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Structural biology of SARS-CoV-1/SARS-CoV-2 main protease

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 76-101 | Received 23 Jun 2022, Accepted 27 Mar 2023, Published online: 23 Jun 2023

References

  • Anand K, Ziebuhr J, Wadhwani P, et al. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 2003;300:1763–1767.
  • Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 2015;1282:1–23.
  • Ziebuhr J, Snijder EJ, Gorbalenya AE. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol. 2000;81:853–879.
  • Douangamath A, Fearon D, Gehrtz P, et al. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun. 2020;11:5047.
  • Günther S, Reinke PYA, Fernández-García Y, et al. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science. 2021;372:642–646.
  • Matthews DA, Smith WW, Ferre RA, et al. Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell. 1994;77:761–771.
  • Mosimann SC, Cherney MM, Sia S, et al. Refined X-ray crystallographic structure of the poliovirus 3C gene product. J Mol Biol. 1997;273:1032–1047.
  • Hegyi A, Ziebuhr J. Conservation of substrate specificities among coronavirus main proteases. J Gen Virol. 2002;83:595–599.
  • Hegyi A, Friebe A, Gorbalenya AE, et al. Mutational analysis of the active centre of coronavirus 3C-like proteases. J Gen Virol. 2002;83:581–593.
  • Ziebuhr J, Heusipp G, Siddell SG. Biosynthesis,: purification, and characterization of the human coronavirus 229E 3C-like proteinase. J Virol. 1997;71:3992–3997.
  • Anand K, Palm GJ, Mesters JR, et al. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J. 2002;21:3213–3224.
  • Drosten C, Günther S, Preiser W, et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003;348:1967–1976.
  • Ksiazek TG, Erdman D, Goldsmith CS, et al. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003;348:1953–1966.
  • Ziebuhr J. Molecular biology of severe acute respiratory syndrome coronavirus. Curr Opin Microbiol. 2004;7:412–419.
  • Yang H, Yang M, Ding Y, et al. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci USA. 2003;100:13190–13195.
  • Jin Z, Du X, Xu Y, et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582:289–293.
  • Qin E, Zhu Q, Yu M, et al. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). Chin Sci Bull. 2003;48:941–948.
  • Hsu M-F, Kuo C-J, Chang K-T, et al. Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem. 2005;280:31257–31266.
  • Ghosh AK, Xi K, Ratia K, et al. Design and synthesis of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease inhibitors. J Med Chem. 2005;48:6767–6771.
  • Pyrc K, Berkhout B, van der Hoek L. The novel human coronaviruses NL63 and HKU1. J Virol. 2007;81:3051–3057.
  • Zaki AM, van Boheemen S, Bestebroer TM, et al. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814–1820.
  • Shi J, Sivaraman J, Song J. Mechanism for controlling the dimer-monomer switch and coupling dimerization to catalysis of the severe acute respiratory syndrome coronavirus 3C-like protease. J Virol. 2008;82:4620–4629.
  • Tan J, Verschueren KHG, Anand K, et al. pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J Mol Biol. 2005;354:25–40.
  • Xue X, Yu H, Yang H, et al. Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. J Virol. 2008;82:2515–2527.
  • Hu T, Zhang Y, Li L, et al. Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure. Virology. 2009;388:324–334.
  • Barrila J, Gabelli SB, Bacha U, et al. Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL(pro). Biochemistry. 2010;49:4308–4317.
  • Muramatsu T, Takemoto C, Kim Y-T, et al. SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc Natl Acad Sci USA. 2016;113:12997–13002.
  • Yang H, Xie W, Xue X, et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 2005;3:e324.
  • Lee T-W, Cherney MM, Huitema C, et al. Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide. J Mol Biol. 2005;353:1137–1151.
  • Lu I-L, Mahindroo N, Liang P-H, et al. Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease. J Med Chem. 2006;49:5154–5161.
  • Verschueren KHG, Pumpor K, Anemüller S, et al. A structural view of the inactivation of the SARS coronavirus main proteinase by benzotriazole esters. Chem Biol. 2008;15:597–606.
  • Akaji K, Konno H, Mitsui H, et al. Structure-based design, synthesis, and evaluation of peptide-mimetic SARS 3CL protease inhibitors. J Med Chem. 2011;54:7962–7973.
