Med Chem (1996) 39, 4349-4353. PubMed Europe PubMed DOI S I
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Wondrak,E.M., Nashed,N.T., Haber,M.T., Jerina,D.M. and Louis,J.M. A transient precursor of the HIV-1 protease. Isolation, characterization, and kinetics of maturation J Biol Chem (1996) 271, 4477-4481. PubMed Europe PubMed

1995

Abbenante,G., March,D.R., Bergman,D.A., Hunt,P.A., Garnham,B., Dancer,R.J., Martin,J.L. and Fairlie,D.P. Regioselective structural and functional mimicry of peptides. Design of hydrolytically-stable cyclic peptidomimetic inhibitors of HIV-1 protease J Am Chem Soc (1995) 117, 10220-10226. DOI S I
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Collins,J.R., Burt,S.K. and Erickson,J.W. Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics Nat Struct Biol (1995) 2, 334-338. PubMed Europe PubMed
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Eberle,J., Bechowsky,B., Rose,D., Hauser,U., von der Helm,K., Gurtler,L. and Nitschko,H. Resistance of HIV type 1 to proteinase inhibitor Ro 31-8959 AIDS Res Hum Retroviruses (1995) 11, 671-676. PubMed Europe PubMed I
Fan,N., Rank,K.B., Leone,J.W., Heinrikson,R.L., Bannow,C.A., Smith,C.W., Evans,D.B., Poppe,S.M., Tarpley,W.G. and Rothrock,D.J. The differential processing of homodimers of reverse transcriptases from human immunodeficiency viruses type 1 and 2 is a consequence of the distinct specificities of the viral proteases J Biol Chem (1995) 270, 13573-13579. PubMed Europe PubMed
Gulnik,S.V., Suvorov,L.I., Liu,B., Yu,B., Anderson,B., Mitsuya,H. and Erickson,J.W. Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure Biochemistry (1995) 34, 9282-9287. PubMed Europe PubMed DOI I
Gustafson,M.E., Junger,K.D., Foy,B.A., Baez,J.A., Bishop,B.F., Rangwala,S.H., Michener,M.L., Leimgruber,R.M., Houseman,K.A. and Mueller,R.A. Large-scale production of HIV-1 protease from Escherichia coli using selective extraction and membrane fractionation Protein Expr Purif (1995) 6, 512-518. PubMed Europe PubMed DOI E
[YEAR:18-8-1995]Hoog,S.S., Zhao,B., Winborne,E., Fisher,S., Green,D.W., DesJarlais,R.L., Newlander,K.A., Callahan,J.F., Moore,M.L. and Huffman,W.F. A check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor J Med Chem (18-8-1995) 38, 3246-3252. PubMed Europe PubMed DOI S I
[YEAR:10-1-1995]Jacobsen,H., Yasargil,K., Winslow,D.L., Craig,J.C., Krohn,A., Duncan,I.B. and Mous,J. Characterization of human immunodeficiency virus type 1 mutants with decreased sensitivity to proteinase inhibitor Ro 31-8959 Virology (10-1-1995) 206, 527-534. PubMed Europe PubMed DOI I
[YEAR:28-3-1995]Kempf,D.J., Marsh,K.C., Denissen,J.F., McDonald,E., Vasavanonda,S., Flentge,C.A., Green,B.E., Fino,L., Park,C.H. and Kong,X.P. ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans Proc Natl Acad Sci U S A (28-3-1995) 92, 2484-2488. PubMed Europe PubMed DOI PMC EPMC I
Kim,E.E., Baker,C.T., Dwyer,M.D., Murcko,M.A., Rao,B.G., Tung,R.D. and Navia,M.A. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme J Am Chem Soc (1995) 117, 1181-1182. DOI S I
Nicholson,L.K., Yamazaki,T., Torchia,D.A., Grzesiek,S., Bax,A., Stahl,S.J., Kaufman,J.D., Wingfield,P.T., Lam,P.Y.S., Jadhav,P.K., Hodge,C.N., Domaille,P.J. and Chang,C.H. Flexibility and function in HIV-1 protease Nat Struct Biol (1995) 2, 274-280. PubMed Europe PubMed
Priestle,J.P., Fassler,A., Rosel,J., Tintelnot-Blomley,M., Strop,P. and Grutter,M.G. Erratum: Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor (vol 3, pg 381, 1995) Structure (1995) 3, 629-629. PubMed Europe PubMed I
Thaisrivongs,S., Watenpaugh,K.D., Howe,W.J., Tomich,P.K., Dolak,L.A., Chong,K.T., Tomich,C.C., Tomasselli,A.G., Turner,S.R. and Strohbach,J.W. Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors J Med Chem (1995) 38, 3624-3637. PubMed Europe PubMed S I
Tisdale,M., Myers,R.E., Maschera,B., Parry,N.R., Oliver,N.M. and Blair,E.D. Cross-resistance analysis of human immunodeficiency virus type 1 variants individually selected for resistance to five different protease inhibitors Antimicrobial Agents Chemother (1995) 39, 1704-1710. PubMed Europe PubMed PMC EPMC I

