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Research Article

Discovery of 3CLpro Inhibitor of SARS-CoV-2 Main Protease

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Article: FSO853 | Received 12 Feb 2023, Accepted 20 Mar 2023, Published online: 06 Apr 2023

References

  • DandachiD , GeigerG , MontgomeryMWet al.Characteristics, comorbidities, and outcomes in a multicenter registry of patients with human immunodeficiency virus and Coronavirus Disease 2019. Clin. Infect. Dis.73(7), E1964–E1972 (2021).
  • ColonaVL , VasilouV , WattJ , NovelliG , ReichardtJKV. Update on human genetic susceptibility to COVID-19: susceptibility to virus and response. Human Genomics15(1), (2021).
  • Our World in Data. https://ourworldindata.org/ (Accessed October 20, 2022).
  • SunHB , LiHJ , HuangSP , ShiLX , XingZH , ShenJ. Case report of China/Tianjin's first novel Coronavirus Variant Omicron. Iran J. of Immunol.19(1), 115–120 (2022).
  • BeraK , ReedaVSJ , BabilaPR , DineshDC , HritzJ , KarthickT. An in silico molecular dynamics simulation study on the inhibitors of SARS-CoV-2 proteases (3CLpro and PLpro) to combat COVID-19. Mol. Simul.47(14), 1168–1184 (2021).
  • BerryM , FieldingB , GamieldienJ. Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: homology modelling and molecular dynamic studies. BMC Struct. Biol.15, 8 (2015).
  • TangBW , HeFM , LiuDPet al.AI-Aided Design of Novel Targeted Covalent Inhibitors against SARS-CoV-2. Biomolecules12(6), 746 (2022).
  • BachaU , BarrilaJ , Velazquez-CampoyA , LeavittSA , FreireE. Identification of Novel Inhibitors of the SARS Coronavirus Main Protease 3CLpro. Biochemistry43(17), 4906–4912 (2004).
  • NovakJ , PotemkinVA. A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study. Mol. Diversity26(5), 2631–2645 (2022).
  • LataS , AkifM. Comparative protein structure network analysis on 3CLpro from SARS-CoV-1 and SARS-CoV-2. Proteins Struct. Funct. Bioinf.89(9), 1216–1225 (2021).
  • KideraA , MoritsuguK , EkimotoT , IkeguchiM. Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble. J. Mol. Biol.433(24), 167324 (2021).
  • ZhaoXH , HeX , ZhongXH. Anti-inflammatory and in-vitro antibacterial activities of Traditional Chinese medicine formula Qingdaisan. BMC Complem. Altern. M.16(1), 503 (2016).
  • YangF , ZhangQ , YuanZSet al.Signaling potential therapeutic herbal medicine prescription for treating COVID-19 by collaborative filtering. Front. Pharmacol.12, 759479 (2021).
  • YaoW , WangF , WangH. Immunomodulation of artemisinin and its derivatives. Sci. Bull.61(18), 1399–1406 (2016).
  • TomaoF , BenedettiPanici P , TomaoS. Paclitaxel and Pazopanib in Ovarian Cancer. JAMA Oncology4(9), 1298–1299 (2018).
  • FanH , HeS-T , HanPet al.Cepharanthine: A Promising Old Drug against SARS-CoV-2. Advanced Biology6(12), 2200148 (2022).
  • SelvarajC , DineshDC , PedoneEMet al.SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors. Briefings Funct. Genomics Doi: 10.1093/bfgp/elac046 (2023) ( Online ahead of print).
  • JacobsJ , Grum-TokarsV , ZhouYet 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.56(2), 534–546 (2013).
  • LockbaumGJ , ReyesAC , LeeJMet al.Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188. Viruses13(2), 174 (2021).
  • DosSantos Correia PR , DonatoDe Souza AH , ChaparroRA , TenorioBarajas AY , PortoSR. Molecular docking, ADMET analysis and molecular dynamics (MD) simulation to identify synthetic isoquinolines as potential inhibitors of SARS-CoV-2 MPRO. Curr. Comput.-Aided Drug Des.19, 1–14 (2023).
  • BehzadiP , GajdácsM. Worldwide Protein Data Bank (wwPDB): a virtual treasure for research in biotechnology. Eur. J. Microbiol. Immu.11(4), 77–86 (2022).
  • GaoL-Q , XuJ , ChenS-D. In Silico screening of potential Chinese herbal medicine against COVID-19 by Targeting SARS-CoV-2 3CLpro and Angiotensin Converting Enzyme II using molecular docking. Chin. J. Integr. Med.26(7), 527–532 (2020).
