Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study

References

• Aanouz, I., Belhassan, A., El-Khatabi, K., Lakhlifi, T., El-Ldrissi, M., & Bouachrine, M. (2020). Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1758790
   Google Scholar
• Abbaspour, H. (2020). Evaluation of efficacy and safety of Sovodak (Sofosbuvir + Daclatasvir) in combination with Ribavirin for mild to moderate hospitalized Covid-19 patients compared to standard care regimen (a randomized controlled trial). IRCT registration number: IRCT20200328046886N1. Retrieved from https://en.irct.ir/trial/46885
   Google Scholar
• Alamri, M. A., Tahir Ul Qamar, M., Mirza, M. U., Bhadane, R., Alqahtani, S. M., Muneer, I., Froeyen, M., & Salo-Ahen, O. M. H. (2020). Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1782768
   Google Scholar
• Alazmi, M., & Motwalli, O. (2020). Molecular basis for drug repurposing to study the interface of the S protein in SARS-CoV-2 and human ACE2 through docking, characterization, and molecular dynamics for natural drug candidates. Journal of Molecular Modeling, 26(12), 338. https://doi.org/10.1007/s00894-020-04599-8
   PubMed Web of Science ®Google Scholar
• Albohy, A., Zahran, E. M., Abdelmohsen, U. R., Salem, M. A., Al-Warhi, T., Al-Sanea, M. M., Abelyan, N., Khalil, H. E., Desoukey, S. Y., Fouad, M. A., & Kamel, M. S. (2020). Multitarget in silico studies of Ocimum menthiifolium, family Lamiaceae against SARS-CoV-2 supported by molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1852964
   Google Scholar
• Anwar, M. U., Adnan, F., Abro, A., Khan, M. R., Rehman, A. U., Osama, M., Javed, S., Baig, A., Shabbir, M. R., & Assir, M. Z. (2020). Combined deep learning and molecular docking simulations approach identifies potentially effective FDA approved drugs for repurposing against SARS-CoV-2 (version 1). ChemRxiv. https://doi.org/10.26434/chemrxiv.12227363.v1
   Google Scholar
• Arya, R., Kumari, S., Pandey, B., Mistry, H., Bihani, S. C., Das, A., Prashar, V., Gupta, G. D., Panicker, L., & Kumar, M. (2021). Structural insights into SARS-CoV-2 proteins. Journal of Molecular Biology, 433(2), 166725. https://doi.org/10.1016/j.jmb.2020.11.024
   PubMed Web of Science ®Google Scholar
• Awad, I. E., Abu-Saleh, A., Sharma, S., Yadav, A., & Poirier, R. A. (2020). High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1835721
   Google Scholar
• Badavath, V. N., Kumar, A., Samanta, P. K., Maji, S., Das, A., Blum, G., Jha, A., & Sen, A. (2020). Determination of potential inhibitors based on isatin derivatives against SARS-CoV-2 main protease (mpro): A molecular docking, molecular dynamics and structure-activity relationship studies. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1845800
   Google Scholar
• Balasubramaniam, M., & Shmookler Reis, R. (2020). Computational target-based drug repurposing of elbasvir, an antiviral drug predicted to bind multiple SARS-CoV-2 proteins (version 2). ChemRxiv, https://doi.org/10.26434/chemrxiv.12084822.v2
   Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2020). Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1766572
   Google Scholar
• Bhardwaj, V. K., Singh, R., Das, P., & Purohit, R. (2021). Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Computers in Biology and Medicine, 128, 104117. https://doi.org/10.1016/j.compbiomed.2020.104117
   PubMed Web of Science ®Google Scholar
• Bzówka, M., Mitusińska, K., Raczyńska, A., Samol, A., Tuszyński, J. A., & Góra, A. (2020). Structural and evolutionary analysis indicate that the SARS-CoV-2 Mpro is a challenging target for small-molecule inhibitor design. International Journal of Molecular Sciences, 21(9), 3099. https://doi.org/10.3390/ijms21093099
   PubMed Web of Science ®Google Scholar
• Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghoreishi, D., Gilson, M. K., Gohlke, H., Goetz, A. W., Greene, D., Harris, R., Homeyer, N., Huang, Y., Izadi, S., Kovalenko, A., Kurtzman, T., … Kollman, P. A. (2019). AMBER 2019 [Computer software]. University of California.