1994

Abdel-Meguid,S.S., Metcalf,B.W., Carr,T.J., Demarsh,P., DesJarlais,R.L., Fisher,S., Green,D.W., Ivanoff,L., Lambert,D.M. and Murthy,K.H. An orally bioavailable HIV-1 protease inhibitor containing an imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis Biochemistry (1994) 33, 11671-11677. PubMed Europe PubMed DOI S I
Cameron,C.E., Ridky,T.W., Shulenin,S., Leis,J., Weber,I.T., Copeland,T., Wlodawer,A., Burstein,H., Bizub-Bender,D. and Skalka,A.M. Mutational analysis of the substrate binding pockets of the Rous sarcoma virus and human immunodeficiency virus-1 proteases J Biol Chem (1994) 269, 11170-11177. PubMed Europe PubMed
[YEAR:14-10-1994]Dorsey,B.D., Levin,R.B., McDaniel,S.L., Vacca,J.P., Guare,J.P., Darke,P.L., Zugay,J.A., Emini,E.A., Schleif,W.A. and Quintero,J.C. L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor J Med Chem (14-10-1994) 37, 3443-3451. PubMed Europe PubMed DOI I
Dunn,B.M., Gustchina,A., Wlodawer,A. and Kay,J. Subsite preferences of retroviral proteinases Methods Enzymol (1994) 241, 254-278. PubMed Europe PubMed V
[YEAR:15-4-1994]Greer,J., Erickson,J.W., Baldwin,J.J. and Varney,M.D. Application of the three-dimensional structures of protein target molecules in structure-based drug design J Med Chem (15-4-1994) 37, 1035-1054. PubMed Europe PubMed I
Harte,W.E., Jr. and Beveridge,D.L. Probing structure-function relationships in human immunodeficiency virus type 1 protease via molecular dynamics simulation Methods Enzymol (1994) 241, 178-195. PubMed Europe PubMed
Hellen,C.U. Assay methods for retroviral proteases Methods Enzymol (1994) 241, 46-58. PubMed Europe PubMed V
Ho,D.D., Toyoshima,T., Mo,H., Kempf,D.J., Norbeck,D., Chen,C.M., Wideburg,N.E., Burt,S.K., Erickson,J.W. and Singh,M.K. Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor J Virol (1994) 68, 2016-2020. PubMed Europe PubMed PMC EPMC I
Hoeprich,P.D., Jr. Chemical synthesis of the aspartic proteinase from human immunodeficiency virus (HIV) Methods Mol Biol (1994) 36, 287-304. PubMed Europe PubMed DOI
Hosur,M.V., Bhat,T.N., Kempf,D.J., Baldwin,E.T., Liu,B., Gulnik,S., Wideburg,N.E., Norbeck,D.W., Appelt,K. and Erickson,J.W. Influence of stereochemistry on activity and binding modes for C2 symmetry-based diol inhibitors of HIV-1 protease J Am Chem Soc (1994) 116, 847-855. I
Katz,R.A. and Skalka,A.M. The retroviral enzymes Annu Rev Biochem (1994) 63, 133-173. PubMed Europe PubMed DOI