  • O'boyleNM , BanckM , JamesCA , MorleyC , VandermeerschT , HutchisonGR. Open Babel: an open chemical toolbox. J. Cheminf.3(1), 33 (2011).
  • NguyenNT , NguyenTH , PhamTNHet al.Autodock Vina adopts more accurate binding poses but Autodock4 forms better binding affinity. J. Chem. Inf. Model.60(1), 204–211 (2020).
  • LiuZ , JiangD , ZhangC , ZhaoH , ZhaoQ , ZhangB. A novel fireworks algorithm for the protein–ligand docking on the AutoDock. Mobile Netw. Appl.26(2), 657–668 (2021).
  • DaouiO , ElkhattabiS , ChtitaS. Rational identification of small molecules derived from 9,10-dihydrophenanthrene as potential inhibitors of 3CLpro enzyme for COVID-19 therapy: a computer-aided drug design approach. Struct. Chem.33(5), 1667–1690 (2022).
  • DaouiO , ElkhattabiS , ChtitaS. Rational design of novel pyridine-based drugs candidates for lymphoma therapy. J. Mol. Struct.1270, 133964 (2022).
  • DaouiO , ElkhattabiS , BakhouchMet al.Cyclohexane-1,3-dione derivatives as future therapeutic agents for NSCLC: QSAR modeling, in Silico ADME-Tox properties, and structure-based drug designing approach. ACS Omega8(4), 4294–4319 (2023).
  • DaouiO , NourH , AbchirO , ElkhattabiS , BakhouchM , ChtitaS. A computer-aided drug design approach to explore novel type II inhibitors of c-Met receptor tyrosine kinase for cancer therapy: QSAR, molecular docking, ADMET and molecular dynamics simulations. J. Biomol. Struct. Dyn.1–18 (2022).
  • DaouiO , ElkhattabiS , ChtitaS. Design and prediction of ADME/Tox properties of novel magnolol derivatives as anticancer agents for NSCLC using 3D-QSAR, molecular docking, MOLCAD and MM-GBSA studies. Lett. Drug Des. Discovery20(5), 545–569 (2023).
  • TumskiyRS , TumskaiaAV. Multistep rational molecular design and combined docking for discovery of novel classes of inhibitors of SARS-CoV-2 main protease 3CLpro. Chem. Phys. Lett.780, 138894 (2021).
  • GoodfordPJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem.28(7), 849–857 (1985).
  • WallaceAC , LaskowskiRA , ThorntonJM. LIGPLOT: a program to generate schematic diagrams of protein–ligand interactions. Protein Eng. Des. Sel.8(2), 127–134 (1995).
  • DaouiO , ElkhattabiS , ChtitaS , ElkhalabiR , ZgouH , BenjellounAT. QSAR, molecular docking and ADMET properties in silico studies of novel 4,5,6,7-tetrahydrobenzo[D]-thiazol-2-Yl derivatives derived from dimedone as potent anti-tumor agents through inhibition of C-Met receptor tyrosine kinase. Heliyon7(7), e07463 (2021).
  • NourH , DaouiO , AbchirO , ElkhattabiS , BelaidiS , ChtitaS. Combined computational approaches for developing new anti-Alzheimer drug candidates: 3D-QSAR, molecular docking and molecular dynamics studies of liquiritigenin derivatives. Heliyon8(12), (2022).
  • HughesJD , BlaggJ , PriceDAet al.Physiochemical drug properties associated with in vivo toxicological outcomes. Bioorg. Med. Chem. Lett.18(17), 4872–4875 (2008).
  • FerreiraLLG , AndricopuloAD. ADMET modeling approaches in drug discovery. Drug Discov. Today24(5), 1157–1165 (2019).
  • NorinderU , BergströmCaS. Prediction of ADMET Properties. Chem. Med. Chem.1(9), 920–937 (2006).
  • PiresDEV , BlundellTL , AscherDB. pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J. Med. Chem.58(9), 4066–4072 (2015).
  • DainaA , MichielinO , ZoeteV. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep.7(1), 42717 (2017).
  • MatsumotoT , KaifuchiN , MizuharaY , WarabiE , WatanabeJ. Use of a Caco-2 permeability assay to evaluate the effects of several Kampo medicines on the drug transporter P-glycoprotein. J. Nat. Med.-Tokyo72(4), 897–904 (2018).
  • LiuL , ZhangL , FengHet al.Prediction of the blood–brain barrier (BBB) permeability of chemicals based on machine-learning and ensemble methods. Chem. Res. Toxicol.34(6), 1456–1467 (2021).
