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 and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1758790
- 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/10.1016/j.softx.2015.06.001
- Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, N.Y.).), 300(5626), 1763–1767. https://doi.org/10.1126/science.1085658
- Arun, K. G., Sharanya, C. S., Abhithaj, J., Francis, D., & Sadasivan, C. (2020). Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2020.1779819
- Beck, B. R., Shin, B., Choi, Y., Park, S., & Kang, K. (2020). Predicting commercially available antiviral 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
- Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F. v., 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
- Bhardwaj, V. K., & Purohit, R. (2020). A new insight into protein-protein interactions and the effect of conformational alterations in PCNA. International Journal of Biological Macromolecules, 148, 999–1009. https://doi.org/10.1016/j.ijbiomac.2020.01.212
- Bhardwaj, V. K., Singh, R., Sharma, J., Das, P., & Purohit, R. (2020). Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase. Computer Methods and Programs in Biomedicine, 194, 105494. https://doi.org/10.1016/j.cmpb.2020.105494
- 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 and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1766572
- Biovia, D. S. (2017). Discovery studio modeling environment. Release.
- Chakraborty, A., Nandi, S. K., Panda, A. K., Mahapatra, P. P., Giri, S., & Biswas, A. (2018). Probing the structure-function relationship of Mycobacterium leprae HSP18 under different UV radiations. International Journal of Biological Macromolecules, 119, 604–616. https://doi.org/10.1016/j.ijbiomac.2018.07.151
- Chen, J. (2016). Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions. RSC Advances, 6(63), 58573–58585. https://doi.org/10.1039/C6RA09201B
- Chen, J., Wang, X., Zhu, T., Zhang, Q., & Zhang, J. Z. (2015). A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods. Journal of Chemical Information and Modeling, 55(9), 1903–1913. https://doi.org/10.1021/acs.jcim.5b00173
- 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. Lancet (London, England), 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
- Chou, K. C., Wei, D. Q., & Zhong, W. Z. (2003). Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochemical and Biophysical Research Communications, 308(1), 148–151. https://doi.org/10.1016/S0006-291X(03)01342-1
- Cucinotta, D., & Vanelli, M. (2020). WHO declares COVID-19 a pandemic. Acta Bio-Medica: Atenei Parmensis, 91(1), 157–160. https://doi.org/10.23750/abm.v91i1.9397
- Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
- Dan, W. J., Zhang, Q., Zhang, F., Wang, W. W., & Gao, J. M. (2019). Benzonate derivatives of acetophenone as potent α-glucosidase inhibitors: synthesis, structure-activity relationship and mechanism. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 937–945. https://doi.org/10.1080/14756366.2019.1604519
- 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., 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1763201
- DeLano, W. (2002). The PyMOL Molecular Graphics System (2002) DeLano Scientific, Palo Alto, CA, USA. http://www.pymol.org.
- Elmezayen, A. D., Al-Obaidi, A., Sahin, A. T., & Yelekci, K. (2020). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1758791
- 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/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/10.1063/1.470117
- Fan, K., Wei, P., Feng, Q., Chen, S., Huang, C., Ma, L., Lai, B., Pei, J., Liu, Y., Chen, J., & Lai, L. (2004). Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase. The Journal of Biological Chemistry, 279(3), 1637–1642. https://doi.org/10.1074/jbc.M310875200
- Frisch, M., & Clemente, F. Gaussian 09, Revision A. 01, MJ Frisch, GW Trucks, HB Schlegel, GE Scuseria, MA Robb, JR Cheeseman, G. Scalmani, V. Barone, B. Mennucci, GA Petersson, H. Nakatsuji, M. Caricato, X. Li, HP Hratchian, AF Izmaylov, J. Bloino, G. Zhe.
- Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2020). Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors - an in silico docking and molecular dynamics simulation study. J Biomol Struct Dyn, 1–13. https://doi.org/10.1080/07391102.2020.1779818
- Gyebi, G. A., Ogunro, O. B., Adegunloye, A. P., Ogunyemi, O. M., & Afolabi, S. O. (2020). Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CL(pro)): An in silico screening of alkaloids and terpenoids from African medicinal plants. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1764868
- Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
- Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/10.1021/ci100275a
- Hsu, M. F., Kuo, C. J., Chang, K. T., Chang, H. C., Chou, C. C., Ko, T. P., Shr, H. L., Chang, G. G., Wang, A. H., & Liang, P. H. (2005). Mechanism of the maturation process of SARS-CoV 3CL protease. The Journal of Biological Chemistry, 280(35), 31257–31266. https://doi.org/10.1074/jbc.M502577200
- Islam, R., Parves, M. 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, 1–12. 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 SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. 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/10.1080/07391102.2020.1760137
- Kamaraj, B., & Purohit, R. (2016). Mutational analysis on membrane associated transporter protein (MATP) and their structural consequences in Oculocutaeous albinism Type 4 (OCA4)-A molecular dynamics approach. Journal of Cellular Biochemistry, 117(11), 2608–2619. https://doi.org/10.1002/jcb.25555
- Kandeel, M., & Al-Nazawi, M. (2020). Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sciences, 251, 117627. https://doi.org/10.1016/j.lfs.2020.117627
- Kim, Y., Liu, H., Galasiti Kankanamalage, A. C., Weerasekara, S., Hua, D. H., Groutas, W. C., Chang, K. O., & Pedersen, N. C. (2016). Reversal of the progression of fatal coronavirus infection in cats by a broad-spectrum coronavirus protease inhibitor. PLoS Pathogens, 12(3), e1005531. https://doi.org/10.1371/journal.ppat.1005531
- Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
- Li, F. (2016). Structure, function, and evolution of coronavirus spike proteins. Annual Review of Virology, 3(1), 237–261. https://doi.org/10.1146/annurev-virology-110615-042301
- 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. Lancet (London, England), 395(10224), 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
- Mahanta, S., Chowdhury, P., Gogoi, N., Goswami, N., Borah, D., Kumar, R., Chetia, D., Borah, P., Buragohain, A. K., & Gogoi, B. (2020). Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: An in silico based approach. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1768902
- Mirza, M. U., & Froeyen, M. (2020). Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. Journal of Pharmaceutical Analysis. https://doi.org/10.1016/j.jpha.2020.04.008
- Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/10.1002/jcc.540130805
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
- Morris, G. M., Huey, R., Olson, A. J. (2008). Using AutoDock for ligand-receptor docking. Curr Protoc Bioinformatics, Chapter 8, Unit 8 14. https://doi.org/10.1002/0471250953.bi0814s24
- 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/10.1080/07391102.2020.1752802
- Nandi, S. K., Chakraborty, A., Panda, A. K., & Biswas, A. (2016). Conformational perturbation, hydrophobic interactions and oligomeric association are responsible for the enhanced chaperone function of Mycobacterium leprae HSP18 under pre-thermal condition [10.1039/C6RA00167J. RSC Advances, 6(67), 62146–62156. https://doi.org/10.1039/C6RA00167J
- Oostenbrink, C., Villa, A., Mark, A. E., & van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
- Park, J. Y., Yuk, H. J., Ryu, H. W., Lim, S. H., Kim, K. S., Park, K. H., Ryu, Y. B., & Lee, W. S. (2017). Evaluation of polyphenols from Broussonetia papyrifera as coronavirus protease inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 504–515. https://doi.org/10.1080/14756366.2016.1265519
- Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
- Pires, D. E., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
- Rajendran, V. (2016). Structural analysis of oncogenic mutation of isocitrate dehydrogenase 1. Molecular Biosystems, 12(7), 2276–2287. https://doi.org/10.1039/c6mb00182c
- Rajendran, V., Gopalakrishnan, C., & Sethumadhavan, R. (2018). Pathological role of a point mutation (T315I) in BCR-ABL1 protein-A computational insight. Journal of Cellular Biochemistry, 119(1), 918–925. https://doi.org/10.1002/jcb.26257
- Ren, L. L., Wang, Y. M., Wu, Z. Q., Xiang, Z. C., Guo, L., Xu, T., Jiang, Y. Z., Xiong, Y., Li, Y. J., Li, X. W., Li, H., Fan, G. H., Gu, X. Y., Xiao, Y., Gao, H., Xu, J. Y., Yang, F., Wang, X. M., Wu, C., … Wang, J. W. (2020). Identification of a novel coronavirus causing severe pneumonia in human: A descriptive study. Chinese Medical Journal, 133(9), 1015–1024. https://doi.org/10.1097/CM9.0000000000000722
- Rota, P. A., Oberste, M. S., Monroe, S. S., Nix, W. A., Campagnoli, R., Icenogle, J. P., Penaranda, S., Bankamp, B., Maher, K., Chen, M. H., Tong, S., Tamin, A., Lowe, L., Frace, M., DeRisi, J. L., Chen, Q., Wang, D., Erdman, D. D., Peret, T. C., … Bellini, W. J. (2003). Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science (New York, N.Y.).), 300(5624), 1394–1399. https://doi.org/10.1126/science.1085952
- Ryu, H. W., Lee, B. W., Curtis-Long, M. J., Jung, S., Ryu, Y. B., Lee, W. S., & Park, K. H. (2010). Polyphenols from Broussonetia papyrifera displaying potent alpha-glucosidase inhibition. Journal of Agricultural and Food Chemistry, 58(1), 202–208. https://doi.org/10.1021/jf903068k
- Ryu, H. W., Lee, J. H., Kang, J. E., Jin, Y. M., & Park, K. H. (2012). Inhibition of xanthine oxidase by phenolic phytochemicals from Broussonetia papyrifera. Journal of the Korean Society for Applied Biological Chemistry, 55(5), 587–594. https://doi.org/10.1007/s13765-012-2143-0
- Schuttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
- Umesh, K. D., Selvaraj, C., Singh, S. K., & Dubey, V. K. (2020). Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1763202
- Venugopal, P. P., Das, B. K., Soorya, E., & Chakraborty, D. (2020). Effect of hydrophobic and hydrogen bonding interactions on the potency of ss-alanine analogs of G-protein coupled glucagon receptor inhibitors. Proteins: Structure, Function, and Bioinformatics, 88(2), 327–344. https://doi.org/10.1002/prot.25807
- Williams, S. J., & Goddard-Borger, E. D. (2020). alpha-glucosidase inhibitors as host-directed antiviral agents with potential for the treatment of COVID-19. Biochemical Society Transactions, https://doi.org/10.1042/BST20200505
- Yu, X., & Yang, R. (2020). COVID-19 transmission through asymptomatic carriers is a challenge to containment. Influenza and Other Respiratory Viruses, 14(4), 474–475. https://doi.org/10.1111/irv.12743
- 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 (New York, N.Y.).), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
- Zhao, X., Guo, F., Comunale, M. A., Mehta, A., Sehgal, M., Jain, P., Cuconati, A., Lin, H., Block, T. M., Chang, J., & Guo, J. T. (2015). Inhibition of endoplasmic reticulum-resident glucosidases impairs severe acute respiratory syndrome coronavirus and human coronavirus NL63 spike protein-mediated entry by altering the glycan processing of angiotensin I-converting enzyme 2. Antimicrobial Agents and Chemotherapy, 59(1), 206–216. https://doi.org/10.1128/AAC.03999-14
- Zheng, J. (2020). SARS-CoV-2: An emerging coronavirus that causes a global threat. International Journal of Biological Sciences, 16(10), 1678–1685. https://doi.org/10.7150/ijbs.45053
- Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., Si, H. R., Zhu, Y., Li, B., Huang, C. L., Chen, H. D., Chen, J., Luo, Y., Guo, H., Jiang, R. D., Liu, M. Q., Chen, Y., Shen, X. R., Wang, X., … Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7
- Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., Tan, W., China Novel Coronavirus, I., & Research, T. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/NEJMoa2001017