Skip to content
2000
Volume 32, Issue 26
  • ISSN: 0929-8673
  • E-ISSN: 1875-533X

Abstract

Aims

This study aimed to explore the potential of natural anticoagulant compounds as synergistic inhibitors of the main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2 and find effective therapies against SARS-CoV-2 by investigating the inhibitory effects of natural anticoagulant compounds on key viral proteases.

Objective

The objectives of this study were to conduct rigorous virtual screening and molecular docking analyses to evaluate the binding affinities and interactions of selected anticoagulant compounds with Mpro and PLpro, to assess the pharmacokinetic and pharmacodynamic profiles of the compounds to determine their viability for therapeutic use, and to employ molecular dynamics simulations to understand the stability of the identified compounds over time.

Methods

In this study, a curated collection of natural anticoagulant compounds was conducted. Virtual screening and molecular docking analyses were performed to assess binding affinities and interactions with Mpro and PLpro. Furthermore, pharmacokinetic and pharmacodynamic analyses were carried out to evaluate absorption, distribution, metabolism, and excretion profiles. Molecular dynamics simulations were performed to elucidate compound stability.

Results

Natural compounds exhibiting significant inhibitory activity against Mpro and PLpro were identified. A dual-target approach was established as a promising strategy for attenuating viral replication and addressing coagulopathic complications associated with SARS-CoV-2 infection.

Conclusion

The study lays a solid foundation for experimental validation and optimization of identified compounds, potentially leading to the development of precise treatments for SARS-CoV-2.

Loading

Article metrics loading...

/content/journals/cmc/10.2174/0109298673331781240829094334
2024-10-03
2025-10-25
Loading full text...

Full text loading...

