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Research Article

Plant Protease Inhibitors Against SARS-CoV-2 Main Protease: An In⟓ilico Approach

, , , , ORCID Icon & ORCID Icon
Pages 439-454 | Received 26 Oct 2022, Accepted 27 Apr 2023, Published online: 07 Jun 2023

References

  • V'kovski P , KratzelA , SteinerS , StalderH , ThielV. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol.19(3), 155–170 (2021).
  • Wang MY , ZhaoR , GaoLJ , GaoXF , WangDP , CaoJM. SARS-CoV-2: structure, biology, and structure-based therapeutics development. Front. Cell. Infect. Microbiol.10(November), 1–17 (2020).
  • Noske GD , NakamuraAM , GawriljukVOet al. A crystallographic snapshot of SARS-CoV-2 main protease maturation process: SARS-CoV-2 Mpro maturation. J. Mol. Biol.433(18), 167118 (2021).
  • Arya R , KumariS , PandeyBet al. Structural insights into SARS-CoV-2 proteins. J. Mol. Biol.433(2), 315–328 (2021).
  • Suárez D , DíazN. SARS-CoV-2 main protease: a molecular dynamics study. J. Chem. Inf. Model60(12), 5815–5831 (2020).
  • Mengist HM , MekonnenD , MohammedA , ShiR , JinT. Potency, safety, and pharmacokinetic profiles of potential inhibitors targeting SARS-CoV-2 main protease. Front. Pharmacol.11(February), 1–8 (2021).
  • Cotabarren J , LufranoD , ParisiMG , ObregónWD. Biotechnological, biomedical, and agronomical applications of plant protease inhibitors with high stability: a systematic review. Plant Science292(December 2019), 110398 (2020).
  • Zhao J , EeKY. In: Protease Inhibitors (Chapter 4, 2nd edition). (Eds). Elsevier (2018).
  • Marathe KR , PatilRH , VishwakarmaKS , ChaudhariAB , MaheshwariVL. In: Protease Inhibitors and Their Applications: An Overview, chapter 2, (1st Edition).Elsevier B.V (2019).
  • Srikanth S , ChenZ. Plant protease inhibitors in therapeutics-focus on cancer therapy. Front. Pharmacol.7(DEC), 1128–1142 (2016).
  • Kanwar SS , GuptaS. Plant protease inhibitors and their antiviral activities - potent therapeutics for introduction classification of plant protease inhibitors. 7, 1–8 (2021).
  • Liu Y , XuXQ , ZhangBet al. Bowman–Birk inhibitor suppresses herpes simplex virus type 2 infection of human cervical epithelial cells. Viruses10(10), 451–463 (2018).
  • Aoki H , AkaikeT , AbeKet al. Antiviral effect of oryzacystatin, a proteinase inhibitor in rice, against herpes simplex virus type 1 in vitro and in vivo. Antimicrob. Agents Chemother.39(4), 846–849 (1995).
  • Ramírez-Aportela E , López-BlancoJR , ChacónP. FRODOCK 2.0: fast protein–protein docking server. Bioinformatics32(15), 2386–2388 (2016).
  • Amaral JL , OliveiraJTA , LopesFESet al. Quantum biochemistry, molecular docking, and dynamics simulation revealed synthetic peptides induced conformational changes affecting the topology of the catalytic site of SARS-CoV-2 main protease. J. Biomol. Struct. Dyn.1(1), 1–13 (2021).
  • Van Der Spoel D , LindahlE , HessB , GroenhofG , MarkAE , BerendsenHJC. GROMACS: fast, flexible, and free. J. Comput. Chem.26(16), 1701–1718 (2005).
  • Moal IH , BatesPA. SwarmDock and the use of normal modes in protein–protein docking. Int. J. Mol. Sci.11(10), 3623–3648 (2010).
  • Robertson MJ , Tirado-RivesJ , JorgensenWL. Improved peptide and protein torsional energetics with the OPLS-AA force field. J. Chem. Theory Comput.11(7), 3499–3509 (2015).
  • Roman AL , MarkBS. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model51, 2778–2786 (2011).
  • Zhang DW , ZhangJZH. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy. J. Chem. Phy.119(7), 3599–3605 (2003).
  • Amaral JL , SantosSJM , SouzaPFNet al. Quantum biochemistry in cancer immunotherapy: new insights about CTLA-4/ipilimumab and design of ipilimumab-derived peptides with high potential in cancer treatment. Mol. Immunol.127(September), 203–211 (2020).
  • Delley B . From molecules to solids with the DMol3 approach. J. Chem. Phy.113(18), 7756–7764 (2000).
  • Tian W , ChenC , LeiX , ZhaoJ , LiangJ. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res.46(W1), W363–W367 (2018).
  • Cusinato J , CauY , CalvaniAM , MoriM. Repurposing drugs for the management of COVID-19. Expert Opin. Ther. Pat.31(4), 295–307 (2021).