  • Zhu L, George S, Schmidt MF, et al. Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease. Antiviral Res. 2011;92:204–212.
  • Jacobs J, Grum-Tokars V, Zhou Y, et al. Discovery, synthesis, and structure-based optimization of a series of N-(tert-butyl)-2-(N-arylamido)-2-(pyridin-3-yl) acetamides (ML188) as potent noncovalent small molecule inhibitors of the severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL protease. J Med Chem. 2013;56:534–546.
  • Chuck C-P, Chen C, Ke Z, et al. Design, synthesis and crystallographic analysis of nitrile-based broad-spectrum peptidomimetic inhibitors for coronavirus 3C-like proteases. Eur J Med Chem. 2013;59:1–6.
  • Turlington M, Chun A, Tomar S, et al. Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding. Bioorg Med Chem Lett. 2013;23:6172–6177.
  • Shimamoto Y, Hattori Y, Kobayashi K, et al. Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors. Bioorg Med Chem. 2015;23:876–890.
  • Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–269.
  • Roe MK, Junod NA, Young AR, et al. Targeting novel structural and functional features of coronavirus protease nsp5 (3CLpro, Mpro) in the age of COVID-19. J Gen Virol. 2021;102:001558.
  • Luttens A, Gullberg H, Abdurakhmanov E, et al. Ultralarge virtual screening identifies SARS-CoV-2 main protease inhibitors with broad-spectrum activity against coronaviruses. J Am Chem Soc. 2022;144:2905–2920.
  • Antonopoulou I, Sapountzaki E, Rova U, et al. Inhibition of the main protease of SARS-CoV-2 (Mpro) by repurposing/designing drug-like substances and utilizing nature’s toolbox of bioactive compounds. Comput Struct Biotechnol J. 2022;20:1306–1344.
  • Jaskolski M, Dauter Z, Shabalin IG, et al. Crystallographic models of SARS-CoV-2 3CLpro: in-depth assessment of structure quality and validation. IUCrJ. 2021;8:238–256.
  • Tekpinar M, Yildirim A. Impact of dimerization and N3 binding on molecular dynamics of SARS-CoV and SARS-CoV-2 main proteases. J Biomol Struct Dyn. 2022;40:6243–6254.
  • Wang H, He S, Deng W, et al. Comprehensive insights into the catalytic mechanism of Middle East respiratory syndrome 3C-like protease and severe acute respiratory syndrome 3C-like protease. ACS Catal. 2020;10:5871–5890.
  • Komatsu TS, Okimoto N, Koyama YM, et al. Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation. Sci Rep. 2020;10:16986.
  • Xiong M, Su H, Zhao W, et al. What coronavirus 3C-like protease tells us: from structure, substrate selectivity, to inhibitor design. Med Res Rev. 2021;41:1965–1998.
  • Huang C, Wei P, Fan K, et al. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry. 2004;43:4568–4574.
  • Paasche A, Zipper A, Schäfer S, et al. Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease. Biochemistry. 2014;53:5930–5946.
  • Kneller DW, Phillips G, Weiss KL, et al. Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography. J Biol Chem. 2020;295:17365–17373.
  • Kneller DW, Phillips G, O’Neill HM, et al. Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: insights into enzyme mechanism and drug design. IUCrJ. 2020;7:1028–1035.
  • Lee J, Worrall LJ, Vuckovic M, et al. Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Nat Commun. 2020;11:5877.
  • Kneller DW, Phillips G, O’Neill HM, et al. Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nat Commun. 2020;11:3202.
  • Ménard R, Storer AC. Oxyanion hole interactions in serine and cysteine proteases. Biol Chem Hoppe-Seyler. 1992;373:393–400.
  • Chen S, Hu T, Zhang J, et al. Mutation of Gly-11 on the dimer interface results in the complete crystallographic dimer dissociation of severe acute respiratory syndrome coronavirus 3C-like protease: crystal structure with molecular dynamics simulations. J Biol Chem. 2008;283:554–564.
  • Dai W, Zhang B, Jiang X-M, et al. Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science. 2020;368:1331–1335.
  • Hattori S-I, Higashi-Kuwata N, Hayashi H, et al. A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun. 2021;12:668.
