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Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.

Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R
Science 368 409-412 (2020)
Related entries: 6y2f, 6y2g, 6y7m

Cited: 1600 times
EuropePMC logo PMID: 32198291

Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (Mpro, also called 3CLpro) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 Mpro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compound in plasma. On the basis of the unliganded structure, we developed the lead compound into a potent inhibitor of the SARS-CoV-2 Mpro The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.

Reviews - 6y2e mentioned but not cited (40)

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  991. Combating Coronavirus Using Resonant Electromagnetic Irradiation. Sayidmarie KH, Mohammed B, Mohammed AJ, Abbosh A. IEEE J Electromagn RF Microw Med Biol 6 477-484 (2022)
  992. Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV. Chang YJ, Le UNP, Liu JJ, Li SR, Chao ST, Lai HC, Lin YF, Hsu KC, Lu CH, Lin CW. Antiviral Res 216 105653 (2023)
  993. Comprehensive Understanding of the Kinetic Behaviors of Main Protease from SARS-CoV-2 and SARS-CoV: New Data and Comparison to Published Parameters. Li F, Fang T, Guo F, Zhao Z, Zhang J. Molecules 28 4605 (2023)
  994. Computer-aided drug design for virtual-screening and active-predicting of main protease (Mpro) inhibitors against SARS-CoV-2. Dai R, Gao H, Su R. Front Pharmacol 14 1288363 (2023)
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  996. Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses. Zvornicanin SN, Shaqra AM, Huang QJ, Ornelas E, Moghe M, Knapp M, Moquin S, Dovala D, Schiffer CA, Kurt Yilmaz N. Viruses 15 781 (2023)
  997. Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor. Luo J, Wang W, Jiang H, Li W, Zeng P, Wang J, Zhou X, Zou X, Chen S, Wang Q, Zhang J, Li J. Acta Biochim Biophys Sin (Shanghai) 55 1257-1264 (2023)
  998. DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors. Jimmidi R, Chamakuri S, Lu S, Ucisik MN, Chen PJ, Bohren KM, Moghadasi SA, Versteeg L, Nnabuife C, Li JY, Qin X, Chen YC, Faver JC, Nyshadham P, Sharma KL, Sankaran B, Judge A, Yu Z, Li F, Pollet J, Harris RS, Matzuk MM, Palzkill T, Young DW. Commun Chem 6 164 (2023)
  999. Design and synthesis of naturally-inspired SARS-CoV-2 inhibitors. Hassan H, Chiavaralli J, Hassan A, Bedda L, Krischuns T, Chen KY, Li ASM, Delpal A, Decroly E, Vedadi M, Naffakh N, Agou F, Mallart S, Arafa RK, Arimondo PB. RSC Med Chem 14 507-519 (2023)
  1000. Design of Potent Inhibitors Targeting the Main Protease of SARS-CoV-2 Using QSAR Modeling, Molecular Docking, and Molecular Dynamics Simulations. Oubahmane M, Hdoufane I, Delaite C, Sayede A, Cherqaoui D, El Allali A. Pharmaceuticals (Basel) 16 608 (2023)
  1001. Design of novel pyrimidine based remdesivir analogues with dual target specificity for SARS CoV-2: A computational approach. Dinesh TV, Malgija B, Ponraj MR, Muralakar P, Thathapudi JJ, Kandasamy R, Alagarmalai J, Balakrishnan AB, Ramar PS, James JV, Bhagavathsingh J. Int J Biol Macromol 242 124443 (2023)
