Target SARS-CoV-2: theoretical exploration on clinical suitability of certain drugs

References

• Atkins, P., Paula, D., & Keeler, J. (2018). Atkins’ physical chemistry. Oxford University Press.
   Google Scholar
• Barros, R. O., Junior, F. L. C. C., Pereira, W. S., Oliveira, N. M. N., & Ramos, R. M. (2020). Interaction of drug candidates with various SARS-CoV-2 receptors: An in-silico study to combat COVID-19. Journal of Proteome Research, 19(11), 4567–4575. https://doi.org/10.1021/acs.jproteome.0c00327
   PubMed Web of Science ®Google Scholar
• Beck, B. R., Shin, B., Choi, Y., Park, S., & Kang, K. (2020). Predicting commercially available anti-viral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. Computational and Structural Biotechnology Journal, 18, 784–790. https://doi.org/10.1016/j.csbj.2020.03.025
   PubMed Web of Science ®Google Scholar
• Biovia, D. S. (2017). Discovery studio visualizer.
   Google Scholar
• Cai, Q., Yang, M., Liu, D., Chen, J., Shu, D., Xia, J., Liao, X., Gu, Y., Cai, Q., Yang, Y., Shen, C., Li, X., Peng, L., Huang, D., Zhang, J., Zhang, S., Wang, S. F., Liu, J., Chen, L., . . . Liu, L. (2020). Experimental treatment with Favipiravir for COVID-19: An open-label control study. Engineering, 6(10), 1192–1198. https://doi.org/10.1016/j.eng.2020.03.007
   Web of Science ®Google Scholar
• Chang, R. (2005). Physical chemistry for the biosciences. University Science Books.
   Google Scholar
• Chellapandi, P., & Saranya, S. (2020). Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery. Medicinal Chemistry Research, 29(10), 1–15. https://doi.org/10.1007/s00044-020-02610-8
   Web of Science ®Google Scholar
• Chen, C., Zhang, Y., Huang, J., Yin, P., Cheng, Z., Wu, J., Chen, S., Zhang, Y., Chen, B., Lu, M., Luo, Y., Ju, L., Zhang, J., & Wang, X. (2020). Favipiravir versus Arbidol for COVID-19: A randomized clinical trial. medRxiv, https://doi.org/10.1101/2020.03.17.20037432
   Google Scholar
• Chen, J. (2020). Pathogenicity and transmissibility10 pt of 2019-nCoV—A quick overview and comparison with other emerging viruses. Microbes and Infection, 22(2), 69–71. https://doi.org/10.1016/j.micinf.2020.01.004
   PubMed Web of Science ®Google Scholar
• Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. The Lancet, 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
   PubMed Web of Science ®Google Scholar
• Chtita, S., Belhassan, A., Aouidate, A., Belaidi, S., Bouachrine, M., & Lakhlifi, T. (2021). Discovery of potent SARS-CoV-2 inhibitors from approved anti-viral drugs via docking screening. Combinatorial Chemistry & High Throughput Screening, 24(3), 441–454. https://doi.org/10.2174/1386207323999200730205447
   PubMed Web of Science ®Google Scholar
• Clercq, E. D., & Li, G. (2016). Approved anti-viral drugs over the past 50 years. Clinical Microbiology Reviews, 29(3), 695–747. https://doi.org/10.1128/CMR.00102-15
   PubMed Web of Science ®Google Scholar
• Coomes, E. A., & Haghbayan, H. (2020). Favipiravir, an anti-viral for COVID-19? Journal of Antimicrobial Chemotherapy, 75(7), 2013–2014. https://doi.org/10.1093/jac/dkaa171
   PubMed Web of Science ®Google Scholar
• Daidone, I., Amadei, A., Roccatano, D., & Nola, A. D. (2003). A Molecular dynamics simulation of protein folding by essential dynamics sampling: Folding landscape of horse heart cytochrome c. Biophysical Journal, 85(5), 2865–2871. https://doi.org/10.1016/S0006-3495(03)74709-2
   PubMed Web of Science ®Google Scholar
• Dodda, L. S., Vaca, C. I., Rives, T. J., & Jorgensen, W. L. (2017). LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Research, 45, 331–336.
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald potential. Journal of Chemical Physics, 103(19), 8577–8592. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Falsafi-Zadeh, S., Karimi, Z., & Galehdari, H. (2012). V.M.D. DisRg: New user-friendly implement for calculation distance and radius of gyration n V.M.D. program. Bioinformation, 8(7), 341–343. https://doi.org/10.6026/97320630008341
   PubMedGoogle Scholar
• Gralinski, L. E., & Menachery, V. D. (2020). Return of the Coronavirus: 2019-nCoV. Viruses, 12(2), 135. https://doi.org/10.3390/v12020135
   PubMed Web of Science ®Google Scholar
• Gurung, B. A., Ali, M. A., Lee, J., Farah, A., & Anazi, M. A. (2020). Structure-based virtual screening of phytochemicals and repurposing of F.D.A. approved anti-viral drugs unravels lead molecules as potential inhibitors of coronavirus 3C-like protease enzyme. Journal of King Saud University, Science., 32(6), 2845–2853. https://doi.org/10.1016/j.jksus.2020.07.007
   PubMed Web of Science ®Google Scholar
• https://en.wikipedia.org/wiki/Root-mean-square_deviation
   Google Scholar
• Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet, 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Jiayi, R., Zhiwei, Y., Nianjue, Z., & Yuan, X. (2017). Effect of force fields and water models on EGFRvIII-MR1 (scFv) complex by molecular dynamics simulation, MM-PBSA calculation, and ITC experiment. Chemical Journal of Chinese Universities, 38, 2070–2076.