  • Yang KS, Ma XR, Ma Y, et al. A quick route to multiple highly potent SARS-CoV-2 main protease inhibitors. ChemMedChem. 2021;16:942–948.
  • MacDonald EA, Frey G, Namchuk MN, et al. Recognition of divergent viral substrates by the SARS-CoV-2 main protease. ACS Infect Dis. 2021;7:2591–2595.
  • Hoffman RL, Kania RS, Brothers MA, et al. Discovery of ketone-based covalent inhibitors of coronavirus 3CL proteases for the potential therapeutic treatment of COVID-19. J Med Chem. 2020;63:12725–12747.
  • Ghosh AK, Xi K, Grum-Tokars V, et al. Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors. Bioorg Med Chem Lett. 2007;17:5876–5880.
  • Zhang C-H, Stone EA, Deshmukh M, et al. Potent noncovalent inhibitors of the main protease of SARS-CoV-2 from molecular sculpting of the drug perampanel guided by free energy perturbation calculations. ACS Cent Sci. 2021;7:467–475.
  • Zhang L, Lin D, Kusov Y, et al. α-Ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication: structure-based design, synthesis, and activity assessment. J Med Chem. 2020;63:4562–4578.
  • Hsu W-C, Chang H-C, Chou C-Y, et al. Critical assessment of important regions in the subunit association and catalytic action of the severe acute respiratory syndrome coronavirus main protease. J Biol Chem. 2005;280:22741–22748.
  • Chou C-Y, Chang H-C, Hsu W-C, et al. Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease. Biochemistry. 2004;43:14958–14970.
  • Zhong N, Zhang S, Zou P, et al. Without its N-finger, the main protease of severe acute respiratory syndrome coronavirus can form a novel dimer through its C-terminal domain. J Virol. 2008;82:4227–4234.
  • Zhong N, Zhang S, Xue F, et al. C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer. Protein Sci. 2009;18:839–844.
  • Chen S, Zhang J, Hu T, et al. Residues on the dimer interface of SARS coronavirus 3C-like protease: dimer stability characterization and enzyme catalytic activity analysis. J Biochem. 2008;143:525–536.
  • Shan Y-F, Li S-F, Xu G-J. A novel auto-cleavage assay for studying mutational effects on the active site of severe acute respiratory syndrome coronavirus 3C-like protease. Biochem Biophys Res Commun. 2004;324:579–583.
  • Ullrich S, Ekanayake KB, Otting G, et al. Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Bioorg Med Chem Lett. 2022;62:128629.
  • Lin P-Y, Chou C-Y, Chang H-C, et al. Correlation between dissociation and catalysis of SARS-CoV main protease. Arch Biochem Biophys. 2008;472:34–42.
  • Noske GD, Nakamura AM, Gawriljuk VO, et al. A crystallographic snapshot of SARS-CoV-2 main protease maturation process. J Mol Biol. 2021;433:167118.
  • Sun Z, Wang L, Li X, et al. An extended conformation of SARS-CoV-2 main protease reveals allosteric targets. Proc Natl Acad Sci USA. 2022;119:e2120913119.
  • Ebrahim A, Riley BT, Kumaran D, et al. The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro). BioRxiv. 2021.
  • Pearce NM, Gros P. A method for intuitively extracting macromolecular dynamics from structural disorder. Nat Commun. 2021;12:5493.
  • Ghosh AK, Osswald HL, 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.
  • de Leuw P, Stephan C. Protease inhibitors for the treatment of hepatitis C virus infection. GMS Infect Dis. 2017;5:Doc08.
  • Zephyr J, Kurt Yilmaz N, Schiffer CA. Viral proteases: structure, mechanism and inhibition. Enzymes. 2021;50:301–333.
  • Lee C-C, Kuo C-J, Ko T-P, et al. Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds. J Biol Chem. 2009;284:7646–7655.
  • Lee T-W, Cherney MM, Liu J, et al. Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase. J Mol Biol. 2007;366:916–932.
  • Yang S, Chen S-J, Hsu M-F, et al. Synthesis, crystal structure, structure-activity relationships, and antiviral activity of a potent SARS coronavirus 3CL protease inhibitor. J Med Chem. 2006;49:4971–4980.
  • Bai B, Belovodskiy A, Hena M, et al. Peptidomimetic α-acyloxymethylketone warheads with six-membered lactam P1 glutamine mimic: SARS-CoV-2 3CL protease inhibition, coronavirus antiviral activity, and in vitro biological stability. J Med Chem. 2022;65:2905–2925.
