1,202
Views
3
CrossRef citations to date
0
Altmetric
Research Articles

Antivirals virtual screening to SARS-CoV-2 non-structural proteins

, , &
Pages 8989-9003 | Received 13 Aug 2020, Accepted 19 Apr 2021, Published online: 05 May 2021

References

  • Alamri, M. A., Tahir Ul Qamar, M., Mirza, M. U., Bhadane, R., Alqahtani, S. M., Muneer, I., Froeyen, M., Salo-Ahen, O. M. H. (2020). Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL pro. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1782768  
  • Angeletti, S., Benvenuto, D., Bianchi, M., Giovanetti, M., Pascarella, S., & Ciccozzi, M. (2020). COVID‐2019: The role of the nsp2 and nsp3 in its pathogenesis. Journal of Medical Virology, 92(6), 584–588. https://doi.org/10.1002/jmv.25719
  • Badri, P. S., Dutta, S., Wang, H., Podsadecki, T. J., Polepally, A. R., Khatri, A., Zha, J., Chiu, Y.-L., Awni, W. M., & Menon, R. M. (2016). Drug interactions with the direct-acting antiviral combination of ombitasvir and paritaprevir-ritonavir. Antimicrobial Agents and Chemotherapy, 60(1), 105–114. https://doi.org/10.1128/AAC.01778-15
  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., 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
  • Case, D. A., Betz, R. M., Cerutti, D. S., & Kollman, P. A. (2016). AMBER 2016. University of California.
  • Cobey, S. (2020). Modeling infectious disease dynamics. Science, 368(6492), 713–714. https://doi.org/10.1126/science.abb5659
  • Colson, P., Rolain, J.-M., Lagier, J.-C., Brouqui, P., & Raoult, D. (2020). Chloroquine and hydroxychloroquine as available weapons to fight COVID-19. International Journal of Antimicrobial Agents, 55(4), 105932. https://doi.org/10.1016/j.ijantimicag.2020.105932
  • Elfiky, A. A. (2020). Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sciences, 253, 117592. https://doi.org/10.1016/j.lfs.2020.117592
  • Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M‐y., Pieper, U., & Sali, A. (2007). Comparative protein structure modeling using MODELLER. Current Protocols in Protein Science, 50(1), 2.9.1–2.9.31. https://doi.org/10.1002/0471140864.ps0209s50
  • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., & Fox, D. J. (2009). Gaussian, Inc., Wallingford CT.
  • Gao, K., Nguyen, D. D., Chen, J., Wang, R., & Wei, G.-W. (2020). Repositioning of 8565 existing drugs for COVID-19. The Journal of Physical Chemistry Letters, 11(13), 5373–5382. https://doi.org/10.1021/acs.jpclett.0c01579
  • 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/10.1517/17460441.2015.1032936
  • Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., O’Meara, M. J., Guo, J. Z., Swaney, D. L., Tummino, T. A., Huettenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., Kim, M., Haas, P., … Krogan, N. J. (2020). A SARS-CoV-2-human protein-protein interaction map reveals drug targets and potential drug-repurposing. BioRxiv, 5. https://doi.org/10.1101/2020.03.22.002386
  • Gordy, J. T., Mazumdar, K., & Dutta, N. K. (2020). Accelerating drug development through repurposed FDA-approved drugs for COVID-19: Speed is important, not haste. Antimicrobial Agents and Chemotherapy, 64(8), 1–3. https://doi.org/10.1128/AAC.00857-20
  • Hakmi. (2020). Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. Bioinformation, 16(4), 301. https://doi.org/10.6026/97320630016301
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Hung, I. F.-N., Lung, K.-C., Tso, E. Y.-K., Liu, R., Chung, T. W.-H., Chu, M.-Y., Ng, Y.-Y., Lo, J., Chan, J., Tam, A. R., Shum, H.-P., Chan, V., Wu, A. K.-L., Sin, K.-M., Leung, W.-S., Law, W.-L., Lung, D. C., Sin, S., Yeung, P., … Yuen, K.-Y. (2020). Triple combination of interferon beta-1b, lopinavir–ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: An open-label, randomised, phase 2 trial. The Lancet, 395(10238), 1695–1704. https://doi.org/10.1016/S0140-6736(20)31042-4
