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Research Articles

Repurposing of the herbal formulations: molecular docking and molecular dynamics simulation studies to validate the efficacy of phytocompounds against SARS-CoV-2 proteins

, , , &
Pages 8405-8419 | Received 11 Dec 2020, Accepted 26 Mar 2021, Published online: 14 May 2021

References

  • Adam, L. (1997). In vitro antiviral activity of indigenous glycyrrhizin, licorice and glycyrrhizic acid (Sigma) on Japanese encephalitis virus. Journal of Communicable Diseases 29(2), 91–99.
  • Ajala, O. S., Jukov, A., & Ma, C.-M. (2014). Hepatitis C virus inhibitory hydrolysable tannins from the fruits of Terminalia chebula. Fitoterapia, 99, 117–123. https://doi.org/10.1016/j.fitote.2014.09.014
  • Badmaev, V., & Nowakowski, M. (2000). Protection of epithelial cells against influenza A virus by a plant derived biological response modifier Ledretan‐96. Phytotherapy Research, 14(4), 245–249. https://doi.org/10.1002/1099-1573(200006)14:4<245::AID-PTR571>3.0.CO;2-O
  • Bag, A. (2013). Anti-inflammatory, anti-lipid peroxidative, antioxidant and membrane stabilizing activities of hydroalcoholic extract of Terminalia chebula fruits. Pharmaceutical Biology, 51(12), 1515–1520. https://doi.org/10.3109/13880209.2013.799709
  • Blankenberg, D., Von Kuster, G., Bouvier, E., Baker, D., Afgan, E., Stoler, N., Taylor, J., & Nekrutenko, A., the Galaxy Team (2014). Dissemination of scientific software with Galaxy ToolShed. Genome Biology, 15, 403. https://doi.org/10.1186/gb4161
  • Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., & Salmon, J. K. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters < SE-END> [Paper presentation].</SE-END>In SC'06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, November) (pp. 43–43). IEEE.
  • Cheng, H. Y., Lin, C. C., & Lin, T. C. (2002). Antiherpes simplex virus type 2 activity of casuarinin from the bark of Terminalia arjuna Linn. Antiviral Research, 55(3), 447–455. https://doi.org/10.1016/s0166-3542(02)00077-3
  • Cheng, V. C. C. (2007). Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clinical Microbiology Reviews, 20(4), 660–694. https://doi.org/10.1128/CMR.00023-07
  • Churiyah, P., Bunga, O., & Rofaani, E. (2015). Antiviral and immunostimulant activities of Andrographis paniculata. HAYATI Journal of Biosciences, 22(2), 67–72. https://doi.org/10.4308/hjb.22.2.67
  • Cinatl, J., Morgenstern, B., Bauer, G., Chandra, P., Rabenau, H., & Doerr, H. W. (2003). Glycyrrhizin, an active component of liquorice roots, and replication of SARS-associated coronavirus. The Lancet , 361(9374), 2045–2046. https://doi.org/10.1016/S0140-6736(03)13615-X
  • Dinesh, D. C.,Chalupska, D.,Silhan, J.,Koutna, E.,Nencka, R.,Veverka, V., &Boura, E. (2020). Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein. PLOS Pathogens, 16(12), e1009100. https://doi.org/10.1371/journal.ppat.1009100
  • Dong, E., Du, H., & Gardner, L. (2020). An interactive web-based dashboard to track COVID-19 in real time. Lancet Infectious Diseases, 26(5), P533–P534. https://doi.org/10.1016/S1473-3099(20)30120-1
  • Ganjhu, R. K. (2015). Herbal plants and plant preparations as remedial approach for viral diseases. Virusdisease, 26(4), 225–236. https://doi.org/10.1007/s13337-015-0276-6
  • Gao, Y. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science, 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
  • Garcia, L. F. (2020). Immune Response, Inflammation, and the Clinical Spectrum of COVID-19. Frontiers in Immunology, 11, 1441.