  • Yin J, Niu C, Cherney MM, et al. A mechanistic view of enzyme inhibition and peptide hydrolysis in the active site of the SARS-CoV 3C-like peptidase. J Mol Biol. 2007;371:1060–1074.
  • Zhang L, Lin D, Sun X, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020;368:409–412.
  • Rathnayake AD, Zheng J, Kim Y, et al. 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Sci Transl Med. 2020;12:eabc5332.
  • Dampalla CS, Kim Y, Bickmeier N, et al. Structure-guided design of conformationally constrained cyclohexane inhibitors of severe acute respiratory syndrome coronavirus-2 3CL protease. J Med Chem. 2021;64:10047–10058.
  • Dampalla CS, Rathnayake AD, Perera KD, et al. Structure-guided design of potent inhibitors of SARS-CoV-2 3CL protease: structural, biochemical, and cell-based studies. J Med Chem. 2021;64:17846–17865.
  • Vuong W, Khan MB, Fischer C, et al. Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun. 2020;11:4282.
  • Sacco MD, Ma C, Lagarias P, et al. Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against Mpro and cathepsin L. Sci Adv. 2020;6:eabe0751.
  • Fu L, Ye F, Feng Y, et al. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat Commun. 2020;11:4417.
  • Ma C, Sacco MD, Hurst B, et al. Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Cell Res. 2020;30:678–692.
  • Arutyunova E, Khan MB, Fischer C, et al. N-Terminal finger stabilizes the S1 pocket for the reversible feline drug GC376 in the SARS-CoV-2 Mpro dimer. J Mol Biol. 2021;433:167003.
  • Shi Y, Shuai L, Wen Z, et al. The preclinical inhibitor GS441524 in combination with GC376 efficaciously inhibited the proliferation of SARS-CoV-2 in the mouse respiratory tract. Emerg Microbes Infect. 2021;10:481–492.
  • Vuong W, Fischer C, Khan MB, et al. Improved SARS-CoV-2 Mpro inhibitors based on feline antiviral drug GC376: structural enhancements, increased solubility, and micellar studies. Eur J Med Chem. 2021;222:113584.
  • Liu H, Iketani S, Zask A, et al. Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nat Commun. 2022;13:1891.
  • Bacha U, Barrila J, Gabelli SB, et al. Development of broad-spectrum halomethyl ketone inhibitors against coronavirus main protease 3CL(pro). Chem Biol Drug Des. 2008;72:34–49.
  • Ullrich S, Sasi VM, Mahawaththa MC, et al. Challenges of short substrate analogues as SARS-CoV-2 main protease inhibitors. Bioorg Med Chem Lett. 2021: 128333.
  • Amporndanai K, Meng X, Shang W, et al. Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat Commun. 2021;12:3061.
  • Su H, Yao S, Zhao W, et al. Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease. Nat Commun. 2021;12:3623.
  • Kitamura N, Sacco MD, Ma C, et al. Expedited approach toward the rational design of noncovalent SARS-CoV-2 main protease inhibitors. J Med Chem. 2022;65:2848–2865.
  • Mslati H, Gentile F, Perez C, et al. Comprehensive consensus analysis of SARS-CoV-2 drug repurposing campaigns. J Chem Inf Model. 2021;61:3771–3788.
  • Lockbaum GJ, Reyes AC, Lee JM, et al. Crystal structure of SARS-CoV-2 main protease in complex with the non-covalent inhibitor ML188. Viruses. 2021;13.
  • Deshmukh MG, Ippolito JA, Zhang C-H, et al. Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease. Structure. 2021;29:823–833.e5.
  • Clyde A, Galanie S, Kneller DW, et al. High-throughput virtual screening and validation of a SARS-CoV-2 main protease noncovalent inhibitor. J Chem Inf Model. 2022;62:116–128.
  • Redhead MA, Owen CD, Brewitz L, et al. Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19. Sci Rep. 2021;11:13208.
  • Iketani S, Forouhar F, Liu H, et al. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nat Commun. 2021;12:2016.
