291
Views
19
CrossRef citations to date
0
Altmetric
Research Articles

Computational Investigations for Identification of Bioactive Molecules from Baccaurea ramiflora and Bergenia ciliata as Inhibitors of SARS-CoV-2 Mpro

, ORCID Icon, ORCID Icon, , &
Pages 2459-2487 | Received 07 Jan 2022, Accepted 17 Feb 2022, Published online: 06 Mar 2022

References

  • M. Mohamadian, H. Chiti, A. Shoghli, S. Biglari, N. Parsamanesh, and A. Esmaeilzadeh, “ COVID-19: Virology, Biology and Novel Laboratory Diagnosis,” The Journal of Gene Medicine 23, no. 2 (2021): e3303. doi:10.1002/jgm.3303.
  • J. Khan, L. A. Asoom, M. Khan, I. Chakrabartty, S. Dandoti, M. Rudrapal, and J. H. Zothantluanga, “Evolution of RNA Viruses from SARS to SARS-CoV-2 and Diagnostic Techniques for COVID-19: A Review,” Beni-Suef University Journal of Basic and Applied Sciences 10, no. 1 (2021): 60. doi:10.1186/s43088-021-00150-7.
  • M. Rudrapal, S. J. Khairnar, L. B. Borse, and A. G. Jadhav, “Coronavirus Disease-2019 (COVID-19): An Updated Review,” Drug Research 70, no. 9 (2020): 389–400. doi:10.1055/a-1217-2397.
  • “WHO Coronavirus (COVID-19) Dashboard,” World Health Organization, last modified February 11, 2022. https://covid19.who.int/ (accessed October 20, 2021).
  • D. Yesudhas, A. Srivastava, and M. M. Gromiha, " “COVID-19 Outbreak: History, Mechanism, Transmission, Structural Studies and Therapeutics,” Infection 49, no. 2 (2021): 199–213. doi:10.1007/s15010-020-01516-2.
  • Z. Abdelrahman, M. Li, and X. Wang, “Comparative Review of SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza a Respiratory Viruses,” Frontiers in Immunology 11 (2020): 552909. doi:10.3389/fimmu.2020.552909.
  • A. A. T. Naqvi, K. Fatima, T. Mohammad, U. Fatima, I. K. Singh, A. Singh, S. M. Atif, G. Hariprasad, G. M. Hasan, and M. I. Hassan, “Insights into SARS-CoV-2 Genome, Structure, Evolution, Pathogenesis and Therapies: Structural Genomics Approach,” Biochimica et Biophysica Acta. Molecular Basis of Disease 1866, no. 10 (2020): 165878. doi:10.1016/j.bbadis.2020.165878.
  • T. Kirby, “New Variant of SARS-CoV-2 in UK Causes Surge of COVID-19,” The Lancet. Respiratory Medicine 9, no. 2 (2021): e20–21. doi:10.1016/S2213-2600(21)00005-9.
  • S. E. Galloway, P. Paul, D. R. MacCannell, M. A. Johansson, J. T. Brooks, A. MacNeil, R. B. Slayton, S. Tong, B. J. Silk, G. L. Armstrong, et al. “Emergence of SARS-CoV-2 B.1.1.7 Lineage - United States, December 29, 2020-January 12, 2021,” MMWR. Morbidity and Mortality Weekly Report 70, no. 3 (2021): 95–9. doi:10.15585/mmwr.mm7003e2.
  • A. Bal, G. Destras, A. Gaymard, K. Stefic, J. Marlet, S. Eymieux, H. Regue, Q. Semanas, C. D’Aubarede, G. Billaud, et al. “Two-Step Strategy for the Identification of SARS-CoV-2 Variant of Concern 202012/01 and Other Variants with Spike Deletion H69–V70, France, August to December 2020,” Eurosurveillance 26, no. 3 (2021): 2100008. doi:10.2807/1560-7917.ES.2021.26.3.2100008.
  • M. D. Knoll and C. Wonodi, “Oxford–AstraZeneca COVID-19 Vaccine Efficacy,” The Lancet 397, no. 10269 (2021): 72–4. doi:10.1016/S0140-6736(20)32623-4.
  • R. L. Soiza, C. Scicluna, and E. C. Thomson, “Efficacy and Safety of COVID-19 Vaccines in Older People,” Age and Ageing 50, no. 2 (2021): 279–83. doi:10.1093/ageing/afaa274.
  • T. A. Rama, A. Moreira, and M. Castells, (2021) “mRNA COVID-19 Vaccine is Well Tolerated in Patients with Cutaneous and Systemic Mastocytosis with Mast Cell Activation Symptoms and Anaphylaxis,” The Journal of Allergy and Clinical Immunology 147, no. 3 (2021): 877–8. doi:10.1016/j.jaci.2021.01.004.
