1,344
Views
10
CrossRef citations to date
0
Altmetric
Research Articles

Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon & ORCID Icon show all
Pages 9347-9360 | Received 26 Jan 2021, Accepted 05 May 2021, Published online: 21 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 3CLpro. Journal of Biomolecular Structure and Dynamics, 0(0), 1–13. https://doi.org/10.1080/07391102.2020.1782768
  • Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, N.Y.), 300(5626), 1763–1767. https://doi.org/10.1126/science.1085658
  • Ashburn, T. T., & Thor, K. B. (2004). Drug repositioning: Identifying and developing new uses for existing drugs. Nature Reviews. Drug Discovery, 3(8), 673–683. https://doi.org/10.1038/nrd1468
  • Bhardwaj, V. K., Singh, R., Das, P., & Purohit, R. (2021). Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Computers in Biology and Medicine, 128, 104117. https://doi.org/10.1016/j.compbiomed.2020.104117
  • Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2020). Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure and Dynamics, 0(0), 1–10. https://doi.org/10.1080/07391102.2020.1766572
  • Case, D. A., Betz, R. M., Cerutti, D. S., Cheatham T. E., Darden, T. A., Duke, R. E., Giese, T. J., Gohlke, H., Goetz, A. W., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T. S., LeGrand, S., Li, P., C., Lin, Luchko, T., … Kollman, P. A. (2016). Amber 2016. University of California.
  • Chen, H., Wei, P., Huang, C., Tan, L., Liu, Y., & Lai, L. (2006). Only one protomer is active in the dimer of SARS 3C-like proteinase. The Journal of Biological Chemistry, 281(20), 13894–13898. https://doi.org/10.1074/jbc.M510745200
  • Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/10.1002/jmv.25681
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Dotolo, S., Marabotti, A., Facchiano, A., & Tagliaferri, R. (2021). A review on drug repurposing applicable to COVID-19. Briefings in Bioinformatics, 22(2), 716–726. https://doi.org/10.1093/bib/bbaa288
  • Elmezayen, A. D., Al-Obaidi, A., Şahin, A. T., & Yelekçi, K. (2021). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure & Dynamics, 39(8), 2913–2980. https://doi.org/10.1080/07391102.2020.1758791
  • Ferenczy, G. G. (2015). Computation of drug-binding thermodynamics. In G. M. Keserü & D. C. Swinney (Eds.), Thermodynamics and kinetics of drug binding (pp. 37–61). Wiley-VCH Verlag GmbH & Co. https://doi.org/10.1002/9783527673025.ch3
  • 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
  • Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. Journal of Molecular Biology, 330(4), 891–913. https://doi.org/10.1016/S0022-2836(03)00610-7 https://doi.org/10.1016/S0022-2836(03)00610-7
  • Gollapalli, P., Sharath, B. S., Rimac, H., Patil, P., Nalilu, S. K., Kandagalla, S., & Shetty, P. (2020). Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2020.1841681
  • Gyebi, G. A., Ogunro, O. B., Adegunloye, A. P., Ogunyemi, O. M., & Afolabi, S. O. (2020). Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): An in silico screening of alkaloids and terpenoids from African medicinal plants. Journal of Biomolecular Structure and Dynamics, 0(0), 1–13. https://doi.org/10.1080/07391102.2020.1764868
  • Handoko, S. D., Ouyang, X., Su, C. T. T., Kwoh, C. K., & Ong, Y. S. (2012). QuickVina: Accelerating AutoDock Vina using gradient-based heuristics for global optimization. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5), 1266–1272. https://doi.org/10.1109/TCBB.2012.82
  • Harrison, C. (2020). Coronavirus puts drug repurposing on the fast track. Nature Biotechnology, 38(4), 379–381. https://doi.org/10.1038/d41587-020-00003-1
  • 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
  • Koulgi, S., Jani, V., Uppuladinne, M., Sonavane, U., Nath, A. K., Darbari, H., & Joshi, R. (2020). Drug repurposing studies targeting SARS-CoV-2: An ensemble docking approach on drug target 3C-like protease (3CLpro). Journal of Biomolecular Structure and Dynamics, 0(0), 1–21. https://doi.org/10.1080/07391102.2020.1792344
