Articles - 3nu4 mentioned but not cited (3)
- Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. Shen CH, Wang YF, Kovalevsky AY, Harrison RW, Weber IT. FEBS J 277 3699-3714 (2010)
- An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings. Maffucci I, Hu X, Fumagalli V, Contini A. Front Chem 6 43 (2018)
- Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities. Ahmad R, Sahidin I, Taher M, Low C, Noor NM, Sillapachaiyaporn C, Chuchawankul S, Sarachana T, Tencomnao T, Iskandar F, Rajab NF, Baharum SN. Sci Rep 8 4202 (2018)
Reviews citing this publication (6)
- Pharmaceutical and medicinal significance of sulfur (SVI)-Containing motifs for drug discovery: A critical review. Zhao C, Rakesh KP, Ravidar L, Fang WY, Qin HL. Eur J Med Chem 162 679-734 (2019)
- Enhancing protein backbone binding--a fruitful concept for combating drug-resistant HIV. Ghosh AK, Anderson DD, Weber IT, Mitsuya H. Angew Chem Int Ed Engl 51 1778-1802 (2012)
- Application of computational methods for anticancer drug discovery, design, and optimization. Prada-Gracia D, Huerta-Yépez S, Moreno-Vargas LM. Bol Med Hosp Infant Mex 73 411-423 (2016)
- Structural and Synthetic Aspects of Small Ring Oxa- and Aza-Heterocyclic Ring Systems as Antiviral Activities. Manna S, Das K, Santra S, Nosova EV, Zyryanov GV, Halder S. Viruses 15 1826 (2023)
- Therapeutic potential of HIV-1 entry inhibitor peptidomimetics. Korie NP, Tandoh KZ, Kwofie SK, Quaye O. Exp Biol Med (Maywood) 246 1060-1068 (2021)
- [Bioinformatics studies on drug resistance against anti-HIV-1 drugs]. Ode H. Uirusu 61 35-47 (2011)
Articles citing this publication (59)
- Molecular Basis for Drug Resistance in HIV-1 Protease. Ali A, Bandaranayake RM, Cai Y, King NM, Kolli M, Mittal S, Murzycki JF, Nalam MNL, Nalivaika EA, Özen A, Prabu-Jeyabalan MM, Thayer K, Schiffer CA. Viruses 2 2509-2535 (2010)
- HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements. Agniswamy J, Shen CH, Aniana A, Sayer JM, Louis JM, Weber IT. Biochemistry 51 2819-2828 (2012)
- Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. Ragland DA, Nalivaika EA, Nalam MN, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA. J Am Chem Soc 136 11956-11963 (2014)
- ePMV embeds molecular modeling into professional animation software environments. Johnson GT, Autin L, Goodsell DS, Sanner MF, Olson AJ. Structure 19 293-303 (2011)
- Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. Ngo ST, Hung HM, Nguyen MT. J Comput Chem 37 2734-2742 (2016)
- Design of Highly Potent, Dual-Acting and Central-Nervous-System-Penetrating HIV-1 Protease Inhibitors with Excellent Potency against Multidrug-Resistant HIV-1 Variants. Ghosh AK, Rao KV, Nyalapatla PR, Kovela S, Brindisi M, Osswald HL, Sekhara Reddy B, Agniswamy J, Wang YF, Aoki M, Hattori SI, Weber IT, Mitsuya H. ChemMedChem 13 803-815 (2018)
- Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics. Agniswamy J, Louis JM, Roche J, Harrison RW, Weber IT. PLoS One 11 e0168616 (2016)
- Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors. Tie Y, Wang YF, Boross PI, Chiu TY, Ghosh AK, Tozser J, Louis JM, Harrison RW, Weber IT. Protein Sci 21 339-350 (2012)
- Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease. de Vera IM, Smith AN, Dancel MC, Huang X, Dunn BM, Fanucci GE. Biochemistry 52 3278-3288 (2013)
- Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran. Agniswamy J, Shen CH, Wang YF, Ghosh AK, Rao KV, Xu CX, Sayer JM, Louis JM, Weber IT. J Med Chem 56 4017-4027 (2013)
- Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir: insights for drug design. Weber IT, Waltman MJ, Mustyakimov M, Blakeley MP, Keen DA, Ghosh AK, Langan P, Kovalevsky AY. J Med Chem 56 5631-5635 (2013)
- Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. Kar P, Knecht V. J Comput Aided Mol Des 26 215-232 (2012)
- Highly potent HIV-1 protease inhibitors with novel tricyclic P2 ligands: design, synthesis, and protein-ligand X-ray studies. Ghosh AK, Parham GL, Martyr CD, Nyalapatla PR, Osswald HL, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. J Med Chem 56 6792-6802 (2013)
- Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors. Raugi DN, Smith RA, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group. J Virol 90 1062-1069 (2016)