  • D. Planas, D. Veyer, A. Baidaliuk, I. Staropoli, F. Guivel-Benhassine, M. M. Rajah, C. Planchais, F. Porrot, N. Robillard, J. Puech, et al. “Reduced Sensitivity of SARS-CoV-2 Variant Delta to Antibody Neutralization,” Nature 596, no. 7871 (2021): 276–80. doi:10.1038/s41586-021-03777-9.
  • L. Forchette, W. Sebastian, and T. Liu, “A Comprehensive Review of COVID-19 Virology, Vaccines, Variants, and Therapeutics,” Current Medical Science 41, no. 6 (2021): 1037–51. doi:10.1007/s11596-021-2395-1.
  • D. Vasireddy, R. Vanaparthy, G. Mohan, S. V. Malayala, and P. Atluri, “Review of COVID-19 Variants and COVID-19 Vaccine Efficacy: What the Clinician Should Know?” Journal of Clinical Medicine Research 13, no. 6 (2021): 317–25. doi:10.14740/jocmr4518.
  • L. R. Baden, H. M. El Sahly, B. Essink, K. Kotloff, S. Frey, R. Novak, D. Diemert, S. A. Spector, N. Rouphael, C. B. Creech, et al. “Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine,” New England Journal of Medicine 384, no. 5 (2021): 403–16. doi:10.1056/NEJMoa2035389.
  • J. Sadoff, M. Le. Gars, G. Shukarev, D. Heerwegh, C. Truyers, A. M. de Groot, J. Stoop, S. Tete, W. Van Damme, I. Leroux-Roels, et al. “Interim Results of a Phase 1-2a Trial of Ad26.COV2.S Covid-19 Vaccine ,” The New England Journal of Medicine 384, no. 19 (2021): 1824–35. doi:10.1056/NEJMoa2034201.
  • F. P. Polack, S. J. Thomas, N. Kitchin, J. Absalon, A. Gurtman, S. Lockhart, J. L. Perez, G. Pérez Marc, E. D. Moreira, C. Zerbini, et al. “Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine,” The New England Journal of Medicine 383, no. 27 (2020): 2603–15. doi:10.1056/NEJMoa2034577.
  • A. Riad, “Oral Side Effects of COVID-19 Vaccine,” British Dental Journal 230, no. 2 (2021): 59. doi:10.1038/s41415-021-2615-x.
  • CDC COVID-19 Response Team, and Food and Drug Administration “Allergic Reactions Including Anaphylaxis after Receipt of the First Dose of Pfizer-BioNTech COVID-19 Vaccine — United States, December 14–23, 2020,” MMWR Morbidity and Mortality Weekly Report 70, no. 2 (2021): 46–51.
  • T. Shimabukuro and N. Nair, “Allergic Reactions Including Anaphylaxis after Receipt of the First Dose of Pfizer-BioNTech COVID-19 Vaccine,” JAMA 325, no. 8 (2021): 780–81. doi:10.1001/jama.2021.0600.
  • K. O. Kwok, K. K. Li, W. I. Wei, A. Tang, S. Y. S. Wong, and S. S. Lee, “Editor's Choice: Influenza Vaccine Uptake, COVID-19 Vaccination Intention and Vaccine Hesitancy among Nurses: A Survey,” International Journal of Nursing Studies 114 (2021): 103854. doi:10.1016/j.ijnurstu.2020.103854.
  • M. Yigit, A. Ozkaya-Parlakay, and E. Senel, “Evaluation of COVID-19 Vaccine Refusal in Parents,” The Pediatric Infectious Disease Journal 40, no. 4 (2021): e134–6. doi:10.1097/INF.0000000000003042.
  • B. Akarsu, D. Canbay Özdemir, D. Ayhan Baser, H. Aksoy, I. Fidancı, and M. Cankurtaran, “While Studies on COVID‐19 Vaccine is Ongoing, the Public’s Thoughts and Attitudes to the Future COVID‐19 Vaccine,” International Journal of Clinical Practice 75, no. 4 (2021): e13891. doi:10.1111/ijcp.13891.
  • A. Shukla, P. Parmar, G. Kapoor, D. Goswami, C. K. Jha, B. Patel, and M. Saraf, “Curse of La Corona: Unravelling the Scientific and Psychological Conundrums of the 21st Century Pandemic,” Molecular Diversity 26 (2021): 555–568. doi:10.1007/s11030-020-10167-2.