  1002. Development of 2-chloroquinoline based heterocyclic frameworks as dual inhibitors of SARS-CoV-2 MPro and PLPro. Kattula B, Reddi B, Jangam A, Naik L, Adimoolam BM, Vavilapalli S, Are S, Thota JR, Jadav SS, Arifuddin M, Addlagatta A. Int J Biol Macromol 242 124772 (2023)
  1003. Development of the Safe and Broad-Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained α, γ-AA Peptide Scaffold. Wang L, Ma C, Sacco MD, Xue S, Mahmoud M, Calcul L, Chen Y, Wang J, Cai J. Chemistry 29 e202300476 (2023)
  1004. Discovery of 2-thiobenzimidazoles as noncovalent inhibitors of SARS-CoV-2 main protease. Deodato D, Asad N, Dore TM. Bioorg Med Chem Lett 72 128867 (2022)
  1005. Discovery of PLpro and Mpro Inhibitors for SARS-CoV-2. Puhl AC, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Oliva G, Ekins S. ACS Omega 8 22603-22612 (2023)
  1006. Discovery of novel inhibitors of SARS-CoV-2 main protease. Zheng L, Chen Y, Bao J, He L, Dong S, Qi Y, Zhang JZH. J Biomol Struct Dyn 40 12526-12534 (2022)
  1007. Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. Rokić F, Trgovec-Greif L, Sučić N, Čemeljić N, Grbeša ĐC, Svedružić Ž, Rukavina T, Vugrek O, Jurak I. Arch Virol 166 1735-1739 (2021)
  1008. Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study. Ahmad S, Mirza MU, Trant JF. J Pharm Anal 13 523-534 (2023)
  1009. Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease. Chan HTH, Oliveira ASF, Schofield CJ, Mulholland AJ, Duarte F. JACS Au 3 1767-1774 (2023)
  1010. E3 ubiquitin ligase ZBTB25 suppresses beta coronavirus infection through ubiquitination of the main viral protease MPro. Lear TB, Boudreau ÁN, Lockwood KC, Chu E, Camarco DP, Cao Q, Nguyen M, Evankovich JW, Finkel T, Liu Y, Chen BB. J Biol Chem 299 105388 (2023)
  1011. Electrochemical Biosensor for the Detection of SARS-CoV-2 Main Protease and Its Inhibitor Ebselen. Zhang Q, Liu G, Ou L. Int J Electrochem Sci 17 220421 (2022)
  1012. Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism. Samanta PN, Majumdar D, Leszczynski J. J Chem Inf Model 63 3404-3422 (2023)
  1013. Endoproteolysis of Oligopeptide-Based Coacervates for Enzymatic Modeling. Jin Z, Ling C, Yim W, Chang YC, He T, Li K, Zhou J, Cheng Y, Li Y, Yeung J, Wang R, Fajtová P, Amer L, Mattoussi H, O'Donoghue AJ, Jokerst JV. ACS Nano 17 16980-16992 (2023)
  1014. Evaluation of RevX solution extract as a potential inhibitor of the main protease of SARS-CoV-2-In vitro study and molecular docking. Chou FP, Liu CC, Huong Giang HN, Huang SC, Hsu HF, Wu TK. Heliyon 8 e09034 (2022)
  1015. Exploring potential SARS-CoV-2 Mpro non-covalent inhibitors through docking, pharmacophore profile matching, molecular dynamic simulation, and MM-GBSA. Shi Y, Dong L, Ju Z, Li Q, Cui Y, Liu Y, He J, Ding X. J Mol Model 29 138 (2023)
  1016. Finding potential inhibitors for Main protease (Mpro) of SARS-CoV-2 through virtual screening and MD simulation studies. Ahamed NA, Arif IA. Saudi J Biol Sci 30 103845 (2023)
  1017. Fluorinated derivatives of tetrahydroaltersolanol molecule on COVID-19, HIV, and HTLV protease by DFT and molecular docking approaches. Azadparvar M, Kheirabadi M, Aliabad HAR. J Mol Model 28 350 (2022)
  1018. Fragment-based inhibitor design for SARS-CoV2 main protease. Andola P, Pagag J, Laxman D, Guruprasad L. Struct Chem 33 1467-1487 (2022)