Kempf,D.J. Design of symmetry-based, peptidomimetic inhibitors of human immunodeficiency virus protease Methods Enzymol (1994) 241, 334-354. PubMed Europe PubMed V I
Lin,X.L., Lin,Y.Z. and Tang,J. Relationships of human immunodeficiency virus protease with eukaryotic aspartic proteases Methods Enzymol (1994) 241, 195-224. PubMed Europe PubMed V
Mildner,A.M., Rothrock,D.J., Leone,J.W., Bannow,C.A., Lull,J.M., Reardon,I.M., Sarcich,J.L., Howe,W.J., Tomich,C.S.C., Smith,C.W., Heinrikson,R.L. and Tomasselli,A.G. The HIV-1 protease as enzyme and substrate: mutagenesis of autolysis sites and generation of a stable mutant with retained kinetic properties Biochemistry (1994) 33, 9405-9413. PubMed Europe PubMed
Polgar,L., Szeltner,Z. and Boros,I. Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease Biochemistry (1994) 33, 9351-9357. PubMed Europe PubMed
Ringe,D. X-ray structures of retroviral proteases and their inhibitor-bound complexes Methods Enzymol (1994) 241, 157-177. PubMed Europe PubMed S
Rose,J.R. and Craik,C.S. Structure-assisted design of nonpeptide human immunodeficiency virus-1 protease inhibitors Am J Respir Crit Care Med (1994) 150, S176-S182. PubMed Europe PubMed DOI I
Sardana,V.V., Schlabach,A.J., Graham,P., Bush,B.L., Condra,J.H., Culberson,J.C., Gotlib,L., Graham,D.J., Kohl,N.E., LaFemina,R.L., Schneider,C.L., Wolanski,B.S., Wolfgang,J.A. and Emini,E.A. Human immunodeficiency virus type 1 protease inhibitors: evaluation of resistance engendered by amino acid substitutions in the enzyme's substrate binding site Biochemistry (1994) 33, 2004-2010. PubMed Europe PubMed I
Thompson,S.K., Murthy,K.H., Zhao,B., Winborne,E., Green,D.W., Fisher,S.M., DesJarlais,R.L., Tomaszek,T.A., Jr., Meek,T.D. and Gleason,J.G. Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'-P2' amide bond isostere J Med Chem (1994) 37, 3100-3107. PubMed Europe PubMed DOI S I
Tomasselli,A.G. and Heinrikson,R.L. Specificity of retroviral proteases: an analysis of viral and nonviral protein substrates Methods Enzymol (1994) 241, 279-301. PubMed Europe PubMed P
Vacca,J.P. Design of tight-binding human immunodeficiency virus type 1 protease inhibitors Methods Enzymol (1994) 241, 311-334. PubMed Europe PubMed I
[YEAR:26-4-1994]Vacca,J.P., Dorsey,B.D., Schleif,W.A., Levin,R.B., McDaniel,S.L., Darke,P.L., Zugay,J., Quintero,J.C., Blahy,O.M. and Roth,E. L-735,524: an orally bioavailable human immunodeficiency virus type 1 protease inhibitor Proc Natl Acad Sci U S A (26-4-1994) 91, 4096-4100. PubMed Europe PubMed PMC EPMC I