  • Geleris, J., Sun, Y., Platt, J., Zucker, J., Baldwin, M., Hripcsak, G., Labella, A., Manson, D. K., Kubin, C., Barr, R. G., Sobieszczyk, M. E., & Schluger, N. W. (2020). Observational study of hydroxychloroquine in hospitalized patients with Covid-19. New England Journal of Medicine, 382(25), 2411–2418. https://doi.org/10.1056/NEJMoa2012410
  • Ghoke, S. S., Sood, R., Kumar, N., Pateriya, A. K., Bhatia, S., Mishra, A., Dixit, R., Singh, V. K., Desai, D. N., Kulkarni, D. D., Dimri, U., & Singh, V. P. (2018). Evaluation of antiviral activity of Ocimum sanctum and Acacia arabica leaves extracts against H9N2 virus using embryonated chicken egg model. BMC Complementary and Alternative Medicine, 18(1), 174. https://doi.org/10.1186/s12906-018-2238-1
  • Grant, B. J.,Rodrigues, A. P. C.,ElSawy, K. M.,McCammon, J. A., &Caves, L. S. D. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. https://doi.org/10.1093/bioinformatics/btl461
  • Guan, W-j.,Ni, Z-y.,Hu, Y.,Liang, W-h.,Ou, C-q.,He, J-x.,Liu, L.,Shan, H.,Lei, C-l.,Hui, D. S.,Du, B.,Li, L-j.,Zeng, G.,Yuen, K.-Y.,Chen, R-c.,Tang, C-l.,Wang, T.,Chen, P-y.,Xiang, J.,…Zhong, N-s. (2020). Clinical characteristics of coronavirus disease 2019 in China. New England journal of medicine, 382(18), 1708–1720.
  • Guidelines for Ayurveda practitioners for COVID 19. https://aiia.gov.in/news/guidelines-for-ayurveda-practitioners-for-covid-19/
  • Gupta, M., Wahl, B., Adhikari, B., Bar-Zeev, N., Bhandari, S., Coria, A., Erchick, D. J., Gupta, N., Hariyani, S., Kagucia, E. W., Killewo, J., Limaye, R. J., McCollum, E. D., Pandey, R., Pomat, W. S., Rao, K. D., Santosham, M., Sauer, M., Wanyenze, R. K., & Peters, D. H. (2020). The need for COVID-19 research in low-and middle-income countries. Global Health Research and Policy, 5(1), 1–4. https://doi.org/10.1186/s41256-020-00159-y
  • Hoever, G. (2005). Antiviral activity of glycyrrhizic acid derivatives against SARS − coronavirus. Journal of Medicinal Chemistry, 48(4), 1256–1259. https://doi.org/10.1021/jm0493008
  • http://ayush.gov.in/
  • https://pubchem.ncbi.nlm.nih.gov/
  • https://www.rcsb.org/
  • Jacobson, M. P., Friesner, R. A., Xiang, Z., & Honig, B. (2002). On the role of crystal packing forces in determining protein sidechain conformations. Journal of Molecular Biology, 320(3), 597–608. https://doi.org/10.1016/S0022-2836(02)00470-9
  • Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins: Structure, Function, and Bioinformatics, 55(2), 351–367. https://doi.org/10.1002/prot.10613
  • Jiang, Z.-Y. (2013). Anti-HBV active constituents from Piper longum. Bioorganic & Medicinal Chemistry Letters, 23(7), 2123–2127. https://doi.org/10.1016/j.bmcl.2013.01.118
  • Kirchdoerfer, R. N., & Ward, A. B. (2019). Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nature Communications, 10(1), 1–9. https://doi.org/10.1038/s41467-019-10280-3
  • Kolla, J. N., Kulkarni, N. M., Kura, R. R., & Theepireddy, S. K. R. (2017). Terminalia chebula Retz.–an important medicinal plant. Herba Polonica, 63(4), 45–56. https://doi.org/10.1515/hepo-2017-0024
  • Komuro, A. (2017). Kampo medicines for infectious diseases. Japanese Kampo Medicines for the Treatment of Common Diseases: Focus on Inflammation, 127–142.
  • Ku, S. K., & Bae, J. S. (2014). Antiplatelet, anticoagulant, and profibrinolytic activities of withaferin A. Vascular Pharmacology, 60(3), 120–126. https://doi.org/10.1016/j.vph.2014.01.009
  • Lalita, B. (2002). In vitro antiviral activity of bael (Aegle marmelos Corr) upon. Journal of Communicable Diseases, 34, 88.
  • Lee, B.-J., Lee, J. A., Kim, K.-I., Choi, J.-Y., & Jung, H.-J. (2020). A consensus guideline of herbal medicine for coronavirus disease 2019. Integrative Medicine Research, 9(3), 100470. https://doi.org/10.1016/j.imr.2020.100470
  • Li, J-y., Cao, H-y., Liu, P., Cheng, G-h., & Sun, M-y. (2014). Glycyrrhizic acid in the treatment of liver diseases: Literature review. BioMed Research International, 2014, 1–15. https://doi.org/10.1155/2014/872139
  • Lin, L.-T. (2013). Broad-spectrum antiviral activity of chebulagic acid and punicalagin against viruses that use glycosaminoglycans for entry. BMC Microbiology, 13(1), 187. https://doi.org/10.1186/1471-2180-13-187
  • Londhe, A. M., Gadhe, C. G., Lim, S. M., & Pae, A. N. (2019). Investigation of molecular details of Keap1-Nrf2 inhibitors using molecular dynamics and umbrella sampling techniques. Molecules, 24(22), 4085. https://doi.org/10.3390/molecules24224085
  • Lugun, O. (2018). Evaluation of antithrombotic activities of Solanum xanthocarpum and Tinospora cordifolia. Pharmacognosy Research, 10(1), 98.
