625
Views
1
CrossRef citations to date
0
Altmetric
Research Article

In Silico Identification of Natural Compounds Against SARS-CoV-2 Main Protease From Chinese Herbal Medicines

, , , , , & show all
Article: FSO873 | Received 27 Mar 2023, Accepted 30 May 2023, Published online: 13 Jun 2023

References

  • FuLF , YeF , FengYet al.Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat. Commun.11(1), 4417 (2020).
  • HuB , GuoH , ZhouP , ShiZL. Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol.19(3), 141–154 (2021).
  • LiCX , NoreenS , ZhangLXet al.A critical analysis of SARS-CoV-2 (COVID-19) complexities, emerging variants, and therapeutic interventions and vaccination strategies. Biomed. Pharmacother.146, 112550 (2022).
  • CosarB , KaragulleogluZY , UnalSet al.SARS-CoV-2 mutations and their viral variants. Cytokine Growth Factor Rev.63, 10–22 (2022).
  • LuR , ZhaoX , LiJet al.Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet395(10224), 565–574 (2020).
  • DaiWH , ZhangB , JiangXMet al.Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science368(6497), 1331–1335 (2020).
  • BahunM , JukicM , OblakDet al.Inhibition of the SARS-CoV-2 3CL(pro) main protease by plant polyphenols. Food Chem.373, 131594 (2021).
  • WangF , ChenC , WangZet al.The structure of the porcine deltacoronavirus main protease reveals a conserved target for the design of antivirals. Viruses-Basel14(3), 486 (2022).
  • ZhaoY , FangC , ZhangQet al.Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332. Protein Cell13, 689–693 (2021).
  • NiuWH , WuF , CaoWYet al.Network pharmacology for the identification of phytochemicals in traditional Chinese medicine for COVID-19 that may regulate interleukin-6. Biosci. Rep.41(1), BSR20202583 (2021).
  • WangZ , YangL. Chinese herbal medicine: fighting SARS-CoV-2 infection on all fronts. J. Ethnopharmacol.270, 113869 (2021).
  • RenX , ShaoXX , LiXXet al.Identifying potential treatments of COVID-19 from traditional Chinese medicine (TCM) by using a data-driven approach. J. Ethnopharmacol.258, 112932 (2020).
  • AljindanRY , Al-SubaieAM , Al-OhaliAI , KumarDT , DossCGP , KamarajB. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput. Biol. Med.135, 104654 (2021).
  • SinghR , BhardwajVK , PurohitR. Inhibition of nonstructural protein 15 of SARS-CoV-2 by golden spice: a computational insight. Cell Biochem. Funct.40(8), 926–934 (2022).
  • SinghR , BhardwajVK , PurohitR. Potential of turmeric-derived compounds against RNA-dependent RNA polymerase of SARS-CoV-2: an in-silico approach. Comput. Biol. Med.139, 104965 (2021).
  • SharmaJ , KumarBhardwaj V , SinghR , RajendranV , PurohitR , KumarS. An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2. Food Chem.346, 128933 (2021).
  • BhardwajVK , SinghR , SharmaJ , RajendranV , PurohitR , KumarS. Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. J. Biomol. Struct. Dyn.39(10), 3449–3458 (2021).
  • SinghR , BhardwajVK , SharmaJ , KumarD , PurohitR. Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Comput. Biol. Med.136, 104631 (2021).
  • SinghR , PurohitR. Multi-target approach against SARS-CoV-2 by stone apple molecules: a master key to drug design. Phytother. Res. [ Early View].
  • BorgioJF , AlsuwatHS , AlOtaibi WMet al.State-of-the-art tools unveil potent drug targets amongst clinically approved drugs to inhibit helicase in SARS-CoV-2. Arch. Med. Sci.16(3), 508–518 (2020).
  • KimS , ChenJ , ChengTet al.PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res.49(D1), D1388–D1395 (2021).
  • RuJ , LiP , WangJet al.TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. J. Cheminf.6(1), 13 (2014).
  • O'boyleNM , BanckM , JamesCA , MorleyC , VandermeerschT , HutchisonGR. Open Babel: an open chemical toolbox. J. Cheminf.3(1), 33 (2011).
  • SannerMF. Python: a programming language for software integration and development. J. Mol. Graphics Modell.17(1), 57–61 (1999).
  • BehzadiP , GajdácsM. Worldwide Protein Data Bank (wwPDB): a virtual treasure for research in biotechnology. Eur. J. Microbiol. Immunol.11(4), 77–86 (2022).
  • Schrodinger, Llc. The PyMOL Molecular Graphics System, Version 1.8. (2015).
  • JohanssonMU , ZoeteV , MichielinO , GuexN. Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinf.13, (2012).
  • TrottO , OlsonAJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem.31(2), 455–461 (2010).
  • SuM , YangQ , DuYet al.Comparative assessment of scoring functions: the CASF-2016 update. J. Chem. Inf. Model.59(2), 895–913 (2019).