  • LiH , YapCW , UngCY , XueY , CaoZW , ChenYZ. Effect of selection of molecular descriptors on the prediction of blood–brain barrier penetrating and nonpenetrating agents by statistical learning methods. J. Chem. Inf. Model.45(5), 1376–1384 (2005).
  • SyedS , ClemensPL , LathersDet al.Lack of effect of brivanib on the pharmacokinetics of midazolam, a CYP3A4 Substrate, administered intravenously and orally in healthy participants. J. Clin. Pharmacol.52(6), 914–921 (2012).
  • XuWD , XiaoMZ , LiJYet al.Hepatoprotective effects of Di Wu Yang Gan: a medicinal food against CCl4-induced hepatotoxicity in vivo and in vitro. Food Chem.327, 127093 (2020).
  • SahuSN , PattanayakSK. Molecular docking and molecular dynamics simulation studies on PLCE1 encoded protein. J. Mol. Struct.1198, 126936 (2019).
  • DeVivo M , MasettiM , BottegoniG , CavalliA. Role of molecular dynamics and related methods in drug discovery. J. Med. Chem.59(9), 4035–4061 (2016).
  • VanDer Spoel D , LindahlE , HessB , GroenhofG , MarkAE , BerendsenHJC. GROMACS: fast, flexible, and free. J. Comput. Chem.26(16), 1701–1718 (2005).
  • CroitoruA , ParkSJ , KumarAet al.Additive CHARMM36 force field for nonstandard amino acids. J. Chem. Theory Comput.17(6), 3554–3570 (2021).
  • ZoeteV , CuendetMA , GrosdidierA , MichielinO. SwissParam: a fast force field generation tool for small organic molecules. J. Comput. Chem.32(11), 2359–2368 (2011).
  • GrotzKK , SchwierzN. Optimized magnesium force field parameters for biomolecular simulations with accurate solvation, ion-binding, and water-exchange properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. J. Chem. Theory Comput.18(1), 526–537 (2022).
  • Mosquera-YuquiF , Lopez-GuerraN , Moncayo-PalacioEA. Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations. J. Biomol. Struct. Dyn.40(5), 2010–2023 (2022).
  • IbrahimMaA , AbdelrahmanAHM , Jaragh-AlhadadLAet al.Exploring Toxins for Hunting SARS-CoV-2 Main Protease Inhibitors: Molecular Docking, Molecular Dynamics, Pharmacokinetic Properties, and Reactome Study. Pharmaceuticals15(2), (2022).
  • Velazquez-LiberaJL , Duran-VerdugoF , Valdes-JimenezA , Nunez-VivancoG , CaballeroJ. LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein–ligand docking. Bioinformatics36(9), 2912–2914 (2020).
  • BorhaniDW , ShawDE. The future of molecular dynamics simulations in drug discovery. J. Comput.-Aided Mol. Des.26(1), 15–26 (2012).
  • FaroukA , BaigMH , KhanMI , ParkT , AlotaibiSS , DongJJ. Screening of inhibitors against SARS-CoV-2 spike protein and their capability to block the viral entry mechanism: a viroinformatics study. Saudi J. Biol. Sci.28(6), 3262–3269 (2021).
  • YamamotoE , AkimotoT , MitsutakeA , MetzlerR. Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution. Phys. Rev. Lett.126(12), (2021).
  • MenendezCA , AccordinoSR , GerbinoDC , AppignanesiGA. Hydrogen bond dynamic propensity studies for protein binding and drug design. PLOS ONE11(10), (2016).
  • LiuK , WatanabeE , KokuboH. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. J. Comput.-Aided Mol. Des.31(2), 201–211 (2017).
  • SongPL , WangG , SuYet al.Strategy and validation of a structure-based method for the discovery of selective inhibitors of PAK isoforms and the evaluation of their anti-cancer activity. Bioorg. Chem.91, 103168 (2019).
  • TianW , ChenC , LeiX , ZhaoJL , LiangJ. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res.46(W1), W363–W367 (2018).
  • KanS , ChenG , HanCet al.Chemical constituents from the roots of Xanthium sibiricum. Nat. Prod. Res.25(13), 1243–1249 (2011).
  • KadanG , GözlerT , HesseM. (+)-Norchelidonine from Chelidonium majus. Planta Med.58(05), 477–477 (1992).
  • KobayashiH , SasanoY , KanohN , KwonE , IwabuchiY. Total synthesis of the proposed structure of turkiyenine. Eur. J. Org. Chem.2016(2), 270–273 (2016).
  • ChagasCM , MossS , AlisaraieL. Drug metabolites and their effects on the development of adverse reactions: Revisiting Lipinski's Rule of Five. Int. J. Pharm.549(1-2), 133–149 (2018).