98
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2

, , &
Received 17 Dec 2023, Accepted 08 Mar 2024, Published online: 09 Apr 2024

References

  • Bestle, D., Heindl, M. R., Limburg, H., Van Lam van, T., Pilgram, O., Moulton, H., Stein, D. A., Hardes, K., Eickmann, M., Dolnik, O., Rohde, C., Klenk, H.-D., Garten, W., Steinmetzer, T., & Böttcher-Friebertshäuser, E. (2020). TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells. Life Science Alliance, 3(9), e202000786. https://doi.org/10.26508/lsa.202000786
  • Bhanushali, A., Rao, P., Raman, V., Kokate, P., Ambekar, A., Mandva, S., Bhatia, S., & Das, B. R. (2018). Status of TMPRSS2–ERG fusion in prostate cancer patients from India: Correlation with clinico-pathological details and TMPRSS2 Met160Val polymorphism. Prostate International, 6(4), 145–150. https://doi.org/10.1016/j.prnil.2018.03.004
  • Bultmann, H., & Brandt, C. R. (2002). Peptides containing membrane-transiting motifs inhibit virus entry. The Journal of Biological Chemistry, 277(39), 36018–36023. https://doi.org/10.1074/jbc.M204849200
  • Cao, Y., Li, L., Feng, Z., Wan, S., Huang, P., Sun, X., Wen, F., Huang, X., Ning, G., & Wang, W. (2020). Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations. Cell Discovery, 6(1), 11. https://doi.org/10.1038/s41421-020-0147-1
  • Chen, Z., Song, X., Li, Q., Xie, L., Guo, T., Su, T., Tang, C., Chang, X., Liang, B., & Huang, D. (2019). Androgen receptor-activated enhancers simultaneously regulate oncogene TMPRSS2 and lncRNA PRCAT38 in prostate cancer. Cells, 8(8), 864. https://doi.org/10.3390/cells8080864
  • Choi, Y., & Chan, A. P. (2015). PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics (Oxford, England), 31(16), 2745–2747. https://doi.org/10.1093/bioinformatics/btv195
  • Eldar, A., Rozenberg, H., Diskin-Posner, Y., Rohs, R., & Shakked, Z. (2013). Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Research, 41(18), 8748–8759. https://doi.org/10.1093/nar/gkt630
  • El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., Sonnhammer, E. L. L., Hirsh, L., Paladin, L., Piovesan, D., Tosatto, S. C. E., & Finn, R. D. (2019). The Pfam protein families database in 2019. Nucleic Acids Research, 47(D1), D427–D432. https://doi.org/10.1093/nar/gky995
  • 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), 2980–2992. https://doi.org/10.1080/07391102.2020.1758791
  • Fuentes-Prior, P. (2021). Priming of SARS-CoV-2 S protein by several membrane-bound serine proteinases could explain enhanced viral infectivity and systemic COVID-19 infection. The Journal of Biological Chemistry, 296, 100135. https://doi.org/10.1074/jbc.REV120.015980
  • Hecht, M., Bromberg, Y., & Rost, B. (2015). Better prediction of functional effects for sequence variants. BMC Genomics, 16(S8), S1. https://doi.org/10.1186/1471-2164-16-S8-S1
  • Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020). SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271–280.e8. https://doi.org/10.1016/j.cell.2020.02.052
  • Hopkins, A. L., Groom, C. R., & Alex, A. (2004). Ligand efficiency: A useful metric for lead selection. Drug Discovery Today, 9(10), 430–431. https://doi.org/10.1016/S1359-6446(04)03069-7
  • Ivanova, L., Tammiku-Taul, J., García-Sosa, A. T., Sidorova, Y., Saarma, M., & Karelson, M. (2018). Molecular dynamics simulations of the interactions between glial cell line-derived neurotrophic factor family receptor GFRα1 and small-molecule ligands. ACS Omega, 3(9), 11407–11414. https://doi.org/10.1021/acsomega.8b01524
  • Joerger, A. C., Ang, H. C., & Fersht, A. R. (2006). Structural basis for understanding oncogenic p53 mutations and designing rescue drugs. Proceedings of the National Academy of Sciences of the United States of America, 103(41), 15056–15061. https://doi.org/10.1073/pnas.0607286103