   Google Scholar
• Chen, H., Zhang, Z., Wang, L., Huang, Z., Gong, F., Li, X., Chen, Y., & Wu, J. J. (2020). First clinical study using HCV protease inhibitor danoprevir to treat COVID-19 patients. Medicine,‌ 99(48), e23357. https://doi.org/10.1097/MD.0000000000023357
   Google Scholar
• Chen, Y. W., Yiu, C. B., & Wong, K. Y. (2020). Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CLpro) structure: Virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Research, 9, 129. https://doi.org/10.12688/f1000research.22457.2
   PubMedGoogle Scholar
• Chikhale, R. V., Gurav, S. S., Patil, R. B., Sinha, S. K., Prasad, S. K., Shakya, A., Shrivastava, S. K., Gurav, N. S., & Prasad, R. S. (2020). Sars-cov-2 host entry and replication inhibitors from Indian ginseng: An in-silico approach. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1778539
   Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Deganutti, G., Prischi, F., & Reynolds, C. A. (2021). Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein. Journal of Computer-Aided Molecular Design, 35(2), 195–207. https://doi.org/10.1007/s10822-020-00356-4
   PubMed Web of Science ®Google Scholar
• Dotolo, S., Marabotti, A., Facchiano, A., & Tagliaferri, R. (2021). A review on drug repurposing applicable to COVID-19. Briefings in Bioinformatics, 22(2), 726–741. https://doi.org/10.1093/bib/bbaa288
   PubMed Web of Science ®Google Scholar
• Dupradeau, F.-Y., Pigache, A., Zaffran, T., Savineau, C., Lelong, R., Grivel, N., Lelong, D., Rosanski, W., & Cieplak, P. (2010). The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building. Physical Chemistry Chemical Physics, 12(28), 7821–7839. https://doi.org/10.1039/c0cp00111b
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A. (2020). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1761882
   Web of Science ®Google Scholar
• El-Gohary, M. A. (2020). Efficacy of sofosbuvir plus ledipasvir in Egyptian patients with COVID-19 compared to standard treatment. ClinicalTrials.gov Identifier: NCT04530422. Retrieved from https://clinicaltrials.gov/ct2/show/NCT04530422
   Google Scholar
• Foroughi, F. (2020). Comparative assessment of the efficacy and safety of addon treatment with “Sofosbuvir-Daclatasvir”, “Lithium”, and “Trifluoprazine” to “standard of care in three groups of patients with COVID-19. IRCT registration number: IRCT20130812014333N147. Retrieved from https://en.irct.ir/trial/46853
   Google Scholar
• Ganesan, A., Coote, M. L., & Barakat, K. (2017). Molecular dynamics-driven drug discovery: Leaping forward with confidence. Drug Discovery Today, 22(2), 249–269. https://doi.org/10.1016/j.drudis.2016.11.001
   PubMed Web of Science ®Google Scholar
• Genheden, S., Kuhn, O., Mikulskis, P., Hoffmann, D., & Ryde, U. (2012). The normal-mode entropy in the MM/GBSA method: Effect of system truncation, buffer region, and dielectric constant. Journal of Chemical Information and Modeling, 52(8), 2079–2088. https://doi.org/10.1021/ci3001919
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2020). Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1841680
   Google Scholar
• Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., … Krogan, N. J. (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), 459–468. https://doi.org/10.1038/s41586-020-2286-9
   PubMed Web of Science ®Google Scholar
• Gottwein, J. M., Pham, L. V., Mikkelsen, L. S., Ghanem, L., Ramirez, S., Scheel, T. K. H., Carlsen, T. H. R., & Bukh, J. (2018). Efficacy of NS5A inhibitors against hepatitis C virus genotypes 1-7 and escape variants. Gastroenterology, 154(5), 1435–1448. https://doi.org/10.1053/j.gastro.2017.12.015
   PubMed Web of Science ®Google Scholar