  • Marzolini, C., Stader, F., Stoeckle, M., Franzeck, F., Egli, A., Bassetti, S., Hollinger, A., Osthoff, M., Weisser, M., Gebhard, C. E., Baettig, V., Geenen, J., Khanna, N., Tschudin-Sutter, S., Mueller, D., Hirsch, H. H., Battegay, M., & Sendi, P. (2020). Effect of systemic inflammatory response to SARS-CoV-2 on lopinavir and hydroxychloroquine plasma concentrations. Antimicrobial Agents and Chemotherapy, 64(9), e01177-20. https://doi.org/10.1128/AAC.01177-20
  • Mendes-Silva, W. (2003). Antithrombotic effect of Glycyrrhizin, a plant-derived thrombin inhibitor. Thrombosis Research, 112(1–2), 93–98. https://doi.org/10.1016/j.thromres.2003.10.014
  • Nirmala, P., & Selvaraj, T. (2011). Anti-inflammatory and anti-bacterial activities of Glycyrrhiza glabra L. Journal of Agricultural Technology, 7(3), 815–823.
  • Oyuntsetseg, N., Khasnatinov, M. A., Molor-Erdene, P., Oyunbileg, J., Liapunov, A. V., & Danchinova, G. A. (2014). Evaluation of direct antiviral activity of the Deva-5 herb formulation and extracts of five Asian plants against influenza A virus H3N8. BMC Complementary and Alternative Medicine 14, 235. https://doi.org/10.1186/1472-6882-14-235
  • Padhi, A. K., Shukla, R., Saudagar, P., & Tripathi, T. (2021). High-throughput rational design of the remdesivir binding site in the RdRp of SARS-CoV-2: Implications for potential resistance. iScience, 24(1), 101992. https://doi.org/10.1016/j.isci.2020.101992
  • Parasuraman, S., Thing, G. S., & Dhanaraj, S. A. (2014). Polyherbal formulation: Concept of ayurveda. Pharmacognosy Reviews, 8(16), 73. https://doi.org/10.4103/0973-7847.134229
  • Peele, K. A., Potla Durthi, C., Srihansa, T., Krupanidhi, S., Ayyagari, V. S., Babu, D. J., Indira, M., Reddy, A. R., & Venkateswarulu, T. C. (2020). Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study. Informatics in Medicine Unlocked, 19, 100345. https://doi.org/10.1016/j.imu.2020.100345
  • Pompei, R., Flore, O., Marccialis, M. A., Pani, A., & Loddo, B. (1979). Glycyrrhizic acid inhibits virus growth and inactivates virus particles. Nature, 281(5733), 689–690. https://doi.org/10.1038/281689a0
  • Pompei, R., Pani, A., Flore, O., Marcialis, M. A., & Loddo, B. (1980). Antiviral activity of glycyrrhizic acid. Experientia, 36, 304–337. https://doi.org/10.1007/BF01952290
  • Rajaram, A. (2018). Anti-inflammatory profile of Aegle marmelos (L) Correa (Bilva) with special reference to young roots grown in different parts of India. Journal of Ayurveda and Integrative Medicine, 9(2), 90–98. https://doi.org/10.1016/j.jaim.2017.03.006
  • Rastogi, S., Pandey, D. N., & Singh, R. H. (2020). COVID-19 Pandemic: A pragmatic plan for Ayurveda Intervention. Journal of Ayurveda and Integrative Medicine, https://doi.org/10.1016/j.jaim.2020.04.002 [Epub ahead of print]
  • Ri, K. C., & Ho Ju, C. (2018). The antithrombotic activity of corilagin purified from Korean herb-Phyllanthus ussuriensis. https://www.researchgate.net/publication/329058540_The_antithrombotic_activity_of_corilagin_purified_from_korean_herb-Phyllanthus_ussuriensis
  • Romeo, A., Iacovelli, F., & Falconi, M. (2020). Targeting the SARS-CoV-2 spike glycoprotein prefusion conformation: Virtual screening and molecular dynamics simulations applied to the identification of potential fusion inhibitors. Virus Research, 286, 198068. https://doi.org/10.1016/j.virusres.2020.198068
  • Saha, S., & Ghosh, S. (2012). Tinospora cordifolia: One plant, many roles. Ancient Science of Life, 31(4), 151. " https://doi.org/10.4103/0257-7941.107344
  • Saleem, U., Latif, N., Fatima, A., & Ahmad, B. (2019). Antithrombotic Potential of Ajwa Dates and Piper Nigrum: In Vitro & In Vivo Studies. PharmacologyOnline, 3, 144–154.
