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Research Articles

In silico screening of potential antiviral inhibitors against SARS-CoV-2 main protease

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 175-185 | Received 21 Jul 2022, Accepted 04 Oct 2022, Published online: 25 Oct 2022

References

  • Kuiken T, Fouchier RAM, Schutten M, et al. Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome. Lancet. 2003;362:263–270.
  • Osterhaus ADME, Fouchier RAM. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814–1820.
  • Lu H, Stratton CW, Tang YW. Outbreak of pneumonia of unknown etiology in Wuhan, China: the mystery and the miracle. J Med Virol. 2020;92:401–402.
  • Sohrabi C, Alsafi Z, O’Neill N, et al. World Health Organization declares global emergency: a review of the 2019 novel coronavirus (COVID-19). Int J Surg. 2020;76:71–76.
  • Wei H, Yin H, Huang M, et al. The 2019 novel cornoavirus pneumonia with onset of oculomotor nerve palsy: a case study. J Neurol. 2020;267:1550–1553.
  • Maier HJ, Bickerton E, Britton P. Coronaviruses: methods and protocols. Coronaviruses Methods Protoc. 2015;1282:1–282.
  • Gorbalenya AE, Baker SC, Baric RS, et al. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020;5:536–544.
  • Patel AB. COVID-19 and angiotensin-converting enzyme inhibitors and angiotensin receptor blockers what is the evidence? JAMA. 2020;323:1769–1770.
  • Forster P, Forster L, Renfrew C, et al. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci. 2020;117:9241–9243.
  • Liu C, Zhou Q, Li Y, et al. Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Cent Sci. 2020;6:315–331.
  • Hosseini-zare MS, Selvam C. Targeting severe acute respiratory syndrome-coronavirus (SARS-CoV-1) with structurally diverse inhibitors: a comprehensive review. RSC Adv. 2020;10: 28287–28299.
  • Callaway E. Making sense of coronavirus mutations. Nature. 2020;585:174–177.
  • Pillaiyar T, Manickam M, Namasivayam V, et al. An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: peptidomimetics and small molecule chemotherapy. J Med Chem. 2016;59:6595–6628.
  • Francés-Monerris A, Hognon C, Miclot T, et al. Molecular basis of SARS-CoV-2 infection and rational design of potential antiviral agents: modeling and simulation approaches. J Proteome Res. 2020;19:4291–4315.
  • 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.
  • Ullrich S, Nitsche C. The SARS-CoV-2 main protease as drug target. Bioorganic Med Chem Lett. 2020;30:127377.
  • 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.
  • Boras B, Jones RM, Anson BJ, et al. Preclinical characterization of an intravenous coronavirus 3CL protease inhibitor for the potential treatment of COVID19. Nat Commun. 2021;12:6055.
  • 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;3:1586–1593.
  • Gautret P, Lagier JC, Parola P, et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents. 2020;56:105949.
  • Parvathaneni V, Gupta V. Utilizing drug repurposing against COVID-19 – efficacy, limitations, and challenges. Life Sci. 2020;259:118275.
  • Quek P. Medicinal plants research in Asia; 2004.
  • Islam MT, Sarkar C, El-kersh DM, et al. Natural products and their derivatives against coronavirus: a review of the non-clinical and pre-clinical data. Phytother Res. 2020;34:2471–2492.
  • My TTA, Loan HTP, Hai NTT, et al. Evaluation of the inhibitory activities of COVID-19 of Melaleuca cajuputi oil using docking simulation. ChemistrySelect. 2020;5:6312–6320.
  • Kumar R, Piya G, Mudgal P, et al. Herbal plants and plant preparations as remedial approach for viral diseases. VirusDisease. 2015;26:225–236.