   Web of Science ®Google Scholar
• Jomah, S., Basheeruddin, S. M., & Yamani, M. J. (2020). Clinical efficacy of anti-virals against novel coronavirus (COVID-19): A review. Journal of Infection and Public Health, 13(9), 1187–1195. https://doi.org/10.1016/j.jiph.2020.07.013
   PubMed Web of Science ®Google Scholar
• Kamps, J. J. A. G., Huang, J., Poater, J., Xu, C., Pieters, B. J. G. E., Dong, A., Min, J., Sherman, W., Beuming, T., Matthias Bickelhaupt, F., Li, H., & Mecinović, J. (2015). The Chemical basis for the recognition of trimethyl lysine by epigenetic reader proteins. Nature Communications, 6(1), 1–12. https://doi.org/10.1038/ncomms9911
   Google Scholar
• Kandeel, M., & Al-Nazawi, M. (2020). Virtual screening and repurposing of F.D.A. approved drugs against COVID-19 main protease. Life Sciences, 251, 117627. https://doi.org/10.1016/j.lfs.2020.117627
   PubMed Web of Science ®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 and Dynamics, 39(8), 2679–2692. https://doi.org/10.1080/07391102.2020.1753577
   Google Scholar
• Khan, S. U., & Htar, T. T. (2020). Deciphering the binding mechanism of Dexamethasone against SARS-CoV-2 Main Protease: Computational molecular modelling approach. Chem Rxiv, https://doi.org/10.26434/chemrxiv.12517535.v1
   Google Scholar
• Kumar, S., Zhi, K., Mukherji, A., & Gerth, K. (2020). Repurposing antiviral protease inhibitors using extracellular vesicles for potential therapy of COVID-19. Viruses, 12(5), 486. https://doi.org/10.3390/v12050486
   PubMed Web of Science ®Google Scholar
• Kumar, Y., Singh, H., & Patel, C. N. (2020). In silico prediction of potential inhibitors for the Main protease of SARS-CoV-2 using molecular docking and dynamics simulation-based drug-repurposing. Journal of Infection and Public Health, S1876-0341(20), 30526–30528. https://doi.org/10.1016/j.jiph.2020.06.016.
   Google Scholar
• Liu, X., & Wang, X. (2020). Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines. Journal of Genetics and Genomics, 47(2), 119–121. https://doi.org/10.1016/j.jgg.2020.02.001
   PubMed Web of Science ®Google Scholar
• Liu, X., Zhang, B., & Jin, Z. (2020). The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein Data Bank.
   Google Scholar
• Md Nayeem, Sk., Sohail, E. M., Ridhima, G., & Reddy, M. S. (2021). Target SARS-CoV-2: Computation of binding energies with drugs of dexamethasone/umifenovir by molecular dynamics using OPLS-AA force field. Research on Biomedical Engineering. https://doi.org/10.1007/s42600-020-00119-y
   Google Scholar
• Moradi, S. Z., Nowroozi, A., Sadrjavadi, K., Moradi, S., Mansouri, K., Hosseinzadeh, L., & Shahlaei, M. (2018). Direct evidence for the groove binding of the Clomifene to double stranded D.N.A. International Journal of Biological Macromolecules, 114, 40–53. https://doi.org/10.1016/j.ijbiomac.2018.03.040
   PubMed Web of Science ®Google Scholar
• Nayeem, S. M., Sohail, E. M., Sudhir, G. P., & Reddy, M. S. (2021). Computational and theoretical exploration for clinical suitability of Remdesivir drug to SARS-CoV-2. European Journal of Pharmacology, 890, 173642. https://doi.org/10.1016/j.ejphar.2020.173642
   PubMed Web of Science ®Google Scholar
• Paraskevis, D., Kostaki, E. G., Magiorkinis, G., Panayiotakopoulos, G., Sourvinos, G., & Tsiodras, S. (2020). Full-genome evolutionary analysis of the novel coronavirus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infection, Genetics and Evolution, 79, 104212. https://doi.org/10.1016/j.meegid.2020.104212
   PubMed Web of Science ®Google Scholar
• Perozzo, R., Folkers, G., & Scapozza, L. (2004). Thermodynamics of protein-ligand interactions: History, presence, and future aspects. Journal of Receptors and Signal Transduction, 24(1–2), 1–52. https://doi.org/10.1081/RRS-120037896
   PubMed Web of Science ®Google Scholar
• Ren, J., Yuan, X., Li, J., Shuian, L., Yang, B., Chen, C., Zhao, J., Zheng, W., Liao, H., Yang, Z., & Qui, Z. (2019). Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. Journal of the Chinese Chemical Society, 67(1), 46–53.