• Gowthaman, R., Guest, J. D., Yin, R., Adolf-Bryfogle, J., Schief, W. R., & Pierce, B. G. (2021). CoV3D: A database of high resolution coronavirus protein structures. Nucleic Acids Research, 49(D1), D282–D287. https://doi.org/10.1093/nar/gkaa731
   PubMed Web of Science ®Google Scholar
• Grottesi, A., Bešker, N., Emerson, A., Manelfi, C., Beccari, A. R., Frigerio, F., Lindahl, E., Cerchia, C., & Talarico, C. (2020). Computational studies of SARS-CoV-2 3CLpro: Insights from MD simulations. International Journal of Molecular Sciences, 21(15), 5346. https://doi.org/10.3390/ijms21155346
   PubMed Web of Science ®Google Scholar
• Hakmi, M., Bouricha, E., Akachar, J., Lmimouni, B., El Harti, J., Belyamani, L., & Ibrahimi, A. (2020). In silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1830175
   Google Scholar
• Hosseini, F. S., & Amanlou, M. (2020). Simeprevir, potential candidate to repurpose for coronavirus infection: Virtual screening and molecular docking study. Preprints, Peer-reviewed version available at Life Sciences 2020. https://doi.org/10.1016/j.lfs.2020.118205
   Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–28. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Ibrahim, T. M., Ismail, M. I., Bauer, M. R., Bekhit, A. A., & Boeckler, F. M. (2020). Supporting SARS-CoV-2 papain-like protease drug discovery: In silico methods and benchmarking. Frontiers in Chemistry, 8, 592289. https://doi.org/10.3389/fchem.2020.592289
   PubMed Web of Science ®Google Scholar
• Jia, C. Y., Li, J. Y., Hao, G. F., & Yang, G. F. (2020). A drug-likeness toolbox facilitates ADMET study in drug discovery. Drug Discovery Today, 25(1), 248–258. https://doi.org/10.1016/j.drudis.2019.10.014
   PubMed Web of Science ®Google Scholar
• Jiménez-Alberto, A., Ribas-Aparicio, R. M., Aparicio-Ozores, G., & Castelán-Vega, J. A. (2020). Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Computational Biology and Chemistry, 88, 107325. https://doi.org/10.1016/j.compbiolchem.2020.107325
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Khan, A., Ali, S. S., Khan, M. T., Saleem, S., Ali, A., Suleman, M., Babar, Z., Shafiq, A., Khan, M., & Wei, D. Q. (2020). Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro). Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1779128
   Google Scholar
• Khan, R. J., Jha, R. K., Singh, E., Jain, M., Amera, G. M., Singh, R. P., Muthukumaran, J., & Singh, A. K. (2020). Identification of promising antiviral drug candidates against non-structural protein 15 (NSP15) from SARS-CoV-2: An in silico assisted drug-repurposing study. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1814870
   Google Scholar
• Khan, R. J., Jha, R. K., Amera, G. M., Jain, M., Singh, E., Pathak, A., Singh, R. P., Muthukumaran, J., & Singh, A. K. (2020). Targeting SARS-CoV-2: A systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2′-O-ribose methyltransferase. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1753577
   Google Scholar
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2019). PubChem 2019 update: Improved access to chemical data. Nucleic Acids Research, 47(D1), D1102–D1109. https://doi.org/10.1093/nar/gky1033
   PubMed Web of Science ®Google Scholar
• Kimura, Y., Ito, H., Ohnishi, R., & Hatano, T. (2010). Inhibitory effects of polyphenols on human cytochrome P450 3A4 and 2C9 activity. Food and Chemical Toxicology, 48(1), 429–435. https://doi.org/10.1016/j.fct.2009.10.041
   PubMed Web of Science ®Google Scholar
• Kumar, D., Kumari, K., Vishvakarma, V. K., Jayaraj, A., Kumar, D., Ramappa, V. K., Patel, R., Kumar, V., Dass, S. K., Chandra, R., & Singh, P. (2020). Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1779131
   Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A.,Lombardo, F.,Dominy, B. W., &Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1. Advanced Drug Delivery Reviews, 46(1–3), 3–26. https://doi.org/10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Liu, X., Shi, D., Zhou, S., Liu, H., Liu, H., & Yao, X. (2018). Molecular dynamics simulations and novel drug discovery. Expert Opinion on Drug Discovery, 13(1), 23–37. https://doi.org/10.1080/17460441.2018.1403419
   PubMed Web of Science ®Google Scholar
• Lokhande, K., Nawani, N., K Venkateswara, S., & Pawar, S. (2020). Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: A molecular docking and molecular dynamics approach. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1858165
   Google Scholar
• Loncharich, R. J., Brooks, B. R., & Pastor, R. W. (1992). Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers, 32(5), 523–535. https://doi.org/10.1002/bip.360320508
   PubMed Web of Science ®Google Scholar
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
   PubMed Web of Science ®Google Scholar
• Maffucci, I., & Contini, A. (2020). In silico drug repurposing for SARS-CoV-2 main proteinase and spike proteins. Journal of Proteome Research, 19(11), 4637–4648. https://doi.org/10.1021/acs.jproteome.0c00383
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). FF14SB: Improving the accuracy of protein side chain and backbone parameters from FF99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Mammen, M., Shakhnovich, E. I., Deutch, J., & Whitesides, G. M. (1998). Estimating the entropic cost of self-assembly of multiparticle hydrogen-bonded aggregates based on the cyanuric acid•melamine lattice. The Journal of Organic Chemistry, 63(12), 3821–3830. https://doi.org/10.1021/jo970944f
   Web of Science ®Google Scholar
• Mariano, G., Farthing, R. J., Lale-Farjat, S., & Bergeron, J. (2020). Structural characterization of SARS-CoV-2: Where we are, and where we need to be. Frontiers in Molecular Biosciences, 7, 605236. https://doi.org/10.3389/fmolb.2020.605236
   PubMed Web of Science ®Google Scholar
• McCauley, J. A., & Rudd, M. T. (2016). Hepatitis C virus NS3/4a protease inhibitors. Current Opinion in Pharmacology, 30, 84–92. https://doi.org/10.1016/j.coph.2016.07.015
   PubMed Web of Science ®Google Scholar
• McQuarrie, D. A. (1976). Statistical mechanics. Harper & Row.
   Google Scholar
• Medhat, M. A., El Kassas, M., Ramadan, H. K. (2020). Sofosbuvir/Ledipasvir and Nitazoxanide for treatment of COVID-19. ClinicalTrials.gov Identifier: NCT04498936. Retrieved from https://clinicaltrials.gov/ct2/show/NCT04498936
   Google Scholar
• Mevada, V., Dudhagara, P., Gandhi, H., Vaghamshi, N., Beladiya, U., & Patel, R. (2020). Drug repurposing of approved drugs elbasvir, ledipasvir, paritaprevir, velpatasvir, antrafenine and ergotamine for combating COVID19 (Version 2). ChemRxiv. https://doi.org/10.26434/chemrxiv.12115251.v2
   Google Scholar
• Miller, B. R., 3rd, McGee, T. D., Jr., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Mishra, A., Pathak, Y., Choudhir, G., Kumar, A., Mishra, S. K., & Tripathi, V. (2020). Natural compounds as potential inhibitors of novel coronavirus (COVID-19) main protease: An in silico study (Version 2). Research Square. https://doi.org/10.21203/rs.3.rs-22839/v2
   Google Scholar
• Mishra, C. B., Pandey, P., Sharma, R. D., Malik, M. Z., Mongre, R. K., Lynn, A. M., Prasad, R., Jeon, R., & Prakash, A. (2021). Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: An integrated computational approach. Briefings in Bioinformatics, 22(2), 1346–1360. https://doi.org/10.1093/bib/bbaa378
   PubMed Web of Science ®Google Scholar
• Mobarak, S. (2020). Comparison of the effect of Sofosbuvir + Daclatasvir (Sovodac) and Ribavirin in Covid-19 patients with severe symptoms. IRCT registration number: IRCT20200324046850N2. Retrieved from https://en.irct.ir/trial/46713
   Google Scholar
