In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing

Zhu, 2020, A novel coronavirus from patients with pneumonia in China, 2019, N Engl J Med, 382, 727, 10.1056/NEJMoa2001017 WHO coronavirus disease (COVID-19) dashboard. n.d. https://covid19.who.int/. [Accessed 15 May 2020]. Hung, 2020, Triple combination of interferon beta-1b, lopinavir–ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: an open-label, randomised, phase 2 trial, Lancet, 0 2020 Chen, 2020, Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study, Lancet, 395, 507, 10.1016/S0140-6736(20)30211-7 Cui, 2019, Origin and evolution of pathogenic coronaviruses, Nat Rev Microbiol, 17, 181, 10.1038/s41579-018-0118-9 CDC, 2020, Coronavirus disease 2019 (COVID-19), Cent Dis Control Prev Hui, 2020, The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — the latest 2019 novel coronavirus outbreak in Wuhan, China, Int J Infect Dis, 91, 264, 10.1016/j.ijid.2020.01.009 Zhou, 2020, Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2, Cell Discov, 6, 1, 10.1038/s41421-020-0153-3 Woo, 2010, Coronavirus genomics and bioinformatics analysis, Viruses, 2, 1804, 10.3390/v2081803 Hussain, 2005, Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus, J Virol, 79, 5288, 10.1128/JVI.79.9.5288-5295.2005 Wong, 2004, A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2, J Biol Chem, 279, 3197, 10.1074/jbc.C300520200 Hilgenfeld, 2014, From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design, FEBS J, 281, 4085, 10.1111/febs.12936 Yang, 2013, A small molecule screen in stem-cell-derived motor neurons identifies a kinase inhibitor as a candidate therapeutic for ALS, Cell Stem Cell, 12, 713, 10.1016/j.stem.2013.04.003 Sun, 2016, Drug combination therapy increases successful drug repositioning, Drug Discov Today, 21, 1189, 10.1016/j.drudis.2016.05.015 Zhang, 2020, Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors, Science, 368, 409, 10.1126/science.abb3405 Kouznetsova, 2014, Identification of 53 compounds that block Ebola virus-like particle entry via a repurposing screen of approved drugs, Emerg Microbes Infect, 3, 1, 10.1038/emi.2014.88 He, 2015, Repurposing of the antihistamine chlorcyclizine and related compounds for treatment of hepatitis C virus infection, Sci Transl Med, 7, 10.1126/scitranslmed.3010286 Barrows, 2016, A screen of FDA-approved drugs for inhibitors of zika virus infection, Cell Host Microbe, 20, 259, 10.1016/j.chom.2016.07.004 Fan, 2020, Repurposing of clinically approved drugs for treatment of coronavirus disease 2019 in a 2019-novel coronavirus-related coronavirus model, Chin Med J (Engl), 133, 1051, 10.1097/CM9.0000000000000797 Cao, 2020, A trial of lopinavir–ritonavir in adults hospitalized with severe Covid-19, N Engl J Med, 382, 1787, 10.1056/NEJMoa2001282 Yang, 2003, The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor, Proc Natl Acad Sci U S A, 100, 13190, 10.1073/pnas.1835675100 Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol Biol Evol, 30, 2725, 10.1093/molbev/mst197 PubChem. PubChem. n.d. https://pubchem.ncbi.nlm.nih.gov/. [Accessed 15 May 2020]. Trott, 2010, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J Comput Chem, 31, 455 Laskowski, 2011, LigPlot+: multiple ligand-protein interaction diagrams for drug discovery, J Chem Inf Model, 51, 2778, 10.1021/ci200227u PyMOL | pymol.org. n.d. https://pymol.org/2/. [Accessed 15 May 2020]. Krieger, 2015, New ways to boost molecular dynamics simulations, J Comput Chem, 36, 996, 10.1002/jcc.23899 Krieger, 2004, Making optimal use of empirical energy functions: force-field parameterization in