Structure-Based Design of Novel Peptidomimetics Targeting the SARS-CoV-2 Spike Protein

Springer Science and Business Media LLC - Tập 14 - Trang 177-185 - 2020
Manikandan Alagumuthu1, Sajjan Rajpoot1, Mirza S. Baig1
1Discipline of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India

Tóm tắt

SARS-CoV-2 is a SARS-like novel coronavirus strain first identified in December 2019 in Wuhan, China. The virus has since spread globally, resulting in the current ongoing coronavirus disease 19 (COVID-19) pandemic. SARS-CoV-2 spike protein is a critical factor in the COVID-19 pathogenesis via interactions with the host cell angiotensin-converting enzyme 2 (ACE2) PD domain. Worldwide, numerous efforts are being made to combat COVID19. In the current study, we identified potential peptidomimetics against the SARS-CoV-2 spike protein. We utilized the information from ACE2-SARS-CoV-2 binary interactions, and based on crucial interacting interface residues, novel peptidomimetics were designed. Top scoring peptidomimetics were found to bind at the ACE2 binding site of the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. The current studies could pave the way for further investigations of these novel and potent compounds against the SARS-CoV-2.

Tài liệu tham khảo

Amanat, F., and F. Krammer. SARS-CoV-2 vaccines: a status report. Immunity 52(4):583–589, 2020. Baig, M. S., M. Alagumuthu, S. Rajpoot, and U. Saqib. Identification of a potential peptide inhibitor of SARS-CoV-2 targeting its entry into the host cells. Drugs R D 20:161–169, 2020. Chen, Y. W., C. B. Yiu, and K. Y. Wong. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000 Research 9:129, 2020. Dassault Systèmes BIOVIA. BIOVIA Workbook, Release 2017; BIOVIA Pipeline Pilot, Release 2017. San Diego: Dassault Systèmes, 2020. Douglas, E. V. P., L. B. Tom, and B. A. David. pkCSM: predicting small-molecule pharmacokinetic properties using graph-based signatures. J Med Chem 58(9):4066–4072, 2015. Fehr, A. R., and S. Perlman. Coronaviruses: an overview of their replication and pathogenesis. Methods in Molecular Biology 1282:1–23, 2015. Floris, M., J. Masciocchi, M. Fanton, and S. Moro. Swimming into peptidomimetic chemical space using pepMMsMIMIC. Nucleic Acids Res. 39:W261–W269, 2011. https://doi.org/10.1093/nar/gkr287. Forli, S., R. Huey, M. E. Pique, M. F. Sanner, D. S. Goodsell, and A. J. Olson. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc. 11(5):905–919, 2016. https://doi.org/10.1038/nprot.2016.051. Gurwitz, D. Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics. Drug Dev Res 2020. https://doi.org/10.1002/ddr.21656. Hoffmann, M., H. Kleine-Weber, S. Schroeder, N. Krüger, T. Herrler, S. Erichsen, T. S. Schiergens, G. Herrler, N. H. Wu, A. Nitsche, M. A. Müller, C. Drosten, and S. Pöhlmann. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 181(2):271–280, 2020. Hsu, K. C., Y. F. Chen, S. R. Lin, and J. M. Yang. iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinformatics. 12(Suppl 1):S33, 2011. https://doi.org/10.1186/1471-2105-12-s1-s33. Johnson, E. R., S. Keinan, P. Mori-Sánchez, J. Contreras-García, A. J. Cohen, and W. Yang. Revealing noncovalent interactions. J Am Chem Soc. 132(18):6498–6506, 2010. Kollman, P. Non-covalent forces of importance in biochemistry, Chapter 2, Editor(s): Michael I. Page. New Comprehensive Biochemistry 6:55–71, 1984. Li, F. Structure, function, and evolution of coronavirus spike proteins. Annual Review of Virology. 3(1):237–261, 2016. Li, G., Y. Fan, Y. Lai, T. Han, Z. Li, P. Zhou, et al. Coronavirus infections and immune responses. Journal of medical virology. 92(4):424–432, 2020. Li, F., W. Li, M. Farzan, and S. C. Harrison. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 309(5742):1864–1868, 2005. Li, Q., and S. Shah. Structure-based virtual screening. Methods Mol Biol. 1558:111–124, 2017. Li, Z., Y. Yi, X. Luo, N. Xiong, Y. Liu, S. Li, et al. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis. J Med Virol 2020. https://doi.org/10.1002/jmv.25727. Lipinski, C. A., F. Lombardo, B. W. Dominy, and P. J. Feeney. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46(1–3):3–26, 2001. Lyne, P. D., M. L. Lamb, and J. C. Saeh. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J. Med. Chem. 49:4805–4808, 2006. Monteil, V., H. Kwon, P. Prado, A. Hagelkrüys, R. A. Wimmer, M. Stahl, et al. Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell. 181(4):905–913, 2020. Muthusamy, K., S. Mohan, S. Nagamani, and C. Kesavan. Identification of novel small molecules that bind to the Loop2 Region of Sclerostin: an in silico computational analysis. Physiol. Res. 65:871–878, 2016. Nagamani, S., and K. Muthusamy. A theoretical insight to understand the molecular mechanism of dual-target ligand CTA-018 in the chronic kidney disease pathogenesis. PLoS ONE 13:e0203194, 2018. O’Boyle, N. M., M. Banck, C. A. James, et al. Open Babel: an open chemical toolbox. J Cheminform 3:33, 2011. https://doi.org/10.1186/1758-2946-3-33. Pettersen, E. F., T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. UCSF Chimera: a visualization system for exploratory research and analysis. J. Comput. Chem. 25:1605–1612, 2004. Procko, E. The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2. bioRxiv 2020. https://doi.org/10.1101/2020.03.16.994236. Robson B. Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus. Comput. Biol. Med. 119:103670, 2020. Sillerud, L. O., and R. S. Larson. Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Curr Protein Pept Sci. 6(2):151–169, 2005. https://doi.org/10.2174/1389203053545462. Thompson, M. A. Molecular docking using ArgusLab, an efficient shape-based search algorithm, and the A Score scoring function. Philadelphia: ACS Meeting, 2004. Trott, O., and A. J. Olson. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 31(2):455–461, 2010. World Health Organization (WHO). Retrieved from on 9th May 9, 2020, https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen. Yan, R., Y. Zhang, et al. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 367:1444–1448, 2020. Yan, R., Y. Zhang, Y. Li, L. Xia, Y. Guo, and Q. Zhou. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science. 367(6485):1444–1448, 2020. Zhou, Y., Y. Hou, J. Shen, Y. Huang, W. Martin, and F. Cheng. Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. 6:14, 2020.