1993

Appelt,K. Crystal structures of HIV-1 protease-inhibitor complexes Perspect Drug Discov Design (1993) 1, 23-48. DOI S I
Athauda,S.B., Ido,E., Arakawa,H., Nishigai,M., Kyushiki,H., Yoshinaka,Y., Takahashi,T., Ikai,A., Tang,J. and Takahashi,K. Entrapment and inhibition of human immunodeficiency virus proteinase by alpha2-macroglobulin and structural changes in the inhibitor J Biochem (1993) 113, 742-746. PubMed Europe PubMed
[YEAR:5-6-1993]Cameron,C.E., Grinde,B., Jacques,P., Jentoft,J., Leis,J., Wlodawer,A. and Weber,I.T. Comparison of the substrate-binding pockets of the Rous sarcoma virus and human immunodeficiency virus type 1 proteases J Biol Chem (5-6-1993) 268, 11711-11720. PubMed Europe PubMed
Dougherty,W.G. and Semler,B.L. Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes Microbiol Rev (1993) 57, 781-822. PubMed Europe PubMed PMC EPMC
Dreyer,G.B., Boehm,J.C., Chenera,B., DesJarlais,R.L., Hassell,A.M., Meek,T.D., Tomaszek,T.A. and Lewis,M. A symmetric inhibitor binds HIV-1 protease asymmetrically Biochemistry (1993) 32, 937-947. PubMed Europe PubMed DOI S I
Erickson,J.W. Design and structure of symmetry-based inhibitors of HIV-1 protease Perspect Drug Discov Design (1993) 1, 109-128. DOI I
Moore,M.L. and Dreyer,G.B. Substrate-based inhibitors of HIV-1 protease Perspect Drug Discov Design (1993) 1, 85-108. DOI I
[YEAR:15-8-1993]Otto,M.J., Garber,S., Winslow,D.L., Reid,C.D., Aldrich,P., Jadhav,P.K., Patterson,C.E., Hodge,C.N. and Cheng,Y.S. In vitro isolation and identification of human immunodeficiency virus (HIV) variants with reduced sensitivity to C-2 symmetrical inhibitors of HIV type 1 protease Proc Natl Acad Sci U S A (15-8-1993) 90, 7543-7547. PubMed Europe PubMed PMC EPMC I
Pettit,S.C., Michael,S.F. and Swanstrom,R. The specificity of the HIV-1 protease Perspect Drug Discov Design (1993) 1, 69-83. DOI P
[YEAR:25-7-1993]Rutenber,E., Fauman,E.B., Keenan,R.J., Fong,S., Furth,P.S., Ortiz,d.M., Meng,E., Kuntz,I.D., DeCamp,D.L. and Salto,R. Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design J Biol Chem (25-7-1993) 268, 15343-15346. PubMed Europe PubMed S I
[YEAR:30-7-1993]Schramm,H.J., Billich,A., Jaeger,E., Rucknagel,K.P., Arnold,G. and Schramm,W. The inhibition of HIV-1 protease by interface peptides Biochem Biophys Res Commun (30-7-1993) 194, 595-600. PubMed Europe PubMed DOI I
[YEAR:23-8-1993]Sham,H.L., Betebenner,D.A., Wideburg,N., Saldivar,A.C., Kohlbrenner,W.E., Craig-Kennard,A., Vasavanonda,S., Kempf,D.J., Clement,J.J. and Erickson,J.E. Pseudo-symmetrical difluoroketones. Highly potent and specific inhibitors of HIV-1 protease FEBS Lett (23-8-1993) 329, 144-146. PubMed Europe PubMed DOI I
Wlodawer,A. and Erickson,J.W. Structure-based inhibitors of HIV-1 protease Annu Rev Biochem (1993) 62, 543-585. PubMed Europe PubMed DOI V I