  1019. Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro. Ruatta SM, Prada Gori DN, Fló Díaz M, Lorenzelli F, Perelmuter K, Alberca LN, Bellera CL, Medeiros A, López GV, Ingold M, Porcal W, Dibello E, Ihnatenko I, Kunick C, Incerti M, Luzardo M, Colobbio M, Ramos JC, Manta E, Minini L, Lavaggi ML, Hernández P, Šarlauskas J, Huerta García CS, Castillo R, Hernández-Campos A, Ribaudo G, Zagotto G, Carlucci R, Medrán NS, Labadie GR, Martinez-Amezaga M, Delpiccolo CML, Mata EG, Scarone L, Posada L, Serra G, Calogeropoulou T, Prousis K, Detsi A, Cabrera M, Alvarez G, Aicardo A, Araújo V, Chavarría C, Mašič LP, Gantner ME, Llanos MA, Rodríguez S, Gavernet L, Park S, Heo J, Lee H, Paul Park KH, Bollati-Fogolín M, Pritsch O, Shum D, Talevi A, Comini MA. Front Pharmacol 14 1193282 (2023)
  1020. High throughput screening for drugs that inhibit 3C-like protease in SARS-CoV-2. Smith E, Davis-Gardner ME, Garcia-Ordonez RD, Nguyen TT, Hull M, Chen E, Yu X, Bannister TD, Baillargeon P, Scampavia L, Griffin P, Farzan M, Spicer TP. SLAS Discov 28 95-101 (2023)
  1021. Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins. Iyengar SM, Barnsley KK, Vu HY, Bongalonta IJA, Herrod AS, Scott JA, Ondrechen MJ. Front Chem 10 1017394 (2022)
  1022. Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. Nemčovičová I, Lopušná K, Štibrániová I, Benedetti F, Berti F, Felluga F, Drioli S, Vidali M, Katrlík J, Pažitná L, Holazová A, Blahutová J, Lenhartová S, Sláviková M, Klempa B, Ondrejovič M, Chmelová D, Legerská B, Miertuš S, Klacsová M, Uhríková D, Kerti L, Frecer V. J Enzyme Inhib Med Chem 39 2301772 (2024)
  1023. Identification of Drug Combination Therapies for SARS-CoV-2: A Molecular Dynamics Simulations Approach. Abdel-Halim H, Hajar M, Hasouneh L, Abdelmalek SMA. Drug Des Devel Ther 16 2995-3013 (2022)
  1024. Identification of Mulberrofuran as a potent inhibitor of hepatitis A virus 3Cpro and RdRP enzymes through structure-based virtual screening, dynamics simulation, and DFT studies. Sureshan M, Brintha S, Jothi A. Mol Divers (2023)
  1025. Identification of Pyrazole Derivatives of Usnic Acid as Novel Inhibitor of SARS-CoV-2 Main Protease Through Virtual Screening Approaches. Roney M, Singh G, Huq AKMM, Forid MS, Ishak WMBW, Rullah K, Aluwi MFFM, Tajuddin SN. Mol Biotechnol (2023)
  1026. Identification of and Mechanistic Insights into SARS-CoV-2 Main Protease Non-Covalent Inhibitors: An In-Silico Study. Shen JX, Du WW, Xia YL, Zhang ZB, Yu ZF, Fu YX, Liu SQ. Int J Mol Sci 24 4237 (2023)
  1027. Identification of non-covalent SARS-CoV-2 main protease inhibitors by a virtual screen of commercially available drug-like compounds. Zhang L, Howland M, Hilgenfeld R, Anderson MO, Eagon S. Bioorg Med Chem Lett 41 127990 (2021)
  1028. Identification of potent inhibitors against transmembrane serine protease 2 for developing therapeutics against SARS-CoV-2. Mamun AA, Akter F, Khan M, Ahmed SS, Uddin MG, Tasfia NT, Efaz FM, Ali MA, Sultana MUC, Halim MA. J Biomol Struct Dyn 40 13049-13061 (2022)
  1029. Identification of the potential association between SARS-CoV-2 infection and acute kidney injury based on the shared gene signatures and regulatory network. Zhou X, Wang N, Liu W, Chen R, Yang G, Yu H. BMC Infect Dis 23 655 (2023)