  • Gimeno A, Mestres-Truyol J, Ojeda-Montes MJ, et al. Prediction of novel inhibitors of the main protease (M-pro) of SARS-CoV-2 through consensus docking and drug reposition. Int J Mol Sci. 2020;21:3793.
  • Han SH, Goins CM, Arya T, et al. Structure-based optimization of ML300-derived, noncovalent inhibitors targeting the severe acute respiratory syndrome coronavirus 3CL protease (SARS-CoV-2 3CLpro). J Med Chem. 2022;65:2880–2904.
  • Llanos MA, Gantner ME, Rodriguez S, et al. Strengths and weaknesses of docking simulations in the SARS-CoV-2 era: the main protease (Mpro) case study. J Chem Inf Model. 2021;61:3758–3770.
  • Tanaka S, Tokutomi S, Hatada R, et al. Dynamic cooperativity of ligand-residue interactions evaluated with the fragment molecular orbital method. J Phys Chem B. 2021;125:6501–6512.
  • Stille JK, Tjutrins J, Wang G, et al. Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CLpro covalent inhibitors. Eur J Med Chem. 2022;229:114046.
  • Zaidman D, Gehrtz P, Filep M, et al. An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor. Cell Chem Biol. 2021;28:1795–1806.e5.
  • Unoh Y, Uehara S, Nakahara K, et al. Discovery of S-217622, a noncovalent oral SARS-CoV-2 3CL protease inhibitor clinical candidate for treating COVID-19. J Med Chem. 2022;65:6499–6512.
  • Shionogi Co., Ltd. New Data for Shionogi’s COVID-19 Once-Daily Oral Antiviral S-217622 Show Rapid Virus Clearance. News. Shionogi Co., Ltd. [Internet]. [cited 2022 May 3]. Available from: https://www.shionogi.com/global/en/news/2022/04/20220424.html.
  • Su H-X, Yao S, Zhao W-F, et al. Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacol Sin. 2020;41:1167–1177.
  • Jin Z, Zhao Y, Sun Y, et al. Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nat Struct Mol Biol. 2020;27:529–532.
  • Li J, Zhou X, Zhang Y, et al. Crystal structure of SARS-CoV-2 main protease in complex with the natural product inhibitor shikonin illuminates a unique binding mode. Sci Bull (Beijing). 2021;66:661–663.
  • Kneller DW, Galanie S, Phillips G, et al. Malleability of the SARS-CoV-2 3CL Mpro active-site cavity facilitates binding of clinical antivirals. Structure. 2020;28:1313–1320.e3.
  • Bai Y, Ye F, Feng Y, et al. Structural basis for the inhibition of the SARS-CoV-2 main protease by the anti-HCV drug narlaprevir. Signal Transduct Target Ther. 2021;6:51.
  • Qiao J, Li Y-S, Zeng R, et al. SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model. Science. 2021;371:1374–1378.
  • Oerlemans R, Ruiz-Moreno AJ, Cong Y, et al. Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics. RSC Med Chem. 2020;12:370–379.
  • Drayman N, DeMarco JK, Jones KA, et al. Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2. Science. 2021;373:931–936.
  • Dementiev A, Joachimiak A, Nguyen H, et al. Molecular mechanism of inhibition of acid ceramidase by carmofur. J Med Chem. 2019;62:987–992.
  • Ma C, Hu Y, Townsend JA, et al. Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin Are nonspecific promiscuous SARS-CoV-2 main protease inhibitors. ACS Pharmacol Transl Sci. 2020;3:1265–1277.
  • Baker JD, Uhrich RL, Kraemer GC, et al. A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV2 main protease. PLoS ONE. 2021;16:e0245962.
  • Xia Z, Sacco M, Hu Y, et al. Rational design of hybrid SARS-CoV-2 main protease inhibitors guided by the superimposed cocrystal structures with the peptidomimetic inhibitors GC-376, telaprevir, and boceprevir. ACS Pharmacol Transl Sci. 2021;4:1408–1421.
  • Owen DR, Allerton CMN, Anderson AS, et al. An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19. Science. 2021;374:1586–1593.
  • Abdelnabi R, Foo CS, Jochmans D, et al. The oral protease inhibitor (PF-07321332) protects Syrian hamsters against infection with SARS-CoV-2 variants of concern. Nat Commun. 2022;13:719.