  • Muratov EN , AmaroR , AndradeCHet al. A critical overview of computational approaches employed for COVID-19 drug discovery. Chem. Soc. Rev.50(16), 9121–9151 (2021).
  • Ministério da Saúde (Brasil) . Comissão Nacional de Incorporação de Tecnologias no SUS (CONITEC). Rendesivir para tratamento de pacientes com COVID-19 hospitalizados com pneumonia e necessidade de suplementação de oxigênio: relatório de recomendação. 1, 59 (2021).
  • Alam S , KamalTB , SarkerMMR , ZhouJR , RahmanSMA , MohamedIN. Therapeutic effectiveness and safety of repurposing drugs for the treatment of COVID-19: position standing in 2021. Front. Pharmacol.12(June), 1–19 (2021).
  • Santoro MG . Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information. (2020).
  • Bugin K , WoodcockJ. Trends in COVID-19 therapeutic clinical trials. Nat. Rev. Drug Discov.20(4), 254–255 (2021).
  • Services H , ServicesH. U.S. Department of Health and Human Services. Depart. Health Human Ser.564, 1–11 (2022).
  • Wang X , LiF , QiuWet al. SYNBIP: synthetic binding proteins for research, diagnosis and therapy. Nucleic Acids Res.50(D1), D560–D570 (2022).
  • Wishart DS , FeunangYD , GuoACet al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res.46(D1), D1074–D1082 (2018).
  • Yin J , LiF , ZhouYet al. INTEDE: interactome of drug–metabolizing enzymes. Nucleic Acids Res.49(D1), D1233–D1243 (2021).
  • Armstrong JF , FaccendaE , HardingSDet al. The IUPHAR/BPS Guide to Pharmacology in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV guide to malaria pharmacology. Nucleic Acids Res.48(D1), D1006–D1021 (2020).
  • Yin J , SunW , LiFet al. VARIDT 1.0: variability of drug transporter database. Nucleic Acids Res.48(D1), D1042–D1050 (2020).
  • Günther S , ReinkePYA , Fernández-GarciáYet al. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 372(6542), 642–646 (2021).
  • Ullrich S , NitscheC. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information. (2020).
  • Sojka D , ŠnebergerováP , RobbertseL. Protease inhibition–an established strategy to combat infectious diseases. Int. J. Mol. Sci.22(11), 1–15 (2021).
  • Banerjee R , PereraL , TillekeratneLMV. Potential SARS-CoV-2 main protease inhibitors. Drug Discov. Today26(3), 804–816 (2021).
  • Zhang L , LinD , SunXet al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors. Science368(6489), 409–412 (2020).
  • Bhat ZA , ChitaraD , IqbalJ , SanjeevBS , MadhumalarA. Targeting allosteric pockets of SARS-CoV-2 main protease Mpro. J. Biomol. Struct. Dyn.2(10), 1–16 (2021).
  • Verma S , PandeyAK. Factual insights of the allosteric inhibition mechanism of SARS-CoV-2 main protease by quercetin: an in silico analysis. 3 Biotech11(2), 1–10 (2021).
  • Crespo A , Rodriguez-GranilloA , LimVT. Quantum-mechanics methodologies in drug discovery: applications of docking and scoring in lead optimization. Curr.Top. Med. Chem.17(23), 25–48 (2017).
  • Tandon H , ChakrabortyT , SuhagV. A brief review on importance of DFT in drug design. Res. Med. Eng. Sci.7(4), 791–795 (2019).
  • Awoonor-Williams E , Abu-SalehAAAA. Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease. Phys. Chem. Chem. Phys.23(11), 6746–6757 (2021).
  • Gyebi GA , OgunroOB , AdegunloyeAP , OgunyemiOM , AfolabiSO. Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants. J. Biomol. Struct. Dyn.39(9), 3396–3408 (2021).
  • Sacco MD , HuY , GongoraMVet al. The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition. BioRxiv15, 898–912 (2022).
  • Vangeel L , ChiuW , DeJonghe Set al. Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern. Antiviral Res.198(January), 10–12 (2022).
  • Mishra UN , ReddyMV , PrasadDT. Plant serine protease inhibitor (SPI): a potent player with bactericidal, fungicidal, nematicidal and antiviral properties. Int. J. Chem. Stud.8(1), 2985–2993 (2020).
  • Sharma A , GuptaSP. Fundamentals of viruses and their proteases. Viral Proteases and Their Inhibitors, 16(January), 1–24 (2017).
  • Bruce Malkowicz S , McKennaWG , VaughnDJet al. Effects of Bowman–Birk Inhibitor Concentrate (BBIC) in patients with benign prostatic hyperplasia. Prostate48(1), 16–28 (2001).

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