  • J. Shang, Y. Wan, C. Luo, G. Ye, Q. Geng, A. Auerbach, and F. Li, “Cell Entry Mechanisms of SARS-CoV-2,” Proceedings of the National Academy of Sciences of the United States of America 117, no. 21 (2020): 11727–34. doi:10.1073/pnas.2003138117.
  • S. A. Amin, S. Banerjee, K. Ghosh, S. Gayen, and T. Jha, " “Protease Targeted COVID-19 Drug Discovery and Its Challenges: Insight into Viral Main Protease (Mpro) and Papain-like Protease (PLpro) Inhibitors,” Bioorganic & Medicinal Chemistry 29 (2021): 115860. doi:10.1016/j.bmc.2020.115860.
  • W. Cui, K. Yang, and H. Yang, “Recent Progress in the Drug Development Targeting SARS-CoV-2 Main Protease as Treatment for COVID-19,” Frontiers in Molecular Biosciences 7 (2020): 616341. doi:10.3389/fmolb.2020.616341.
  • J. Lei and R. Hilgenfeld, “RNA-Virus Proteases Counteracting Host Innate Immunity,” FEBS Letters 591, no. 20 (2017): 3190–210. doi:10.1002/1873-3468.12827.
  • D. Lai, A. Wang, Y. Cao, K. Zhou, Z. Mao, X. Dong, J. Tian, D. Xu, J. Dai, Y. Peng, et al. “Bioactive Dibenzo-α-Pyrone Derivatives from the Endophytic Fungus Rhizopycnis Vagum Nitaf22,” Journal of Natural Products 79, no. 8 (2016): 2022–31. doi:10.1021/acs.jnatprod.6b00327.
  • J. Prajapati, R. Patel, D. Goswami, M. Saraf, and R. M. Rawal, “Sterenin M as a Potential Inhibitor of SARS-CoV-2 Main Protease Identified from MeFSAT Database Using Molecular Docking, Molecular Dynamics Simulation and Binding Free Energy Calculation,” Computers in Biology and Medicine 135 (2021): 104568. doi:10.1016/j.compbiomed.2021.104568.
  • B. Adhikari, B. P. Marasini, B. Rayamajhee, B. R. Bhattarai, G. Lamichhane, K. Khadayat, A. Adhikari, S. Khanal, and N. Parajuli, “Potential Roles of Medicinal Plants for the Treatment of Viral Diseases Focusing on COVID‐19: A Review,” Phytotherapy Research 35, no. 3 (2021): 1298–312. doi:10.1002/ptr.6893.
  • C. Zannella, R. Giugliano, A. Chianese, C. Buonocore, G. A. Vitale, G. Sanna, F. Sarno, A. Manzin, A. Nebbioso, P. Termolino, et al. “Antiviral Activity of Vitis vinifera Leaf Extract against SARS-CoV-2 and HSV-1,” Viruses 13, no. 7 (2021): 1263. doi:10.3390/v13071263.
  • S. Yu, Y. Zhu, J. Xu, G. Yao, P. Zhang, M. Wang, Y. Zhao, G. Lin, H. Chen, L. Chen, et al. “Glycyrrhizic Acid Exerts Inhibitory Activity against the Spike Protein of SARS-CoV-2,” Phytomedicine: International Journal of Phytotherapy and Phytopharmacology 85 (2021): 153364. doi:10.1016/j.phymed.2020.153364.
  • S. Vardhan and S. K. Sahoo, “In Silico ADMET and Molecular Docking Study on Searching Potential Inhibitors from Limonoids and Triterpenoids for COVID-19,” Computers in Biology and Medicine 124 (2020): 103936. doi:10.1016/j.compbiomed.2020.103936.
  • S. K. Sinha, S. K. Prasad, M. A. Islam, S. S. Gurav, R. B. Patil, N. A. AlFaris, T. S. Aldayel, N. M. AlKehayez, S. M. Wabaidur, and A. Shakya, “Identification of Bioactive Compounds from Glycyrrhiza Glabra as Possible Inhibitor of SARS-CoV-2 Spike Glycoprotein and Non-Structural Protein-15: A Pharmacoinformatics Study,” Journal of Biomolecular Structure & Dynamics 39, no. 13 (2021): 4686–700. doi:10.1080/07391102.2020.1779132.
  • M. Rudrapal, I. Celik, J. Khan, M. A. Ansari, M. N. Alomary, F. A. Alatawi, R. Yadav, T. Sharma, T. E. Tallei, P. K. Pasala, et al. “Identification of Bioactive Molecules from Triphala (Ayurvedic Herbal Formulation) as Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro) through Computational Investigations,” Journal of King Saud University. Science 34, no. 3 (2022): 101826. doi:10.1016/j.jksus.2022.101826.