  • Jones, J. C., Settles, E. W., Brandt, C. R., & Schultz-Cherry, S. (2011). Identification of the minimal active sequence of an anti-influenza virus peptide. Antimicrobial Agents and Chemotherapy, 55(4), 1810–1813. https://doi.org/10.1128/AAC.01428-10
  • Jones, J. C., Turpin, E. A., Bultmann, H., Brandt, C. R., & Schultz-Cherry, S. (2006). Inhibition of influenza virus infection by a novel antiviral peptide that targets viral attachment to cells. Journal of Virology, 80(24), 11960–11967. https://doi.org/10.1128/JVI.01678-06
  • Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. https://doi.org/10.1021/ja9621760
  • Kumar, S., Clarke, D., & Gerstein, M. B. (2019). Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures. Proceedings of the National Academy of Sciences of the United States of America, 116(38), 18962–18970. https://doi.org/10.1073/pnas.1901156116
  • Laporte, M., & Naesens, L. (2017). Airway proteases: An emerging drug target for influenza and other respiratory virus infections. Current Opinion in Virology, 24, 16–24. https://doi.org/10.1016/j.coviro.2017.03.018
  • Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., Xing, X., Xiang, N., Wu, Y., Li, C., Chen, Q., Li, D., Liu, T., Zhao, J., Liu, M., … Feng, Z. (2020). Early transmission dynamics in wuhan, China, of novel coronavirus-infected pneumonia. The New England Journal of Medicine, 382(13), 1199–1207. https://doi.org/10.1056/NEJMoa2001316
  • Martyna, G. J., Klein, M. L., & Tuckerman, M. (1992). Nosé–Hoover chains: The canonical ensemble via continuous dynamics. The Journal of Chemical Physics, 97(4), 2635–2643. https://doi.org/10.1063/1.463940
  • Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
  • Meyer, D., Sielaff, F., Hammami, M., Böttcher-Friebertshäuser, E., Garten, W., & Steinmetzer, T. (2013). Identification of the first synthetic inhibitors of the type II transmembrane serine protease TMPRSS2 suitable for inhibition of influenza virus activation. The Biochemical Journal, 452(2), 331–343. https://doi.org/10.1042/BJ20130101
  • Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J. L., Merz, K. M., Oprea, T. I., Poroikov, V., Schneider, G., Todd, M. H., Varnek, A., Winkler, D. A., Zakharov, A. V., Cherkasov, A., & Tropsha, A. (2021). A critical overview of computational approaches employed for COVID-19 drug discovery. Chemical Society Reviews, 50(16), 9121–9151. https://doi.org/10.1039/d0cs01065k
  • Ofoegbu, T. C., David, A., Kelley, L. A., Mezulis, S., Islam, S. A., Mersmann, S. F., Strömich, L., Vakser, I. A., Houlston, R. S., & Sternberg, M. J. E. (2019). PhyreRisk: A dynamic web application to bridge genomics, proteomics and 3d structural data to guide interpretation of human genetic variants. Journal of Molecular Biology, 431(13), 2460–2466. https://doi.org/10.1016/j.jmb.2019.04.043
  • Paniri, A., Hosseini, M. M., & Akhavan-Niaki, H. (2020). First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations. Journal of Biomolecular Structure & Dynamics, 39(10), 3576–3593. https://doi.org/10.1080/07391102.2020.1767690
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera?A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Prajapat, M., Sarma, P., Shekhar, N., Prakash, A., Avti, P., Bhattacharyya, A., Kaur, H., Kumar, S., Bansal, S., Sharma, A. R., & Medhi, B. (2020). Update on the target structures of SARS-nCoV-2: A systematic review. Indian Journal of Pharmacology, 52(2), 142–149. https://doi.org/10.4103/ijp.IJP_338_20