  • Kumar S, Sharma PP, Shankar U, et al. Discovery of new hydroxyethylamine analogs against 3CL pro protein target of SARS-CoV-2: molecular docking, molecular dynamics simulation, and structure–activity relationship studies. J Chem Inf Model. 2020;60:5754–5770.
  • Gahlawat A, Kumar N, Kumar R, et al. Structure-based virtual screening to discover potential lead molecules for the SARS-CoV-2 main protease. J Chem Inf Model. 2020;60:5781–5793.
  • Singam ERA, La Merrill MA, Durkin KA, et al. Structure-based virtual screening of a natural product database to identify several possible SARS-CoV-2 main protease inhibitors. ChemRxiv.
  • Thi B, Thuy P, Thi T, et al. Investigation into SARS-CoV-2 resistance of compounds in garlic essential oil. ACS Omega. 2020;5:8312–8320.
  • Kulkarni SA, Nagarajan SK, Ramesh V, et al. Computational evaluation of major components from plant essential oils as potent inhibitors of SARS-CoV-2 spike protein. J Mol Struct. 2020;1221:128823.
  • Gutierrez-Villagomez JM, Campos-García T, Molina-Torres J, et al. Alkamides and piperamides as potential antivirals against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Phys Chem Lett. 2020;11:8008–8016.
  • Palanisamy K, Rubavathy SME, Prakash M, et al. RSC advances antiviral activities of natural compounds and ionic liquids to inhibit the Mpro of SARS-CoV-2: a computational approach. RSC Adv. 2022;12:3687–3695.
  • Wu D, Koganti R, Lambe UP, et al. Vaccines and therapies in development for SARS-CoV-2 infections. J Clin Med. 2020;9:1885.
  • Linlin Z, Daizong L, Xinyuanyuan S, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020;3405:1–9.
  • Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 16, revision A. 03. Wallingford (CT); 2016.
  • Meng X, Zhang H, Mezei M, et al. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput-Aid Drug Des. 2011;7:146–157.
  • Garrett M, Ruth H, William L, et al. Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2012;32:174–182.
  • Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:1–13.
  • Pires DEV, Blundell TL, Ascher DB. pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem. 2015;58:4066–4072.
  • Lindorff-Larsen K, Piana S, Palmo K, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins Struct Funct Bioinforma. 2010;78:1950–1958.
  • Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general Amber force field. J Comput Chem. 2004;56531:1157–1174.
  • Da Silva AW S, Vranken WF. ACPYPE – AnteChamber PYthon Parser interfacE. BMC Res Notes. 2012;5:1–8.
  • Bayly CI, Cieplak P, Cornell WD, et al. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem. 1993;97:10269–10280.
  • Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun. 1995;91:43–56.
  • Kumari R, Kumar R, Lynn A. G-mmpbsa – a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 2014;54:1951–1962.
  • DeLano WL. PyMOL: an open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr. 2002;40:82–92.
  • Ricker EW. VMD: visual molecular dynamics. J Fish Res Board Canada. 1954;11:559–623.
  • Mengist HM, Fan X, Jin T. Designing of improved drugs for COVID-19: crystal structure of SARS-CoV-2 main protease Mpro. Signal Transduct Target Ther. 2020;5:2–3.
  • Nguyen NT, Nguyen TH, Pham TNH, et al. Autodock Vina adopts more accurate binding poses but Autodock4 forms better binding affinity. J Chem Inf Model. 2020;60:204–211.
  • Huynh T, Wang H, Luan B. In silico exploration of the molecular mechanism of clinically oriented drugs for possibly inhibiting SARS-CoV-2’s main protease. J Phys Chem Lett. 2020;11:4413–4420.