• Naqvi, A., Mohammad, T., Hasan, G. M., & Hassan, M. I. (2018). Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships. Current Topics in Medicinal Chemistry, 18(20), 1755–1768. https://doi.org/10.2174/1568026618666181025114157
   PubMed Web of Science ®Google Scholar
• O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• de Oliveira, O. V., Rocha, G. B., Paluch, A. S., & Costa, L. T. (2020). Repurposing approved drugs as inhibitors of SARS-CoV-2S-protein from molecular modeling and virtual screening. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1772885
   Google Scholar
• Olsson, M. H. M., Søndergaard, C. R., Rostkowski, M., & Jensen, J. H. (2011). PROPKA3: Consistent treatment of internal and surface residues in empirical pKa Predictions. Journal of Chemical Theory and Computation, 7(2), 525–537. https://doi.org/10.1021/ct100578z
   PubMed Web of Science ®Google Scholar
• Pan, X., Tan, N., Zeng, G., Zhang, Y., & Jia, R. (2005). Amentoflavone and its derivatives as novel natural inhibitors of human Cathepsin B. Bioorganic & Medicinal Chemistry, 13(20), 5819–5825. https://doi.org/10.1016/j.bmc.2005.05.071
   PubMed Web of Science ®Google Scholar
• Patil, R., Chikhale, R., Khanal, P., Gurav, N., Ayyanar, M., Sinha, S., Prasad, S., Dey, Y. N., Wanjari, M., & Gurav, S. S. (2021). Computational and network pharmacology analysis of bioflavonoids as possible natural antiviral compounds in COVID-19. Informatics in Medicine Unlocked, 22, 100504. https://doi.org/10.1016/j.imu.2020.100504
   PubMedGoogle Scholar
• Peterson, L. (2020). COVID-19 and flavonoids: In silico molecular dynamics docking to the active catalytic site of SARS-CoV and SARS-CoV-2 main protease. https://doi.org/10.2139/ssrn.3599426
   Google Scholar
• Pinzi, L., & Rastelli, G. (2019). Molecular docking: Shifting paradigms in drug discovery. International Journal of Molecular Sciences, 20(18), 4331. https://doi.org/10.3390/ijms20184331
   PubMed Web of Science ®Google Scholar
• Puttaswamy, H., Gowtham, H. G., Ojha, M. D., Yadav, A., Choudhir, G., Raguraman, V., Kongkham, B., Selvaraju, K., Shareef, S., Gehlot, P., Ahamed, F., & Chauhan, L. (2020). In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis. Scientific Reports, 10(1), 20584. https://doi.org/10.1038/s41598-020-77602-0
   PubMed Web of Science ®Google Scholar
• Rameshkumar, M. R., Indu, P., Arunagirinathan, N., Venkatadri, B., El-Serehy, H. A., & Ahmad, A. (2021). Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study. Saudi Journal of Biological Sciences, 28(1), 448–458. https://doi.org/10.1016/j.sjbs.2020.10.028
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Roozbeh, F. (2020). The effect of adding SOVODAK (sofosbuvir + daclatasvir) to the treatment protocol of COVID-19 outpatients: A clinical trial study. IRCT registration number: IRCT20200403046926N1. Retrieved from https://en.irct.ir/trial/46926
   Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Ryu, Y. B., Jeong, H. J., Kim, J. H., Kim, Y. M., Park, J.-Y., Kim, D., Nguyen, T. T. H., Park, S.-J., Chang, J. S., Park, K. H., Rho, M.-C., & Lee, W. S. (2010). Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition. Bioorganic & Medicinal Chemistry, 18(22), 7940–7947. https://doi.org/10.1016/j.bmc.2010.09.035
   PubMed Web of Science ®Google Scholar
• Sadeghi, A. (2020). A prospective randomized controlled trial comparing Sovodak (Sofosbuvir plus Daclatasvir) in participants with moderate to severe Coronavirus disease (COVID-19) compared to standard of care treatment. IRCT registration number: IRCT20200128046294N2. Retrieved from https://en.irct.ir/trial/46463
   Google Scholar
• Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
   PubMed Web of Science ®Google Scholar
• Sanner, M. F. (1999). Python: A programming language for software integration and development. Journal of Molecular Graphics & Modelling, 17(1), 57–61.