crystal space, Proteins, 57, 678, 10.1002/prot.20251 Desai, 2015, Receptor-guided de novo design of dengue envelope protein inhibitors, Appl Biochem Biotechnol, 177, 861, 10.1007/s12010-015-1784-y Kiemer, 2004, Coronavirus 3CLproproteinase cleavage sites: possible relevance to SARS virus pathology, BMC Bioinformatics, 5, 10.1186/1471-2105-5-72 Anand, 2003, Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs, Science, 300, 1763, 10.1126/science.1085658 De Luca, 2019, Clinical use, efficacy, and durability of maraviroc for antiretroviral therapy in routine care: a European survey, PLoS One, 14, 10.1371/journal.pone.0225381 Foolad, 2018, Letermovir for the prevention of cytomegalovirus infection in adult cytomegalovirus-seropositive hematopoietic stem cell transplant recipients, Expert Rev Clin Pharmacol, 11, 931, 10.1080/17512433.2018.1500897 Hayden, 2018, Baloxavir Marboxil for uncomplicated influenza in adults and adolescents, N Engl J Med, 379, 913, 10.1056/NEJMoa1716197 Agarwal, 2018, 96 weeks treatment of tenofovir alafenamide vs. tenofovir disoproxil fumarate for hepatitis B virus infection, J Hepatol, 68, 672, 10.1016/j.jhep.2017.11.039 Blair, 2018, Dolutegravir/rilpivirine: a review in HIV-1 infection, Drugs, 78, 1741, 10.1007/s40265-018-1005-4 Yamamoto, 2004, HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus, Biochem Biophys Res Commun, 318, 719, 10.1016/j.bbrc.2004.04.083 Zhang, 2020, Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors, Science, 368, 409, 10.1126/science.abb3405 Del Puente, 2020, Comment on: dual therapy combining raltegravir with etravirine maintains a high level of viral suppression over 96 weeks in long-term experienced HIV-infected individuals over 45 years on a PI-based regimen: results from the Phase II ANRS 163 ETRAL study, J Antimicrob Chemother, 10.1093/jac/dkaa120 Plosker, 2003, Tipranavir, Drugs, 63, 1611, 10.2165/00003495-200363150-00009 Brites, 2018, Raltegravir versus lopinavir/ritonavir for treatment of HIV-infected late-presenting pregnant women, HIV Clin Trials, 19, 94, 10.1080/15284336.2018.1459343 WHO Director-General’s remarks at the media briefing on 2019-nCoV on 11 February 2020. n.d. https://www.who.int/dg/speeches/detail/who-director-general-s-remarks-at-the-media-briefing-on-2019-ncov-on-11-february-2020. [Accessed 15 May 2020]. Forster, 2020, Phylogenetic network analysis of SARS-CoV-2 genomes, Proc Natl Acad Sci U S A, 117, 9241, 10.1073/pnas.2004999117 2020, Coronavirus outbreak: top coronavirus drugs and vaccines in development, Clin Trials Arena Walls, 2020, Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein, Cell, 181, 10.1016/j.cell.2020.02.058 Chen, 2020, Structure analysis of the receptor binding of 2019-nCoV, Biochem Biophys Res Commun, 525, 135, 10.1016/j.bbrc.2020.02.071 Doyon, 2005, Selection and characterization of HIV-1 showing reduced susceptibility to the non-peptidic protease inhibitor tipranavir, Antiviral Res, 68, 27, 10.1016/j.antiviral.2005.07.003 Larder, 2000, Tipranavir inhibits broadly protease inhibitor-resistant HIV-1 clinical samples, AIDS Lond Engl, 14, 1943, 10.1097/00002030-200009080-00009 Walmsley, 2013, Dolutegravir plus abacavir-lamivudine for the treatment of HIV-1 infection, N Engl J Med, 369, 1807, 10.1056/NEJMoa1215541 Cottrell, 2013, Clinical pharmacokinetic, pharmacodynamic and drug-interaction profile of the integrase inhibitor dolutegravir, Clin Pharmacokinet, 52, 981, 10.1007/s40262-013-0093-2 Marty, 2017, Letermovir prophylaxis for cytomegalovirus in hematopoietic-cell transplantation, N Engl J Med, 377, 2433, 10.1056/NEJMoa1706640