Molecular docking and dynamic simulations of some medicinal plants compounds against SARS-CoV-2: an in silico study

References

• Chan JFW, Yuan S, Kok KH, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020;395:514–523. doi:10.1016/S0140-6736(20)30154-9.
   PubMed Web of Science ®Google Scholar
• Zhou P, Lou Yang X, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–273. doi:10.1038/s41586-020-2012-7.
   PubMed Web of Science ®Google Scholar
• WHO, Coronavirus (COVID-19) events as they happen, https://www.who.int/emergencies/diseases/novel-coronavirus-2019/Events-as-They-Happen. (2020) https://www.who.int/emergencies/diseases/novel-cor. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen (accessed May 18, 2020).
   Google Scholar
• (World Health Organisation), Coronavirus (COVID-19) events as they happen, (n.d.). https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen (accessed June 30, 2020).
   Google Scholar
• Mousavizadeh L, Ghasemi S. Genotype and phenotype of COVID-19: their roles in pathogenesis. J Microbiol Immunol Infect. 2020: 0–4. doi:10.1016/j.jmii.2020.03.022.
   PubMedGoogle Scholar
• Niranjani Iyer, Decoding the SARS-CoV-2 Genomes – Diagnostic Testing, (2020). https://blogs.3ds.com/biovia/decoding-the-sars-cov-2-genomes-diagnostic-testing/?utm_medium=email&utm_source=promotional&utm_campaign=bioviaeflashsendinwaves_OP53851&utm_content=2020-05-biovia-newsletter-en_DM960160 (accessed May 21, 2020).
   Google Scholar
• Vankadari N, Wilce JA. Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26. Emerg Microbes Infect. 2020;9:601–604. doi:10.1080/22221751.2020.1739565.
   PubMed Web of Science ®Google Scholar
• Habibzadeh P, Stoneman EK. The novel coronavirus: a bird’s eye view. Int J Occup Environ Med. 2020;11:65–71. doi:10.15171/ijoem.2020.1921.
   PubMed Web of Science ®Google Scholar
• Jin Z, Du X, Xu Y, et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature. 2020. doi:10.1038/s41586-020-2223-y.
   Web of Science ®Google Scholar
• Wang M, Cao R, Zhang L, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30:269–271. doi:10.1038/s41422-020-0282-0.
   PubMed Web of Science ®Google Scholar
• Moore N. Chloroquine for COVID-19 infection. Drug Saf. 2020;43:393–394. doi:10.1007/s40264-020-00933-4.
   Web of Science ®Google Scholar
• Strodel B, Jülich F, Olubiyi OO, et al. High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2 Mechanistic study View project Sickle cell disease (SCD) drug discovery View project High throughput virtual screening for M pro inhibitors A PREPR, Researchgate.Net. (2020). doi:10.20944/preprints202004.0161.v1.
   Google Scholar
• Tallei T, Tumilaar S, Niode N, et al. Potential of plant bioactive compounds as SARS-CoV-2 main protease (Mpro) and spike (S) glycoprotein inhibitors: a molecular docking study. Preprints. 2020: 1–18. doi:10.20944/preprints202004.0102.v1.
   Google Scholar
• Okereke SC, Ijeh II, Arunsi UO. Determination of bioactive constituents of Rauwolfia vomitoria Afzel (Asofeyeje) roots using gas chromatography-mass spectrometry (GC-MS) and Fourier transform infrared spectrometry (FT-IR). African J Pharm Pharmacol. 2017;11:25–31. doi:10.5897/ajpp2016.4712.
   Google Scholar
• Ganjhu RK, Mudgal PP, Maity H, et al. Herbal plants and plant preparations as remedial approach for viral diseases. VirusDisease. 2015;26:225–236. doi:10.1007/s13337-015-0276-6.
   PubMedGoogle Scholar
• Ali I, Alharbi OML. COVID-19: disease, management, treatment, and social impact. Sci Total Environ. 2020;728:138861. doi:10.1016/j.scitotenv.2020.138861.
   PubMed Web of Science ®Google Scholar
• Okunade AL. Ageratum conyzoides L. (Asteraceae). Fitoterapia. 2002;73:1–16. doi:10.1016/S0367-326X(01)00364-1.
