References
- Ahmed, M. A., Azam, F., Rghigh, A. M., Gbaj, A., & Zetrini, A. E. (2012). Structure-based design, synthesis, molecular docking, and biological activities of 2-(3-benzoylphenyl) propanoic acid derivatives as dual mechanism drugs. Journal of Pharmacy & Bioallied Sciences, 4(1), 43. https://doi.org/https://doi.org/10.4103/0975-7406.92728
- Ahmed, M., Azam, F., Gbaj, A., Zetrini, A. E., Abodlal, A. S., Rghigh, A., Elmahdi, E., Hamza, A., Salama, M., & Bensaber, S. M. (2016). Ester prodrugs of ketoprofen: Synthesis, in vitro stability, in vivo biological evaluation and in silico comparative docking studies against COX-1 and COX-2. Current Drug Discovery Technologies, 13(1), 41–57.
- Azam, F., Abodabos, H. S., Taban, I. M., Rfieda, A. R., Mahmood, D., Anwar, M. J., Khan, S., Sizochenko, N., Poli, G., Tuccinardi, T., & Ali, H. I. (2019). Rutin as promising drug for the treatment of Parkinson’s disease: An assessment of MAO-B inhibitory potential by docking, molecular dynamics and DFT studies. Molecular Simulation, 45(18), 1563–1571. https://doi.org/https://doi.org/10.1080/08927022.2019.1662003
- Azam, F., Alabdullah, N. H., Ehmedat, H. M., Abulifa, A. R., Taban, I., & Upadhyayula, S. (2018). NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer’s disease: An investigation by docking, molecular dynamics, and DFT studies. Journal of Biomolecular Structure and Dynamics, 36(8), 2099–2117. https://doi.org/https://doi.org/10.1080/07391102.2017.1338164
- Azam, F., Amer, A. M., Rabulifa, A., & Elzwawi, M. M. (2014). Ginger components as new leads for the design and development of novel multi-targeted anti-Alzheimer’s drugs: A computational investigation. Drug Design, Development and Therapy, 8, 2045–2059. https://doi.org/https://doi.org/10.2147/DDDT.S67778
- Azam, F., Mohamed, N., & Alhussen, F. (2015). Molecular interaction studies of green tea catechins as multitarget drug candidates for the treatment of Parkinson's disease: Computational and structural insights. Network (Bristol, England), 26(3–4), 97–115. https://doi.org/https://doi.org/10.3109/0954898X.2016.1146416
- Azam, F., Vijaya Vara Prasad, M., Thangavel, N., Kumar Shrivastava, A., & Mohan, G. (2012). Structure-based design, synthesis and molecular modeling studies of thiazolyl urea derivatives as novel anti-Parkinsonian agents. Medicinal Chemistry (Shariqah (United Arab Emirates)), 8(6), 1057–1068. https://doi.org/https://doi.org/10.2174/1573406411208061057
- Borkotoky, S., & Banerjee, M. (2020). A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem). Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1774419
- Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. SC’06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing.
- Caly, L., Druce, J. D., Catton, M. G., Jans, D. A., & Wagstaff, K. M. (2020). The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Research, 178, 104787. https://doi.org/https://doi.org/10.1016/j.antiviral.2020.104787
- Chandel, V., Sharma, P. P., Raj, S., Choudhari, R., Rathi, B., & Kumar, D. (2020). Structure-based drug repurposing for targeting Nsp9 replicase and spike proteins of severe acute respiratory syndrome coronavirus 2. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1811773
- 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 and Dynamics, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.1772885
- Desmond Molecular Dynamics System. (2020). Schrödinger LLC.
