Protease inhibitors targeting the main protease and papain-like protease of coronaviruses

References

• Romagnoli S, Peris A, De Gaudio AR, et al. SARS-CoV-2 and COVID-19: from the bench to the bedside. Physiol Rev. 2020;100(4):1455–1466.
   PubMed Web of Science ®Google Scholar
• Chakraborty I, Maity P. COVID-19 outbreak: migration, effects on society, global environment and prevention. Sci Total Environ. 2020;728:138882.
   PubMed Web of Science ®Google Scholar
• Cascella M, Rajnik M, Cuomo A, et al. Features, evaluation, and treatment of coronavirus (COVID-19). Treasure Island (FL): StatPearls; 2020.
   Google Scholar
• Yang Y, Peng F, Wang R, et al. Corrigendum to “The deadly coronaviruses: the 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China” [J. Autoimmun. 109C (2020) 102434]. J Autoimmun. 2020;111:102487.
   PubMedGoogle Scholar
• Mori M, Capasso C, Carta F, et al. A deadly spillover: SARS-CoV-2 outbreak. Expert Opin Ther Pat. 30(7): 481–485. 2020.
   PubMed Web of Science ®Google Scholar
• Peeri NC, Shrestha N, Rahman MS, et al. The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: what lessons have we learned? Int J Epidemiol. 2020;49(3):717–726.
   PubMed Web of Science ®Google Scholar
• Liu J, Xie W, Wang Y, et al. A comparative overview of COVID-19, MERS and SARS: review article. Int J Surg. 2020;81:1–8.
   PubMed Web of Science ®Google Scholar
• Latinne A, Hu B, Olival KJ, et al. Origin and cross-species transmission of bat coronaviruses in China. Nat Commun. 11(1): 4235. 2020.
   PubMed Web of Science ®Google Scholar
• Fan Y, Zhao K, Shi ZL, et al. Bat coronaviruses in China. Viruses. 2019;11:210.
   Web of Science ®Google Scholar
• Satarker S, Nampoothiri M. Structural proteins in severe acute respiratory syndrome coronavirus-2. Arch Med Res. 2020;51(6):482–491.
   PubMed Web of Science ®Google Scholar
• Jiang F, Deng L, Zhang L, et al. Review of the clinical characteristics of coronavirus disease 2019 (COVID-19). J Gen Intern Med. 2020;35(5):1545–1549.
   PubMed Web of Science ®Google Scholar
• Pal M, Berhanu G, Desalegn C, et al. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): an update. Cureus. 2020;12:e7423.
   PubMed Web of Science ®Google Scholar
• Schoeman D, Fielding BC. Coronavirus envelope protein: current knowledge. Virol J. 2019;16:69.
   PubMed Web of Science ®Google Scholar
• Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon. 2020;6(8):e04743.
   PubMedGoogle Scholar
• Hu T, Liu Y, Zhao M, et al. A comparison of COVID-19, SARS and MERS. PeerJ. 2020;8:e9725
   PubMed Web of Science ®Google Scholar
• Hoffmann M, Kleine-Weber H, Schroeder S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 181(2): 271–280 e278. 2020.
   PubMed Web of Science ®Google Scholar
• Petrosillo N, Viceconte G, Ergonul O, et al. COVID-19, SARS and MERS: are they closely related? Clin Microbiol Infect. 2020;26(6):729–734.
   PubMed Web of Science ®Google Scholar
• Chauhan S. Comprehensive review of coronavirus disease 2019 (COVID-19). Biomed J. 2020;43(4):334–340.
   PubMed Web of Science ®Google Scholar
• Rudrapal M, Khairnar SJ, Borse LB, et al. Coronavirus disease-2019 (COVID-19): an updated review. Drug Res (Stuttg). 2020;70(9):389–400.
   PubMedGoogle Scholar
• Harapan H, Itoh N, Yufika A, et al. Coronavirus disease 2019 (COVID-19): a literature review. J Infect Public Health. 2020;13(5):667–673.
   PubMed Web of Science ®Google Scholar
• Giannis D, Ziogas IA, Gianni P. Coagulation disorders in coronavirus infected patients: COVID-19, SARS-CoV-1, MERS-CoV and lessons from the past. J Clin Virol. 2020;127:104362.
   PubMed Web of Science ®Google Scholar
• Li Y, Zhang Z, Yang L, et al. The MERS-CoV Receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike. iScience. 2020;23(8):101400.