   PubMed Web of Science ®Google Scholar
• Churiyah, Pongtuluran OB, Rofaani E, et al. Antiviral and immunostimulant activities of andrographis paniculata. HAYATI J Biosci. 2015;22:67–72. doi:10.4308/hjb.22.2.67.
   Google Scholar
• Benoy GK, Animesh DK, Aninda M, et al. An overview on andrographis paniculata (burm. F.) Nees. Int J Res Ayurveda Pharm. 2012;3:752–760. doi:10.7897/2277-4343.03610.
   Google Scholar
• Tang LIC, Ling APK, Koh RY, et al. Screening of anti-dengue activity in methanolic extracts of medicinal plants. BMC Complement Altern Med. 2012;12:3. doi:10.1186/1472-6882-12-3.
   PubMed Web of Science ®Google Scholar
• Wintachai P, Kaur P, Lee RCH, et al. Activity of andrographolide against chikungunya virus infection. Sci Rep. 2015;5:1–14. doi:10.1038/srep14179.
   Web of Science ®Google Scholar
• Dubey S, Kashyap P. Azadirachta indica: a plant with versatile potential. Rajiv Gandhi Univ Heal Sci J Pharm Sci. 2014;4:39–46. doi:10.5530/rjps.2014.2.2.
   Google Scholar
• Emmanuel O, Agbaji AS, Williams IS, et al. An overview of Neem, Azadirachta indica research in Nigeria. Niger J Sci. 2015;49:1–9.
   Google Scholar
• Ahmad A, Javed MR, Rao AQ, et al. Designing and screening of universal drug from neem (Azadirachta indica) and standard drug chemicals against influenza virus nucleoprotein. BMC Complement Altern Med. 2016;16:1–8. doi:10.1186/s12906-016-1469-2.
   PubMed Web of Science ®Google Scholar
• Bharti Sarin AM, Verma N, PedroMartín J. An overview of important ethnomedicinal herbs of phyllanthus species: present status and future prospects. Sci World J. 2014;2014:12. doi:10.1155/2014/839172.
   Google Scholar
• Pongthanapisith V, Ikuta K, Puthavathana P, et al. Antiviral protein of Momordica charantia L. inhibits different subtypes of influenza A. Evidence-Based Complement Altern Med. 2013;2013; doi:10.1155/2013/729081.
   Web of Science ®Google Scholar
• Tang LIC, Ling APK, Voon KGL. Screening of anti-dengue activity in methanolic extracts of medicinal plants Background Methods Plant materials and extraction. BMC Complement Altern Med. 2014: 1–13.
   Google Scholar
• Salehi B, Anil Kumar NV, Şener B, et al. Medicinal plants used in the treatment of human immunodeficiency virus. Int J Mol Sci. 2018;19. doi:10.3390/ijms19051459.
   Web of Science ®Google Scholar
• Yeh SF, Hong CY, Huang YL, et al. Effect of an extract from Phyllanthus amarus on hepatitis B surface antigen gene expression in human hepatoma cells. Antiviral Res. 1993;20:185–192. doi:10.1016/0166-3542(93)90019-F.
   PubMed Web of Science ®Google Scholar
• Londhe JS, Devasagayam TPA, Foo LY, et al. Antioxidant activity of some polyphenol constituents of the medicinal plant Phyllanthus amarus Linn. Redox Rep. 2008;13:199–207. doi:10.1179/135100008X308984.
   PubMed Web of Science ®Google Scholar
• Yeo SG, Song JH, Hong EH, et al. Antiviral effects of Phyllanthus urinaria containing corilagin against human enterovirus 71 and Coxsackievirus A16 in vitro. Arch Pharm Res. 2015;38:193–202. doi:10.1007/s12272-014-0390-9.
   PubMed Web of Science ®Google Scholar
• Patel JR, Tripathi P, Sharma V, et al. Phyllanthus amarus: ethnomedicinal uses, phytochemistry and pharmacology: a review. J Ethnopharmacol. 2011;138:286–313. doi:10.1016/j.jep.2011.09.040.
   PubMed Web of Science ®Google Scholar
• PubChem, (n.d.). https://pubchem.ncbi.nlm.nih.gov/ (accessed June 27, 2020).