  • M. Rudrapal, N. Gogoi, D. Chetia, J. Khan, S. Banwas, B. Alshehri, M. A. Alaidarous, U. D. Laddha, S. J. Khairnar, and S. G. Walode, (2021) “Repurposing of Phytomedicine-Derived Bioactive Compounds with Promising Anti-SARS-CoV-2 Potential: Molecular Docking, MD Simulation and Drug-Likeness/ADMET Studies,” Saudi Journal of Biological Sciences (2021). doi:10.1016/j.sjbs.2021.12.018.
  • C. N. Patel, D. Goswami, D. G. Jaiswal, R. M. Parmar, H. A. Solanki, and H. A. Pandya, “Pinpointing the Potential Hits for Hindering Interaction of SARS-CoV-2 S-Protein with ACE2 from the Pool of Antiviral Phytochemicals Utilizing Molecular Docking and Molecular Dynamics (MD) Simulations,” Journal of Molecular Graphics & Modelling 105 (2021): 107874. doi:10.1016/j.jmgm.2021.107874.
  • C. N. Patel, S. P. Kumar, H. A. Pandya, and R. M. Rawal, “Identification of Potential Inhibitors of Coronavirus Hemagglutinin-Esterase Using Molecular Docking, Molecular Dynamics Simulation and Binding Free Energy Calculation,” Molecular Diversity 25, no. 1 (2021): 421–33. doi:10.1007/s11030-020-10135-w.
  • P. Rao, R. Patel, A. Shukla, P. Parmar, R. M. Rawal, M. Saraf, and D. Goswami, “Identifying Structural–Functional Analogue of GRL0617, the Only Well-Established Inhibitor for Papain-like Protease (PLpro) of SARS-CoV2 from the Pool of Fungal Metabolites Using Docking and Molecular Dynamics Simulation,” Molecular Diversity 26, no. 1 (2021): 1–21. doi:10.1007/s11030-021-10220-8.
  • A. Basu, A. Sarkar, and U. Maulik, “Molecular Docking Study of Potential Phytochemicals and Their Effects on the Complex of SARS-CoV2 Spike Protein and Human ACE2,” Scientific Reports 10, no. 1 (2020): 17699. doi:10.1038/s41598-020-74715-4.
  • B. K. Kumar, Faheem, K. V. G. C. Sekhar, R. Ojha, V. K. Prajapati, A. Pai, and S. Murugesan, “Pharmacophore Based Virtual Screening, Molecular Docking, Molecular Dynamics and MM-GBSA Approach for Identification of Prospective SARS-CoV-2 Inhibitor from Natural Product Databases,” Journal of Biomolecular Structure and Dynamics 40, no. 3 (2022): 1363–8. doi:10.1080/07391102.2020.1824814.
  • O. Noureddine, N. Issaoui, and O. Al-Dossary, “DFT and Molecular Docking Study of Chloroquine Derivatives as Antiviral to Coronavirus COVID-19,” Journal of King Saud University. Science 33, no. 1 (2021): 101248. doi:10.1016/j.jksus.2020.101248.
  • D. Douche, Y. Sert, S. A. Brandán, A. A. Kawther, B. Bilmez, N. Dege, E. A. Louzi, K. Bougrin, K. Karrouchi, and B. Himmi, “5-((1H-Imidazol-1-yl)Methyl)Quinolin-8-ol as Potential Antiviral SARS-CoV-2 Candidate: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT and Molecular Docking Studies,” Journal of Molecular Structure 1232 (2021): 130005. doi:10.1016/j.molstruc.2021.130005.
  • M. Gümüş, S. N. Babacan, Y. Demir, Y. Sert, I. Koca, and I. Gülçin, “Discovery of Sulfadrug–Pyrrole Conjugates as Carbonic Anhydrase and Acetylcholinesterase Inhibitors,” Archiv Der Pharmazie 355, no. 1 (2022): 2100242. doi:10.1002/ardp.202100242.
  • I. Çapan, S. Servi, I. Yıldırım, and Y. Sert, “Synthesis, DFT Study, Molecular Docking and Drug‐Likeness Analysis of the New Hydrazine‐1‐Carbothioamide, Triazole and Thiadiazole Derivatives: Potential Inhibitors of HSP90,” ChemistrySelect 6, no. 23 (2021): 5838–46. doi:10.1002/slct.202101086.
  • I. Çapan, M. Gümüş, H. Gökce, H. Çetin, Y. Sert, and I. Koca, “Synthesis, Dielectric Properties, Molecular Docking and ADME Studies of Pyrrole-3-Ones,” Journal of Biomolecular Structure and Dynamics (2021): 1–17. doi:10.1080/07391102.2021.1914174.
