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Volume 18   Issue 2   Year 2023
Satpathy R., Acharya S.

Exploring the Mangrove Based Phytochemicals as Potential Viral RNA Helicase Inhibitors by in silico Docking and Molecular Dynamics Simulation Methods

Mathematical Biology & Bioinformatics. 2023;18(2):405-417.

doi: 10.17537/2023.18.405.

References

  1. Shang Y., Li H., Zhang R. Effects of pandemic outbreak on economies: evidence from business history context. Front. Public Health. 2021;9:632043. doi: 10.3389/fpubh.2021.632043
  2. Qiu W., Rutherford S., Mao A., Chu C. The pandemic and its impacts. Health. Cult. Soc. 2017;9:1–11. doi: 10.5195/HCS.2017.221
  3. Schlicksup C.J., Zlotnick A. Viral structural proteins as targets for antivirals. Curr. Opin. Virol. 2020;45:43–50. doi: 10.1016/j.coviro.2020.07.001
  4. Shi S.T., Lai M.M.C. Viral and cellular proteins involved in coronavirus replication. Curr. Top. Microbiol. Immunol. 2005;287:95–131. doi: 10.1007/3-540-26765-4_4
  5. Ranji A., Boris-Lawrie K. RNA helicases: emerging roles in viral replication and the host innate response. RNA Biol. 2010;7(6):775–787. doi: 10.4161/rna.7.6.14249
  6. Ghosh D., Basu A. Present perspectives on flaviviral chemotherapy. Drug Discov. Today. 2008;13(13–14):619–624. doi: 10.1016/j.drudis.2008.04.001
  7. Kim J., Park S.J., Park J., Shin H., Jang Y.S., Woo J.S., Min D.H. Identification of a direct-acting antiviral agent targeting RNA helicase via a graphene oxide nanobiosensor. ACS Appl. Mater. Interfaces. 2021;13(22):25715–25726. doi: 10.1021/acsami.1c04641
  8. De Clercq E. Strategies in the design of antiviral drugs. Nat. Rev. Drug Discov. 2002;1(1):13–25. doi: 10.1038/nrd703
  9. Spratt A.N., Gallazzi F., Quinn T.P., Lorson C.L., Sönnerborg A., Singh K. Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents. Expert Opin. Ther. Pat. 2021;31(4):339–350. doi: 10.1080/13543776.2021.1884224
  10. Kannan S.R., Spratt A.N., Quinn T.P., Heng X., Lorson C.L., Sönnerborg A., Byrareddy S.N., Singh K. Infectivity of SARS-CoV-2: there is something more than D614G? J. Neuroimmune Pharmacol. 2020;15(4):574–577. doi: 10.1007/s11481-020-09954-3
  11. Shadrick W.R., Ndjomou J., Kolli R., Mukherjee S., Hanson A.M., Frick D.N. Discovering new medicines targeting helicases: challenges and recent progress. J. Biomol. Screen. 2013;18(7):761–781. doi: 10.1177/1087057113482586
  12. Ortega S.S., Cara L.C., Salvador M.K. In silico pharmacology for a multidisciplinary drug discovery process. Drug Metab. Drug Interact. 2012;27(4):199–207. doi: 10.1515/dmdi-2012-0021
  13. Song C.M., Lim S.J., Tong J.C. Recent advances in computer-aided drug design. Brief. Bioinform. 2009;10(5):579–591. doi: 10.1093/bib/bbp023
  14. Shaker B., Ahmad S., Lee J., Jung C., Na D. In silico methods and tools for drug discovery. Comput. Biol. Med. 2021;137:104851. doi: 10.1016/j.compbiomed.2021.104851
  15. Kumar Y., Singh H., Patel C.N. In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing. J. Infect. Public Health. 2020;13(9):1210–1223. doi: 10.1016/j.jiph.2020.06.016
  16. White M.A., Lin W., Cheng X. Discovery of COVID-19 inhibitors targeting the SARS-CoV-2 Nsp13 helicase. J. Phys. Chem. Lett. 2020;11(21):9144–9151. doi: 10.1021/acs.jpclett.0c02421
  17. Satpathy R., Acharya S. Development of a database of RNA helicase inhibitors (VHIMDB) of pathogenic viruses and in silico screening for the potential drug molecules. Eurobiotech J. 2022;6(3):116–125. doi: 10.2478/ebtj-2022-0012
  18. Ibrahim A.K., Youssef A.I., Arafa A.S., Ahmed S.A. Anti-H5N1 virus flavonoids from Capparis sinaica Veill. Nat. Prod. Res. 2013;27(22):2149–2153. doi: 10.1080/14786419.2013.790027