  • Li J, Lin C, Zhou X, et al. Structural basis of the main proteases of coronavirus bound to drug candidate PF-07321332. J Virol. 2022;96:e0201321.
  • Goetz DH, Choe Y, Hansell E, et al. Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the SARS coronavirus. Biochemistry. 2007;46:8744–8752.
  • Konno S, Kobayashi K, Senda M, et al. 3CL protease inhibitors with an electrophilic arylketone moiety as anti-SARS-CoV-2 agents. J Med Chem. 2022;65:2926–2939.
  • Li J, Lin C, Zhou X, et al. Structural basis of main proteases of coronavirus bound to drug candidate PF-07304814. J Mol Biol. 2022;434:167706.
  • Ma Y, Yang KS, Geng ZZ, et al. A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals. Eur J Med Chem. 2022;240:114570.
  • Bai B, Arutyunova E, Khan MB, et al. Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors. RSC Med Chem. 2021;12:1722–1730.
  • Sacco MD, Hu Y, Gongora MV, et al. The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition. Cell Res. 2022;32:498–500.
  • Dampalla CS, Rathnayake AD, Galasiti Kankanamalage AC, et al. Structure-guided design of potent spirocyclic inhibitors of severe acute respiratory syndrome coronavirus-2 3C-like protease. J Med Chem. 2022;65:7818–7832.
  • Lee C-C, Kuo C-J, Hsu M-F, et al. Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors. FEBS Lett. 2007;581:5454–5458.
  • Pillaiyar T, Flury P, Krüger N, et al. Small-molecule thioesters as SARS-CoV-2 main protease inhibitors: enzyme inhibition, structure-activity relationships, antiviral activity, and X-ray structure determination. J Med Chem. 2022;65:9376–9395.
  • Fu L, Shao S, Feng Y, et al. Mechanism of microbial metabolite leupeptin in the treatment of COVID-19 by traditional Chinese medicine herbs. MBio. 2021;12:e0222021.
  • Andi B, Kumaran D, Kreitler DF, et al. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep. 2022;12:12197.
  • Kneller DW, Phillips G, Weiss KL, et al. Direct observation of protonation state modulation in SARS-CoV-2 main protease upon inhibitor binding with neutron crystallography. J Med Chem. 2021;64:4991–5000.
  • Lockbaum GJ, Henes M, Lee JM, et al. Pan-3C protease inhibitor rupintrivir binds SARS-CoV-2 main protease in a unique binding mode. Biochemistry. 2021;60:2925–2931.
  • Kuzikov M, Costanzi E, Reinshagen J, et al. Identification of inhibitors of SARS-CoV-2 3CL-Pro enzymatic activity using a small molecule in vitro repurposing screen. ACS Pharmacol Transl Sci. 2021;4:1096–1110.
  • Costanzi E, Kuzikov M, Esposito F, et al. Structural and biochemical analysis of the dual inhibition of MG-132 against SARS-CoV-2 main protease (Mpro/3CLpro) and human cathepsin-L. Int J Mol Sci. 2021;22:11779.
  • Ghosh AK, Raghavaiah J, Shahabi D, et al. Indole chloropyridinyl ester-derived SARS-CoV-2 3CLpro inhibitors: enzyme inhibition, antiviral efficacy, structure-activity relationship, and X-ray structural studies. J Med Chem. 2021;64:14702–14714.
  • Malla TR, Brewitz L, Muntean D-G, et al. Penicillin derivatives inhibit the SARS-CoV-2 main protease by reaction with its nucleophilic cysteine. J Med Chem. 2022;65:7682–7696.
  • Ma C, Xia Z, Sacco MD, et al. Discovery of di- and trihaloacetamides as covalent SARS-CoV-2 main protease inhibitors with high target specificity. J Am Chem Soc. 2021;143:20697–20709.
  • Alugubelli YR, Geng ZZ, Yang KS, et al. A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals. Eur J Med Chem. 2022;240:114596.
  • Zhao Y, Fang C, Zhang Q, et al. Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332. Protein Cell. 2022;13:689–693.
  • Kneller D, Li H, Phillips G, et al. Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity. [Preprint]. Res Sq. 2022.
  • Greasley SE, Noell S, Plotnikova O, et al. Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. J Biol Chem. 2022: 101972.