  • M. Ahmad, M. A. Butt, G. Zhang, S. Sultana, A. Tariq, and M. Zafar, “Bergenia ciliata: A Comprehensive Review of Its Traditional Uses, Phytochemistry, Pharmacology and Safety,” Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie 97 (2018): 708–21. doi:10.1016/j.biopha.2017.10.141.
  • M. L. Nesa, S. M. S. Karim, K. Api, M. M. R. Sarker, M. M. Islam, A. Kabir, M. K. Sarker, K. Nahar, M. Asadujjaman, and M. S. Munir, “Screening of Baccaurea ramiflora (Lour.) Extracts for Cytotoxic, Analgesic, Anti-Inflammatory, Neuropharmacological and Antidiarrheal Activities,” BMC Complementary and Alternative Medicine 18, no. 1 (2018): 35. doi:10.1186/s12906-018-2100-5.
  • P. K. Mukherjee and A. A. Mao, "Compendium of the Anti-Viral Medicinal Plants of Northeast India.", 2021. https://dbtindia.gov.in/latest-announcement/compendium-anti-viral-medicinal-plants-northeast-india (accessed October 12, 2021).
  • X. W. Yang, J. S. Wang, Y. L. Ma, H. T. Xiao, Y. Q. Zuo, H. Lin, H. P. He, L. Li, and X. J. Hao, “Bioactive Phenols from the Leaves of Baccaurea ramiflora,” Planta Medica 73, no. 13 (2007): 1415–17. doi:10.1055/s-2007-990235.
  • T. Usha, S. Middha, M. Bhattacharya, P. Lokesh, and A. Goyal, “Rosmarinic Acid, a New Polyphenol from Baccaurea ramiflora Lour. Leaf: A Probable Compound for Its Anti-Inflammatory Activity,” Antioxidants (Basel, Switzerland) 3, no. 4 (2014): 830–42. doi:10.3390/antiox3040830.
  • Z. H. Pan, D. S. Ning, S. S. Huang, Y. F. Wu, T. Ding, and L. Luo, “A New Picrotoxane sesquiterpene from the Berries of Baccaurea ramiflora with Antifungal Activity against Colletotrichum gloeosporioides,” Natural Product Research 29, no. 14 (2015): 1323–7. doi:10.1080/14786419.2014.999335.
  • X. W. Yang, H. P. He, Y. L. Ma, F. Wang, Y. Q. Zuo, H. Lin, S. L. Li, L. Li, and X. J. Hao, “Three New Vanilloid Derivatives from the Stems of Baccaurea ramiflora,” Planta Medica 76, no. 1 (2010): 88–90. doi:10.1055/s-0029-1185901.
  • R. Zafar, H. Ullah, M. Zahoor, and A. Sadiq, “Isolation of Bioactive Compounds from Bergenia ciliata (Haw.) Sternb Rhizome and Their Antioxidant and Anticholinesterase Activities,” BMC Complementary and Alternative Medicine 19, no. 1 (2019): 296. doi:10.1186/s12906-019-2679-1.
  • A. Du, R. Zheng, C. Disoma, S. Li, Z. Chen, S. Li, P. Liu, Y. Zhou, Y. Shen, S. Liu, et al. “Epigallocatechin-3-Gallate, an Active Ingredient of Traditional Chinese Medicines, Inhibits the 3CLpro Activity of SARS-CoV-2,” International Journal of Biological Macromolecules 176 (2021): 1–12. doi:10.1016/j.ijbiomac.2021.02.012.
  • L. Henss, A. Auste, C. Schürmann, C. Schmidt, C. von Rhein, M. D. Mühlebach, and B. S. Schnierle, “The Green Tea Catechin Epigallocatechin Gallate Inhibits SARS-CoV-2 Infection,” The Journal of GeneralVirology 102, no. 4 (2021): 001574.
  • J. Liu, B. H. Bodnar, F. Meng, A. I. Khan, X. Wang, S. Saribas, T. Wang, S. C. Lohani, P. Wang, Z. Wei, et al. “Epigallocatechin Gallate from Green Tea Effectively Blocks Infection of SARS-CoV-2 and New Variants by Inhibiting Spike Binding to ACE2 Receptor,” Cell & Bioscience 11, no. 1 (2021): 168.
  • S. Ghosh, D. Chetia, N. Gogoi, and M. Rudrapal, “Design, Molecular Docking, Drug-Likeness, and Molecular Dynamics Studies of 1,2,4-Trioxane Derivatives as Novel Plasmodium falciparum Falcipain-2 (FP-2) Inhibitors,” BioTechnologia 102, no. 3 (2021): 257–75. doi:10.5114/bta.2021.108722.