   PubMed Web of Science ®Google Scholar
• Cohen FS. How viruses invade cells. Biophys J. 2016;110(5):1028–1032.
   PubMed Web of Science ®Google Scholar
• Benvenuto D, Giovanetti M, Ciccozzi A, et al. The 2019-new coronavirus epidemic: evidence for virus evolution. J Med Virol. 2020;92(4):455–459.
   PubMed Web of Science ®Google Scholar
• Schubert K, Karousis ED, Jomaa A, et al. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol. 2020;27(10):959–966.
   PubMed Web of Science ®Google Scholar
• Thoms M, Buschauer R, Ameismeier M, et al. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science. 2020;369(6508):1249–1255.
   PubMed Web of Science ®Google Scholar
• Shi M, Wang L, Fontana P, et al. SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism. bioRxiv. 2020 Sep;18:2020.09.18.302901.
   Google Scholar
• Banerjee AK, Blanco MR, Bruce EA, et al. SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses. Cell. 2020 Oct 8;S0092-8674(20)31310–6. DOI:10.1016/j.cell.2020.10.004.
   PubMed Web of Science ®Google Scholar
• Shin D, Mukherjee R, Grewe D, et al. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 2020;587(in press):657–662.
   PubMedGoogle Scholar
• Gao X, Qin B, Chen P, et al. Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharm Sin B. 2020. DOI:10.1016/j.apsb.2020.08.014.
   Web of Science ®Google Scholar
• Wolff G, Limpens RWAL, Zevenhoven-Dobbe JC, et al. A molecular pore spans the double membrane of the coronavirus replication organelle. Science. 2020;369(6509):1395–1398.
   PubMed Web of Science ®Google Scholar
• Jin Z, Du X, Xu Y, et al. Structure of M(pro) from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582:289–293.
   PubMed Web of Science ®Google Scholar
• Ullrich S, Nitsche C. The SARS-CoV-2 main protease as drug target. Bioorg Med Chem Lett. 2020;30(17):127377.
   PubMed Web of Science ®Google Scholar
• Hillen HS, Kokic G, Farnung L, et al. Structure of replicating SARS-CoV-2 polymerase. Nature. 2020;584(7819):154–156.
   PubMed Web of Science ®Google Scholar
• Chandel V, Sharma PP, Raj S, et al. Structure-based drug repurposing for targeting Nsp9 replicase and spike proteins of severe acute respiratory syndrome coronavirus 2. J Biomol Struct Dyn. 2020;1–14. DOI:10.1080/07391102.2020.1811773.
   Web of Science ®Google Scholar
• Shu T, Huang M, Wu D, et al. SARS-coronavirus-2 Nsp13 possesses NTPase and RNA helicase activities that can be inhibited by bismuth salts. Virol Sin. 2020;35(3):321–329.
   PubMed Web of Science ®Google Scholar
• Sheahan TP, Sims AC, Leist SR, et al. Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nat Commun. 2020;11(1):222.
   PubMed Web of Science ®Google Scholar
• Edwards JK, Cole SR, Adimora AA. Remdesivir and COVID-19. Lancet. 2020;396(10256):953.
   PubMedGoogle Scholar
• O’Malley PA. A potential antiviral treatment for COVID-19: remdesivir. Clin Nurse Spec. 2020;34:257–260.
   PubMed Web of Science ®Google Scholar
• Davies M, Osborne V, Lane S, et al. Remdesivir in treatment of COVID-19: a systematic benefit-risk assessment. Drug Saf. 2020;43(7):645–656.
   PubMed Web of Science ®Google Scholar
• Arabi YM, Mandourah Y, Al-Hameed F, et al. Corticosteroid therapy for critically ill patients with middle east respiratory syndrome. Am J Respir Crit Care Med. 2018;197(6):757–767.
   PubMed Web of Science ®Google Scholar
• Chun-Wing Lau A, So LK, Yam LY, et al. Response to published article, “The use of corticosteroid as treatment in SARS was associated with adverse outcomes: a retrospective cohort study.”. J Infect. 2006;52(4):309–310.
   PubMedGoogle Scholar
• Xu YD, Jiang M, Chen RC, et al. Evaluation of the efficacy and safety of corticosteroid in the treatment of severe SARS in Guangdong province with multi-factor regression analysis. Zhongguo Wei Zhong Bing Ji Jiu Yi Xue. 2008;20:84–87.
