95
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

Exploiting Modeling Studies for Evaluating the Potential Antiviral Activities of some Clinically Approved Drugs and Herbal Materials against SARS-CoV-2: Theoretical Studies toward Hindering the Virus and Blocking the Human Cellular Receptor

, , &
Pages 1209-1220 | Received 22 Jul 2022, Accepted 03 Mar 2023, Published online: 20 Mar 2023

References

  • C.C. Lai, T.P. Shih, W.C. Ko, H.J. Tang, and P.R. Hsueh, “Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Coronavirus Disease-2019 (COVID-19): The Epidemic and the Challenges,” International Journal of Antimicrobial Agents 55, no. 3 (2020): 105924.
  • T.E. Tallie, S.G. Tumilaar, T.J. Niode, F. Fatimawali, B.J. Kepel, R. Idroes, Y. Effendi, S.A. Sakib, and T.B. Emran, “Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) glycoprotein Inhibitors: A Molecular Docking Study,” Scientifica 2020 (2020): 6307457.
  • M. Tahir Ul Qamar, S.M. Alqahtani, M.A. Alamri, and L.-L. Chen, “Structural Basis of SARS-CoV-2 3CL(Pro) and anti-COVID-19 Drug Discovery from Medicinal Plants,” Journal of Pharmaceutical Analysis 10, no. 4 (2020): 313–9.
  • K. Sharun, R. Tiwari, K. Dhama, T. B. Emran, A. A. Rabban, and A. Al Mutair, “Emerging SARS-CoV-2 Variants: Impact on Vaccine Efficacy and Neutralizing Antibodies,” Human Vaccines Immunotherapy 17 (2021): 1–4.
  • M. Romano, A. Ruggiero, F. Squeglia, G. Maga, and R. Berisio, “A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading, and Final Capping,” Cells 9 (2020): 1267.
  • K. Khairan, R. Idroes, T.E. Tallie, M.J. Nasim, and C. Jacob, “Bioactive Compounds from Medicinal Plants and Their Possible Effect as Therapeutics Agents against COVID-19: A Review,” Current Research in Nutrition and Food Science 17 (2021): 621–33.
  • A. Rakib, P. Arkajyoti, N.C. Uddin, S.A. Sami, S.K. Baral, M. Majumder, A.M. Tareq, M.N. Amin, A. Shahriar, Z. Uddin, et al, “Biochemical and Computational Approach of Selected Phytocompounds from Tinospora Crispa in the Management of COVID-19,” Molecules 25 (2020): 3936.
  • R. Yadav, J.K. Chaudhary, N. Jain, P.K. Chaudhary, S. Khanra, P. Dhamija, A. Sharma, A. Kumar, and S. Hadu, “Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19,” Cells 10 (2021): 821.
  • W. Li, M.J. Moore, N. Vasilieva, J. Sui, S.K. Wong, M.A. Berne, M. Somasundaran, J.L. Sullivan, K. Luzuriaga, T. C. Greenough, et al, “Angiotensin-Converting Enzyme 2 is a Functional Receptor for the SARS Coronavirus,” Nature 426, no. 6965 (2003): 450–4.
  • X. Ou, Y. Liu, X. Lei, P. Li, D. Mi, L. Ren, L. Guo, R. Guo, T. Chen, J. Hu, et al, “Characterization of Spike Glycoprotein of SARS-CoV-2 on Virus Entry and Its Immune Cross-Reactivity with SARS-CoV,” Nature Communications. 11, no. 1 (2020): 12.
  • J. Lan, J. Ge, J. Yu, S. Shan, H. Zhou, S. Fan, Q. Zhang, X. Shi, Q. Wang, L. Zhang, et al, “Structure of the SARS-CoV-2 Spike Receptor-Binding Domain Bound to the ACE2 Receptor,” Nature 581, no. 7807 (2020): 215–20.
  • A.M. Rabie, “Discovery of (E)-N-(4-Cyanobenzylidene)-6-Fluoro-3-Hydroxypyrazine-2-Carboxamide (Cyanorona-20): The First Potent and Specific anti-COVID-19 Drug,” Chemicke Zvesti 75, no. 9 (2021): 4669–85.
  • C. Laffeber, K. de Koning, R. Kanaar, and J.H.G. Lebbink, “Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants,” Journal of Molecular Biology 433, no. 15 (2021): 167058.