  • J. A. Junejo, K. Zaman, M. Rudrapal, I. Celik, and E. I. Attah, “Antidiabetic Bioactive Compounds from Tetrastigma angustifolia (Roxb.) Deb and Oxalis debilis Kunth.: Validation of Ethnomedicinal Claim by In Vitro and In Silico Studies,” South African Journal of Botany 143 (2021): 164–75. doi:10.1016/j.sajb.2021.07.023.
  • M. Rudrapal, A. R. Issahaku, C. Agoni, A. R. Bendale, A. Nagar, M. E. S. Soliman, and D. Lokwani, “In Silico Screening of Phytopolyphenolics for the Identification of Bioactive Compounds as Novel Protease Inhibitors Effective against SARS-CoV-2,” Journal of Biomolecular Structure and Dynamics (2021): 1–17. doi:10.1080/07391102.2021.1944909.
  • I. M. M. Othman, M. H. Mahross, M. A. M. Gad-Elkareem, M. Rudrapal, N. Gogoi, D. Chetia, K. Aouadi, M. Snoussi, and A. Kadri, “Toward a Treatment of Antibacterial and Antifungal Infections: Design, Synthesis and In Vitro Activity of Novel Arylhydrazothiazolylsulfonamides Analogues and Their Insight of DFT, Docking and Molecular Dynamic Simulations,” Journal of Molecular Structure 1243 (2021): 130862. doi:10.1016/j.molstruc.2021.130862.
  • S. E. St. John, S. Tomar, S. R. Stauffer, and A. D. Mesecar, “Targeting Zoonotic Viruses: Structure-Based Inhibition of the 3C-like Protease from Bat Coronavirus HKU4—the Likely Reservoir Host to the Human Coronavirus That Causes Middle East Respiratory Syndrome (MERS),” Bioorganic & Medicinal Chemistry 23, no. 17 (2015): 6036–48. doi:10.1016/j.bmc.2015.06.039.
  • G. Gabutti, E. d'Anchera, F. Sandri, M. Savio, and A. Stefanati, “Coronavirus: Update Related to the Current Outbreak of COVID-19,” Infectious Diseases and Therapy 9, no. 2 (2020): 241–53. doi:10.1007/s40121-020-00295-5.
  • A. V. Anand, B. Balamuralikrishnan, M. Kaviya, K. Bharathi, A. Parithathvi, M. Arun, N. Senthilkumar, S. Velayuthaprabhu, M. Saradhadevi, N. A. Al-Dhabi, et al. “Medicinal Plants, Phytochemicals, and Herbs to Combat Viral Pathogens Including SARS-CoV-2,” Molecules 26, no. 6 (2021): 1775. doi:10.3390/molecules26061775.
  • S. K. Das, S. Mahanta, B. Tanti, H. Tag, and P. K. Hui, “Identification of Phytocompounds from Houttuynia cordata Thunb. as Potential Inhibitors for SARS-CoV-2 Replication Proteins through GC–MS/LC–MS Characterization, Molecular Docking and Molecular Dynamics Simulation,” Molecular Diversity 26, no. 1 (2021). doi:10.1007/s11030-021-10226-2.
  • R. K. Mohapatra, L. Perekhoda, M. Azam, M. Suleiman, A. K. Sarangi, A. Semenets, L. Pintilie, and S. I. Al-Resayes, “Computational Investigations of Three Main Drugs and Their Comparison with Synthesized Compounds as Potent Inhibitors of SARS-CoV-2 Main Protease (Mpro): DFT, QSAR, Molecular Docking, and In Silico Toxicity Analysis,” Journal of King Saud University. Science 33, no. 2 (2021): 101315. doi:10.1016/j.jksus.2020.101315.
  • T. S. Ram, M. Munikumar, V. N. Raju, P. Devaraj, N. K. Boiroju, R. Hemalatha, P. V. V. Prasad, M. Gundeti, B. S. Sisodia, S. Pawar, et al. “In Silico Evaluation of the Compounds of the Ayurvedic Drug, AYUSH-64, for the Action against the SARS-CoV-2 Main Protease,” Journal of Ayurveda and Integrative Medicine 13, no. 1 (2022): 100413. doi:10.1016/j.jaim.2021.02.004.
  • K. L. Forrestall, D. E. Burley, M. K. Cash, I. R. Pottie, and S. Darvesh, “2-Pyridone Natural Products as Inhibitors of SARS-CoV-2 Main Protease,” Chemico-Biological Interactions 335 (2021): 109348. doi:10.1016/j.cbi.2020.109348.