- Eid, E., Alanazi, A., Koosha, S., Alrasheedy, A., Azam, F., Taban, I., Khalilullah, H., Sadiq Al-Qubaisi, M., Alshawsh, M., Eid, E., Alanazi, A., Koosha, S., Alrasheedy, A., Azam, F., Taban, I., Khalilullah, H., Sadiq Al-Qubaisi, M., & Alshawsh, M. (2019). Zerumbone induces apoptosis in breast cancer cells by targeting αvβ3 integrin upon co-administration with TP5-iRGD peptide. Molecules, 24(14), 2554. https://doi.org/https://doi.org/10.3390/molecules24142554
- Fahmy, N. M., Al-Sayed, E., Moghannem, S., Azam, F., El-Shazly, M., & Singab, A. N. (2020). Breaking down the barriers to a natural antiviral agent: Antiviral activity and molecular docking of erythrina speciosa extract, fractions, and the major compound. Chemistry & Biodiversity, 17(2), e1900511. https://doi.org/https://doi.org/10.1002/cbdv.201900511
- Fraser, J. E., Watanabe, S., Wang, C., Chan, W. K. K., Maher, B., Lopez-Denman, A., Hick, C., Wagstaff, K. M., Mackenzie, J. M., Sexton, P. M., Vasudevan, S. G., & Jans, D. A. (2014). A nuclear transport inhibitor that modulates the unfolded protein response and provides in vivo protection against lethal dengue virus infection. The Journal of Infectious Diseases, 210(11), 1780–1791. https://doi.org/https://doi.org/10.1093/infdis/jiu319
- Gaillard, T. (2018). Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark. Journal of Chemical Information and Modeling, 58(8), 1697–1706. https://doi.org/https://doi.org/10.1021/acs.jcim.8b00312
- 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/https://doi.org/10.1517/17460441.2015.1032936
- 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/https://doi.org/10.1038/s41586-020-2286-9
- Görlich, D., Henklein, P., Laskey, R. A., & Hartmann, E. (1996). A 41 amino acid motif in importin-alpha confers binding to importin-beta and hence transit into the nucleus. The EMBO Journal, 15(8), 1810–1817.
- Götz, V., Magar, L., Dornfeld, D., Giese, S., Pohlmann, A., Höper, D., Kong, B.-W., Jans, D. A., Beer, M., Haller, O., & Schwemmle, M. (2016). Influenza A viruses escape from MxA restriction at the expense of efficient nuclear vRNP import. Scientific Reports, 6(1), 23138. https://doi.org/https://doi.org/10.1038/srep23138
- Harder, E., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J. Y., Wang, L., Lupyan, D., Dahlgren, M. K., Knight, J. L., Kaus, J. W., Cerutti, D. S., Krilov, G., Jorgensen, W. L., Abel, R., & Friesner, R. A. (2016). OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation, 12(1), 281–296. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00864
- Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review. A, General Physics, 31(3), 1695–1697. https://doi.org/https://doi.org/10.1103/physreva.31.1695
- Hospital, A., Goñi, J. R., Orozco, M., & Gelpí, J. L. (2015). Molecular dynamics simulations: Advances and applications. Advances and Applications in Bioinformatics and Chemistry: AABC, 8, 37–47. https://doi.org/https://doi.org/10.2147/AABC.S70333
- Humphreys, D. D., Friesner, R. A., & Berne, B. J. (1994). A multiple-time-step molecular dynamics algorithm for macromolecules. The Journal of Physical Chemistry, 98(27), 6885–6892. https://doi.org/https://doi.org/10.1021/j100078a035
- Hussain, M. S., Azam, F., Ahamed, K. F. H. N., Ravichandiran, V., & Alkskas, I. (2016). Anti-endotoxin effects of terpenoids fraction from Hygrophila auriculata in lipopolysaccharide-induced septic shock in rats. Pharmaceutical Biology, 54(4), 628–636. https://doi.org/https://doi.org/10.3109/13880209.2015.1070877
- Jans, D. A., Martin, A. J., & Wagstaff, K. M. (2019). Inhibitors of nuclear transport. Current Opinion in Cell Biology, 58, 50–60. https://doi.org/https://doi.org/10.1016/j.ceb.2019.01.001
