The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective
Open accessAbstract
New treatment against SARS-CoV-2 now is a must. Nowadays, the world encounters a huge health crisis by the COVID-19 viral infection. Nucleotide inhibitors gave a lot of promising results in terms of its efficacy against different viral infections. In this work, molecular modeling, docking, and dynamics simulations are used to build a model for the viral protein RNA-dependent RNA polymerase (RdRp) and test its binding affinity to some clinically approved drugs and drug candidates. Molecular dynamics is used to equilibrate the system upon binding calculations to ensure the successful reproduction of previous results, to include the dynamics of the RdRp, and to understand how it affects the binding. The results show the effectiveness of Sofosbuvir, Ribavirin, Galidesivir, Remdesivir, Favipiravir, Cefuroxime, Tenofovir, and Hydroxychloroquine, in binding to SARS-CoV-2 RdRp. Additionally, Setrobuvir, YAK, and IDX-184, show better results, while four novel IDX-184 derivatives show promising results in attaching to the SARS-CoV-2 RdRp. There is an urgent need to specify drugs that can selectively bind and subsequently inhibit SARS-CoV-2 proteins. The availability of a punch of FDA-approved anti-viral drugs can help us in this mission, aiming to reduce the danger of COVID-19. The compounds 2 and 3 may tightly bind to the SARS-CoV-2 RdRp and so may be successful in the treatment of COVID-19.
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UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828
Trott, O., & Olson, A. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21334 · Cited by 38,412
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak
Rothan, H. A., & Byrareddy, S. N. (2020) · Journal of Autoimmunity · doi:10.1016/j.jaut.2020.102433 · Cited by 5,840
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
Laskowski, R., Rullmann, J. A., MacArthur, M., Kaptein, R., & Thornton, J. (1996) · Journal of Biomolecular NMR · doi:10.1007/bf00228148 · Cited by 5,502
PubChem Substance and Compound databases
Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku340 · Cited by 4,632
Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
Mark, P., & Nilsson, L. (2001) · The Journal of Physical Chemistry A · doi:10.1021/jp003020w · Cited by 4,571
Hui, D. S., I Azhar, E., Madani, T. A., Ntoumi, F., Kock, R., Dar, O., Ippolito, G., Mchugh, T. D., Memish, Z. A., Drosten, C., et al. (2020) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2020.01.009 · Cited by 3,809
Stewart, J. J. P. (2007) · Journal of Molecular Modeling · doi:10.1007/s00894-007-0233-4 · Cited by 3,619
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Yan, W., Zheng, Y., Zeng, X., He, B., & Cheng, W. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00884-5 · Cited by 291
Pandey, P., Rane, J. S., Chatterjee, A., Kumar, A., Khan, R., Prakash, A., & Ray, S. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1796811 · Cited by 258
Bignon, E., Marazzi, M., Grandemange, S., & Monari, A. (2022) · Chemical Science · doi:10.1039/d2sc00108j · Cited by 13
Koulgi, S., Jani, V., V N, M. U., Sonavane, U., & Joshi, R. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1894985 · Cited by 12
Influence of contact map topology on RNA structure prediction
Faber, C., Upadhyay, U., Taubert, O., & Schug, A. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1370 · Cited by 1
Metadata
- Authors
- Elfiky, A. A.
- Venue
- Journal of Biomolecular Structure and Dynamics
- Publisher
- Informa UK Limited
- Published
- 2020-05-06
- Volume
- 39
- Issue
- 9
- Pages
- 3204-3212
- ISSN
- 0739-1102 (ISSN-L)
- 1538-0254
- OpenAlex
- W3020358199
- Cited by
- 284
- References
- 51
- FWCI
- 31.68
- Type
- journal article
- Language
- en
- Open access
- green
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