   Google Scholar
• R. Quarcoo, A. Court, C. Division, Search list, (2014) 2013–2015. https://phytochem.nal.usda.gov/phytochem/search (accessed June 6, 2020).
   Google Scholar
• 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. doi:10.1016/j.addr.2012.09.019.
   Web of Science ®Google Scholar
• Veber DF, Johnson SR, Cheng HY, et al. Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem. 2002;45:2615–2623. doi:10.1021/jm020017n.
   PubMed Web of Science ®Google Scholar
• Giménez BG, Santos MS, Ferrarini M, et al. Evaluation of blockbuster drugs under the rule-of-five. Pharmazie. 2010;65:148–152. doi:10.1691/ph.2010.9733.
   PubMed Web of Science ®Google Scholar
• 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. doi:10.1038/srep42717.
   PubMed Web of Science ®Google Scholar
• Walls AC, Park YJ, Tortorici MA, et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020;181:281–292.e6. doi:10.1016/j.cell.2020.02.058.
   PubMed Web of Science ®Google Scholar
• Wang Q, Zhang Y, Wu L, et al. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell. 2020: 1–11. doi:10.1016/j.cell.2020.03.045.
   Google Scholar
• Protein Data Bank, RCSB PDB: Homepage, Rcsb Pdb. (2019) 1. https://www.rcsb.org/ (accessed June 30, 2020).
   Google Scholar
• Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron. 1980;36:3219–3228. doi:10.1016/0040-4020(80)80168-2.
   Web of Science ®Google Scholar
• Allouche A. Software news and updates Gabedit — a graphical user interface for computational chemistry softwares. J Comput Chem. 2012;32:174–182. doi:10.1002/jcc.
   Web of Science ®Google Scholar
• Sabe VT, Tolufashe GF, Ibeji CU, et al. Identification of potent L,D-transpeptidase 5 inhibitors for Mycobacterium tuberculosis as potential anti-TB leads: virtual screening and molecular dynamics simulations. J Mol Model. 2019;25; doi:10.1007/s00894-019-4196-z.
   Web of Science ®Google Scholar
• Baker EN, Hubbard RE. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol. 1984;44:97–179. doi:10.1016/0079-6107(84)90007-5.
   PubMed Web of Science ®Google Scholar
• Srinivasan J, Cheatham TE, Cieplak P, et al. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc. 1998;120:9401–9409. doi:10.1021/ja981844+.
   Web of Science ®Google Scholar
• Kollman PA, Massova I, Reyes C, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33:889–897. doi:10.1021/ar000033j.
   PubMed Web of Science ®Google Scholar
• Gohlke H, Case DA, Biology M, et al. Converging free energy estimates: MM-PB (GB) SA studies on the protein – protein complex Ras – Raf. J Comput Chem. 2003: 238–250.
   Web of Science ®Google Scholar
• Liu K, Watanabe E, Kokubo H. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. J Comput Aided Mol Des. 2017;31:201–211. doi:10.1007/s10822-016-0005-2.
   PubMed Web of Science ®Google Scholar
• Aier I, Varadwaj PK, Raj U. Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Sci Rep. 2016;6:1–10. doi:10.1038/srep34984.
   PubMed Web of Science ®Google Scholar
• Sun H, Li Y, Tian S, et al. Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Phys Chem Chem Phys. 2014;16:16719–16729. doi:10.1039/c4cp01388c.
   PubMed Web of Science ®Google Scholar
• Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov. 2015;10:449–461. doi:10.1517/17460441.2015.1032936.
   PubMed Web of Science ®Google Scholar
• Cournia Z, Allen B, Sherman W. Relative binding free energy calculations in drug discovery: recent advances and practical considerations. J Chem Inf Model. 2017;57:2911–2937. doi:10.1021/acs.jcim.7b00564.
   PubMed Web of Science ®Google Scholar
• Cho IH, Gong JH, Kang MK, et al. Astragalin inhibits airway eotaxin-1 induction and epithelial apoptosis through modulating oxidative stress-responsive MAPK signaling. BMC Pulm Med. 2014;14:1–11. doi:10.1186/1471-2466-14-122.
   Web of Science ®Google Scholar