  19. Yarmolinsky L., Huleihel M., Zaccai M., Ben-Shabat S. Potent antiviral flavone glycosides from Ficus benjamina leaves. Fitoterapia. 2012;83(2):362–367. doi: 10.1016/j.fitote.2011.11.014
  20. Ben-Shabat S., Yarmolinsky L., Porat D., Dahan A. Antiviral effect of phytochemicals from medicinal plants: applications and drug delivery strategies. Drug Deliv. Transl. Res. 2020;10(2):354–367. doi: 10.1007/s13346-019-00691-6
  21. Abeysinghe P.D. Antibacterial activity of some medicinal mangroves against antibiotic resistant pathogenic bacteria. Indian J. Pharm. Sci. 2010;72(2):167–172. doi: 10.4103/0250-474X.65019
  22. Satpathy R., Acharya S. Phytochemicals from mangroves and their antiviral applications. In: Handbook of Research on advanced phytochemicals and plant-based drug discovery. IGI Global, 2022. P. 350–365. doi: 10.4018/978-1-6684-5129-8.ch018
  23. Aljahdali M.O., Molla M.H.R., Ahammad F. Compounds identified from marine mangrove plant (Avicennia Alba) as potential antiviral drug candidates against WDSV, an in-silico approach. Mar. Drugs. 2021;19(5):253. doi: 10.3390/md19050253
  24. Mitra S., Naskar N., Chaudhuri P. A review on potential bioactive phytochemicals for novel therapeutic applications with special emphasis on mangrove species. Phytomed. Plus. 2021;1(4):100107. doi: 10.1016/j.phyplu.2021.100107
  25. Abeysinghe P.D., Wanigatunge R.P., Pathirana R.N. Evaluation of antibacterial activity of different mangrove plant extracts. Ruhuna J. Sci. 2006;1:104–112. doi: 10.4038/rjs.v1i0.70
  26. Lipinski C.A. Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov. Today Technol. 2004;1(4):337–341. doi: 10.1016/j.ddtec.2004.11.007
  27. Morris G.M., Lim-Wilby M. Molecular docking. In: Molecular modeling of proteins. Humana Press, 2008. P. 365–382. doi: 10.1007/978-1-59745-177-2_19
  28. Satpathy R. Application of molecular docking methods on endocrine disrupting chemicals: a review. J. Appl. Biotechnol. Rep. 2020;7(2):74–80. doi: Cite to nonCR doi: 10.30491/JABR.2020.108287
  29. Huey R., Morris G.M., Forli S. Using AutoDock 4 and AutoDock vina with AutoDockTools: A tutorial, 92037. Vol. 1000. Scripps Research Institute Molecular Graphics Laboratory, 2012. P. 10550.
  30. Kumari R., Kumar R. Open Source Drug Discovery Consortium, Lynn A. g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model. 2014;54(7):1951–1962. doi: 10.1021/ci500020m
  31. Kushwaha P.P., Singh A.K., Bansal T., Yadav A., Prajapati K.S., Shuaib M., Kumar S. Identification of natural inhibitors against SARS-CoV-2 drugable targets using molecular docking, molecular dynamics simulation, and MM-PBSA approach. Front. Cell. Infect. Microbiol. 2021;11:730288. doi: 10.3389/fcimb.2021.730288
  32. Gupta S., Singh A.K., Kushwaha P.P., Prajapati K.S., Shuaib M., Senapati S., Kumar S. Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. J. Biomol. Struct. Dyn. 2021;39(12):4334–4345. doi: 10.1080/07391102.2020.1776157
  33. Garg S., Anand A., Lamba Y., Roy A. Molecular docking analysis of selected phytochemicals against SARS-CoV-2 M pro receptor. Vegetos. 2020;33(4):766–781. doi: 10.1007/s42535-020-00162-1
  34. Liu K., Kokubo H. Exploring the stability of ligand binding modes to proteins by Molecular Dynamics simulations: A cross-docking study. J. Chem. Inf. Model. 2017;57(10):2514–2522. doi: 10.1021/acs.jcim.7b00412
  35. Alamri M.A., Tahir U.l. Qamar M., Mirza M.U., Alqahtani S.M., Froeyen M., Chen L.L. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches. J. Pharm. Anal. 2020;10(6):546–559. doi: 10.1016/j.jpha.2020.08.012
  36. McGillewie L., Soliman ME. The binding landscape of plasmepsin V and the implications for flap dynamics. Mol. Biosyst. 2016;12(5):1457–1467. doi: 10.1039/C6MB00077K