   PubMedGoogle Scholar
• Brotherton H, Usuf E, Nadjm B, et al. Dexamethasone for COVID-19: data needed from randomised clinical trials in Africa. Lancet Glob Health. 2020;8(9):e1125–e1126.
   PubMed Web of Science ®Google Scholar
• Simpson CR, Thomas BD, Challen K, et al. The UK hibernated pandemic influenza research portfolio: triggered for COVID-19. Lancet Infect Dis. 2020;20(7):767–769.
   PubMed Web of Science ®Google Scholar
• Group RC, Horby P, Lim WS, et al. Dexamethasone in hospitalized patients with covid-19 - preliminary report. N Engl J Med. 2020.
   Web of Science ®Google Scholar
• Tan T, Khoo B, Mills EG, et al. Association between high serum total cortisol concentrations and mortality from COVID-19. Lancet Diabetes Endocrinol. 2020;8(8):659–660.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Bastard P, Liu Z, et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science. 2020;370(6515):eabd4570.
   PubMed Web of Science ®Google Scholar
• Bastard P, Rosen LB, Zhang Q, et al. Auto-antibodies against type I IFNs in patients with life-threatening COVID-19. Science. 2020;370(6515):eabd4585.
   PubMed Web of Science ®Google Scholar
• Liu YJ. IPC: professional type 1 interferon-producing cells and plasmacytoid dendritic cell precursors. Annu Rev Immunol. 2005;23(1):275–306.
   PubMedGoogle Scholar
• Solaimanzadeh I. Acetazolamide, nifedipine and phosphodiesterase inhibitors: rationale for their utilization as adjunctive countermeasures in the treatment of coronavirus disease 2019 (COVID-19). Cureus. 2020;12:e7343.
   PubMed Web of Science ®Google Scholar
• Mishra CB, Tiwari M, Supuran CT. Progress in the development of human carbonic anhydrase inhibitors and their pharmacological applications: where are we today? Med Res Rev. 2020;40(6):2485–2565.
   PubMed Web of Science ®Google Scholar
• Anand K, Ziebuhr J, Wadhwani P, et al. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 2003;300(5626):1763–1767.
   PubMed Web of Science ®Google Scholar
• 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(13):3213–3224.
   PubMed Web of Science ®Google Scholar
• 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 U S A. 2003;100(23):13190–13195
   PubMed Web of Science ®Google Scholar
• Lim L, Shi J, Mu Y, et al. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain. PLoS One. 2014;9(7):e101941.
   PubMed Web of Science ®Google Scholar
• Yang H, Xie W, Xue X, et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 2005;3(10):e324.
   PubMed Web of Science ®Google Scholar
• 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(6489):409–412.
   PubMed Web of Science ®Google Scholar
• Ho B-L, Cheng S-C, Shi L, et al. Critical assessment of the important residues involved in the dimerization and catalysis of MERS coronavirus main protease. PLoS One. 2015;10(12):e0144865.
   PubMed Web of Science ®Google Scholar
• Sulea T, Lindner HA, Purisima EO, et al. Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease? J Virol. 2005;79(7):4550–4551.
   PubMed Web of Science ®Google Scholar
• Freitas BT, Durie IA, Murray J, et al. Characterization and noncovalent inhibition of the deubiquitinase and deISGylase activity of SARS-CoV-2 papain-like protease. ACS Infect Dis. 2020;6(8):2099–2109.
   PubMed Web of Science ®Google Scholar
• Krishna SS, Majumdar I, Grishin NV. Structural classification of zinc fingers: survey and summary. Nucleic Acids Res. 2003;31(2):532–550.
   PubMed Web of Science ®Google Scholar
• Lei J, Mesters JR, Drosten C, et al. Crystal structure of the papain-like protease of MERS coronavirus reveals unusual, potentially druggable active-site features. Antiviral Res. 2014;109:72–82.
   PubMed Web of Science ®Google Scholar
• Mastrolorenzo A, Rusconi S, Scozzafava A, et al. 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 Web of Science ®Google Scholar
• Tzoupis H, Leonis G, Megariotis G, et al. Dual inhibitors for aspartic proteases HIV-1 PR and renin: advancements in AIDS-hypertension-diabetes linkage via molecular dynamics, inhibition assays, and binding free energy calculations. J Med Chem. 2012;55(12):5784–5796.