References

  1. CuiJ. LiF. ShiZ.L. Origin and evolution of pathogenic coronaviruses.Nat. Rev. Microbiol.201917318119210.1038/s41579‑018‑0118‑930531947
    [Google Scholar]
  2. MollicaV. RizzoA. MassariF. The pivotal role of TMPRSS2 in coronavirus disease 2019 and prostate cancer.Future Oncol.202016272029203310.2217/fon‑2020‑057132658591
    [Google Scholar]
  3. RizzoA. PalmiottiG. SARS-CoV-2 Omicron variant in cancer patients: an insight into the vaccine booster debate.Future Oncol.202218111301130210.2217/fon‑2022‑002435109688
    [Google Scholar]
  4. SuH. ZhouF. HuangZ. MaX. NatarajanK. ZhangM. HuangY. SuH. Molecular insights into small- molecule drug discovery for SARS-CoV-2.Angew. Chem. Int. Ed.202160189789980210.1002/anie.20200883532729180
    [Google Scholar]
  5. BrantA.C. TianW. MajerciakV. YangW. ZhengZ.M. SARS-CoV-2: from its discovery to genome structure, transcription, and replication.Cell Biosci.202111113610.1186/s13578‑021‑00643‑z34281608
    [Google Scholar]
  6. HuB. GuoH. ZhouP. ShiZ.L. Characteristics of SARS-CoV-2 and COVID-19.Nat. Rev. Microbiol.202119314115410.1038/s41579‑020‑00459‑733024307
    [Google Scholar]
  7. HuQ. XiongY. ZhuG.H. ZhangY.N. ZhangY.W. HuangP. GeG.B. The SARS-CoV-2 main protease (Mpro): Structure, function, and emerging therapies for COVID-19.MedComm.202233e15110.1002/mco2.15135845352
    [Google Scholar]
  8. ClementzM.A. ChenZ. BanachB.S. WangY. SunL. RatiaK. Baez-SantosY.M. WangJ. TakayamaJ. GhoshA.K. LiK. MesecarA.D. BakerS.C. Deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases.J. Virol.20108494619462910.1128/JVI.02406‑0920181693
    [Google Scholar]
  9. YevsieievaL.V. LohachovaK.O. KyrychenkoA. KovalenkoS.M. IvanovV.V. KaluginO.N. Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2.RSC Advances20231350355003552410.1039/D3RA06479D38077980
    [Google Scholar]
  10. Khazeei TabariM.A. IranpanahA. BahramsoltaniR. RahimiR. Flavonoids as promising antiviral agents against SARS-CoV-2 Infection: A mechanistic review.Molecules20212613390010.3390/molecules2613390034202374
    [Google Scholar]
  11. YamariI. AbchirO. NourH. El KoualiM. ChtitaS. Identification of new dihydrophenanthrene derivatives as promising antiSARS-CoV-2 drugs through in silico investigations.Main Group Chem.202322522012710.3233/MGC‑220127
    [Google Scholar]
  12. AfricaJ.G. ArturoH.C. BernardoL.J. ChingJ.K.A. de la CruzO.C. HernandezJ.B. MagsipocR.J. SalesC.T. AgbayJ.C. NeriG.L. QuimqueM.T. MacabeoA.P. In silico triple targeting of SARS-CoV-2 3CLᵖʳᵒ, PLᵖʳᵒ, and RdRp by Philippine antitubercular natural products libraries.Philipp. J. Sci.20211511.10.56899/151.01.04
    [Google Scholar]
  13. IslamM.T. SarkarC. El-KershD.M. JamaddarS. UddinS.J. ShilpiJ.A. MubarakM.S. Natural products and their derivatives against coronavirus: A review of the non- clinical and pre-clinical data.Phytother. Res.202034102471249210.1002/ptr.670032248575
    [Google Scholar]
  14. RamanK. RajagopalK. IslamF. DhawanM. MitraS. AparnaB. VarakumarP. ByranG. ChoudharyO.P. EmranT.B. Role of natural products towards the SARS-CoV-2: A critical review.Ann. Med. Surg.20228010406210.1016/j.amsu.2022.10406235814035
    [Google Scholar]
  15. XianY. ZhangJ. BianZ. ZhouH. ZhangZ. LinZ. XuH. Bioactive natural compounds against human coronaviruses: A review and perspective.Acta Pharm. Sin. B20201071163117410.1016/j.apsb.2020.06.00232834947
    [Google Scholar]
  16. VlachouE.E.N. LitinasK.E. An overview on pyranocoumarins: Synthesis and biological activities.Curr. Org. Chem.202023242679272110.2174/1385272823666191025151236
    [Google Scholar]
  17. KhandyM.T. SofronovaA.K. GorpenchenkoT.Y. ChirikovaN.K. Plant pyranocoumarins: description, biosynthesis, application.Plants20221122313510.3390/plants1122313536432864
    [Google Scholar]
  18. VenugopalaK.N. RashmiV. OdhavB. Review on natural coumarin lead compounds for their pharmacological activity.BioMed. Res. Int.2013201311410.1155/2013/96324823586066
    [Google Scholar]
  19. HassanM.Z. OsmanH. AliM.A. AhsanM.J. Therapeutic potential of coumarins as antiviral agents.Eur. J. Med. Chem.201612323625510.1016/j.ejmech.2016.07.05627484512
    [Google Scholar]
  20. KashmanY. GustafsonK.R. FullerR.W. CardellinaJ.H.II McMahonJ.B. CurrensM.J. BuckheitR.W. HughesS.H. CraggG.M. BoydM.R. HIV inhibitory natural products. Part 7. The calanolides, a novel HIV-inhibitory class of coumarin derivatives from the tropical rainforest tree, Calophyllum lanigerum.J. Med. Chem.199235152735274310.1021/jm00093a0041379639
