Repurposing antibiotics as potent multi-drug candidates for SARS-CoV-2 delta and omicron variants: molecular docking and dynamics

References

• 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
   Google Scholar
• Baildya, N., Khan, A. A., Ghosh, N. N., Dutta, T., & Chattopadhyay, A. P. (2021). Screening of potential drug from Azadirachta Indica (Neem) extracts for SARS-CoV-2: An insight from molecular docking and MD-simulation studies. Journal of Molecular Structure, 1227, 129390. https://doi.org/10.1016/j.molstruc.2020.129390
   PubMed Web of Science ®Google Scholar
• Benarous, K., Bombarda, I., Iriepa, I., Moraleda, I., Gaetan, H., Linani, A., Tahri, D., Sebaa, M., & Yousfi, M. (2015). Harmaline and hispidin from Peganum harmala and Inonotus hispidus with binding affinity to Candida rugosa lipase: In silico and in vitro studies. Bioorganic Chemistry, 62, 1–7. https://doi.org/10.1016/j.bioorg.2015.06.005
   PubMed Web of Science ®Google Scholar
• BIOVIA Discovery Studio. (2016). Discovery Studio Modeling Environment, Release 2017. BIOVIA.
   Google Scholar
• Cavalheiro, J. P. d V. H. (2015). Optimization of a MM-PBSA/GBSA protocol for the prediction of binding free energy of Bcl-xL inhibitors.
   Google Scholar
• El Bakri, Y., Musrat Kurbanova, M., Ali Siddique, S., Ahmad, S., & Goumri-Said, S. (2022). One-pot synthesis, X-ray crystal structure, and identification of potential molecules against COVID-19 main protease through structure-guided modeling and simulation approach. Arabian Journal of Chemistry, 15(11), 104230. https://doi.org/10.1016/j.arabjc.2022.104230
   PubMed Web of Science ®Google Scholar
• Falsafi-Zadeh, S., Karimi, Z., & Galehdari, H. (2012). VMD DisRg: New user-friendly Implement for calculation distance and radius of gyration in VMD program. Bioinformation, 8(7), 341–343. https://doi.org/10.6026/97320630008341
   PubMedGoogle Scholar
• FDA. (2020). FDA Approves First Treatment for COVID-19, https://www.fda.gov/news-events/press-announcements/fda-approves-first-treatment-covid-19
   Google Scholar
• Gallagher, T. M., & Buchmeier, M. J. (2001). Coronavirus spike proteins in viral entry and pathogenesis. Virology, 279(2), 371–374. https://doi.org/10.1006/viro.2000.0757
   PubMed Web of Science ®Google Scholar
• GISAID Database. (2022). Global initiative on sharing all influenza data: https://www.gisaid.org/hcov19-variants/
   Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Kong, W. H., Li, Y., Peng, M. W., Kong, D. G., Yang, X. B., Wang, L., & Liu, M. Q. (2020). SARS-CoV-2 detection in patients with influenza-like illness. Nature Microbiology, 5(5), 675–678.
   PubMed Web of Science ®Google Scholar
• Lau, S. K. P., & Chan, J. F. W. (2015). Coronaviruses: Emerging and re-emerging pathogens in humans and animals. Virology Journal, 12, 209. https://doi.org/10.1186/s12985-015-0432-z
   PubMed Web of Science ®Google Scholar
• Lemkul, J. (2019). From proteins to perturbed Hamiltonians: A suite of tutorials for the GROMACS-2018 molecular simulation package [Article v1.0]. Living Journal of Computational Molecular Science,1(1), 1–53. https://doi.org/10.33011/livecoms.1.1.5068
   Google Scholar
• Linani, A., Benarous, K., Bou-Salah, L., Yousfi, M., & Goumri-Said, S. (2022). Exploring structural mechanism of COVID-19 treatment with glutathione as a potential peptide inhibitor to the main protease: molecular dynamics simulation and MM/PBSA free energy calculations study. International Journal of Peptide Research and Therapeutics, 28(2), 55. https://doi.org/10.1007/s10989-022-10365-6
   PubMed Web of Science ®Google Scholar
• Lindahl, E., Abraham, M. J., Hess, B., & Spoel, V. D. (2022). GROMACS 2021.5 Manual. https://doi.org/10.5281/ZENODO.5849961
   Google Scholar
• Lindahl, E., Hess, B., & Van Der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7(8), 306–317. https://doi.org/10.1007/s008940100045
   Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Autodock4 and AutoDock Tools4: Automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Nandekar, P. P., Tumbi, K. M., Bansal, N., Rathod, V. P., Labhsetwar, L. B., Soumya, N., Singh, S., & Sangamwar, A. T. (2013). Chem-bioinformatics and in vitro approaches for candidate optimization: A case study of NSC745689 as a promising antitumor agent. Medicinal Chemistry Research, 22(8), 3728–3742. https://doi.org/10.1007/s00044-012-0364-8
   Web of Science ®Google Scholar
• Naresh, G. K., & Guruprasad, L. (2022). Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor. Journal of Biomolecular Structure and Dynamics, 41 (1),1–14. https://doi.org/10.1080/07391102.2022.2032354
   Google Scholar