1992

Ainsztein,A.M. and Purich,D.L. Cleavage of bovine brain microtubule-associated protein-2 by human immunodeficiency virus proteinase J Neurochem (1992) 59, 874-880. PubMed Europe PubMed
Grinde,B., Cameron,C.E., Leis,J., Weber,I.T., Wlodawer,A., Burstein,H. and Skalka,A.M. Analysis of substrate interactions of the Rous sarcoma virus wild type and mutant proteases and human immunodeficiency virus-1 protease using a set of systematically altered peptide substrates J Biol Chem (1992) 267, 9491-9498. PubMed Europe PubMed
[YEAR:5-6-1992]Milton,R.C., Milton,S.C. and Kent,S.B. Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected] Science (5-6-1992) 256, 1445-1448. PubMed Europe PubMed
[YEAR:15-11-1992]Murthy,K.H., Winborne,E.L., Minnich,M.D., Culp,J.S. and Debouck,C. The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations J Biol Chem (15-11-1992) 267, 22770-22778. PubMed Europe PubMed S I
Tam,T.F., Carriere,J., MacDonald,I.D., Castelhano,A.L., Pliura,D.H., Dewdney,N.J., Thomas,E.M., Bach,C., Barnett,J. and Chan,H. Intriguing structure-activity relations underlie the potent inhibition of HIV protease by norstatine-based peptides J Med Chem (1992) 35, 1318-1320. PubMed Europe PubMed DOI I
Thanki,N., Rao,J.K., Foundling,S.I., Howe,W.J., Moon,J.B., Hui,J.O., Tomasselli,A.G., Heinrikson,R.L., Thaisrivongs,S. and Wlodawer,A. Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling Protein Sci (1992) 1, 1061-1072. PubMed Europe PubMed DOI PMC EPMC S I
Tomaszek,T.A., Jr., Moore,M.L., Strickler,J.E., Sanchez,R.L., Dixon,J.S., Metcalf,B.W., Hassell,A., Dreyer,G.B., Brooks,I. and Debouck,C. Proteolysis of an active site peptide of lactate dehydrogenase by human immunodeficiency virus type 1 protease Biochemistry (1992) 31, 10153-10168. PubMed Europe PubMed DOI P
Urban,J., Konvalinka,J., Stehlikova,J., Gregorova,E., Majer,P., Soucek,M., Andreansky,M., Fabry,M. and Strop,P. Reduced-bond tight-binding inhibitors of HIV-1 protease. Fine tuning of the enzyme subsite specificity FEBS Lett (1992) 298, 9-13. PubMed Europe PubMed DOI I

1991

Craig,J.C., Duncan,I.B., Hockley,D., Grief,C., Roberts,N.A. and Mills,J.S. Antiviral properties of Ro 31-8959, an inhibitor of human immunodeficiency virus (HIV) proteinase Antiviral Res (1991) 16, 295-305. PubMed Europe PubMed DOI I
Debouck,C. Substrate specificity of the human (type 1) and simian immunodeficiency virus proteases Adv Exp Med Biol (1991) 306, 407-415. PubMed Europe PubMed
Goobar,L., Danielson,U.H., Brodin,P., Grundstrom,T., Oberg,B. and Norrby,E. High-yield purification of HIV-1 proteinase expressed by a synthetic gene in Escherichia coli Protein Expr Purif (1991) 2, 15-23. PubMed Europe PubMed E