  • Huynh, T., Wang, H., & Luan, B. (2020). In silico exploration of the molecular mechanism of clinically oriented drugs for possibly inhibiting SARS-CoV-2’s Main Protease. The Journal of Physical Chemistry Letters, 11(11), 4413–4420. https://doi.org/10.1021/acs.jpclett.0c00994
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Khan, R. J., Jha, R. K., Amera, G. M., Jain, M., Singh, E., Pathak, A., Singh, R. P., Muthukumaran, J., Singh, A. K. (2020). Targeting SARS-CoV-2: A systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2′-O-ribose methyltransferase. Journal of Biomolecular Structure and Dynamics, 39(8), 1–14. https://doi.org/10.1080/07391102.2020.1753577
  • Kim, Y., Jedrzejczak, R., Maltseva, N. I., Wilamowski, M., Endres, M., Godzik, A., Michalska, K., & Joachimiak, A. (2020). Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV ‐2. Protein Science, 29(7), 1596–1605. https://doi.org/10.1002/pro.3873
  • Krichel, B., Falke, S., Hilgenfeld, R., Redecke, L., & Uetrecht, C. (2020). Processing of the SARS-CoV pp1a/ab nsp7–10 region. Biochemical Journal, 477(5), 1009–1019. https://doi.org/10.1042/BCJ20200029
  • Kumar, R., Hsiang, J. C., Tan, J., & Thurairajah, P. H. (2019). Ombitasvir/paritaprevir/ritonavir + dasabuvir and ribavirin associated drug-induced liver injury and syndrome of inappropriate secretion of anti-diuretic hormone: A case report. Clinical and Molecular Hepatology, 25(3), 326–330. https://doi.org/10.3350/cmh.2018.0063
  • Kumar, S., Sharma, P. P., Shankar, U., Kumar, D., Joshi, S. K., Pena, L., Durvasula, R., Kumar, A., Kempaiah, P., Poonam., & Rathi, B. (2020). Discovery of new hydroxyethylamine analogs against 3CLpro protein target of SARS-CoV-2: molecular docking, molecular dynamics simulation, and structure-activity relationship studies. Journal of Chemical Information and Modeling, 60(12), 5754–5770. https://doi.org/10.1021/acs.jcim.0c00326
  • Lawitz, E. J., O'Riordan, W. D., Asatryan, A., Freilich, B. L., Box, T. D., Overcash, J. S., Lovell, S., Ng, T. I., Liu, W., Campbell, A., Lin, C.-W., Yao, B., & Kort, J. (2016). Potent antiviral activities of the direct-acting antivirals ABT-493 and ABT-530 with three-day monotherapy for Hepatitis C virus genotype 1 infection. Antimicrobial Agents and Chemotherapy, 60(3), 1546–1555. https://doi.org/10.1128/AAC.02264-15
  • Lei, J., Kusov, Y., & Hilgenfeld, R. (2018). Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. Antiviral Research, 149, 58–74. https://doi.org/10.1016/j.antiviral.2017.11.001
  • Leung, N. H. L., Chu, D. K. W., Shiu, E. Y. C., Chan, K.-H., McDevitt, J. J., Hau, B. J. P., Yen, H.-L., Li, Y., Ip, D. K. M., Peiris, J. S. M., Seto, W.-H., Leung, G. M., Milton, D. K., & Cowling, B. J. (2020). Respiratory virus shedding in exhaled breath and efficacy of face masks. Nature Medicine, 26(5), 676–680. https://doi.org/10.1038/s41591-020-0843-2
  • 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/10.1016/j.isci.2020.101258
  • Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., & Albaiu, D. (2020). Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Science, 6(3), 315–331. https://doi.org/10.1021/acscentsci.0c00272
  • 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. The Lancet, 395(10224), 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
  • Mahdian, S., Ebrahim-Habibi, A., & Zarrabi, M. (2020). Drug repurposing using computational methods to identify therapeutic options for COVID-19. Journal of Diabetes & Metabolic Disorders, 19(2), 691–699. https://doi.org/10.1007/s40200-020-00546-9
  • 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/10.1021/acs.jctc.5b00255
  • Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py : An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
  • 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
  • Pant, S., Singh, M., Ravichandiran, V., Murty, U. S. N., & Srivastava, H. K. (2020). Peptide-like and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure and Dynamics, 39(8), 1–10. https://doi.org/10.1080/07391102.2020.1757510