  1030. Impact of Sulfur Fumigation on Ginger: Chemical and Biological Evidence. Zhang WH, Luo HY, Fang J, Zhao CL, Chan KC, Chan YM, Dong CX, Chen HB, Zhao ZZ, Li SL, Xu J. J Agric Food Chem 70 12577-12586 (2022)
  1031. In Silico Identification of Potential Inhibitors of the SARS-CoV-2 Main Protease among a PubChem Database of Avian Infectious Bronchitis Virus 3CLPro Inhibitors. Soulère L, Barbier T, Queneau Y. Biomolecules 13 956 (2023)
  1032. In silico Study of Antiviral Activity of Polyphenol Compounds from Ocimum basilicum by Molecular Docking, ADMET, and Drug-Likeness Analysis. Kurnia D, Putri SA, Tumilaar SG, Zainuddin A, Dharsono HDA, Amin MF. Adv Appl Bioinform Chem 16 37-47 (2023)
  1033. In silico approach for the development of novel antiviral compounds based on SARS-COV-2 protease inhibition. Ničkčović VP, Nikolić GR, Nedeljković BM, Mitić N, Danić SF, Mitić J, Marčetić Z, Sokolović D, Veselinović AM. Chem Zvesti 76 4393-4404 (2022)
  1034. In silico evaluation of Philippine Natural Products against SARS-CoV-2 Main Protease. Cheng AJT, Macalino SJY, Billones JB, Balolong MP, Murao LAE, Carrillo MCO. J Mol Model 28 345 (2022)
  1035. In silico studies of anti-oxidative and hot temperament-based phytochemicals as natural inhibitors of SARS-CoV-2 Mpro. Naderi Beni R, Elyasi-Ebli P, Gharaghani S, Seyedarabi A. PLoS One 18 e0295014 (2023)
  1036. In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro. Saleh NA. 3 Biotech 13 185 (2023)
  1037. In-vitro antiviral activity and in-silico targeted study of quinoline-3-carboxylate derivatives against SARS-Cov-2 isolate. Mittal RK, Purohit P, Sankaranarayanan M, Muzaffar-Ur-Rehman M, Taramelli D, Signorini L, Dolci M, Basilico N. Mol Divers (2023)
  1038. Insights into targeting SARS-CoV-2: design, synthesis, in silico studies and antiviral evaluation of new dimethylxanthine derivatives. Mohamed AR, Mostafa A, El Hassab MA, Hedeab GM, Mahmoud SH, George RF, Georgey HH, Abdel Gawad NM, El-Ashrey MK. RSC Med Chem 14 899-920 (2023)
  1039. Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors. Aniana A, Nashed NT, Ghirlando R, Coates L, Kneller DW, Kovalevsky A, Louis JM. Commun Biol 6 1159 (2023)
  1040. Interactions of the Anti-SARS-CoV-2 Agents Molnupiravir and Nirmatrelvir/Paxlovid with Human Drug Transporters. Bakos É, Temesszentandrási-Ambrus C, Özvegy-Laczka C, Gáborik Z, Sarkadi B, Telbisz Á. Int J Mol Sci 24 11237 (2023)
  1041. Investigating novel thiazolyl-indazole derivatives as scaffolds for SARS-CoV-2 MPro inhibitors. Airas J, Bayas CA, N'Ait Ousidi A, Ait Itto MY, Auhmani A, Loubidi M, Esseffar M, Pollock JA, Parish CA. Eur J Med Chem Rep 4 100034 (2022)
  1042. Investigation on the Essential Oils of the Achillea Species: From Chemical Analysis to the In Silico Uptake against SARS-CoV-2 Main Protease. Angourani HR, Zarei A, Moghadam MM, Ramazani A, Mastinu A. Life (Basel) 13 378 (2023)
  1043. Korupensamine A, but not its atropisomer, korupensamine B, inhibits SARS-CoV-2 in vitro by targeting its main protease (Mpro). Sayed AM, Ibrahim AH, Tajuddeen N, Seibel J, Bodem J, Geiger N, Striffler K, Bringmann G, Abdelmohsen UR. Eur J Med Chem 251 115226 (2023)
  1044. Lab-on-a-chip for the easy and visual detection of SARS-CoV-2 in saliva based on sensory polymers. Arnaiz A, Guirado-Moreno JC, Guembe-García M, Barros R, Tamayo-Ramos JA, Fernández-Pampín N, García JM, Vallejos S. Sens Actuators B Chem 379 133165 (2023)