  • Xiong M, Nie T, Shao Q, et al. In silico screening-based discovery of novel covalent inhibitors of the SARS-CoV-2 3CL protease. Eur J Med Chem. 2022;231:114130.
  • Cantrelle F-X, Boll E, Brier L, et al. NMR spectroscopy of the main protease of SARS-CoV-2 and fragment-based screening identify three protein hotspots and an antiviral fragment. Angew Chem Int Ed. 2021;60:25428–25435.
  • Kneller DW, Li H, Galanie S, et al. Structural, electronic, and electrostatic determinants for inhibitor binding to subsites S1 and S2 in SARS-CoV-2 main protease. J Med Chem. 2021;64:17366–17383.
  • Zhong B, Peng W, Du S, et al. Oridonin inhibits sars-cov-2 by targeting its 3c-like protease. Small Sci. 2022;2:2100124.
  • Rossetti GG, Ossorio MA, Rempel S, et al. Non-covalent SARS-CoV-2 Mpro inhibitors developed from in silico screen hits. Sci Rep. 2022;12:2505.
  • Zhang Y, Gao H, Hu X, et al. Structure-based discovery and structural basis of a novel broad-spectrum natural product against the main protease of coronavirus. J Virol. 2022;96:e0125321.
  • Yang KS, Alex Kuo S-T, Blankenship LR, et al. Repurposing halicin as a potent covalent inhibitor for the SARS-CoV-2 main protease. Curr Res Chem Biol. 2022;2:100025.
  • Shaqra AM, Zvornicanin SN, Huang QYJ, et al. Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nat Commun. 2022;13:3556.
  • Vangeel L, Chiu W, De Jonghe S, et al. Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 omicron and other variants of concern. Antiviral Res. 2022;198:105252.
  • Sidebottom DB, Smith DD, Gill D. Safety and efficacy of antivirals against SARS-CoV-2. Br Med J. 2021;375:n2611.
  • Ye C, Bian P, Zhang J, et al. Structure-based discovery of antiviral inhibitors targeting the E dimer interface of Japanese encephalitis virus. Biochem Biophys Res Commun. 2019;515:366–371.
  • Pietrucci F, Vargiu AV, Kranjc A. HIV-1 Protease dimerization dynamics reveals a transient druggable binding pocket at the interface. Sci Rep. 2015;5:18555.
  • Bannwarth L, Kessler A, Pèthe S, et al. Molecular tongs containing amino acid mimetic fragments: new inhibitors of wild-type and mutated HIV-1 protease dimerization. J Med Chem. 2006;49:4657–4664.
  • Brzezinski D, Kowiel M, Cooper DR, et al. Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models. Protein Sci. 2021;30:115–124.
  • Croll TI, Diederichs K, Fischer F, et al. Making the invisible enemy visible. Nat Struct Mol Biol. 2021;28:404–408.
  • Guven O, Gul M, Ayan E, et al. Case study of high-throughput drug screening and remote data collection for SARS-CoV-2 main protease by using serial femtosecond X-ray crystallography. Crystals. 2021;11:1579.
  • Chamakuri S, Lu S, Ucisik MN, et al. DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 Mpro inhibitors. Proc Natl Acad Sci USA. 2021;118:e2111172118.
  • Gildea RJ, Beilsten-Edmands J, Axford D, et al. Xia2.multiplex: a multi-crystal data-analysis pipeline. Acta Crystallogr D Struct Biol. 2022;78:752–769.
  • Narayanan A, Narwal M, Majowicz SA, et al. Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay. Commun Biol. 2022;5:169.
  • Sutanto F, Shaabani S, Oerlemans R, et al. Combining high-throughput synthesis and high-throughput protein crystallography for accelerated Hit identification. Angew Chem Int Ed. 2021;60:18231–18239.
  • Deetanya P, Hengphasatporn K, Wilasluck P, et al. Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification. Comput Struct Biotechnol J. 2021;19:3364–3371.
  • Moghadasi SA, Esler MA, Otsuka Y, et al. Gain-of-signal assays for probing inhibition of SARS-CoV-2 Mpro/3CLpro in living cells. MBio. 2022;13:e0078422.
  • Tomasello G, Armenia I, Molla G. The protein imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities. Bioinformatics. 2020;36:2909–2911.
  • Omasits U, Ahrens CH, Müller S, et al. Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. 2014;30:884–886.

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