  • Qureshi, A., Thakur, N., Tandon, H., & Kumar, M. (2014). AVPdb: A database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Research, 42(Database issue), D1147–D1153. https://doi.org/10.1093/nar/gkt1191
  • Ramachandran, B., Jeyakanthan, J., & Lopes, B. S. (2020). Molecular docking, dynamics and free energy analyses of Acinetobacter baumannii OXA class enzymes with carbapenems investigating their hydrolytic mechanisms. Journal of Medical Microbiology, 69(8), 1062–1078. https://doi.org/10.1099/jmm.0.001233
  • Reusken, C. B. E. M., Haagmans, B. L., Müller, M. A., Gutierrez, C., Godeke, G.-J., Meyer, B., Muth, D., Raj, V. S., Smits-De Vries, L., Corman, V. M., Drexler, J.-F., Smits, S. L., El Tahir, Y. E., De Sousa, R., van Beek, J., Nowotny, N., van Maanen, K., Hidalgo-Hermoso, E., Bosch, B.-J., … Koopmans, M. P. G. (2013). Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: A comparative serological study. The Lancet. Infectious Diseases, 13(10), 859–866. https://doi.org/10.1016/S1473-3099(13)70164-6
  • Sanfelice, D., De Simone, A., Cavalli, A., Faggiano, S., Vendruscolo, M., & Pastore, A. and AP. (2014). Characterization of the conformational fluctuations in the josephin domain of ataxin-3. Biophysical Journal, 107(12), 2932–2940. https://doi.org/10.1016/j.bpj.2014.10.008
  • Sankar, M., Ramachandran, B., Pandi, B., Mutharasappan, N., Ramasamy, V., Prabu, P. G., Shanmugaraj, G., Wang, Y., Muniyandai, B., Rathinasamy, S., Chandrasekaran, B., Bayan, M. F., Jeyaraman, J., Halliah, G. P., & Ebenezer, S. K. (2021). In silico screening of natural phytocompounds towards identification of potential lead compounds to treat COVID-19. Frontiers in Molecular Biosciences, 8, 637122. https://doi.org/10.3389/fmolb.2021.637122
  • Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research, 33(Web Server issue), W363–W367. https://doi.org/10.1093/nar/gki481
  • Shulla, A., Heald-Sargent, T., Subramanya, G., Zhao, J., Perlman, S., & Gallagher, T. (2011). A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry. Journal of Virology, 85(2), 873–882. https://doi.org/10.1128/JVI.02062-10
  • Sonawane, K., Barale, S. S., Dhanavade, M. J., Waghmare, S. R., Nadaf, N. H., & Kamble, S. A. (2020). Homology modeling and docking studies of TMPRSS2 with experimentally known inhibitors camostat mesylate, nafamostat and bromhexine hydrochloride to control SARS-Coronavirus-2. ChemRxiv [Preprint]. https://doi.org/10.26434/chemrxiv.12162360.v1
  • 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
  • Yamamoto, M., Matsuyama, S., Li, X., Takeda, M., Kawaguchi, Y., Inoue, J.-I., & Matsuda, Z. (2016). Identification of nafamostat as a potent inhibitor of middle east respiratory syndrome coronavirus S protein-mediated membrane fusion using the split-protein-based cell-cell fusion assay. Antimicrobial Agents and Chemotherapy, 60(11), 6532–6539. https://doi.org/10.1128/AAC.01043-16
  • Yamaya, M., Shimotai, Y., Hatachi, Y., Lusamba Kalonji, N., Tando, Y., Kitajima, Y., Matsuo, K., Kubo, H., Nagatomi, R., Hongo, S., Homma, M., & Nishimura, H. (2015). The serine protease inhibitor camostat inhibits influenza virus replication and cytokine production in primary cultures of human tracheal epithelial cells. Pulmonary Pharmacology & Therapeutics, 33, 66–74. https://doi.org/10.1016/j.pupt.2015.07.001
  • Yan, Y., Zhang, D., Zhou, P., Li, B., & Huang, S.-Y. (2017). HDOCK: A web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research, 45(W1), W365–W373. https://doi.org/10.1093/nar/gkx407
  • Zumla, A., Chan, J. F. W., Azhar, E. I., Hui, D. S. C., & Yuen, K.-Y. (2016). Coronaviruses - Drug discovery and therapeutic options. Nature Reviews. Drug Discovery, 15(5), 327–347. https://doi.org/10.1038/nrd.2015.37

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.