  1045. Luteolin is a potential inhibitor of COVID-19: An in silico analysis. Wang W, Yang C, Xia J, Li N, Xiong W. Medicine (Baltimore) 102 e35029 (2023)
  1046. MO-MEMES: A method for accelerating virtual screening using multi-objective Bayesian optimization. Mehta S, Goel M, Priyakumar UD. Front Med (Lausanne) 9 916481 (2022)
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  1048. Molecular Dynamics Simulation of Ligands from Anredera cordifolia (Binahong) to the Main Protease (M pro) of SARS-CoV-2. Fatriansyah JF, Boanerges AG, Kurnianto SR, Pradana AF, Fadilah, Surip SN. J Trop Med 2022 1178228 (2022)
  1049. Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein. Liu P, Li Y, Liu Y, Liu J, Dong K, Jia Q. J Phys Chem B 127 4396-4405 (2023)
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  1052. Multi-target direct-acting SARS-CoV-2 antivirals against the nucleotide-binding pockets of virus-specific proteins. Rani R, Long S, Pareek A, Dhaka P, Singh A, Kumar P, McInerney G, Tomar S. Virology 577 1-15 (2022)
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  1057. New Chemicals Suppressing SARS-CoV-2 Replication in Cell Culture. Sulimov A, Ilin I, Kutov D, Shikhaliev K, Shcherbakov D, Pyankov O, Stolpovskaya N, Medvedeva S, Sulimov V. Molecules 27 5732 (2022)
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  1059. Novel Approach to the Synthesis of 3-amino-4-arylpyridin-2(1H)-one Derivatives. Shuvalov VY, Chernenko SА, Shatsauskas AL, Samsonenko AL, Dmitriev MV, Fisyuk AS. Chem Heterocycl Compd (N Y) 57 764-771 (2021)
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  1061. Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2. Medrano FJ, de la Hoz-Rodríguez S, Martí S, Arafet K, Schirmeister T, Hammerschmidt SJ, Müller C, González-Martínez Á, Santillana E, Ziebuhr J, Romero A, Zimmer C, Weldert A, Zimmermann R, Lodola A, Świderek K, Moliner V, González FV. Commun Chem 7 15 (2024)
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  1071. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Magn Reson (Gott) 3 169-182 (2022)
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  1077. Targeting DPP4-RBD interactions by sitagliptin and linagliptin delivers a potential host-directed therapy against pan-SARS-CoV-2 infections. Mani S, Kaur A, Jakhar K, Kumari G, Sonar S, Kumar A, Das S, Kumar S, Kumar V, Kundu R, Pandey AK, Singh UP, Majumdar T. Int J Biol Macromol 245 125444 (2023)
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  1081. The hope and hype of ellagic acid and urolithins as ligands of SARS-CoV-2 Nsp5 and inhibitors of viral replication. Bianconi E, Gidari A, Souma M, Sabbatini S, Grifagni D, Bigiotti C, Schiaroli E, Comez L, Paciaroni A, Cantini F, Francisci D, Macchiarulo A. J Enzyme Inhib Med Chem 38 2251721 (2023)
  1082. Ultrasound assisted Cu-catalyzed Ullmann-Goldberg type coupling-cyclization in a single pot: Synthesis and in silico evaluation of 11H-pyrido[2,1-b]quinazolin-11-ones against SARS-CoV-2 RdRp. Manikanttha M, Deepti K, Tej MB, Tej MB, Gopi Reddy A, Kapavarapu R, Barange DK, V Basaveswara Rao M, Pal M. J Mol Struct 1280 135044 (2023)
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