Graves,B.J., Hatada,M.H., Miller,J.K., Graves,M.C., Roy,S., Cook,C.M., Krohn,A., Martin,J.A. and Roberts,N.A. The three-dimensional x-ray crystal structure of HIV-1 protease complexed with a hydroxyethylene inhibitor Adv Exp Med Biol (1991) 306, 455-460. PubMed Europe PubMed S I
Ido,E., Han,H.P., Kezdy,F.J. and Tang,J. Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S J Biol Chem (1991) 266, 24359-24366. PubMed Europe PubMed
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Kempf,D.J., Marsh,K.C., Paul,D.A., Knigge,M.F., Norbeck,D.W., Kohlbrenner,W.E., Codacovi,L., Vasavanonda,S., Bryant,P. and Wang,X.C. Antiviral and pharmacokinetic properties of C2 symmetric inhibitors of the human immunodeficiency virus type 1 protease Antimicrob Agents Chemother (1991) 35, 2209-2214. PubMed Europe PubMed PMC EPMC I
Meier,U.C., Billich,A., Mann,K., Schramm,H.J. and Schramm,W. alpha2-Macroglobulin is cleaved by HIV-1 protease in the bait region but not in the C-terminal inter-domain region Biol Chem Hoppe Seyler (1991) 372, 1051-1056. PubMed Europe PubMed
Oswald,M. and von der Helm,K. Fibronectin is a non-viral substrate for the HIV proteinase FEBS Lett (1991) 292, 298-300. PubMed Europe PubMed DOI
Pettit,S.C., Simsic,J., Loeb,D.D., Everitt,L., Hutchison,C.A., III and Swanstrom,R. Analysis of retroviral protease cleavage sites reveals two types of cleavage sites and the structural requirements of the P1 amino acid J Biol Chem (1991) 266, 14539-14547. PubMed Europe PubMed
Poorman,R.A., Tomasselli,A.G., Heinrikson,R.L. and Kezdy,F.J. A cumulative specificity model for proteases from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base J Biol Chem (1991) 266, 14554-14561. PubMed Europe PubMed
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Spinelli,S., Liu,Q.Z., Alzari,P.M., Hirel,P.H. and Poljak,R.J. The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU Biochimie (1991) 73, 1391-1396. PubMed Europe PubMed DOI S
Tomasselli,A.G., Howe,W.J., Hui,J.O., Sawyer,T.K., Reardon,I.M., DeCamp,D.L., Craik,C.S. and Heinrikson,R.L. Calcium-free calmodulin is a substrate of proteases from human immunodeficiency viruses 1 and 2 Proteins (1991) 10, 1-9. PubMed Europe PubMed DOI
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Weber,I.T. Modeling of structure of human immunodeficiency virus-1 protease with substrate based on crystal structure of Rous sarcoma virus protease Methods Enzymol (1991) 202, 727-741. PubMed Europe PubMed

