263
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

In silico and in vitro studies on inhibitors for SARS-CoV-2 non-structural proteins with dual herbal combination of Withania somnifera with five rasayana herbs

ORCID Icon, ORCID Icon & ORCID Icon
Pages 3265-3280 | Received 06 Jun 2021, Accepted 20 Feb 2022, Published online: 08 Mar 2022

References

  • Astuti, I. & Ysrafil. (2020). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response. Diabetes & Metabolic Syndrome, 14(4), 407–412. https://doi.org/10.1016/j.dsx.2020.04.020
  • Benedec, D., Oniga, I., Oprean, R., & Tamas, M. (2009). Chemical composition of the essential oils of Ocimum basilicum L. Cultivated in Romania, 57, 625–629.
  • Bhargavi, S., & Shankar, S. R. M. (2021). Dual herbal combination of Withania somnifera and five Rasayana herbs: A phytochemical, antioxidant, and chemometric profiling. Journal of Ayurveda and Integrative Medicine, 12(2), 283–293. https://doi.org/10.1016/j.jaim.2020.10.001
  • Ch, M., Naz, S., Sharif, A., Akram, M., & Saeed, M. (2015). Biological and pharmacological properties of the sweet basil (Ocimum basilicum). British Journal of Pharmaceutical Research, 7(5), 330–339. https://doi.org/10.9734/BJPR/2015/16505
  • Chakrabarti, S., Jayachandran, U., Bonneau, F., Fiorini, F., Basquin, C., Domcke, S., Le Hir, H., & Conti, E. (2011). Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2. Molecular Cell, 41(6), 693–703. https://doi.org/10.1016/j.molcel.2011.02.010
  • Chawla, R., Redon, S., Raftopoulou, C., Wischnewski, H., Gagos, S., & Azzalin, C. M. (2011). Human UPF1 interacts with TPP1 and telomerase and sustains telomere leading-strand replication. The EMBO Journal, 30(19), 4047–4058. https://doi.org/10.1038/emboj.2011.280
  • Clasman, J. R., Báez-Santos, Y. M., Mettelman, R. C., O’Brien, A., Baker, S. C., & Mesecar, A. D. (2017). X-ray structure and enzymatic activity profile of a core papain-like protease of MERS coronavirus with utility for structure-based drug design. Scientific Reports, 7(1), 40292. https://doi.org/10.1038/srep40292
  • Deyama, T. (1983). The constituents of eucommia ulmoides OLIV. I. Isolation of (+)-medioresinol Di-O-β-D-glucopyranoside. Chemical and Pharmaceutical Bulletin, 31(9), 2993–2997. https://doi.org/10.1248/cpb.31.2993
  • Dummer, W., Niethammer, A. G., Baccala, R., Lawson, B. R., Wagner, N., Reisfeld, R. A., & Theofilopoulos, A. N. (2002). T cell homeostatic proliferation elicits effective antitumor autoimmunity. The Journal of Clinical Investigation, 110(2), 185–192. https://doi.org/10.1172/JCI15175
  • Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science (New York, N.Y.), 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
  • Gu, M., & Lima, C. D. (2005). Processing the message: structural insights into capping and decapping mRNA. Current Opinion in Structural Biology, 15(1), 99–106. https://doi.org/10.1016/j.sbi.2005.01.009
  • Han, Y., Zhang, J., Hu, C. Q., Zhang, X., Ma, B., & Zhang, P. (2019). In silico ADME and toxicity prediction of ceftazidime and its impurities. Frontiers in Pharmacology, 10, 404–412. https://doi.org/10.3389/fphar.2019.00434
  • Hasselbalch, H. C., Skov, V., Kjaer, L., Ellervik, C., Poulsen, A., Poulsen, T. D., & Nielsen, C. H. (2021). COVID-19 as a mediator of interferon deficiency and hyperinflammation: Rationale for the use of JAK1/2 inhibitors in combination with interferon. Cytokine & Growth Factor Reviews, 60, 28–45. https://doi.org/10.1016/j.cytogfr.2021.03.006
  • Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
  • Joshi, C., Chaudhari, A., Joshi, C., Joshi, M., & Bagatharia, S. (2021). Repurposing of the herbal formulations: molecular docking and molecular dynamics simulation studies to validate the efficacy of phytocompounds against SARS-CoV-2 proteins. Journal of Biomolecular Structure and Dynamics, 2021, 1–15. https://doi.org/10.1080/07391102.2021.1922095
  • Kessler, D. S., Levy, D. E., & Darnell, J. E., Jr. (1988). Two interferon-induced nuclear factors bind a single promoter element in interferon-stimulated genes. Proceedings of the National Academy of Sciences of the United States of America, 85(22), 8521–8525. https://doi.org/10.1073/pnas.85.22.8521