  • LaskowskiRA , SwindellsMB. LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. J. Chem. Inf. Model.51(10), 2778–2786 (2011).
  • LipinskiCA. Lead- and drug-like compounds: the rule-of-five revolution. Drug Discovery Today: Technol.1(4), 337–341 (2004).
  • 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).
  • AbrahamMJ , MurtolaT , SchulzRet al.GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX1–2, 19–25 (2015).
  • YuY , KramerA , VenableRMet al.Semi-automated optimization of the CHARMM36 lipid force field to include explicit treatment of long-range dispersion. J. Chem. Theory Comput.17(3), 1562–1580 (2021).
  • ZoeteV , CuendetMA , GrosdidierA , MichielinO. SwissParam: a fast force field generation tool for small organic molecules. J. Comput. Chem.32(11), 2359–2368 (2011).
  • Valdés-TresancoMS , Valdés-TresancoME , ValientePA , MorenoE. gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS. J. Chem. Theory Comput.17(10), 6281–6291 (2021).
  • OwenDR , AllertonCMN , AndersonASet al.An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19. Science374(6575), 1586–1593 (2021).
  • SonTung N , NgocQuynh Anh P , LyThi L , Duc-HungP , VuVV. Computational determination of potential inhibitors of SARS-CoV-2 main protease. J. Chem. Inf. Model.60(12), 5771–5780 (2020).
  • DainaA , MichielinO , ZoeteV. iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. J. Chem. Inf. Model.54(12), 3284–3301 (2014).
  • DelaneyJS. ESOL: estimating aqueous solubility directly from molecular structure. J. Chem. Inf. Comput. Sci.44(3), 1000–1005 (2004).
  • DainaA , ZoeteV. A BOILED-egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem11(11), 1117–1121 (2016).
  • MadlC , MadlU. Gastrointestinal motility in critically ill patients. Med. Klin-Intensivmed.113(5), 433–442 (2018).
  • ShakerB , YuMS , SongJSet al.LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM. Bioinformatics37(8), 1135–1139 (2021).
  • SongYR , LiCX , LiuGZet al.Drug-metabolizing cytochrome P450 enzymes have multifarious influences on treatment outcomes. Clin. Pharmacokinet.60(5), 585–601 (2021).
  • DasS , SarmahS , HazarikaZet al.Targeting the heme protein hemoglobin by (−)-epigallocatechin gallate and the study of polyphenol–protein association using multi-spectroscopic and computational methods. PCCP22(4), 2212–2228 (2020).
  • DasS , SinghA , SamantaSK , SinghaRoy A. Naturally occurring anthraquinones as potential inhibitors of SARS-CoV-2 main protease: an integrated computational study. Biologia77(4), 1121–1134 (2022).
  • DasS , BoraN , RohmanMA , SharmaR , JhaAN , SinghaRoy A. Molecular recognition of bio-active flavonoids quercetin and rutin by bovine hemoglobin: an overview of the binding mechanism, thermodynamics and structural aspects through multi-spectroscopic and molecular dynamics simulation studies. PCCP20(33), 21668–21684 (2018).
  • DasS , SinghA , SamantaSK , RoyAS. Naturally occurring anthraquinones as potential inhibitors of SARS-CoV-2 main protease: an integrated computational study. Biologia doi:10.1007/s11756-021-01004-4
  • BharadwajS , AzharEI , KamalMAet al.SARS-CoV-2 M-pro inhibitors: identification of anti-SARS-CoV-2 M-pro compounds from FDA approved drugs. J. Biomol. Struct. Dyn.40(6), 2769–2784 (2022).
  • KuangY , MaX , ShenW , RaoQ , YangS. Discovery of 3CLpro inhibitor of SARS-CoV-2 main protease. Future Sci. OA9(4), FSO853 (2023).
  • ChoudharyMI , ShaikhM , Tul-WahabA , Ur-RahmanA. In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation. PLOS ONE15(7), e0235030 (2020).
  • LoganathanY , JainM , ThiyagarajanSet al.An Insilico evaluation of phytocompounds from Albizia amara and Phyla nodiflora as cyclooxygenase-2 enzyme inhibitors. DARU29(2), 311–320 (2021).
  • XiaoT , WeiYL , CuiMQet al.Effect of dihydromyricetin on SARS-CoV-2 viral replication and pulmonary inflammation and fibrosis. Phytomedicine91, (2021).
  • FerreiraJC , FadlS , VillanuevaAJ , RabehWM. Catalytic dyad residues His41 and Cys145 impact the catalytic activity and overall conformational fold of the main SARS-CoV-2 protease 3-chymotrypsin-like protease. Front. Chem.9, (2021).
  • LamTTY , JiaN , ZhangYWet al.Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature583(7815), 282–285 (2020).
  • Al-MomaniH , AolymatI , AlmasriM , MahmoudSA , MashalS. Prevalence of gastro-intestinal symptoms among COVID-19 patients and the association with disease clinical outcomes. Future Sci. OA9(5), FSO858 (2023).