- Khan, M. T., Ali, A., Wang, Q., Irfan, M., Khan, A., Zeb, M. T., Zhang, Y.-J., Chinnasamy, S., & Wei, D.-Q. (2020). Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2—a molecular dynamic study. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1769733
- Kobe, B. (1999). Autoinhibition by an internal nuclear localization signal revealed by the crystal structure of mammalian importin alpha. Nature Structural Biology, 6(4), 388–397. https://doi.org/https://doi.org/10.1038/7625
- Kong, R., Yang, G., Xue, R., Liu, M., Wang, F., Hu, J., Guo, X., & Chang, S. (2020). COVID-19 Docking Server: A meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19. Bioinformatics, 1–3. https://doi.org/https://doi.org/10.1093/bioinformatics/btaa645
- Kosyna, F. K., Nagel, M., Kluxen, L., Kraushaar, K., & Depping, R. (2015). The importin α/β-specific inhibitor Ivermectin affects HIF-dependent hypoxia response pathways. Biological Chemistry, 396(12), 1357–1367. https://doi.org/https://doi.org/10.1515/hsz-2015-0171
- Littler, D. R., Gully, B. S., Colson, R. N., & Rossjohn, J. (2020). Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9. iScience, 23(7), 101258. https://doi.org/https://doi.org/10.1016/j.isci.2020.101258
- Lundberg, L., Pinkham, C., Baer, A., Amaya, M., Narayanan, A., Wagstaff, K. M., Jans, D. A., & Kehn-Hall, K. (2013). Nuclear import and export inhibitors alter capsid protein distribution in mammalian cells and reduce Venezuelan Equine Encephalitis Virus replication. Antiviral Research, 100(3), 662–672. https://doi.org/https://doi.org/10.1016/j.antiviral.2013.10.004
- Luvira, V., Watthanakulpanich, D., & Pittisuttithum, P. (2014). Management of Strongyloides stercoralis: A puzzling parasite. International Health, 6(4), 273–281. https://doi.org/https://doi.org/10.1093/inthealth/ihu058
- Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. https://doi.org/https://doi.org/10.1021/jm060522a
- 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/https://doi.org/10.1080/07391102.2020.1768902
- Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/https://doi.org/10.1063/1.467468
- Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. https://doi.org/https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14 < 1639::AID-JCC10 > 3.0.CO;2-B
- 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(1), 33. https://doi.org/https://doi.org/10.1186/1758-2946-3-33
- Pumroy, R. A., & Cingolani, G. (2015). Diversification of importin-α isoforms in cellular trafficking and disease states. The Biochemical Journal, 466(1), 13–28. https://doi.org/https://doi.org/10.1042/BJ20141186
- Romano, M., Ruggiero, A., Squeglia, F., Maga, G., & Berisio, R. (2020). A structural view of SARS-CoV-2 RNA replication machinery: RNA synthesis, proofreading and final capping. Cells, 9(5), 1267. https://doi.org/https://doi.org/10.3390/cells9051267
- Schenone, M., Dančík, V., Wagner, B. K., & Clemons, P. A. (2013). Target identification and mechanism of action in chemical biology and drug discovery. Nature Chemical Biology, 9(4), 232–240. https://doi.org/https://doi.org/10.1038/nchembio.1199
- Sgobba, M., Caporuscio, F., Anighoro, A., Portioli, C., & Rastelli, G. (2012). Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations. European Journal of Medicinal Chemistry, 58, 431–440. https://doi.org/https://doi.org/10.1016/j.ejmech.2012.10.024
- Shushni, M. A. M., Azam, F., & Lindequist, U. (2013). Oxasetin from Lophiostoma sp. of the Baltic Sea: Identification, in silico binding mode prediction and antibacterial evaluation against fish pathogenic bacteria. Natural Product Communications, 8(9), 1934578X1300800.