   PubMed Web of Science ®Google Scholar
• Barbaro G, Scozzafava A, Mastrolorenzo A, et al. Highly active antiretroviral therapy: current state of the art, new agents and their pharmacological interactions useful for improving therapeutic outcome. Curr Pharm Des. 2005;11(14):1805–1843.
   PubMed Web of Science ®Google Scholar
• Alazard-Dany N, Denolly S, Boson B, et al. Overview of HCV life cycle with a special focus on current and possible future antiviral targets. Viruses. 2019;11(1):30.
   Web of Science ®Google Scholar
• McCauley JA, Rudd MT. Hepatitis C virus NS3/4a protease inhibitors. Curr Opin Pharmacol. 2016;30:84–92.
   PubMed Web of Science ®Google Scholar
• Miao M, Jing X, De Clercq E, et al. Danoprevir for the treatment of hepatitis C virus infection: design, development, and place in therapy. Drug Des Devel Ther. 2020;14:2759–2774.
   PubMed Web of Science ®Google Scholar
• Gil C, Ginex T, Maestro I, et al. COVID-19: drug targets and potential treatments. J Med Chem. 2020;63(21):12359–12386.
   Web of Science ®Google Scholar
• Kania RS, Mitchell LJ Jr, Nieman JA. Anticoronaviral compounds and compositions, their pharmaceutical uses and materials for their synthesis. WO2006/061714
   Google Scholar
• Schubert U, Gunther S. Mittel zur behandlung von infektionen mit coronaviridae. DE2005/61945.
   Google Scholar
• Liu H, Nian Y, Li J, et al. Aldehyde and preparation and application thereof. WO2017/114509.
   Google Scholar
• Dai W, Zhang B, Jiang XM, et al. Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science. 2020;368(6497):1331–1335.
   PubMed Web of Science ®Google Scholar
• He M, Kania RS, Lou J, et al. Inhibitors of SARS 3C like protease. US2006/0014821
   Google Scholar
• Fuhrman S, Matthews DA, Patick AK, et al. Inhibitors of severe acute respiratory syndrome (SARS) 3C-like proteinase. US2004/0235952
   Google Scholar
• Fuhrman S, Matthews DA, Patick AK, et al. Inhibitors of SARS related coronavirus proteinase. WO2004/093860.
   Google Scholar
• Hoffman RA, Kania RS, Nieman JA, et al. Anticoronaviral compounds and compositions, their pharmaceutical uses and materials for their synthesis. WO2005/113580.
   Google Scholar
• Botyanszky J, Catalano JG, Chong PY, et al. Compounds that inhibit 3C and 3CL proteases and methods of use thereof. WO2018/042343.
   Google Scholar
• Greenbaum DC. Novel alpha-helical peptidomimetic inhibitors and methods using same. US2015/0133367.
   Google Scholar
• 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(9):4562–4578.
   PubMed Web of Science ®Google Scholar
• Lin MH, Moses DC, Hsieh CH, et al. Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes. Antiviral Res. 2018;150:155–163.
   PubMed Web of Science ®Google Scholar
• Wang L, Bao BB, Song GQ, et al. Discovery of unsymmetrical aromatic disulfides as novel inhibitors of SARS-CoV main protease: chemical synthesis, biological evaluation, molecular docking and 3D-QSAR study. Eur J Med Chem. 2017;137:450–461.
   PubMed Web of Science ®Google Scholar
• Karypidou K, Ribone SR, Quevedo MA. Synthesis, biological evaluation and molecular modeling of a novel series of fused 1,2,3-triazoles as potential anti-coronavirus agents. Bioorg Med Chem Lett. 2018;28(21):3472–3476.
   PubMed Web of Science ®Google Scholar
• Jo S, Kim S, Shin DH, et al. Inhibition of SARS-CoV 3CL protease by flavonoids. J Enzyme Inhib Med Chem. 2020;35(1):145–151.
   PubMed Web of Science ®Google Scholar
• Lu W, Shang J, Wang J, et al. Asymmetric aromatic disulfide compound and application thereof for preparing medicine for resisting SARS (severe acute respiratory syndrome) coronaviral infection. CN2016/106187933.
   Google Scholar
• Bao B, Cai Y, Chen C, et al. Application of asymmetric aromatic disulfide compound containing five-membered heterocycle to preparation of medicine for treating SARS. CN2016/106166153.
