References
- Aanouz, I., Belhassan, A., El Khatabi, K., Lakhlifi, T., El Idrissi, M., & Bouachrine, M. (2020). Moroccan medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/https://doi.org/10.1080/07391102.2020.1758790
- Abdelli, I., Hassani, F., Bekkel Brikci, S., & Ghalem, S. (2020). In silico study the inhibition of Angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from western Algeria. Journal of Biomolecular Structure and Dynamics, 1–17. https://doi.org/https://doi.org/10.1080/07391102.2020.1763199
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/https://doi.org/10.1016/j.softx.2015.06.001
- Åkerström, S., Mousavi-Jazi, M., Klingström, J., Leijon, M., Lundkvist, Å., & Mirazimi, A. (2005). Nitric oxide inhibits the replication cycle of severe acute respiratory syndrome coronavirus. Journal of Virology, 79(3), 1966–1969. https://doi.org/https://doi.org/10.1128/JVI.79.3.1966-1969.2005
- Åkerström, S., Gunalan, V., Keng, C. T., Tan, Y. J., & Mirazimi, A. (2009). Dual effect of nitric oxide on SARS-CoV replication: Viral RNA production and palmitoylation of the S protein are affected. Virology, 395(1), 1–9. https://doi.org/https://doi.org/10.1016/j.virol.2009.09.007
- Al-Khafaji, K., Al-DuhaidahawiL, D., & Taskin Tok, T. (2020). Using Integrated Computational Approaches to Identify Safe and Rapid Treatment for SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1764392
- Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1758788
- Chen, L., Liu, P., Gao, H., Sun, B., Chao, D., Wang, F., Zhu, Y., Hedenstierna, G., & Wang, C. G. (2004). Inhalation of nitric oxide in the treatment of severe acute respiratory syndrome: A rescue trial in Beijing. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 39(10), 1531–1535. https://doi.org/https://doi.org/10.1086/425357
- Cheng, F. (2019). In silico oncology drug repositioning and polypharmacology. In Cancer Bioinformatics. Humana Press. 1878, 243–261 https://doi.org/https://doi.org/10.1007/978-1-4939-8868-6_15
- Das, S., Sarmah, S., Lyndem, S., & Singha Roy, A. (2020). An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. Journal of Biomolecular Structure and Dynamics, 1–18. https://doi.org/https://doi.org/10.1080/07391102.2020.1763201
- Elfiky, A. A. (2020a). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/https://doi.org/10.1080/07391102.2020.1761882
- Elfiky, A. A. (2020b). Natural products may interfere with SARSCoV-2 attachment to the host cell. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1761881
- Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure and Dynamics, 1–7. https://doi.org/https://doi.org/10.1080/07391102.2020.1760136
- Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/https://doi.org/10.1063/1.470117
- Gasco, A., Fruttero, R., Sorba, G., Di Stilo, A., & Calvino, R. (2004). NO donors: Focus on furoxan derivatives. Pure and Applied Chemistry, 76(5), 973–981. https://doi.org/https://doi.org/10.1351/pac200476050973
- Ghosh, A. K., Brindisi, M., Shahabi, D., Chapman, M. E., & Mesecar, A. D. (2020). Drug Development and Medicinal Chemistry Efforts Toward SARS‐Coronavirus and Covid‐19 Therapeutics. ChemMedChem., 15(11), 907–932. https://doi.org/https://doi.org/10.1002/cmdc.202000223
- Gyebi, G. A., Ogunro, O. B., Adegunloye, A. P., Ogunyemi, O. M., & Afolabi, S. O. (2020). Potential Inhibitors of Coronavirus 3-Chymotrypsin-Like Protease (3CLpro): An in silico screening of Alkaloids and Terpenoids from African medicinal plants. Journal of Biomolecular Structure and Dynamics, 1–19. https://doi.org/https://doi.org/10.1080/07391102.2020.1764868
- Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
- Islam, R., Parves, R., Paul, A. S., Uddin, N., Rahman, M. S., Mamun, A. A., Hossain, M. N., Ali, M. A., & Halim, M. A. (2020). A Molecular Modeling Approach to Identify Effective Antiviral Phytochemicals against the Main Protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–20. https://doi.org/https://doi.org/10.1080/07391102.2020.1761883
- Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature, 582(7811), 289–293. (2019). https://doi.org/https://doi.org/10.1038/s41586-020-2223-y
- Joshi, R. S., Jagdale, S. S., Bansode, S. B., Shankar, S. S., Tellis, M. B., Pandya, V. K., Chugh, A., Giri, A. P., & Kulkarni, M. J. (2020). Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/https://doi.org/10.1080/07391102.2020.1760137
- Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487. https://doi.org/https://doi.org/10.1021/jp003919d
- Keyaerts, E., Vijgen, L., Chen, L., Maes, P., Hedenstierna, G., & Van Ranst, M. (2004). Inhibition of SARS-coronavirus infection in vitro by S-nitroso-N-acetylpenicillamine, a nitric oxide donor compound. International Journal of Infectious Diseases : IJID : official Publication of the International Society for Infectious Diseases, 8(4), 223–226. https://doi.org/https://doi.org/10.1016/j.ijid.2004.04.012
- Khan, R. J., Jha, R. K., Amera, G., Jain, M., Singh, E., Pathak, A., Singh, R. P., Muthukumaran, J., & Singh, A. K. (2020a). 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, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1753577
- Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020b). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.1751298.
- Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/https://doi.org/10.1021/ci500020m
- Lobo-Galo, N., Terrazas-López, M., Martínez-Martínez, A., & Díaz-Sánchez, Á. G. (2020). FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/https://doi.org/10.1080/07391102.2020.1764393
- Lu, H. (2020). Drug treatment options for the 2019-new coronavirus (2019-nCoV). Bioscience Trends, 14(1), 69–71. https://doi.org/https://doi.org/10.5582/bst.2020.01020
- Mannick, J. B. (1995). The antiviral role of nitric oxide. Research in Immunology, 146(9), 693–697. https://doi.org/https://doi.org/10.1016/0923-2494(96)84920-0
- Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/https://doi.org/10.1080/07391102.2020.1752802.
- Pant, S., Singh, M., Ravichandiran, V., Murty, U. S. N., & Srivastava, H. K. (2020). Peptidelike and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.1757510
- Parulekar, R. S., & Sonawane, K. D. (2018a). Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains. Journal of Cellular Biochemistry, 119(3), 2679–2695. https://doi.org/https://doi.org/10.1002/jcb.26435
- Parulekar, R. S., & Sonawane, K. D. (2018b). Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus: In silico and in vitro perspective. Journal of Cellular Biochemistry, 119(11), 9444–9461. https://doi.org/https://doi.org/10.1002/jcb.27261
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084
- Prabhuling, S., Tamboli, Y., Choudhari, P. B., Bhatia, M. S., Mohanta, T. K., Al-Harrasi, A., & Pudukulathan, Z. K. (2020). Synthesis and Modeling Studies of Furoxan Coupled Spiro-Isoquinolino Piperidine Derivatives as NO Releasing PDE 5 Inhibitors. Biomedicines, 8(5), 121. https://doi.org/https://doi.org/10.3390/biomedicines8050121
- Pudukulatham, Z., Zhang, F. X., Gadotti, V. M., M’Dahoma, S., Swami, P., Tamboli, Y., & Zamponi, G. W. (2016). Synthesis and characterization of a disubstitutedpiperazine derivative with T-type channel blocking action and analgesic properties. Molecular Pain, 12, 174480691664167. https://doi.org/https://doi.org/10.1177/1744806916641678
- Reiss, C. S., & Komatsu, T. (1998). Does nitric oxide play a critical role in viral infections? Journal of Virology, 72(6), 4547–4551. https://doi.org/https://doi.org/10.1128/JVI.72.6.4547-4551.1998
- Sarma, P., Sekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., Singh, S., Kumar, H., Prakash, A., & Dhibar, D. P. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure and Dynamics (Just-Accepted), 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1753580
- Saura, M., Zaragoza, C., McMillan, A., Quick, R. A., Hohenadl, C., Lowenstein, J. M., & Lowenstein, C. J. (1999). An antiviral mechanism of nitric oxide: Inhibition of a viral protease. Immunity, 10(1), 21–28. https://doi.org/https://doi.org/10.1016/S1074-7613(00)80003-5
- Serafim, R. A. M., Primi, M. C., Trossini, G. H. G., & Ferreira, E. I. (2012). Nitric oxide: State of the art in drug design. Current Medicinal Chemistry, 19(3), 386–405. https://doi.org/https://doi.org/10.2174/092986712803414321
- Sinha, S. K., Shakya, A., Prasad, S. K., Singh, S., Gurav, N. S., Prasad, R. S., & Gurav, S. S. (2020). An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1762741
- 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/https://doi.org/10.1002/jcc.21334
- Van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. https://doi.org/https://doi.org/10.1007/BF00355047
- Wahedi, H. M., Ahmad, S., & Abbasi, S. W. (2020). Stilbene-based natural compounds as promising drug candidates against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/https://doi.org/10.1080/07391102.2020.1762743
- www.rcsb.org
- www.vlifesciences.com
- Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 368(6489), 409–412. https://doi.org/https://doi.org/10.1126/science.abb3405