  • Li, C., Teng, X., Qi, Y., Tang, B., Shi, H., Ma, X., & Lai, L. (2016). Conformational flexibility of a short loop near the active site of the SARS-3CLpro is essential to maintain catalytic activity. Scientific Reports, 6(January), 20918. https://doi.org/10.1038/srep20918
  • Lim, L., Shi, J., Mu, Y., & Song, J. (2014). Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain. PLoS One, 9(7), e101941. https://doi.org/10.1371/journal.pone.0101941
  • Machado, M. R., & Pantano, S. (2020). Split the charge difference in two! A rule of thumb for adding proper amounts of ions in MD simulations. Journal of Chemical Theory and Computation, 16(3), 1367–1372. https://doi.org/10.1021/acs.jctc.9b00953
  • 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
  • Novak, J., Rimac, H., Kandagalla, S., Grishina, M. A., & Potemkin, V. A. (2021). Can natural products stop the SARS-CoV-2 virus? A docking and molecular dynamics study of a natural product database. Future Medicinal Chemistry, 13(4), 363–378. https://doi.org/10.4155/fmc-2020-0248
  • Nukoolkarn, V., Lee, V. S., Malaisree, M., Aruksakulwong, O., & Hannongbua, S. (2008). Molecular dynamic simulations analysis of ritronavir and lopinavir as SARS-CoV 3CLpro inhibitors. Journal of Theoretical Biology, 254(4), 861–867. https://doi.org/10.1016/j.jtbi.2008.07.030
  • 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/10.1186/1758-2946-3-33
  • Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., & Pirmohamed, M. (2019). Drug repurposing: Progress, challenges and recommendations. Nature Reviews. Drug Discovery, 18(1), 41–58. https://doi.org/10.1038/nrd.2018.168
  • Rastelli, G., Rio, A. D., Degliesposti, G., & Sgobba, M. (2010). Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. Journal of Computational Chemistry, 31(4), 797–810. https://doi.org/10.1002/jcc.21372
  • 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. C. (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
  • Sang, P., Tian, S. H., Meng, Z. H., & Yang, L. Q. (2020). Anti-HIV drug repurposing against SARS-CoV-2. RSC Advances, 10(27), 15775–15783. https://doi.org/10.1039/D0RA01899F
  • Shi, J., & Song, J. (2006). The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain. The FEBS Journal, 273(5), 1035–1045. https://doi.org/10.1111/j.1742-4658.2006.05130.x
  • Vanhaelen, Q. (2019). Computational methods for drug repurposing (Vol. 1903). Springer New York. https://doi.org/10.1007/978-1-4939-8955-3
  • Volkamer, A., Kuhn, D., Grombacher, T., Rippmann, F., & Rarey, M. (2012). Combining global and local measures for structure-based druggability predictions. Journal of Chemical Information and Modeling, 52(2), 360–372. https://doi.org/10.1021/ci200454v
  • Wei, P., Fan, K., Chen, H., Ma, L., Huang, C., Tan, L., Xi, D., Li, C., Liu, Y., Cao, A., & Lai, L. (2006). The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase. Biochemical and Biophysical Research Communications, 339(3), 865–872. https://doi.org/10.1016/j.bbrc.2005.11.102
  • Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/10.1038/s41586-020-2008-3
  • Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W., & Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China. Life Sciences, 63(3), 457–460. https://doi.org/10.1007/s11427-020-1637-5
  • Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R., & Rao, Z. (2003). The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proceedings of the National Academy of Sciences of the United States of America, 100(23), 13190–13195. https://doi.org/10.1073/pnas.1835675100
  • 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 (New York, N.Y.), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
  • Zhong, N., Zhang, S., Zou, P., Chen, J., Kang, X., Li, Z., Liang, C., Jin, C., & Xia, B. (2008). Without its N-finger, the main protease of severe acute respiratory syndrome coronavirus can form a novel dimer through its C-terminal domain. Journal of Virology, 82(9), 4227–4234. https://doi.org/10.1128/JVI.02612-07
  • Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7
  • 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. New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/NEJMoa2001017

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.