  • Peele, K. A., Potla Durthi, C., Srihansa, T., Krupanidhi, S., Ayyagari, V. S., Babu, D. J., Indira, M., Reddy, A. R., & Venkateswarulu, T. C. (2020). Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study. Informatics in Medicine Unlocked, 19, 100345. https://doi.org/10.1016/j.imu.2020.100345
  • Peng, Q., Peng, R., Yuan, B., Zhao, J., Wang, M., Wang, X., Wang, Q., Sun, Y., Fan, Z., Qi, J., Gao, G. F., & Shi, Y. (2020). Structural and biochemical characterization of the nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2. Cell Reports, 31(11), 107774. https://doi.org/10.1016/j.celrep.2020.107774
  • 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/10.1021/ct400341p
  • Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
  • Shah, B., Modi, P., & Sagar, S. R. (2020). In silico studies on therapeutic agents for COVID-19: Drug repurposing approach. Life Sciences, 252, 117652. https://doi.org/10.1016/j.lfs.2020.117652
  • Shamsi, A., Mohammad, T., Anwar, S., AlAjmi, M. F., Hussain, A., Rehman, M. T., Islam, A., & Hassan, M. I. (2020). Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: Possible implication in COVID-19 therapy. Bioscience Reports, 40(6), 1–8. https://doi.org/10.1042/BSR20201256
  • Subissi, L., Posthuma, C. C., Collet, A., Zevenhoven-Dobbe, J. C., Gorbalenya, A. E., Decroly, E., Snijder, E. J., Canard, B., & Imbert, I. (2014). One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proceedings of the National Academy of Sciences, 111(37), E3900–E3909. https://doi.org/10.1073/pnas.1323705111
  • 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, 1–14. https://doi.org/10.1080/07391102.2020.1779133
  • 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/10.1002/jcc.21334
  • Uberuaga, B. P., Anghel, M., & Voter, A. F. (2004). Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation. The Journal of Chemical Physics, 120(14), 6363–6374. https://doi.org/10.1063/1.1667473
  • Verity, R., Okell, L. C., Dorigatti, I., Winskill, P., Whittaker, C., Imai, N., Cuomo-Dannenburg, G., Thompson, H., Walker, P. G. T., Fu, H., Dighe, A., Griffin, J. T., Baguelin, M., Bhatia, S., Boonyasiri, A., Cori, A., Cucunubá, Z., FitzJohn, R., Gaythorpe, K., … Ferguson, N. M. (2020). Estimates of the severity of coronavirus disease 2019: A model-based analysis. The Lancet Infectious Diseases, 20(6), 669–677. https://doi.org/10.1016/S1473-3099(20)30243-7
  • Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–212. https://doi.org/10.1016/j.cell.2020.02.058
  • Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
  • Wang, J. (2020). Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study. Journal of Chemical Information and Modeling, 60(6), 3277–3286. https://doi.org/10.1021/acs.jcim.0c00179
  • Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B, 10(5), 766–788. https://doi.org/10.1016/j.apsb.2020.02.008
  • Xu, Y., Cong, L., Chen, C., Wei, L., Zhao, Q., Xu, X., Ma, Y., Bartlam, M., & Rao, Z. (2009). Crystal Structures of Two Coronavirus ADP-Ribose-1″-monophosphatases and their complexes with ADP-Ribose: A systematic structural analysis of the viral ADRP Domain. Journal of Virology, 83(2), 1083–1092. https://doi.org/10.1128/JVI.01862-08
  • Yaras, S., Ucbilek, E., Ozdogan, O., Ates, F., Altintas, E., & Sezgin, O. (2019). Real-life results of treatment with ombitasvir, paritaprevir, dasabuvir, and ritonavir combination in patients with chronic renal failure infected with HCV in Turkey. The Turkish Journal of Gastroenterology, 30(4), 331–335. https://doi.org/10.5152/tjg.2018.18269
  • 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
  • Yoshimoto, F. K. (2020). The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19. The Protein Journal, 39(3), 198–216. https://doi.org/10.1007/s10930-020-09901-4
  • 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, 368(6489), 409–412. https://doi.org/10.1126/science.abb3405

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.