  • Kim, Y., Wower, J., Maltseva, N., Chang, C., Jedrzejczak, R., Wilamowski, M., … Joachimiak, A. (2020). Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. BioRxiv. https://doi.org/10.1101/2020.06.26.173872
  • Kong, R., Yang, G., Xue, R., Liu, M., Wang, F., Hu, J., Guo, X., & Chang, S. (2020). COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19. Bioinformatics (Oxford, England), 36(20), 5009–5104. https://doi.org/10.1093/bioinformatics/btaa645
  • Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • L DeLano, W. (2002). Pymol: An open-source molecular graphics tool. {CCP4} Newsletter on Protein Crystallography, 40, 1–8. http://www.ccp4.ac.uk/newsletters/newsletter40/11_pymol.pdf
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). {\it PROCHECK}: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science, 27(1), 129–134. https://doi.org/10.1002/pro.3289
  • Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., & Albaiu, D. (2020). Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Science, 6(3), 315–331. https://doi.org/10.1021/acscentsci.0c00272
  • Ma, Y., Wu, L., Shaw, N., Gao, Y., Wang, J., Sun, Y., Lou, Z., Yan, L., Zhang, R., & Rao, Z. (2015). Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proceedings of the National Academy of Sciences of the United States of America, 112(30), 9436–9441. https://doi.org/10.1073/pnas.1508686112
  • Majumder, R., & Mandal, M. (2022). Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: An in silico docking and molecular dynamics simulation approach. Journal of Biomolecular Structure and Dynamics, 40(2), 606–616. https://doi.org/10.1080/07391102.2020.1817787
  • Mirjalili, M. H., Moyano, E., Bonfill, M., Cusido, R. M., & Palazón, J. (2009). Steroidal lactones from Withania somnifera, an ancient plant for novel medicine. Molecules (Basel, Switzerland), 14(7), 2373–2393. https://doi.org/10.3390/molecules14072373
  • Mirtaleb, M. S., Mirtaleb, A. H., Nosrati, H., Heshmatnia, J., Falak, R., & Zolfaghari Emameh, R. (2021). Potential therapeutic agents to COVID-19: An update review on antiviral therapy, immunotherapy, and cell therapy. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 138, 111518. https://doi.org/10.1016/j.biopha.2021.111518
  • Nimgampalle, M., Devanathan, V., & Saxena, A. (2020). Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets. Journal of Biomolecular Structure & Dynamics, 2020, 1–13. https://doi.org/10.1080/07391102.2020.1782265
  • Panda, P. K., Arul, M. N., Patel, P., Verma, S. K., Luo, W., Rubahn, H., Mishra, Y. K., Suar, M., & Ahuja, R. (2020). Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. Science Advances, 6(28), eabb8097.
  • Panda, S. K., Sen Gupta, P. S., Biswal, S., Ray, A. K., & Rana, M. K. (2021). ACE-2-derived biomimetic peptides for the inhibition of spike protein of SARS-CoV-2. Journal of Proteome Research, 20(2), 1296–1303. https://doi.org/10.1021/acs.jproteome.0c00686
  • Pestka, S., Langer, J. A., Zoon, K. C., & Samuel, C. E. (1987). Interferons and their actions. Annual Review of Biochemistry, 56, 727–777. https://doi.org/10.1146/annurev.bi.56.070187.003455
  • Pfizenmaier, K., Jung, H., Starzinski-Powitz, A., Röllinghoff, M., & Wagner, H. (1977). The role of T cells in anti-herpes simplex virus immunity. Journal of Immunology (Baltimore, Md. : 1950), 119(3), 939–944. https://www.jimmunol.org/content/119/3/939
  • Purushothaman, B., Prasannasrinivasan, R., Suganthi, P., Ranganathan, B., Gimbun, J., & Shanmugam, K. (2018). A comprehensive review on Ocimum basilicum. Journal of Natural Remedies, 18(3), 71–85. https://doi.org/10.18311/jnr/2018/21324
  • Rodero, M. P., Decalf, J., Bondet, V., Hunt, D., Rice, G. I., Werneke, S., McGlasson, S. L., Alyanakian, M.-A., Bader-Meunier, B., Barnerias, C., Bellon, N., Belot, A., Bodemer, C., Briggs, T. A., Desguerre, I., Frémond, M.-L., Hully, M., van den Maagdenberg, A. M. J. M., Melki, I., … Duffy, D. (2017). Detection of interferon alpha protein reveals differential levels and cellular sources in disease. The Journal of Experimental Medicine, 214(5), 1547–1555. https://doi.org/10.1084/jem.20161451