  • T. Serseg, K. Benarous, and M. Yousfi, “Hispidin and Lepidine E: Two Natural Compounds and Folic Acid as Potential Inhibitors of 2019-novel Coronavirus Main Protease (2019- nCoVMpro), Molecular Docking and SAR Study ,” Current Computer-Aided Drug Design 17, no. 3 (2021): 469–79. doi:10.2174/1573409916666200422075440.
  • Z. Fakhar, S. Khan, S. Y. AlOmar, A. Alkhuriji, and A. Ahmad, “ABBV-744 as a Potential Inhibitor of SARS-CoV-2 Main Protease Enzyme against COVID-19,” Scientific Reports 11, no. 1 (2021): 234. doi:10.1038/s41598-020-79918-3.
  • P. N. Pandya, S. P. Kumar, K. Bhadresha, C. N. Patel, S. K. Patel, R. M. Rawal, and A. U. Mankad, “Identification of Promising Compounds from Curry Tree with Cyclooxygenase Inhibitory Potential Using a Combination of Machine Learning, Molecular Docking, Dynamics Simulations and Binding Free Energy Calculations,” Molecular Simulation 46, no. 11 (2020): 812–22. doi:10.1080/08927022.2020.1764552.
  • P. Parmar, A. Shukla, P. Rao, M. Saraf, B. Patel, and D. Goswami, “The Rise of Gingerol as Anti-QS Molecule: Darkest Episode in the LuxR-Mediated Bioluminescence Saga,” Bioorganic Chemistry 99 (2020): 103823. doi:10.1016/j.bioorg.2020.103823.
  • J. Gopala Krishna and K. Roy, “QSPR Modeling of Absorption Maxima of Dyes Used in Dye Sensitized Solar Cells (DSSCs),” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 265 (2022): 120387. doi:10.1016/j.saa.2021.120387.
  • A. Nath, P. De, and K. Roy, “QSAR Modelling of Inhalation Toxicity of Diverse Volatile Organic Molecules Using No Observed Adverse Effect Concentration (NOAEC) as the Endpoint,” Chemosphere 287, no. Pt 1 (2022): 131954. doi:10.1016/j.chemosphere.2021.131954.
  • B. S. Aswal, A. K. Goel, D. K. Kulshrestha, B. N. Mehrotra, and G. K. Patnaik, “Screening of Indian Plants for Biological Activity: Part XV,” Indian Journal of Experimental Biology 34, no. 5 (1996): 444–67.
  • M. Rajbhandari, R. Mentel, P. K. Jha, R. P. Chaudhary, S. Bhattarai, M. B. Gewali, N. Karmacharya, M. Hipper, and U. Lindequist, “Antiviral Activity of Some Plants Used in Nepalese Traditional Medicine,” Evidence-Based Complementary and Alternative Medicine: eCAM 6, no. 4 (2009): 517–22.
  • A. Sadat, G. Uddin, M. Alam, A. Ahmad, and B. S. Siddiqui, “Structure Activity Relationship of Bergenin, p-Hydroxybenzoyl Bergenin, 11-O-Galloylbergenin as Potent Antioxidant and Urease Inhibitor Isolated from Bergenia ligulata,” Natural Product Research 29, no. 24 (2015): 2291–4. doi:10.1080/14786419.2015.1004173.
  • D. W. Kneller, G. Phillips, H. M. O'Neill, R. Jedrzejczak, L. Stols, P. Langan, A. Joachimiak, L. Coates, and A. Kovalevsky, “Structural Plasticity of SARS-CoV-2 3CL Mpro Active Site Cavity Revealed by Room Temperature X-Ray Crystallography,” Nature Communications 11, no. 1 (2020): 3202. doi:10.1038/s41467-020-16954-7.
  • N. Forouzesh and N. Mishra, “An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor,” Molecules 26, no. 8 (2021): 2383. doi:10.3390/molecules26082383.
  • A. Ongaro, E. Oselladore, M. Memo, G. Ribaudo, and A. Gianoncelli, “Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein-Protein Docking, Molecular Dynamics, and MM-GBSA Calculations,” Journal of Chemical Information and Modeling 61, no. 6 (2021): 2780–7. doi:10.1021/acs.jcim.1c00198.
  • A. Czyrski, “Determination of the Lipophilicity of Ibuprofen, Naproxen, Ketoprofen, and Flurbiprofen with Thin-Layer Chromatography,” Journal of Chemistry 2019 (2019): 1–6. doi:10.1155/2019/3407091.
  • S. Ishtiaq, M. Akram, S. H. Kamran, U. Hanif, M. S. K. Afridi, Sajid-Ur-Rehman, A. Afzal, A. Asif, M. Younus, and S. Akbar, “Acute and Sub-Acute Toxicity Study of a Pakistani Polyherbal Formulation,” BMC Complementary and Alternative Medicine 17 (2017): 387. doi:10.1186/s12906-017-1889-7.