   Google Scholar
• Roberts, A., Deming, D., Paddock, C. D., Cheng, A., Yount, B., Vogel, L., Herman, B. D., Sheahan, T., Heise, M., Genrich, G. L., Zaki, S. R., Baric, R., & Rao, K. S. (2007). A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice. PLoS Pathogens, 3(1), e5. https://doi.org/10.1371/journal.ppat.0030005
   PubMed Web of Science ®Google Scholar
• Robertson, M., Tirado-Rives, J., & Jorgensen, W. (2015). Improved peptide and protein torsional energetics with the OPLS-AA Force Field. Journal of Chemical Theory and Computation, 11(7), 3499–3509. https://doi.org/10.1021/acs.jctc.5b00356
   PubMed Web of Science ®Google Scholar
• Salsbury, F. R. Jr. (2010). Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Current Opinion in Pharmacology, 10(6), 738–744. https://doi.org/10.1016/j.coph.2010.09.016
   PubMed Web of Science ®Google Scholar
• Sanders, J. M., Monogue, M. L., Jodlowski, T. Z., & Cutrell, J. B. (2020). Pharmacologic treatments for coronavirus disease 2019 (COVID-19): A review. JAMA, 323, 1824–1836.
   PubMed Web of Science ®Google Scholar
• Schauperl, M., Podewitz, M., Waldner, B. J., & Liedl, K. R. (2016). Enthalpic and entropic contributions to hydrophobicity. Journal of Chemical Theory and Computation, 12(9), 4600–4610. https://doi.org/10.1021/acs.jctc.6b00422
   PubMed Web of Science ®Google Scholar
• Shamsi, A., Mohammad, T., Anwar, S., Ajmi, A. M. F., Hussain, A., Rehman, M. T., Slam, A., & Hassan, M. I. (2020). Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: Possible implication in COVID-19 therapy. Bioscience Reports, 40(6), BSR20201256. https://doi.org/10.1042/BSR20201256
   PubMed Web of Science ®Google Scholar
• Shannon, B., Selisko, B., Le, N. T., Huchting, J., Touret, F., Piorkowski, G., Fattorini, V., Ferron, F., Decroly, E., Meier, C., Coutard, B., Peersen, O., & Canard, B. (2020). Favipiravir strikes the SARS-CoV-2 at its Achilles heel, the RNA polymerase. bioRxiv. https://doi.org/10.1101/2020.05.15.098731
   PubMedGoogle Scholar
• Sun, H., Li, Y., Shen, M., Shen, M., Tian, S., Xu, L., Pan, P., Guan, Y., & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Physical Chemistry Chemical Physics, 16(40), 22035–22045. https://doi.org/10.1039/C4CP03179B
   PubMed Web of Science ®Google Scholar
• Tachoua, W., & Kabrine, M. (2020). Molecular docking study of COVID-19 main protease with clinically approved drugs. ChemRxiv. https://doi.org/10.26434/chemrxiv
   Google Scholar
• Tikellis, C., & Thomas, M. C. (2012). Angiotensin-converting enzyme 2 (ACE2) is a key modulator of the renin-angiotensin system in health and disease. International Journal of Peptides, 2012, 1–8. https://doi.org/10.1155/2012/256294
   Google Scholar
• Tipnis, S. R., Hooper, N. M., Hyde, R., Karran, E., Christie, G., & Turner, A. J. (2000). A human homolog of angiotensin-converting enzyme cloning and functional expression as a captopril-insensitive carboxypeptidase. Journal of Biological Chemistry, 275(43), 33238–33243. https://doi.org/10.1074/jbc.M002615200
   PubMed Web of Science ®Google Scholar
• Ton, A.‐T., Gentile, F., Hsing, M., Ban, F., & Cherkasov, A. (2020). Rapid identification of potential inhibitors of SARS‐CoV‐2 main protease by deep docking of 1.3 billion compounds. Molecular Informatics, 39(8), e2000028. https://doi.org/10.1002/minf.202000028
   Web of Science ®Google Scholar
• Tu, Y.-F., Chien, C.-S., Yarmishyn, A. A., Lin, Y.-Y., Luo, Y.-H., Lin, Y.-T., Lai, W.-Y., Yang, D.-M., Chou, S.-J., Yang, Y.-P., Wang, M.-L., & Chiou, S.-H. (2020). A review of SARS-CoV-2 and the ongoing clinical trials. International Journal of Molecular Sciences, 21(7), 2657. https://doi.org/10.3390/ijms21072657
   PubMed Web of Science ®Google Scholar
• Yanai, H. (2020). Favipiravir: A possible pharmaceutical treatment for COVID-19. Journal of Endocrinology and Metabolism, 10(2), 33–34. https://doi.org/10.14740/jem645
   Web of Science ®Google Scholar
• Yavuz, S. S., & Unal, S. (2020). Anti-viral treatment of COVID-19. Turkish Journal of Medical Sciences, 50(SI-1), 611–619. https://doi.org/10.3906/sag-2004-145
   PubMedGoogle Scholar