1990

[YEAR:15-3-1990]Cheng,Y.S., McGowan,M.H., Kettner,C.A., Schloss,J.V., Erickson-Viitanen,S. and Yin,F.H. High-level synthesis of recombinant HIV-1 protease and the recovery of active enzyme from inclusion bodies Gene (15-3-1990) 87, 243-248. PubMed Europe PubMed DOI E
Cheng,Y.S., Yin,F.H., Foundling,S., Blomstrom,D. and Kettner,C.A. Stability and activity of human immunodeficiency virus protease: comparison of the natural dimer with a homologous, single-chain tethered dimer Proc Natl Acad Sci U S A (1990) 87, 9660-9664. PubMed Europe PubMed DOI PMC EPMC
[YEAR:31-5-1990]Copeland,T.D., Wondrak,E.M., Tozser,J., Roberts,M.M. and Oroszlan,S. Substitution of proline with pipecolic acid at the scissile bond converts a peptide substrate of HIV proteinase into a selective inhibitor Biochem Biophys Res Commun (31-5-1990) 169, 310-314. PubMed Europe PubMed DOI I
DesJarlais,R.L., Seibel,G.L., Kuntz,I.D., Furth,P.S., Alvarez,J.C., Ortiz de Montellano,P.R., DeCamp,D.L., Babe,L.M. and Craik,C.S. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease Proc Natl Acad Sci U S A (1990) 87, 6644-6648. PubMed Europe PubMed PMC EPMC I
[YEAR:3-8-1990]Erickson,J., Neidhart,D.J., VanDrie,J., Kempf,D.J., Wang,X.C., Norbeck,D.W., Plattner,J.J., Rittenhouse,J.W., Turon,M. and Wideburg,N. Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease Science (3-8-1990) 249, 527-533. PubMed Europe PubMed I
[YEAR:29-6-1990]Grobelny,D., Wondrak,E.M., Galardy,R.E. and Oroszlan,S. Selective phosphinate transition-state analogue inhibitors of the protease of human immunodeficiency virus Biochem Biophys Res Commun (29-6-1990) 169, 1111-1116. PubMed Europe PubMed DOI I
[YEAR:20-8-1990]Gustchina,A. and Weber,I.T. Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap FEBS Lett (20-8-1990) 269, 269-272. PubMed Europe PubMed DOI S
Kempf,D.J., Norbeck,D.W., Codacovi,L., Wang,X.C., Kohlbrenner,W.E., Wideburg,N.E., Paul,D.A., Knigge,M.F., Vasavanonda,S. and Craig-Kennard,A. Structure-based, C2 symmetric inhibitors of HIV protease J Med Chem (1990) 33, 2687-2689. PubMed Europe PubMed I
[YEAR:26-1-1990]McQuade,T.J., Tomasselli,A.G., Liu,L., Karacostas,V., Moss,B., Sawyer,T.K., Heinrikson,R.L. and Tarpley,W.G. A synthetic HIV-1 protease inhibitor with antiviral activity arrests HIV-like particle maturation Science (26-1-1990) 247, 454-456. PubMed Europe PubMed I
Phylip,L.H., Richards,A.D., Kay,J., Konvalinka,J., Strop,P., Blaha,I., Velek,J., Kostka,V., Ritchie,A.J., Broadhurst,A.V., Farmerie,W.G., Scarborough,P.E. and Dunn,B.M. Hydrolysis of synthetic chromogenic substrates by HIV-1 and HIV- 2 proteinases Biochem Biophys Res Commun (1990) 171, 439-444. PubMed Europe PubMed DOI A P
Rao,J.K.M. and Wlodawer,A. Is the pseudo-dyad in retroviral proteinase monomers structural or evolutionary? FEBS Lett (1990) 260, 201-205. PubMed Europe PubMed
[YEAR:15-5-1990]Richards,A.D., Phylip,L.H., Farmerie,W.G., Scarborough,P.E., Alvarez,A., Dunn,B.M., Hirel,P.H., Konvalinka,J., Strop,P. and Pavlickova,L. Sensitive, soluble chromogenic substrates for HIV-1 proteinase J Biol Chem (15-5-1990) 265, 7733-7736. PubMed Europe PubMed
[YEAR:20-4-1990]Roberts,N.A., Martin,J.A., Kinchington,D., Broadhurst,A.V., Craig,J.C., Duncan,I.B., Galpin,S.A., Handa,B.K., Kay,J. and Krohn,A. Rational design of peptide-based HIV proteinase inhibitors Science (20-4-1990) 248, 358-361. PubMed Europe PubMed I
Swain,A.L., Miller,M.M., Green,J., Rich,D.H., Schneider,J., Kent,S.B. and Wlodawer,A. X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor Proc Natl Acad Sci U S A (1990) 87, 8805-8809. PubMed Europe PubMed DOI PMC EPMC I
[YEAR:25-8-1990]Tomasselli,A.G., Hui,J.O., Sawyer,T.K., Staples,D.J., Bannow,C., Reardon,I.M., Howe,W.J., DeCamp,D.L., Craik,C.S. and Heinrikson,R.L. Specificity and inhibition of proteases from human immunodeficiency viruses 1 and 2 J Biol Chem (25-8-1990) 265, 14675-14683. PubMed Europe PubMed

