References
- Abdullah, J. A., Aldahham, B. J. M., Rabeea, M. A., Asmary, F. A., Alhajri, H. M., & Islam, M. A. (2021). Synthesis, characterization and in-silico assessment of novel thiazolidinone derivatives for cyclin-dependent kinases-2 inhibitors. Journal of Molecular Structure, 1223, 129311. https://doi.org/https://doi.org/10.1016/j.molstruc.2020.129311
- Al-Khafaji, K., & Taskin Tok, T. (2020a). Amygdalin as multi-target anticancer drug against targets of cell division cycle: Double docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1742792
- Al-Khafaji, K., & Taskin Tok, T. (2020b). Understanding the mechanism of amygdalin’s multifunctional anti-cancer action using computational approach. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1736159
- Amer, A. M., El-Eraky, W. I., & Mahgoub, S. (2018). Synthesis, characterization and antimicrobial activity of some novel quinoline derivatives bearing pyrazole and pyridine moieties. Egyptian Journal of Chemistry, 61, 1–8. https://doi.org/https://doi.org/10.21608/ejchem.2018.3941.1345
- Andersen, H. C. (1983). Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52(1), 24–34. https://doi.org/https://doi.org/10.1016/0021-9991(83)90014-1
- Anderson, S. L. (2014). Dapagliflozin efficacy and safety: A perspective review. Therapeutic Advances in Drug Safety, 5(6), 242–254. https://doi.org/https://doi.org/10.1177/2042098614551938
- Becke, A. D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A, General Physics, 38(6), 3098–3100. https://doi.org/https://doi.org/10.1103/physreva.38.3098
- 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/https://doi.org/10.1093/nar/28.1.235
- Case, D. A., Belfon, K., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Giambasu, G., Gilson, M. K., Gohlke, H., Goetz, A. W., Harris, R., Izadi, S., Izmailov, S. A., Kasavajhala, K., Kovalenko, A., Krasny, R., . . . Kollman, P. A. (2020). AMBER 2020. University of California.
- Cavasotto, C. N., & Di Filippo, J. I. (2020). In silico drug repurposing for COVID-19: Targeting SARS-CoV-2 proteins through docking and consensus ranking. Molecular Informatics, 39, 2000115. https://doi.org/https://doi.org/10.1002/minf.202000115
- Chikhale, R. V., Gupta, V. K., Eldesoky, G. E., Wabaidur, S. M., Patil, S. A., & Islam, M. A. (2020). Identification of potential anti-TMPRSS2 natural products through homology modelling, virtual screening and molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1798813
- Cocco, M. T., Congiu, C., & Onnis, V. (2000). Synthesis and antitumour activity of 4-hydroxy-2-pyridone derivatives. European Journal of Medicinal Chemistry, 35(5), 545–552. https://doi.org/https://doi.org/10.1016/S0223-5234(00)00149-5
- Culletta, G., Gulotta, M. R., Perricone, U., Zappalà, M., Almerico, A. M., & Tutone, M. (2020). Exploring the SARS-CoV-2 proteome in the search of potential inhibitors via structure-based pharmacophore modeling/docking approach. Computation, 8(3), 77. https://doi.org/https://doi.org/10.3390/computation8030077
- 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/https://doi.org/10.1038/srep42717
- Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ort, J. V., . . . Fox, D. J. (2016). Gaussian 09, Revision A.02. Gaussian, Inc.
- 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
- Jiang, C., You, Q., Li, Z., & Guo, Q. (2006). Kinesin spindle protein inhibitors as anticancer agents. In. Expert Opinion on Therapeutic Patents, 16(11), 1517–1532. https://doi.org/https://doi.org/10.1517/13543776.16.11.1517
- Kadioglu, O., Saeed, M., Greten, H. J., & Efferth, T. (2020). Identification of novel compounds against three targets of SARS CoV2 coronavirus by combined virtual screening and supervised machine learning. Bull World Health Organ.