- Sk, M. F., Roy, R., Jonniya, N. A., Poddar, S., & Kar, P. (2020). Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1768149
- Snijder, E. J., Decroly, E., & Ziebuhr, J. (2016). Chapter Three - The nonstructural proteins directing Coronavirus RNA synthesis and processing. In V. R. Ziebuhr (Ed.), Coronaviruses (Vol. 96, pp. 59–126). Academic Press. https://doi.org/https://doi.org/10.1016/bs.aivir.2016.08.008
- Tay, M. Y. F., Fraser, J. E., Chan, W. K. K., Moreland, N. J., Rathore, A. P., Wang, C., Vasudevan, S. G., & Jans, D. A. (2013). Nuclear localization of dengue virus (DENV) 1-4 non-structural protein 5; protection against all 4 DENV serotypes by the inhibitor Ivermectin. Antiviral Research, 99(3), 301–306. https://doi.org/https://doi.org/10.1016/j.antiviral.2013.06.002
- Tay, M. Y. F., Smith, K., Ng, I. H. W., Chan, K. W. K., Zhao, Y., Ooi, E. E., Lescar, J., Luo, D., Jans, D. A., Forwood, J. K., & Vasudevan, S. G. (2016). The C-terminal 18 amino acid region of dengue virus NS5 regulates its subcellular localization and contains a conserved arginine residue essential for infectious virus production. PLoS Pathogens, 12(9), e1005886. https://doi.org/https://doi.org/10.1371/journal.ppat.1005886
- 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
- Vihinen, M. (1987). Relationship of protein flexibility to thermostability. Protein Engineering, 1(6), 477–480. https://doi.org/https://doi.org/10.1093/protein/1.6.477
- Vijayakumar, B., Parasuraman, S., Raveendran, R., & Velmurugan, D. (2014). Identification of natural inhibitors against angiotensin I converting enzyme for cardiac safety using induced fit docking and MM-GBSA studies. Pharmacognosy Magazine, 10(Suppl 3), S639–S644. https://doi.org/https://doi.org/10.4103/0973-1296.139809
- Wagstaff, K. M., Sivakumaran, H., Heaton, S. M., Harrich, D., & Jans, D. A. (2012). Ivermectin is a specific inhibitor of importin α/β-mediated nuclear import able to inhibit replication of HIV-1 and dengue virus. The Biochemical Journal, 443(3), 851–856. https://doi.org/https://doi.org/10.1042/BJ20120150
- WHO. (2020). Coronavirus disease 2019 (COVID-19) Situation report. World Health Organization. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200914-weekly-epi-update-5.pdf?sfvrsn=cf929d04_2
- Yamasmith, E. (2018). Efficacy and safety of ivermectin against dengue infection: A phase III, randomized, double-blind, placebo-controlled trial. In He 34th Annual Meeting the Royal College of Physicians of Thailand. Internal Medicine and One Health.
- Yang, C.-W., Peng, T.-T., Hsu, H.-Y., Lee, Y.-Z., Wu, S.-H., Lin, W.-H., Ke, Y.-Y., Hsu, T.-A., Yeh, T.-K., Huang, W.-Z., Lin, J.-H., Sytwu, H.-K., Chen, C.-T., & Lee, S.-J. (2020). Repurposing old drugs as antiviral agents for coronaviruses. Biomedical Journal, 43(4), 368–374. https://doi.org/https://doi.org/10.1016/j.bj.2020.05.003
- Yang, S. N. Y., Atkinson, S. C., Fraser, J. E., Wang, C., Maher, B., Roman, N., Forwood, J. K., Wagstaff, K. M., Borg, N. A., & Jans, D. A. (2019). Novel flavivirus antiviral that targets the host nuclear transport importin α/β1 heterodimer. Cells, 8(3), 281. https://doi.org/https://doi.org/10.3390/cells8030281
- Yang, S. N. Y., Atkinson, S. C., Wang, C., Lee, A., Bogoyevitch, M. A., Borg, N. A., & Jans, D. A. (2020). The broad spectrum antiviral ivermectin targets the host nuclear transport importin α/β1 heterodimer. Antiviral Research, 177, 104760. https://doi.org/https://doi.org/10.1016/j.antiviral.2020.104760
- Zeng, Z., Deng, F., Shi, K., Ye, G., Wang, G., Fang, L., Xiao, S., Fu, Z., & Peng, G. (2018). Dimerization of Coronavirus nsp9 with diverse modes enhances its nucleic acid binding affinity. Journal of Virology, 92(17), e00692-18. https://doi.org/https://doi.org/10.1128/JVI.00692-18