    [Google Scholar]
  21. MinS.J. LeeH. ShinM.S. LeeJ.W. Synthesis and biological properties of pyranocoumarin derivatives as potent anti-inflammatory agents.Int. J. Mol. Sci.202324121002610.3390/ijms24121002637373174
    [Google Scholar]
  22. StefanachiA. LeonettiF. PisaniL. CattoM. CarottiA. Coumarin: A natural, privileged and versatile scaffold for bioactive compounds.Molecules201823225010.3390/molecules2302025029382051
    [Google Scholar]
  23. MJ. JoyF. NizamA. Naidu KrishnaS.B. Multicomponent synthesis strategies, catalytic activities, and potential therapeutic applications of pyranocoumarins: A comprehensive review.Chem. Biodivers.20232010e20230083610.1002/cbdv.202300836
    [Google Scholar]
  24. XiangX. FengX. LuS. JiangB. HaoD. PeiQ. XieZ. JingX. Indocyanine green potentiated paclitaxel nanoprodrugs for imaging and chemotherapy.Exploration2022242022000810.1002/EXP.2022000837325605
    [Google Scholar]
  25. TruongP.L. YinY. LeeD. KoS.H. Advancement in COVID-19 detection using nanomaterial-based biosensors.Exploration2023312021023210.1002/EXP.2021023237323622
    [Google Scholar]
  26. PerkinElmer ChemOffice Professional PerkinElmer ChemOffice Professional 16.0.2011Available from: https://perkinelmer-chemoffice-professional.software.informer.com/16.0/ (Accessed on 19-8-2024)
  27. Avogadro: an open-source molecular builder and visualization tool.2022Available from: https://avogadro.cc/ (Accessed on 19-8-2024)
  28. BermanH.M. WestbrookJ. FengZ. GillilandG. BhatT.N. WeissigH. ShindyalovI.N. BourneP.E. The protein data bank.Nucleic Acids Res.200028123524210.1093/nar/28.1.23510592235
    [Google Scholar]
  29. Swiss-PdbViewer 2019.Available from: https://spdbv.unil.ch/ (Accessed on 19-8-2024)
  30. MorrisG.M. HueyR. OlsonA.J. Using AutoDock for ligand-receptor docking.Curr. Protoc. Bioinformatics20082411410.1002/0471250953.bi0814s2419085980
    [Google Scholar]
  31. PyMOL by Schrödinger. Available from:https://pymol.org/2/ (Accessed on 19-8-2024)
  32. Dassault systéme. Discovery Studio. Biovia, Software.2021Available from: https://discover.3ds.com/discovery-studio-visualizer-download (Accessed on 15-8-2024)
  33. WiniwarterS. AhlbergE. WatsonE. OprisiuI. MogemarkM. NoeskeT. GreeneN. In silico ADME in drug design – enhancing the impact.ADMET DMPK2018611510.5599/admet.6.1.470
    [Google Scholar]
  34. DainaA. MichielinO. ZoeteV. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.Sci. Rep.2017714271710.1038/srep4271728256516
    [Google Scholar]
  35. PiresD.E.V. BlundellT.L. AscherD.B. pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures.J. Med. Chem.20155894066407210.1021/acs.jmedchem.5b0010425860834
    [Google Scholar]
  36. Schrödinger2021Available from: https://doi.org/software (Accessed on 19-8-2024)
  37. RoosK. WuC. DammW. ReboulM. StevensonJ.M. LuC. DahlgrenM.K. MondalS. ChenW. WangL. AbelR. FriesnerR.A. HarderE.D. OPLS3e: Extending force field coverage for drug-like small molecules.J. Chem. Theory Comput.20191531863187410.1021/acs.jctc.8b0102630768902
    [Google Scholar]
  38. MarkP. NilssonL. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K.J. Phys. Chem. A2001105439954996010.1021/jp003020w
    [Google Scholar]
  39. KeQ. GongX. LiaoS. DuanC. LiL. Effects of thermostats/barostats on physical properties of liquids by molecular dynamics simulations.J. Mol. Liq.202236512011610.1016/j.molliq.2022.120116
    [Google Scholar]
  40. LipinskiC.A. LombardoF. DominyB.W. FeeneyP.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169- 409X(96)00423-1.Adv. Drug Deliv. Rev.2001461-332610.1016/S0169‑409X(00)00129‑011259830
    [Google Scholar]
  41. VeberD.F. JohnsonS.R. ChengH.Y. SmithB.R. WardK.W. KoppleK.D. Molecular properties that influence the oral bioavailability of drug candidates.J. Med. Chem.200245122615262310.1021/jm020017n12036371
    [Google Scholar]
  42. EganW.J. MerzK.M.Jr. BaldwinJ.J. Prediction of drug absorption using multivariate statistics.J. Med. Chem.200043213867387710.1021/jm000292e11052792
    [Google Scholar]
/content/journals/cmc/10.2174/0109298673331781240829094334
Loading
/content/journals/cmc/10.2174/0109298673331781240829094334
Loading

Data & Media loading...

Supplements

Supplementary material is available on the publisher's website along with the published article.


  • Article Type:
    Research Article
Keyword(s): ADMET; dynamics simulation; molecular docking; papain-like protease; Protease; SARS-CoV-2
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test