- Kandwal, S., & Fayne, D. (2020). Repurposing drugs for treatment of SARS-CoV-2 infection: Computational design insights into mechanisms of action. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1825232
- Leonard, J. T., Gangadhar, R., Gnanasam, S. K., Ramachandran, S., Saravanan, M., & Sridhar, S. K. (2002). Synthesis and pharmacological activities of 1,8-naphthyridine derivatives. Biological and Pharmaceutical Bulletin, 25(6), 798–802. https://doi.org/https://doi.org/10.1248/bpb.25.798
- Lipsitch, M., Swerdlow, D. L., & Finelli, L. (2020). Defining the epidemiology of Covid-19 — studies needed. The New England Journal of Medicine, 382(13), 1194–1196. https://doi.org/https://doi.org/10.1056/NEJMp2002125
- 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/https://doi.org/10.1021/acs.jctc.5b00255
- Marchese, A., Debbia, E. A., & Schito, G. C. (2000). Comparative in vitro potency of gemifloxacin against European respiratory tract pathogens isolated in the Alexander Project. Journal of Antimicrobial Chemotherapy, 46(suppl 3), 11–15. https://doi.org/https://doi.org/10.1093/oxfordjournals.jac.a020888
- Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. Journal of Physical Chemistry A,105, 9954-9960. https://doi.org/https://doi.org/10.1021/jp003020w
- Mekheimer, R. A., Hameed, A. M. A., & Sadek, K. U. (2007). 8-Naphthyridines II: Synthesis of novel polyfunctionally substituted 1,8-naphthyridinones and their degradation to 6-aminopyridones. Arkivoc, 2007(13), 269–281. https://doi.org/https://doi.org/10.3998/ark.5550190.0008.d30
- Morris, G. M., Goodsell, D. S., Pique, M. E., Lindstrom, W., Lindy Huey, R., Forli, S., Hart, W., Halliday, E., Belew, S., & Olson, R. A. J. (2009). Autodock4 and AutoDockTools4: Automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/https://doi.org/10.1002/jcc.21256
- Mukherjee, S., Kumar, V., Prasad, A. K., Raj, H. G., Bracke, M. E., Olsen, C. E., Jain, S. C., & Parmar, V. S. (2001). Synthetic and biological activity evaluation studies on novel 1,3-diarylpropenones. Bioorganic and Medicinal Chemistry, 9, 337-345.
- Narender, T., Shweta, Tanvir, K., Srinivasa Rao, M., Srivastava, K., & Puri, S. K. (2005). Prenylated chalcones isolated from Crotalaria genus inhibits in vitro growth of the human malaria parasite Plasmodium falciparum. Bioorganic and Medicinal Chemistry Letters, 15, 2453-2455. https://doi.org/https://doi.org/10.1016/j.bmcl.2005.03.081
- Ojha, P. K., Kar, S., Krishna, J. G., Roy, K., & Leszczynski, J. (2020). Therapeutics for COVID-19: From computation to practices—Where we are, where we are heading to. Molecular Diversity. https://doi.org/https://doi.org/10.1007/s11030-020-10134-x
- Peramo, A. (2016). Solvated and generalised Born calculations differences using GPU CUDA and multi-CPU simulations of an antifreeze protein with AMBER. Molecular Simulation, 42(15), 1263–1273. https://doi.org/https://doi.org/10.1080/08927022.2016.1183000
- Petersen, H. G. (1995). Accuracy and efficiency of the particle mesh Ewald method. The Journal of Chemical Physics, 103(9), 3668–3679. https://doi.org/https://doi.org/10.1063/1.470043
- Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J., & Sanner, M. F. (2015). AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility. PLoS Computational Biology, 11(12), e1004586. https://doi.org/https://doi.org/10.1371/journal.pcbi.1004586
- Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
- Rosas-Lemus, M., Minasov, G., Shuvalova, L., Inniss, N., Kiryukhina, O., Wiersum, G., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Jaroszewski, L., Godzik, A., Joachimiak, A., & Satchell, K. (2020). The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine. BioRxiv : The Preprint Server for Biology. https://doi.org/https://doi.org/10.1101/2020.04.17.047498
- Saleh, M., Ayoub, A., & Hammady, A. (2020). Synthesis biological studies of some new heterocyclic compound derived from 2-chloro-3-formyl quinoline and 4-(benzyl sulfonyl) acetophenone. Egyptian Journal of Chemistry. https://doi.org/https://doi.org/10.21608/ejchem.2020.26354.2535
- 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/https://doi.org/10.1093/nar/gkv315
- Singh, I. P., Kumar, S., & Gupta, S. (2017). Naphthyridines with antiviral activity - a review. Medicinal Chemistry, 13(5), 430-438. https://doi.org/https://doi.org/10.2174/1573406412666161228112127
- Taha, M. O., Habash, M., Al-Hadidi, Z., Al-Bakri, A., Younis, K., & Sisan, S. (2011). Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies. Journal of Chemical Information and Modeling, 51(3), 647–669. https://doi.org/https://doi.org/10.1021/ci100368t
- Tazikeh-Lemeski, E., Moradi, S., Raoufi, R., Shahlaei, M., Janlou, M. A. M., & Zolghadri, S. (2020). Targeting SARS-COV-2 non-structural protein 16: A virtual drug repurposing study. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1779133
- Träg, J., & Zahn, D. (2019). Improved GAFF2 parameters for fluorinated alkanes and mixed hydro- and fluorocarbons. Journal of Molecular Modeling, 25(2), 39. https://doi.org/https://doi.org/10.1007/s00894-018-3911-5
- Weiss, S. R., & Leibowitz, J. L. (2011). Coronavirus pathogenesis. In Advances in virus research. Elsvier. https://doi.org/https://doi.org/10.1016/B978-0-12-385885-6.00009-2
- 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. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017