  • Rohaim, M. A., El Naggar, R. F., Clayton, E., & Munir, M. (2021). Structural and functional insights into non-structural proteins of coronaviruses. Microbial Pathogenesis, 150, 104641. https://doi.org/10.1016/j.micpath.2020.104641
  • Rut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S. J., El Oualid, F., Huang, T. T., Bekes, M., Drag, M., & Olsen, S. K. (2020). Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design. Science Advances, 6(42), 1–13. https://doi.org/10.1126/sciadv.abd4596
  • Shah, B., Modi, P., & Sagar, S. R. (2020). In silico studies on therapeutic agents for COVID-19: Drug repurposing approach. Life Sciences, 252, 117652. https://doi.org/10.1016/j.lfs.2020.117652
  • Sharanya, C. S., Sabu, A., & Haridas, M. (2021). Potent phytochemicals against COVID-19 infection from phyto-materials used as antivirals in complementary medicines: a review. Future Journal of Pharmaceutical Sciences, 7(1), 113. https://doi.org/10.1186/s43094-021-00259-7
  • Shuman, S. (2002). What messenger RNA capping tells us about eukaryotic evolution. Nature Reviews. Molecular Cell Biology, 3(8), 619–625. https://doi.org/10.1038/nrm880
  • Singh, N., Bhalla, M., De Jager, P., & Gilca, M. (2011). An overview on ashwagandha: A rasayana (rejuvenator) of ayurveda. African Journal of Traditional, Complementary, and Alternative Medicines: AJTCAM, 8(5 Suppl), 208–213. https://doi.org/10.4314/ajtcam.v8i5S.9
  • Subissi, L., Posthuma, C. C., Collet, A., Zevenhoven-Dobbe, J. C., Gorbalenya, A. E., Decroly, E., Snijder, E. J., Canard, B., & Imbert, I. (2014). One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proceedings of the National Academy of Sciences of the United States of America, 111(37), E3900–E3909. https://doi.org/10.1073/pnas.1323705111
  • Tachoua, W., Kabrine, M., Mushtaq, M., & Ul-Haq, Z. (2020). An in-silico evaluation of COVID-19 main protease with clinically approved drugs. Journal of Molecular Graphics & Modelling, 101, 107758. https://doi.org/10.1016/j.jmgm.2020.107758
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • van Boxel-Dezaire, A. H. H., Rani, M. R. S., & Stark, G. R. (2006). Complex modulation of cell type-specific signaling in response to type I interferons. Immunity, 25(3), 361–372. https://doi.org/10.1016/j.immuni.2006.08.014
  • Vardhan, S., & Sahoo, S. K. (2020). In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19. Computers in Biology and Medicine, 124, 103936. https://doi.org/10.1016/j.compbiomed.2020.103936
  • Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., & Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30(3), 269–271. https://doi.org/10.1038/s41422-020-0282-0
  • World Health Organization. (2021, January). COVID-19 weekly epidemiological update 22. World Health Organization, pp. 1–3. https://www.who.int/docs/default-source/coronaviruse/situation-reports/weekly_epidemiological_update_22.pdf
  • Xie, L.-H., Akao, T., Hamasaki, K., Deyama, T., & Hattori, M. (2003). Biotransformation of pinoresinol diglucoside to mammalian lignans by human intestinal microflora, and isolation of Enterococcus faecalis strain PDG-1 responsible for the transformation of (+)-pinoresinol to (+)-lariciresinol. Chemical & Pharmaceutical Bulletin, 51(5), 508–515. https://doi.org/10.1248/cpb.51.508
  • Yoshimoto, F. K. (2020). The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the cause of COVID-19. The Protein Journal, 39(3), 198–216. https://doi.org/10.1007/s10930-020-09901-4
  • Yu, D., Du, Z., Li, W., Chen, H., Ye, S., Hoffman, A. R., Cui, J., & Hu, J.-F. (2017). Targeting Jurkat T lymphocyte leukemia cells by an engineered interferon-alpha hybrid molecule. Cellular Physiology and Biochemistry, 42(2), 519–529. https://doi.org/10.1159/000477601
  • Zhou, J.-T., Li, C.-Y., Wang, C.-H., Wang, Y.-F., Wang, X.-D., Wang, H.-T., Zhu, Y., Jiang, M.-M., & Gao, X.-M. (2015). Phenolic compounds from the roots of rhodiola crenulata and their antioxidant and inducing IFN-γ production activities. Molecules (Basel, Switzerland), 20(8), 13725–13739. https://doi.org/10.3390/molecules200813725

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.