  • Peele KA, Potla Durthi C, Srihansa T, et al. Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: a computational study. Informatics Med Unlocked. 2020;19:100345.
  • Srinivasan K. Black pepper and its pungent principle-piperine: a review of diverse physiological effects. Crit Rev Food Sci Nutr. 2007;47:735–748.
  • Zaveri M, Khandhar A, Patel S, et al. Chemistry and pharmacology of Piper longum L. Int J Pharm Sci Rev Res. 2010;5:67–76.
  • Lee HS, Koo YC, Suh HJ, et al. Preventive effects of chebulic acid isolated from Terminalia chebula on advanced glycation endproduct-induced endothelial cell dysfunction. J Ethnopharmacol. 2010;131:567–574.
  • Laphookhieo S, Phungpanya C, Tantapakul C, et al. Chemical constituents from Aegle marmelos. J Braz Chem Soc. 2011;22:176–178.
  • Sahu J, Rathi B, Koul S, et al. Solanum trilobatum (Solanaceae) – an overview. J Nat Remedies. 2013;13:76–80.
  • Kaur R, Kaur H, Dhindsa AS. Glycyrrhiza glabra: a phytopharmacological review. Int J Pharm Sci Res. 2013;4:2470–2477.
  • Salentin S, Schreiber S, Haupt VJ, et al. PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015;43:443–447.
  • Lipinski CA, Lombardo F, Dominy BW, et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2012;64:4–17.
  • Ad ABAW, Downie AC, Fink CS. Inhibition of growth and stimulation of apoptosis by ß-sitosterol treatment of MDA-MB-231 human breast cancer cells in culture. Int J Mol Med. 2000;5:541–545.
  • Velazco O, Chamorro G. Genotoxic and cytotoxic studies of beta-sitosterol and pteropodine in mouse. J Biomed Biotechnol. 2005;3:242–247.
  • Saeidnia S, Manayi A, Gohari AR. The story of beta-sitosterol – a review. Eur J Med Plants. 2014;4:590–609.
  • Meneses-Sagrero SE, Navarro-Navarro M, Ruiz-Bustos E, et al. Antiproliferative activity of spinasterol isolated of Stegnosperma halimifolium (Benth, 1844). Saudi Pharm J. 2017;25:1137–1143.
  • Sedky NK, El Gammal ZH, Wahba AE, et al. The molecular basis of cytotoxicity of α-spinasterol from Ganoderma resinaceum: induction of apoptosis and overexpression of p53 in breast and ovarian cancer cell lines. J Cell Biochem. 2018;119:3892–3902.
  • Flekhter OB, Boreko EI, Nigmatullina LR, et al. Synthesis and antiviral activity of lupane triterpenoids and their derivatives. Pharm Chem J. 2004;38:355–358.
  • Saleem M. Lupeol, a novel anti-inflammatory and anti-cancer dietary triterpene. Cancer Lett. 2009;285:109–115.
  • Fukai T, Satoh K, Nomura T, et al. Preliminary evaluation of antinephritis and radical scavenging activities of glabridin from Glycyrrhiza glabra. Fitoterapia. 2003;74:624–629.
  • Wang L, Yang R, Yuan B, et al. The antiviral and antimicrobial activities of licorice, a widely-used Chinese herb. Acta Pharm Sin B. 2015;5:310–315.
  • Jeong M, Kim HM, Lee JS, et al. (−)-Asarinin from the roots of Asarum sieboldii induces apoptotic cell death via caspase activation in human ovarian cancer cells. Molecules. 2018;23:1849.
  • Sankar M, Ramachandran B, Pandi B, et al. In silico screening of natural phytocompounds towards identification of potential lead compounds to treat COVID-19. Front Mol Biosci. 2021;8:637122.
  • Zubair MS, Maulana S, Widodo A, et al. Gc-ms, lc-ms/ms, docking and molecular dynamics approaches to identify potential sars-cov-2 3-chymotrypsin-like protease inhibitors from Zingiber officinale roscoe. Molecules. 2021;26:5230.
  • Lakhera S, Devlal K, Ghosh A, et al. In silico investigation of phytoconstituents of medicinal herb “Piper longum” against SARS-CoV-2 by molecular docking and molecular dynamics analysis. Results Chem. 2021;3:100199.

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