  37. Keum Y.S., Jeong Y.J. Development of chemical inhibitors of the SARS coronavirus: viral helicase as a potential target. Biochem. Pharmacol. 2012;84(10):1351–1358. doi: 10.1016/j.bcp.2012.08.012
  38. Byler K.G., Ogungbe I.V., Setzer W.N. In-silico screening for anti-Zika virus phytochemicals. J. Mol. Graph. Model. 2016;69:78–91. doi: 10.1016/j.jmgm.2016.08.011
  39. Vivek-Ananth R.P., Krishnaswamy S., Samal A. Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: A molecular docking and dynamic simulation study. Mol. Divers. 2022;26(1):429–442. doi: 10.1007/s11030-021-10251-1
  40. Bhowmik D., Chiranjib Y.J., Tripathi K.K., Kumar K.S. Herbal remedies of Azadirachta indica and its medicinal application. J. Chem. Pharm. Res. 2010;2(1):62–72.
  41. Amraiz D., Zaidi N.S., Fatima M. Antiviral evaluation of an Hsp90 inhibitor, gedunin, against dengue virus. Trop. J. Pharm. Res. 2017;16(5):997–1004. doi: 10.4314/tjpr.v16i5.5
  42. Kumar A.H. Molecular docking of natural compounds from tulsi (Ocimum sanctum) and neem (Azadirachta indica) against SARS-CoV-2 protein targets. BEMS Reports. 2020;6(1):11–13. doi: 10.5530/bems.6.1.4
  43. Dwivedi V.D., Singh A., El-Kafraway S.A., Alandijany T.A., Faizo A.A., Bajrai L.H., Kamal M.A., Azhar E.I. Mechanistic insights into the Japanese encephalitis virus RNA dependent RNA polymerase protein inhibition by bioflavonoids from Azadirachta indica. Sci. Rep. 2021;11(1):18125. doi: 10.1038/s41598-021-96917-0
  44. Kushwaha P.P., Singh A.K., Prajapati K.S., Shuaib M., Gupta S., Kumar S. Phytochemicals present in Indian ginseng possess potential to inhibit SARS-CoV-2 virulence: A molecular docking and MD simulation study. Microb. Pathog. 2021;157:104954. doi: 10.1016/j.micpath.2021.104954
  45. Uma Reddy B.U., Routhu N.K., Kumar A. Multifaceted role of plant derived small molecule inhibitors on replication cycle of sars-cov-2. Microb. Pathog. 2022;168:105512. doi: 10.1016/j.micpath.2022.105512
  46. Braga T.M., Rocha L., Chung T.Y., Oliveira R.F., Pinho C., Oliveira A.I., Morgado J., Cruz A. Biological activities of gedunin–A limonoid from the Meliaceae family. Molecules. 2020;25(3):493. doi: 10.3390/molecules25030493
  47. Bray D.H., Warhurst D.C., Connolly J.D., O’Neill M.J., Phillipson J.D. Plants as sources of antimalarial drugs. Part 7. Activity of some species of Meliaceae plants and their constituent limonoids. Phytother Res. 1990;4(1):29–35. doi: 10.1002/ptr.2650040108
  48. Omar S., Godard K., Ingham A., Hussain H., Wongpanich V., Pezzuto J., Durst T., Eklu C., Gbeassor M., Sanchez‐Vindas P. et al. Antimalarial activities of gedunin and 7‐methoxygedunin and synergistic activity with dillapiol. Ann. Appl. Biol. 2003;143(2):135–141. doi: 10.1111/j.1744-7348.2003.tb00279.x
  49. Tharmarajah L., Samarakoon S.R., Ediriweera M.K., Piyathilaka P., Tennekoon K.H., Senathilake K.S., Rajagopalan U., Galhena P.B., Thabrew I. In vitro anticancer effect of gedunin on human teratocarcinomal (NTERA-2) cancer stem-like cells. BioMed Res. Int. 2017;2017:2413197. doi: 10.1155/2017/2413197
  50. Khalid S.A., Dawood M., Boulos J.C., Wasfi M., Drif A., Bahramimehr F., Shahhamzehei N., Shan L., Efferth T. Identification of gedunin from a phytochemical depository as a novel multidrug resistance-bypassing tubulin inhibitor of cancer cells. Molecules. 2022;27(18):5858. doi: 10.3390/molecules27185858
Table of Contents Original Article
Math. Biol. Bioinf.
2023;18(2):405-417
doi: 10.17537/2023.18.405
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References
Supplementary data

 

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