• Nur, E., Gaartman, A. E., Tuijn, C. F. J., Tang, M. W., & Biemond, B. J. (2020). Vaso‐occlusive crisis and acute chest syndrome in sickle cell disease due to 2019 Novel Coronavirus Disease (COVID‐19). American Journal of Hematology, 95(6), 725–726. https://doi.org/10.1002/ajh.25821
   PubMed Web of Science ®Google Scholar
• Ou, J., Lan, W., Wu, X., Zhao, T., Duan, B., Yang, P., Ren, Y., Quan, L., Zhao, W., Seto, D., Chodosh, J., Luo, Z., Wu, J., & Zhang, Q. (2022). Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events. Signal Transduction and Targeted Therapy, 7(1), 1–9. https://doi.org/10.1038/s41392-022-00992-2
   PubMed Web of Science ®Google Scholar
• Sargsyan, K., Grauffel, C., & Lim, C. (2017). How molecular size impacts RMSD applications in molecular dynamics simulations. Journal of Chemical Theory and Computation, 13(4), 1518–1524. https://doi.org/10.1021/acs.jctc.7b00028
   PubMed Web of Science ®Google Scholar
• Serseg, T., & Benarous, K. (2018). The inhibitory effect of some drugs on Candida rugosa lipase and human pancreatic li-pase: In vitro and in silico studies. Endocrine, Metabolic & Immune Disorders Drug Targets, 18(6), 602–609. https://doi.org/10.2174/1871530318666180319093342
   PubMed Web of Science ®Google Scholar
• Serseg, T., Benarous, K., Serseg, M., Rehman, H. M., Bakri, Y. E., & Goumri-Said, S. (2022). Discovery of inhibitors against SARS- CoV-2 associated fungal coinfections via virtual screening, ADMET evaluation, PASS, molecular docking, dynamics and pharmacophore studies. Arab Journal of Basic and Applied Sciences, 29(1), 337–350. https://doi.org/10.1080/25765299.2022.2126588
   Google Scholar
• Serseg, T., Benarous, K., & Yousfi, M. (2021). Hispidin and Lepidine E: Two natural compounds and folic acid as potential inhibitors of 2019-novel coronavirus main protease (2019-nCoVMpro), molecular docking and SAR study. Current Computer-Aided Drug Design, 17(3), 469–479. https://doi.org/10.2174/1573409916666200422075440
   PubMed Web of Science ®Google Scholar
• Sun, H., Li, Y., Tian, S., Xu, L., & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Physical Chemistry Chemical Physics : PCCP, 16(31), 16719–16729.https://doi.org/10.1039/C4CP01388C
   PubMed Web of Science ®Google Scholar
• Surti, M., Patel, M., Adnan, M., Moin, A., Ashraf, S. A., Siddiqui, A. J., Snoussi, M., Deshpande, S., & Reddy, M. N. (2020). Ilimaquinone (marine sponge metabolite) as a novel inhibitor of SARS-CoV-2 key target proteins in comparison with suggested COVID-19 drugs: Designing, docking and molecular dynamics simulation study. RSC Advances, 10(62), 37707–37720. https://doi.org/10.1039/d0ra06379g
   PubMed Web of Science ®Google Scholar
• Turner, P. J. (2005). XMGRACE, Version 5.1. 19. Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology
   Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., Mackerell, A. D. Jr. (2009). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem., 31(4), 671-90. https://doi.org/10.1002/jcc.21367. PMID: 19575467; PMCID: PMC2888302.
   Google Scholar
• Wang, Z., Kang, Y., Li, D., Sun, H., Dong, X., Yao, X., Xu, L., Chang, S., Li, Y., & Hou, T. (2018). Benchmark study based on 2P2IDB to gain insights into the discovery of small-molecule PPI inhibitors. The Journal of Physical Chemistry. B, 122(9), 2544–2555.https://doi.org/10.1021/acs.jpcb.7b12658
   PubMed Web of Science ®Google Scholar
• Wang, Z., Pan, H., Sun, H., Kang, Y., Liu, H., Cao, D., & Hou, T. (2022). fastDRH: a webserver to predict and analyze protein–ligand complexes based on molecular docking and MM/PB (GB) SA computation. Briefings in Bioinformatics, 23(5), bbac201. https://doi.org/10.1093/bib/bbac201
   Google Scholar
• WHO. (2021). World Health Organization; Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern; https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
   Google Scholar
• Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, N.Y.), 367(6485), 1444–1448. https://doi.org/10.1126/science.abb2762
   PubMed Web of Science ®Google Scholar
• Yin, W., Mao, C., Luan, X., Shen, D.-D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.-C., Tian, G., Jiang, H.-W., Tao, S.-C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., … Xu, H. E. (2020). Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science, 368(6498), 1499–1504. https://doi.org/10.1126/science.abc1560
   PubMed Web of Science ®Google Scholar
• Yu, Z., Kan, R., Ji, H., Wu, S., Zhao, W., Shuian, D., Liu, J., & Li, J. (2021). Identification of tuna protein-derived peptides as potent SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation. Food Chemistry, 342, 128366. https://doi.org/10.1016/j.foodchem.2020.128366
   PubMed Web of Science ®Google Scholar