   Google Scholar
• Sun C, Wang J, Xu F Application of benzopentanedione in preparation of SARS-CoV protease inhibitor. CN2014/104069090.
   Google Scholar
• Chen W, Liu H, Liu W, et al. Isatin-5-amide inhibiting agent with inhibition effect against SARS coronavirus main protease. CN2013/103159665.
   Google Scholar
• Chen W, Feng J, Li J, et al. Application of biphenyl cyclooctene lignin in anti-SARS coronavirus infection. CN2016/103156828.
   Google Scholar
• Hwang SW, Kim DM, Ryu H, et al. Inhibitors of SARS-coronavirus 3CL protease for severe acute respiratory syndrome and method for screening thereof. KR2014/0002975.
   Google Scholar
• Halcomb R, Roethle P. Derivatives of purine or deazapurine useful for the treatment of (inter alia) viral infections. CA2016/2777824.
   Google Scholar
• Chong YH, Jeong YJ, Lee CW. Pharmaceutical compositions comprising dihydroxychromone derivatives as an active ingredient for treating and preventing diseases caused by coronaviruses. KR2011/0006083.
   Google Scholar
• Chang Z, Fei X, Ming M, et al. Diterpenes diterpenoids natural product inhibitor for main protease of coronaviruses such as SARS and screen method thereof. CN2011/101418334.
   Google Scholar
• Lai LL, Changkang H, Hao C, et al. 3CL protease inhibitor of non-peptide SARS coronavirus and use thereof. CN2009/1965833.
   Google Scholar
• Hirota H, Kurane I, Matsumoto T, et al. Protease inhibitor. JP2008/133190A
   Google Scholar
• Fan K, Lai LL, Liu Y, et al. SARS coronavirus 3CL protease inhibitor and its use. CN2006/1569841.
   Google Scholar
• Song G, Wang J, Wu R. Aromatic thioether compounds as well as pesticides containing same and medical application thereof. CN2019/10911405.
   Google Scholar
• Frieman M, Basu D, Matthews K, et al. Yeast based small molecule screen for inhibitors of SARS-CoV. PLoS One. 2011;6(12):e28479.
   PubMed Web of Science ®Google Scholar
• Chen X, Chou CY, Chang GG. Thiopurine analogue inhibitors of severe acute respiratory syndrome-coronavirus papain-like protease, a deubiquitinating and deISGylating enzyme. Antivir Chem Chemother. 2009;19(4):151–156.
   PubMedGoogle Scholar
• Park JY, Kim JH, Kim YM, et al. Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorg Med Chem. 2012;20(19):5928–5935.
   PubMed Web of Science ®Google Scholar
• Park JY, Jeong HJ, Kim JH, et al. Diarylheptanoids from Alnus japonica inhibit papain-like protease of severe acute respiratory syndrome coronavirus. Biol Pharm Bull. 2012;35(11):2036–2042.
   PubMed Web of Science ®Google Scholar
• Cho JK, Curtis-Long MJ, Lee KH, et al. Geranylated flavonoids displaying SARS-CoV papain-like protease inhibition from the fruits of Paulownia tomentosa. Bioorg Med Chem. 2013;21(11):3051–3057.
   PubMed Web of Science ®Google Scholar
• Ratia K, Kilianski A, Baez-Santos YM, et al. Structural basis for the ubiquitin-linkage specificity and deISGylating activity of SARS-CoV papain-like protease. PLoS Pathog. 2014;10(5):e1004113.
   PubMed Web of Science ®Google Scholar
• Lee H, Lei H, Santarsiero BD, et al. Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV. ACS Chem Biol. 2015;10:1456–1465.
   PubMed Web of Science ®Google Scholar
• Rut W, Lv Z, Zmudzinski M, et al. Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design. bioRxiv. 2020 Apr;29:2020.04.29.068890.
   Google Scholar
• Cho JK, Kim DW, Park HH, et al. Novel tomentin derivates from paulownia tomentosa and using thereof. KR2014/101458465B1
   Google Scholar
• Choi SD, Prasanna V, Shah M, et al. Composition for preventing or treating middle east respiratory syndrome-coronavirus MERS-CoV infection. KR2018/101934199B1
   Google Scholar
• Quammen D. Spillover: animal infections and the next human pandemic. New York: W.W. Norton and Co.; 2012. p. 1–608.
   Google Scholar