  • Selvaraj, C., Dinesh, D. C., Panwar, U., Abhirami, R., Boura, E., & Singh, S. K. (2020). Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19. Journal of Biomolecular Structure and Dynamics 1–12. https://doi.org/10.1080/07391102.2020.1778535
  • Shukla, R., Shukla, H., & Tripathi, T. (2019). Structural and energetic understanding of novel natural inhibitors of Mycobacterium tuberculosis malate synthase. Journal of Cellular Biochemistry, 120(2), 2469–2482. https://doi.org/10.1002/jcb.27538
  • Tan, W. C., Jaganath, I. B., Manikam, R., & Sekaran, S. D. (2013). Evaluation of antiviral activities of four local Malaysian Phyllanthus species against herpes simplex viruses and possible antiviral target. International Journal of Medical Sciences, 10(13), 1817–1829. https://doi.org/10.7150/ijms.6902
  • Tang, N., Li, D., Wang, X., & Sun, Z. (2020). Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia. Journal of Thrombosis and Haemostasis, 18(4), 844–847. https://doi.org/10.1111/jth.14768
  • Tiwari, V., Darmani, N. A., Yue, B. Y. J. T., & Shukla, D. (2010). In vitro antiviral activity of neem (Azardirachta indica L.) bark extract against herpes simplex virus type‐1 infection. Phytotherapy Research, 24(8), 1132–1140. https://doi.org/10.1002/ptr.3085
  • 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
  • Upadhyay, A. K., Kumar, K., Kumar, A., & Mishra, H. S. (2010). Tinospora cordifolia (Willd.) Hook. f. and Thoms. (Guduchi)–validation of the Ayurvedic pharmacology through experimental and clinical studies. International Journal of Ayurveda Research, 1(2), 112. https://doi.org/10.4103/0974-7788.64405
  • Vellingiri, B., Jayaramayya, K., Iyer, M., Narayanasamy, A., Govindasamy, V., Giridharan, B., Ganesan, S., Venugopal, A., Venkatesan, D., Ganesan, H., Rajagopalan, K., Rahman, P. K. S. M., Cho, S.-G., Kumar, N. S., & Subramaniam, M. D. (2020). COVID-19: A promising cure for the global panic. Science of the Total Environment, 725, 138277. https://doi.org/10.1016/j.scitotenv.2020.138277
  • Wang, Y., Zhang, D., Du, G., Du, R., Zhao, J., Jin, Y., Fu, S., Gao, L., Cheng, Z., Lu, Q., Hu, Y., Luo, G., Wang, K., Lu, Y., Li, H., Wang, S., Ruan, S., Yang, C., Mei, C., … Wang, C. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. The Lancet, 395(10236), 1569–1578. https://doi.org/10.1016/S0140-6736(20)31022-9
  • Wichmann, D., Sperhake, J.-P., Lütgehetmann, M., Steurer, S., Edler, C., & Heinemann, A. (2020). Autopsy findings and venous thromboembolism in patients with COVID-19: A prospective cohort study. Annals of Internal Medicine, 173(12), 1030. https://doi.org/10.7326/L20-1206
  • WHO. (2020). Clinical management of severe acute respiratory infection (SARI) when the COVID-19 disease is suspected: Interim Guidance (Version 1.2), 13 March 2020 released by World Health Organization (WHO/2019- nCoV/clinical/2020.4).
  • World Health Organization. (2020). https://www.who.int/publications/m/item/weekly-epidemiological-update–-19-january-2021
  • Yan, R. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science, 367(6485), 1444–1448. https://doi.org/10.1126/science.abb2762
  • Yang, Y., Islam, M. S., Wang, J., Li, Y., & Chen, X. (2020). Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): A review and perspective. International Journal of Biological Sciences, 16(10), 1708. https://doi.org/10.7150/ijbs.45538
  • Yuan, H., Ma, Q., Ye, L., & Piao, G. (2016). The traditional medicine and modern medicine from natural products. Molecules, 21(5), 559. https://doi.org/10.3390/molecules21050559
  • Zhang, W., Zhao, Y., Zhang, F., Wang, Q., Li, T., Liu, Z., Wang, J., Qin, Y., Zhang, X., Yan, X., Zeng, X., & Zhang, S. (2020). The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The experience of clinical immunologists from China. Clinical Immunology, 214, 108393. https://doi.org/10.1016/j.clim.2020.108393
  • Zhou, F., Yu, T., Du, R., Fan, G., Liu, Y., Liu, Z., Xiang, J., Wang, Y., Song, B., Gu, X., Guan, L., Wei, Y., Li, H., Wu, X., Xu, J., Tu, S., Zhang, Y., Chen, H., & Cao, B. (2020). Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. The Lancet, 395(10229), 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3

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