  • A. Shakya, S. K. Chaudhary, H. R. Bhat, and S. K. Ghosh, (2020) “Acute and Sub-Chronic Toxicity Studies of Benincasa hispida (Thunb.) Cogniaux Fruit Extract in Rodents,” Regulatory Toxicology and Pharmacology: RTP 118 (2020): 104785. doi:10.1016/j.yrtph.2020.104785.
  • J. O. Unuofin, G. A. Otunola, and A. J. Afolayan, “Acute and Subacute Toxicity of Aqueous Extract of the Tuber of Kedrostis africana (L.) Cogn in Wistar Rats,” Journal of Complementary and Integrative Medicine 15, no. 4 (2018).
  • F. Yan and F. Gao, “An Overview of Potential Inhibitors Targeting Non-Structural Proteins 3 (PLpro and Mac1) and 5 (3CLpro/Mpro) of SARS-CoV-2,” Computational and Structural Biotechnology Journal 19 (2021): 4868–83. doi:10.1016/j.csbj.2021.08.036.
  • Z. Jin, X. Du, Y. Xu, Y. Deng, M. Liu, Y. Zhao, B. Zhang, X. Li, L. Zhang, C. Peng, et al. “Structure of Mpro from SARS-CoV-2 and Discovery of Its Inhibitors,” Nature 582, no. 7811 (2020): 289–93. doi:10.1038/s41586-020-2223-y.
  • S. Beura and P. Chetti, “In-Silico Strategies for Probing Chloroquine Based Inhibitors against SARS-CoV-2,” Journal of Biomolecular Structure & Dynamics 39, no. 10 (2021): 3747–59. doi:10.1080/07391102.2020.1772111.
  • K. J. Bowers, F. D. Sacerdoti, J. K. Salmon, Y. Shan, D. E. Shaw, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, et al. “Molecular Dynamics–Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters” (Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, New York, 2006).   doi:10.1145/1188455.1188544.
  • J. Li, R. Abel, K. Zhu, Y. Cao, S. Zhao, and R. A. Friesner, “The VSGB 2.0 Model: A Next Generation Energy Model for High Resolution Protein Structure Modeling,” Proteins 79, no. 10 (2011): 2794–812. doi:10.1002/prot.23106.
  • A. D. Becke, “Density‐Functional Thermochemistry. III. The Role of Exact Exchange,” The Journal of Chemical Physics 98, no. 7 (1993): 5648–52. doi:10.1063/1.464913.
  • M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, G. Scalmani, and D. Fox, Gaussian 09 (2009). https://gaussian.com/g09citation/.
  • R. K. Mohapatra, M. M. El-Ajaily, F. S. Alassbaly, A. K. Sarangi, D. Das, A. A. Maihub, S. F. Ben-Gweirif, A. Mahal, M. Suleiman, L. Perekhoda, et al. “DFT, Anticancer, Antioxidant and Molecular Docking Investigations of Some Ternary Ni(II) Complexes with 2-[(E)-[4-(Dimethylamino)Phenyl]Methyleneamino]Phenol,” Chemical Papers 75, no. 3 (2021): 1005–19. doi:10.1007/s11696-020-01342-8.
  • B. B. Mahapatra, R. R. Mishra, and A. K. Sarangi, “Synthesis, Characterisation, XRD, Molecular Modelling and Potential Antibacterial Studies of Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II) Complexes with Bidentate Azodye Ligand,” Journal of Saudi Chemical Society 20, no. 6 (2016): 635–43. doi:10.1016/j.jscs.2013.07.002.
  • A. K. Sarangi, B. B. Mahapatra, R. K. Mohapatra, S. K. Sethy, D. Das, L. Pintilie, M. Kudrat‐E‐Zahan, M. Azam, and H. Meher, “Synthesis and Characterization of Some Binuclear Metal Complexes with a Pentadentate Azodye Ligand: An Experimental and Theoretical Study,” Applied Organometallic Chemistry 34, no. 8 (2020): e5693. doi:10.1002/aoc.5693.
  • A. Daina, O. Michielin, and V. Zoete, “SwissADME: A Free Web Tool to Evaluate Pharmacokinetics, Drug-Likeness and Medicinal Chemistry Friendliness of Small Molecules,” Scientific Reports 7 (2017): 42717. doi:10.1038/srep42717.
  • P. Banerjee, A. O. Eckert, A. K. Schrey, and R. Preissner, “ProTox-II: A Webserver for the Prediction of Toxicity of Chemicals,” Nucleic Acids Research 46, no. W1 (2018): W257–63. doi:10.1093/nar/gky318.

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.