  • S. Jiang, C. Hillyer, and L. Du, “Neutralizing Antibodies against SARS-CoV-2 and Other Human Coronaviruses,” Trends in Immunology 41, no. 5 (2020): 355–9.
  • A. Rakib, Z. Nain, M.A. Islam, S.A. Sami, S. Mahmud, A. Islam, S. Ahmed, A.B.F. Siddiqui, S. M.O.F. Babu, P. Hossain, et al, “A Molecular Modelling Approach for Identifying Antiviral Selenium-Containing Heterocyclic Compounds That Inhibit the Main Protease of SARS-CoV-2: An in Silico Investigation,” Briefings in Bioinformatics 22, no. 2 (2021): 1476–98.
  • M. Dutta, A.M. Tareq, A. Rakib, S. Mahmud, S.A. Sami, J. Mallick, M.N. Islam, M. Majumder, M.Z. Uddin, A. Alsubaie, et al, “Phytochemicals from Leucas Zeylanica Targeting Main Protease of SARS–CoV–2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations,” Biology 10 (2021): 789.
  • K.H. Chowdhury, R. Chowdhury, S. Mahmud, A.M. Tareq, N.B. Hanif, N. Banu, A.S.M. Reza, T.B. Emran, and J. Simal-Gandara, “Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease,” Biology 10 (2021): 2.
  • D. Guo, “Old Weapon for New Enemy: Drug Repurposing for Treatment of Newly Emerging Viral Diseases,” Virologica Sinica 35, no. 3 (2020): 253–5.
  • T.P. Sheahan, A.C. Sims, S.R. Leist, A. Schafer, J. Won, A.J. Brown, S.A. Montgomery, A. Hogg, D. Babusis, M.O. Clarke, et al, “Comparative Therapeutic Efficacy of Remdesivir and Combination Lopinavir, Ritonavir, and Interferon-Beta against MERS-CoV,” Nature Communications 11, no. 1 (2020): 222.
  • M. Wang, R. Cao, L. Zhang, X. Yang, J. Liu, M. Xu, Z. Shi, Z. Hu, W. Zhong, and G. Xiao, “Remdesivir and Chloroquine Effectively Inhibit the Recently Emerged Novel Coronavirus (2019-nCoV) In Vitro,” Cell Research. 30 (2020): 269.
  • D.S. Moirangthem and L. Surbala, “Remdesivir (GS-5734) in COVID-19 Therapy: The Fourth Chance,” Current Drug Targets 22, no. 12 (2021): 1346–56.
  • V.C. Yan and F.L. Muller, “Advantages of the Parent Nucleoside GS441524 over Remdesivir for Covid-19 Treatment,” ACS Medicinal Chemistry Letters 11, no. 7 (2020): 1361–6.
  • L. Brunotte, S. Zheng, A. Mecate-Zambrano, J. Tang, S. Ludwig, U. Rescher, and S. Schloer, “Combination Therapy with Fluoxetine and the Nucleoside Analog GS-441524 Exerts Synergistic Antiviral Effects against Different SARS-CoV-2 Variants in Vitro,” Pharmaceutics 13 (2021): 1400.
  • Q. Cai, M. Yang, D. Liu, J. Chen, D. Shu, J. Xia, X. Liao, Y. Gu, Q. Cai, Y. Yang, et al, “Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study,” Engineering 6, no. 10 (2020): 1192–8.
  • A.M. Rabie, “Cyanorona-20: The First Potent anti-SARS-CoV-2 Agent,” International Immunopharmacology 98 (2021): 107831.
  • M. Tahir Ul Qamar, A. Maryam, and I. Muneer, “Computational Screening of Medicinal Plant Phytochemicals to Discover Potent Pan-Serotype Inhibitors against Dengue Virus,” Scientific Reports. 9, no. 1 (2019): 16.
  • H. Dabbagh-Bazarbachi, G. Clergeaud, I.M. Quesada, M. Ortiz, C.K. O'Sullivan, and J.B. Fernández-Larrea, “Zinc Ionophore Activity of Quercetin and Epigallocatechin-Gallate: From Hepa 1-6 Cells to a Liposome Model,” Journal of Agricultural and Food Chemistry 62, no. 32 (2014): 8085–93.
  • M.L. Lestari and G. Indrayanto, “Curcumin. Profiles Drug Subst,” Excipients and Related Methodology 39 (2014): 113–204.
  • G.B. Mahady, S.L. Pendland, G. Yun, and Z.Z. Lu, “Turmeric (Curcuma Longa) and Curcumin Inhibit the Growth of Helicobacter pylori, a Group 1 Carcinogen,” Anticancer Research 22, no. 6C (2002): 4179–81.