- Conformational variation of an extreme drug resistant mutant of HIV protease. Shen CH, Chang YC, Agniswamy J, Harrison RW, Weber IT. J Mol Graph Model 62 87-96 (2015)
- Design of HIV-1 protease inhibitors with C3-substituted hexahydrocyclopentafuranyl urethanes as P2-ligands: synthesis, biological evaluation, and protein-ligand X-ray crystal structure. Ghosh AK, Chapsal BD, Parham GL, Steffey M, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. J Med Chem 54 5890-5901 (2011)
- Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance. Naicker P, Achilonu I, Fanucchi S, Fernandes M, Ibrahim MA, Dirr HW, Soliman ME, Sayed Y. J Biomol Struct Dyn 31 1370-1380 (2013)
- Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps. Zhang Y, Chang YC, Louis JM, Wang YF, Harrison RW, Weber IT. ACS Chem Biol 9 1351-1358 (2014)
- The L76V drug resistance mutation decreases the dimer stability and rate of autoprocessing of HIV-1 protease by reducing internal hydrophobic contacts. Louis JM, Zhang Y, Sayer JM, Wang YF, Harrison RW, Weber IT. Biochemistry 50 4786-4795 (2011)
- 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. Ghosh AK, R Nyalapatla P, Kovela S, Rao KV, Brindisi M, Osswald HL, Amano M, Aoki M, Agniswamy J, Wang YF, Weber IT, Mitsuya H. J Med Chem 61 4561-4577 (2018)
- Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K. Gerlits O, Keen DA, Blakeley MP, Louis JM, Weber IT, Kovalevsky A. J Med Chem 60 2018-2025 (2017)
- Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50. Mittal S, Bandaranayake RM, King NM, Prabu-Jeyabalan M, Nalam MN, Nalivaika EA, Yilmaz NK, Schiffer CA. J Virol 87 4176-4184 (2013)
- Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics. Sheik Amamuddy O, Bishop NT, Tastan Bishop Ö. Sci Rep 8 17938 (2018)
- Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. J Phys Chem B 120 8743-8756 (2016)
- Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors. Braz AS, Tufanetto P, Perahia D, Scott LP. Proteins 80 2680-2691 (2012)
- Structure-based design of potent HIV-1 protease inhibitors with modified P1-biphenyl ligands: synthesis, biological evaluation, and enzyme-inhibitor X-ray structural studies. Ghosh AK, Yu X, Osswald HL, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. J Med Chem 58 5334-5343 (2015)
- Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors. Ghosh AK, Chapsal BD, Steffey M, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. Bioorg Med Chem Lett 22 2308-2311 (2012)
- Inhibition Profiling of Retroviral Protease Inhibitors Using an HIV-2 Modular System. Mahdi M, Szojka Z, Mótyán JA, Tőzsér J. Viruses 7 6152-6162 (2015)
- Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Retrovirology 17 13 (2020)
- Protocol for rational design of covalently interacting inhibitors. Schmidt TC, Welker A, Rieger M, Sahu PK, Sotriffer CA, Schirmeister T, Engels B. Chemphyschem 15 3226-3235 (2014)
- Structure-Based Design of Highly Potent HIV-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-ray Structural Studies. Ghosh AK, Kovela S, Osswald HL, Amano M, Aoki M, Agniswamy J, Wang YF, Weber IT, Mitsuya H. J Med Chem 63 4867-4879 (2020)
- Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism. Meher BR, Wang Y. J Mol Graph Model 38 430-445 (2012)
- Capturing the reaction pathway in near-atomic-resolution crystal structures of HIV-1 protease. Shen CH, Tie Y, Yu X, Wang YF, Kovalevsky AY, Harrison RW, Weber IT. Biochemistry 51 7726-7732 (2012)
- 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. Ghosh AK, Williams JN, Ho RY, Simpson HM, Hattori SI, Hayashi H, Agniswamy J, Wang YF, Weber IT, Mitsuya H. J Med Chem 61 9722-9737 (2018)
- Structural and biochemical characterization of the inhibitor complexes of xenotropic murine leukemia virus-related virus protease. Li M, Gustchina A, Matúz K, Tözsér J, Namwong S, Goldfarb NE, Dunn BM, Wlodawer A. FEBS J 278 4413-4424 (2011)
- 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. Ghosh AK, Martyr CD, Osswald HL, Sheri VR, Kassekert LA, Chen S, Agniswamy J, Wang YF, Hayashi H, Aoki M, Weber IT, Mitsuya H. J Med Chem 58 6994-7006 (2015)
- Synthesis and biological evaluation of novel amprenavir-based P1-substituted bi-aryl derivatives as ultra-potent HIV-1 protease inhibitors. Yan J, Huang N, Li S, Yang LM, Xing W, Zheng YT, Hu Y. Bioorg Med Chem Lett 22 1976-1979 (2012)
- Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations. Kneller DW, Agniswamy J, Harrison RW, Weber IT. FEBS J 287 3235-3254 (2020)
- Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study. Honarparvar B, Pawar SA, Alves CN, Lameira J, Maguire GE, Silva JR, Govender T, Kruger HG. J Biomed Sci 22 15 (2015)
- Potent HIV-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-ray Structural Studies. Ghosh AK, Xia Z, Kovela S, Robinson WL, Johnson ME, Kneller DW, Wang YF, Aoki M, Takamatsu Y, Weber IT, Mitsuya H. ChemMedChem 14 1863-1872 (2019)
- Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I. Pawar S, Wang YF, Wong-Sam A, Agniswamy J, Ghosh AK, Harrison RW, Weber IT. Biochem Biophys Res Commun 514 974-978 (2019)
- Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field. Duan R, Lazim R, Zhang D. J Comput Chem 36 1885-1892 (2015)
- A combined 3D-QSAR and docking studies for the In-silico prediction of HIV-protease inhibitors. Ul-Haq Z, Usmani S, Shamshad H, Mahmood U, Halim SA. Chem Cent J 7 88 (2013)
- Design, synthesis, biological evaluation and X-ray structural studies of HIV-1 protease inhibitors containing substituted fused-tetrahydropyranyl tetrahydrofuran as P2-ligands. Ghosh AK, Martyr CD, Kassekert LA, Nyalapatla PR, Steffey M, Agniswamy J, Wang YF, Weber IT, Amano M, Mitsuya H. Org Biomol Chem 13 11607-11621 (2015)
- Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation. Ghosh AK, Osswald HL, Glauninger K, Agniswamy J, Wang YF, Hayashi H, Aoki M, Weber IT, Mitsuya H. J Med Chem 59 6826-6837 (2016)
- Design, Synthesis, Biological Evaluation, and X-ray Studies of HIV-1 Protease Inhibitors with Modified P2' Ligands of Darunavir. Ghosh AK, Fyvie WS, Brindisi M, Steffey M, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. ChemMedChem 12 1942-1952 (2017)
- Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach. Ngo ST, Hong ND, Quynh Anh LH, Hiep DM, Tung NT. RSC Adv 10 7732-7739 (2020)
- Prediction of HIV drug resistance based on the 3D protein structure: Proposal of molecular field mapping. Ota R, So K, Tsuda M, Higuchi Y, Yamashita F. PLoS One 16 e0255693 (2021)
- Teaching foundational topics and scientific skills in biochemistry within the conceptual framework of HIV protease. Johnson RJ. Biochem Mol Biol Educ 42 299-304 (2014)
- Virtual Screening on Marine Natural Products for Discovering TMPRSS2 Inhibitors. Mahmudpour M, Nabipour I, Keshavarz M, Farrokhnia M. Front Chem 9 722633 (2021)
- Selection of HIV-1 for resistance to fifth-generation protease inhibitors reveals two independent pathways to high-level resistance. Spielvogel E, Lee SK, Zhou S, Lockbaum GJ, Henes M, Sondgeroth A, Kosovrasti K, Nalivaika EA, Ali A, Yilmaz NK, Schiffer CA, Swanstrom R. Elife 12 e80328 (2023)
- Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Laville P, Petitjean M, Regad L. Molecules 26 611 (2021)
- Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds. Zhou S, Liu Y, Wang S, Wang L. Sci Rep 13 13741 (2023)
- Design, Synthesis and X-Ray Structural Studies of Potent HIV-1 Protease Inhibitors Containing C-4 Substituted Tricyclic Hexahydro-Furofuran Derivatives as P2 Ligands. Ghosh AK, Kovela S, Sharma A, Shahabi D, Ghosh AK, Hopkins DR, Yadav M, Johnson ME, Agniswamy J, Wang YF, Hattori SI, Higashi-Kuwata N, Aoki M, Amano M, Weber IT, Mitsuya H. ChemMedChem 17 e202200058 (2022)
- Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. Ghosh AK, Jadhav RD, Simpson H, Kovela S, Osswald H, Agniswamy J, Wang YF, Hattori SI, Weber IT, Mitsuya H. Eur J Med Chem 160 171-182 (2018)
- Elasticity-Associated Functionality and Inhibition of the HIV Protease. Sherry D, Worth R, Sayed Y. Adv Exp Med Biol 1371 79-108 (2022)
- Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation. Ghosh AK, Mishevich JL, Kovela S, Shaktah R, Ghosh AK, Johnson M, Wang YF, Wong-Sam A, Agniswamy J, Amano M, Takamatsu Y, Hattori SI, Weber IT, Mitsuya H. Eur J Med Chem 255 115385 (2023)
- HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics. Wong-Sam A, Wang YF, Kneller DW, Kovalevsky AY, Ghosh AK, Harrison RW, Weber IT. J Mol Graph Model 117 108315 (2022)
- Theoretical Study on the Alkylimino-Substituted Sulfonamides with Potential Biological Activity. Brzeski J, Ciesielska A, Makowski M. J Phys Chem B 127 6620-6627 (2023)