   PubMed Web of Science ®Google Scholar
• Saravanan, K. M., Zhang, H., Senthil, R., Vijayakumar, K. K., Sounderrajan, V., Wei, Y., & Shakila, H. (2020). Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1834457
   Google Scholar
• Sharma, J., Bhardwaj, V. K., Singh, R., Rajendran, V., Purohit, R., & Kumar, S. (2021). An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2. Food Chemistry, 346, 128933. https://doi.org/10.1016/j.foodchem.2020.128933
   PubMed Web of Science ®Google Scholar
• Sitkoff, D., Sharp, K. A., & Honig, B. (1994). Accurate calculation of hydration free energies using macroscopic solvent models. The Journal of Physical Chemistry, 98(7), 1978–1988. https://doi.org/10.1021/j100058a043
   Web of Science ®Google Scholar
• Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. Jr. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. https://doi.org/10.1124/pr.112.007336
   PubMed Web of Science ®Google Scholar
• Søndergaard, C. R., Olsson, M. H., Rostkowski, M., & Jensen, J. H. (2011). Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. Journal of Chemical Theory and Computation, 7(7), 2284–2295. https://doi.org/10.1021/ct200133y
   PubMed Web of Science ®Google Scholar
• Sterling, T., & Irwin, J. J. (2015). ZINC 15 – Ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
   PubMed Web of Science ®Google Scholar
• Swargiary, A., Mahmud, S., & Saleh, M. A. (2020). Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: An in silico approach to combat COVID-19. Journal of Biomolecular Structure & Dynamics. Advance online publication. https://doi.org/10.1080/07391102.2020.1835729
   Google Scholar
• Tao, W.-T., Yu, Q., Li, Y.-L., Ge, M., Zhao, Y.-L., & Shi, T. (2021). Exploring the interaction between vancomycin/teicoplanin and receptor binding domain (RBD) of SARS-CoV-2. Frontiers in Chemistry, 8, 1310. https://doi.org/10.3389/fchem.2020.639918
   Google Scholar
• Tariq, A.,Mateen, R. M.,Afzal, M. S., &Saleem, M. (2020). Paromomycin: A potential dual targeted drug effectively inhibits both spike (S1) and main protease of COVID-19. International Journal of Infectious Diseases, 98, 166–175. https://doi.org/10.1016/j.ijid.2020.06.063
   PubMed Web of Science ®Google Scholar
• Trezza, A., Iovinelli, D., Santucci, A., Prischi, F., & Spiga, O. (2020). An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors. Scientific Reports, 10(1), 13866. https://doi.org/10.1038/s41598-020-70863-9
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Ullrich, S., & Nitsche, C. (2020). The SARS-CoV-2 main protease as drug target. Bioorganic & Medicinal Chemistry Letters, 30(17), 127377. https://doi.org/10.1016/j.bmcl.2020.127377
   PubMed Web of Science ®Google Scholar
• Unni, S., Aouti, S., Thiyagarajan, S., & Padmanabhan, B. (2020). Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods. Journal of Biosciences, 45(1), 130. https://doi.org/10.1007/s12038-020-00102-w
   PubMed Web of Science ®Google Scholar
• Wang, C., Nguyen, P. H., Pham, K., Huynh, D., Le, T. B., Wang, H., Ren, P., & Luo, R. (2016). Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. Journal of Computational Chemistry, 37(27), 2436–2446. https://doi.org/10.1002/jcc.24467
   PubMed Web of Science ®Google Scholar
• Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
   PubMed Web of Science ®Google Scholar
• Wang, H. W., & Wang, J. W. (2017). How cryo-electron microscopy and X-ray crystallography complement each other. Protein Science, 26(1), 32–39. https://doi.org/10.1002/pro.3022
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wei, T.-Z., Wang, H., Wu, X.-Q., Lu, Y., Guan, S.-H., Dong, F.-Q., Dong, C-l., Zhu, G.-L., Bao, Y.-Z., Zhang, J., Wang, G.-Y., & Li, H.-Y. (2020). In silico screening of potential spike glycoprotein inhibitors of SARS-CoV-2 with drug repurposing strategy. Chinese Journal of Integrative Medicine, 26(9), 663–669. https://doi.org/10.1007/s11655-020-3427-6
   PubMed Web of Science ®Google Scholar
• Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W., & Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China. Life Sciences, 63(3), 457–460. https://doi.org/10.1007/s11427-020-1637-5
   PubMed Web of Science ®Google Scholar
• Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (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
   PubMed Web of Science ®Google Scholar
• Yu, S., Yan, H., Zhang, L., Shan, M., Chen, P., Ding, A., & Li, S. F. (2017). A review on the phytochemistry, pharmacology, and pharmacokinetics of amentoflavone, a naturally-occurring biflavonoid. Molecules, 22(2), 299. https://doi.org/10.3390/molecules22020299
   PubMed Web of Science ®Google Scholar
• Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target. Intensive Care Medicine, 46(4), 586–590. https://doi.org/10.1007/s00134-020-05985-9
   PubMed Web of Science ®Google Scholar