1989

Blumenstein,J.J., Copeland,T.D., Oroszlan,S. and Michejda,C.J. Synthetic non-peptide inhibitors of HIV protease Biochem Biophys Res Commun (1989) 163, 980-987. PubMed Europe PubMed I
Copeland,T.D., Wondrak,E.M., Tozser,J., Roberts,M.M. and Oroszlan,S. Substitution of proline with pipecolic acid at the scissile bond converts a peptide substrate of HIV proteinase into selective inhibitor Biochem Biophys Res Commun (1989) 169, 310-314. I
Hatfield,D., Feng,Y.X., Lee,B.J., Rein,A., Levin,J.G. and Oroszlan,S. Chromatographic analysis of the aminoacyl-tRNAs which are required for translation of codons at and around the ribosomal frameshift sites of HIV, HTLV-1, and BLV Virology (1989) 173, 736-742. PubMed Europe PubMed DOI
[YEAR:30-6-1989]Hostomsky,Z., Appelt,K. and Ogden,R.C. High-level expression of self-processed HIV-1 protease in Escherichia coli using a synthetic gene Biochem Biophys Res Commun (30-6-1989) 161, 1056-1063. PubMed Europe PubMed E
Lapatto,R., Blundell,T., Hemmings,A., Overington,J., Wilderspin,A., Wood,S., Merson,J.R., Whittle,P.J., Danley,D.E., Geoghegan,K.F., Hawrylik,S.J., Lee,S.E., Scheld,K.G. and Hobart,P.M. X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes Nature (1989) 342, 299-302. PubMed Europe PubMed DOI S
Loeb,D.D., Hutchison,C.A., III, Edgell,M.H., Farmerie,W.G. and Swanstrom,R. Mutational analysis of human immunodeficiency virus type 1 protease suggests functional homology with aspartic proteinases J Virol (1989) 63, 111-121. PubMed Europe PubMed PMC EPMC
[YEAR:5-2-1989]McKeever,B.M., Navia,M.A., Fitzgerald,P.M., Springer,J.P., Leu,C.T., Heimbach,J.C., Herbert,W.K., Sigal,I.S. and Darke,P.L. Crystallization of the aspartylprotease from the human immunodeficiency virus, HIV-1 J Biol Chem (5-2-1989) 264, 1919-1921. PubMed Europe PubMed
[YEAR:16-2-1989]Navia,M.A., Fitzgerald,P.M., McKeever,B.M., Leu,C.T., Heimbach,J.C., Herber,W.K., Sigal,I.S., Darke,P.L. and Springer,J.P. Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1 Nature (16-2-1989) 337, 615-620. PubMed Europe PubMed DOI S
[YEAR:10-4-1989]Richards,A.D., Roberts,R., Dunn,B.M., Graves,M.C. and Kay,J. Effective blocking of HIV-1 proteinase activity by characteristic inhibitors of aspartic proteinases FEBS Lett (10-4-1989) 247, 113-117. PubMed Europe PubMed DOI I

1988

Kohl,N.E., Emini,E.A., Schleif,W.A., Davis,L.J., Heimbach,J.C., Dixon,R.A., Scolnick,E.M. and Sigal,I.S. Active human immunodeficiency virus protease is required for viral infectivity Proc Natl Acad Sci U S A (1988) 85, 4686-4690. PubMed Europe PubMed PMC EPMC
Krausslich,H.G. and Wimmer,E. Viral proteinases Annu Rev Biochem (1988) 57, 701-754. PubMed Europe PubMed DOI
Le Grice,S.F., Mills,J. and Mous,J. Active site mutagenesis of the AIDS virus protease and its alleviation by trans complementation EMBO J (1988) 7, 2547-2553. PubMed Europe PubMed PMC EPMC
Nutt,R.F., Brady,S.F., Darke,P.L., Ciccarone,T.M., Colton,C.D., Nutt,E.M., Rodkey,J.A., Bennett,C.D., Waxman,L.H. and Sigal,I.S. Chemical synthesis and enzymatic activity of a 99-residue peptide with a sequence proposed for the human immunodeficiency virus protease Proc Natl Acad Sci U S A (1988) 85, 7129-7133. PubMed Europe PubMed PMC EPMC
[YEAR:29-7-1988]Schneider,J. and Kent,S.B. Enzymatic activity of a synthetic 99 residue protein corresponding to the putative HIV-1 protease Cell (29-7-1988) 54, 363-368. PubMed Europe PubMed
Seelmeier,S., Schmidt,H., Turk,V. and von der Helm,K. Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A Proc Natl Acad Sci U S A (1988) 85, 6612-6616. PubMed Europe PubMed PMC EPMC I

1987

Debouck,C., Gorniak,J.G., Strickler,J.E., Meek,T.D., Metcalf,B.W. and Rosenberg,M. Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor Proc Natl Acad Sci U S A (1987) 84, 8903-8906. PubMed Europe PubMed PMC EPMC I

1985

Sanchez-Pescador,R., Power,M.D., Barr,P.J., Steimer,K.S., Stempien,M.M., Brown-Shimer,S.L., Gee,W.W., Renard,A., Randolph,A. and Levy,J.A. Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2) Science (1985) 227, 484-492. PubMed Europe PubMed
Wain-Hobson,S., Sonigo,P., Danos,O., Cole,S. and Alizon,M. Nucleotide sequence of the AIDS virus, LAV Cell (1985) 40, 9-17. PubMed Europe PubMed