  • R.C. Reddy, P.G. Vatsala, V.G. Keshamouni, G. Padmanaban, and P.N. Rangarajan, “Curcumin for Malaria Therapy,” Biochemical and Biophysical Research Communications 326, no. 2 (2005): 472–4.
  • L. Vera-Ramirez, P. Perez-Lopez, A. Varela-Lopez, M. Ramirez-Tortosa, M. Battino, and J.L. Quiles, “Curcumin and Liver Disease,” BioFactors 39, no. 1 (2013): 88–100.
  • M.S.A. Abdel-Mottaleb and Y. Abdel-Mottaleb, “Impact of Magnesium, Zinc, Selenium, Copper, and Iodine Food Supplements on SARS-CoV, SARS-CoV-2 Viruses and Their Adducts with Human ACE2 Enzyme: A Computational Based Investigation,” Egyptian Journal of Chemistry. 64 (2021): 989–96.
  • Y. Ma, E. Frutos-Beltrán, D. Kang, C. Pannecouque, E. De Clercq, L. Menéndez-Arias, X. Liu, and P. Zhan, “Medicinal Chemistry Strategies for Discovering Antivirals Effective against Drug-Resistant Viruses,” Chemical Society Reviews 50, no. 7 (2021): 4514–40.
  • J.-D. Chai and M. Head-Gordon, “Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections,” Physical Chemistry Chemical Physics 10, no. 44 (2008): 6615–20.
  • M. Cossi, N. Rega, G. Scalmani, and V. Barone, “Energies, Structures, and Electronic Properties of Molecules in Solution with the C-PCM Solvation Model,” Journal of Computational Chemistry 24, no. 6 (2003): 669–81.
  • C.R. Corbeil, C.I. Williams, and P. Labute, “Variability in Docking Success Rates Due to Dataset Preparation,” Journal of Computer-Aided Molecular Design 26, no. 6 (2012): 775–86.
  • A. Kumar, M. Parveen, and M.A. Shahabuddin, “Reaction of 7α-Bromo-6-Nitrocholest-5-Enes with Hydrazine: Formation of Steroidal Pyrazolines and Molecular Docking against SARS-CoV-2 Omicron Protease,” Steroids 188 (2022): 109120.
  • I. Soo Moon and M. Alam, “Aluminum Chloride-Functionalized Silica Gel Synthesis as a Catalyst for the Preparation of Biologically Active Oxazolidinethiones: Antioxidant and Molecular Docking Studies,” Journal of Saudi Chemical Society 24, no. 11 (2022): 906–14.
  • M. Abdalla, R.K. Mohapatra, A.K. Sarangi, P.K. Mohapatra, W.A. Eltayb, M. Alam, A.A. El-Arabey, M. Azam, S.I. Al-Resayes, V. Seidel, et al, “In Silico Studies on Phytochemicals to Combat the Emerging COVID-19 Infection,” Journal of Saudi Chemical Society 25, no. 12 (2021): 101367.
  • A. Ahmed, A. Saeed, S.A. Ejaz, M. Aziz, M.Z. Hashmi, P.A. Channar, Q. Abbas, H. Raza, Z. Shafiq, and H.R. El-Seedi, “Novel Adamantyl Clubbed Iminothiazolidinones as Promising Elastase Inhibitors: Design, Synthesis, Molecular Docking, ADMET and DFT Studies,” RSC Advances 12, no. 19 (2022): 11974–91.
  • I. Fleming, “Frontier Orbitals and Organic Chemical Reactions,” John Wiley and Sons 320 (1976), 879–80.
  • F. Zielinski, “Condensed Descriptors for Reactivity: A Methodological Study,” Chemical Physics Letters. 527 (2012): 67–72.
  • S. Lakhera, K. Devlal, A. Ghosh, P Chowdhury, and M. Rana, “Modeling the DFT Structural and Reactivity Study of Feverfew and Evaluation of Its Potential Antiviral Activity against COVID‑19 Using Molecular Docking and MD Simulations,” Chemical Papers 15 (2020): 1–18.
  • Y.Y. Gu, M. Zhang, H. Cen, Y.F. Wu, Z. Lu, F. Lu, X.S. Liu, and H.Y. Lan, “Quercetin as a Potential Treatment for COVID-19-Induced Acute Kidney Injury: Based on Network Pharmacology and Molecular Docking Study,” PLOS One 16, no. 1 (2021): e0245209.

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.