Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2
Jacopo Sgrignani, Andrea Cavalli
Frontiers in Molecular Biosciences, doi:10.3389/fmolb.2021.666626
Camostat, nafamostat, and bromhexine are inhibitors of the transmembrane serine protease TMPRSS2. The inhibition of TMPRSS2 has been shown to prevent the viral infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses. However, while camostat and nafamostat inhibit TMPRSS2 by forming a covalent adduct, the mode of action of bromhexine remains unclear. TMPRSS2 is autocatalytically activated from its inactive form, zymogen, through a proteolytic cleavage that promotes the binding of Ile256 to a putative allosteric pocket (Apocket). Computer simulations, reported here, indicate that Ile256 binding induces a conformational change in the catalytic site, thus providing the atomistic rationale to the activation process of the enzyme. Furthermore, computational docking and molecular dynamics simulations indicate that bromhexine competes with the N-terminal Ile256 for the same binding site, making it a potential allosteric inhibitor. Taken together, these findings provide the atomistic basis for the development of more selective and potent TMPRSS2 inhibitors.
AUTHOR CONTRIBUTIONS JS designed the study, performed and analyzed simulations and experiments, and wrote and revised the manuscript. AC designed the study, analyzed the results of simulations and experiments, and wrote and revised the manuscript. Both authors contributed to the article and approved the submitted version.
SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmolb. 2021.666626/full#supplementary-material
Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
References
Afar, Vivanco, Hubert, Kuo, Chen et al., Catalytic cleavage of the androgen-regulated TMPRSS2 protease results in its secretion by prostate and prostate cancer epithelia, Cancer Res
Amaro, Baron, Mccammon, An improved relaxed complex scheme for receptor flexibility in computer-aided drug design, J. Comput. Aided Mol. Des,
doi:10.1007/s10822-007-9159-2Amaro, Baudry, Chodera, Demir, Mccammon et al., Effect of bromhexine on clinical outcomes and mortality in COVID-19 patients: a randomized clinical trial, Biophys. J,
doi:10.34172/bi.2020.27Bertram, Glowacka, Blazejewska, Soilleux, Allen et al., TMPRSS2 and TMPRSS4 facilitate trypsin-independent spread of influenza virus in Caco-2 cells, J. Virol,
doi:10.1128/jvi.00239-10Bestle, Heindl, Limburg, Van Lam Van, Pilgram et al., TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells, Life Sci. Alliance,
doi:10.26508/lsa.202000786Chen, Lee, Lucht, Chou, Huang et al., TMPRSS2, a serine protease expressed in the prostate on the apical surface of luminal epithelial cells and released into semen in prostasomes, is misregulated in prostate cancer cells, Am. J. Pathol,
doi:10.2353/ajpath.2010.090665Depfenhart, De Villiers, Lemperle, Meyer, Somma, Potential new treatment strategies for COVID-19: is there a role for bromhexine as add-on therapy?, Intern. Emerg. Med,
doi:10.1007/s11739-020-02383-3Fassi, Sgrignani, D'agostino, Cecchinato, Garofalo et al., Oxidation state dependent conformational changes of HMGB1 regulate the formation of the CXCL12/HMGB1 Heterocomplex, Comput. Struct. Biotechnol. J,
doi:10.1016/j.csbj.2019.06.020Friesner, Banks, Murphy, Halgren, Klicic et al., Glide: a new approach for rapid, accurate docking and scoring
Fu, Sahakyan, Camilloni, Tartaglia, Paci et al., ALMOST: an all atom molecular simulation toolkit for protein structure determination, J. Comput. Chem,
doi:10.1002/jcc.23588Guarnera, Berezovsky, Toward comprehensive allosteric control over protein activity, Structure
Habtemariam, Nabavi, Ghavami, Cismaru, Berindan-Neagoe et al., Possible use of the mucolytic drug, bromhexine hydrochloride, as a prophylactic agent against SARS-CoV-2 infection based on its action on the Transmembrane Serine Protease 2, Pharmacol. Res,
doi:10.1016/j.phrs.2020.104853Halgren, Halgren, New method for fast and accurate binding-site identification and analysis, J. Chem. Inform. Modell,
doi:10.1021/ci800324mHammamy, Haase, Hammami, Hilgenfeld, Steinmetzer, Development and characterization of new peptidomimetic inhibitors of the West Nile virus NS2B-NS3 protease, ChemMedChem,
doi:10.1002/cmdc.201200497Harder, Damm, Maple, Wu, Reboul et al., OPLS3: a force field providing broad coverage of drug-like small molecules and proteins, J. Chem. Theory Comput,
doi:10.1021/acs.jctc.5b00864Hoffmann, Kleine-Weber, Schroeder, Krüger, Herrler et al., SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and Is blocked by a clinically proven protease inhibitor, Cell
Huber, How I chose research on proteases or, more correctly, how it chose me, Angew. Chem. Int. Ed. Engl,
doi:10.1002/anie.201205629Ishida, Kato, Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process, J. Am. Chem. Soc,
doi:10.1021/ja021369mIvanova, Hardes, Kallis, Dahms, Than et al., Optimization of substrate-analogue furin inhibitors, ChemMedChem,
doi:10.1002/cmdc.201700596Jerabek-Willemsen, Wienken, Braun, Baaske, Duhr, Molecular interaction studies using microscale thermophoresis, Assay Drug. Dev. Technol,
doi:10.1089/adt.2011.0380Jiménez, Doerr, Martínez-Rosell, Rose, De Fabritiis, DeepSite: protein-binding site predictor using 3D-convolutional neural networks, Bioinformatics,
doi:10.1093/bioinformatics/btx350Jorgensen, Chandrasekhar, Madura, Impey, Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys,
doi:10.1063/1.445869Kots, Lushchekina, Varfolomeev, Nemukhin, Role of protein dimeric interface in allosteric inhibition of N-Acetyl-aspartate hydrolysis by human aspartoacylase, J. Chem. Inform. Modell,
doi:10.1021/acs.jcim.7b00133Kozakov, Grove, Hall, Bohnuud, Mottarella et al., The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins, Nat. Protoc,
doi:10.1038/nprot.2015.043Laporte, Naesens, Airway proteases: an emerging drug target for influenza and other respiratory virus infections, Curr. Opin. Virol,
doi:10.1016/j.coviro.2017.03.018Li, Sun, Zhang, Zheng, Jiang et al., Bromhexine hydrochloride tablets for the treatment of moderate COVID-19: an open-label randomized controlled pilot study, Clin. Transl. Sci,
doi:10.1111/cts.12881Lucas, Heinlein, Kim, Hernandez, Malik et al., The androgen-regulated protease TMPRSS2 activates a proteolytic cascade involving components of the tumor microenvironment and promotes prostate cancer metastasis, Cancer Discov,
doi:10.1158/2159-8290.cd-13-1010Maggio, Corsini, Repurposing the mucolytic cough suppressant and TMPRSS2 protease inhibitor bromhexine for the prevention and management of SARS-CoV-2 infection, Pharmacol. Res,
doi:10.1016/j.phrs.2020.104837Martyna, Klein, Tuckerman, Nosé-hoover chains: the canonical ensemble via continuous dynamics, J. Chem. Phys,
doi:10.1063/1.463940Martyna, Tobias, Klein, Constant pressure molecular dynamics algorithms, J. Chem. Phys,
doi:10.1063/1.467468Meyer, Sielaff, Hammami, Böttcher-Friebertshäuser, Garten et al., Identification of the first synthetic inhibitors of the type II transmembrane serine protease TMPRSS2 suitable for inhibition of influenza virus activation, Biochem. J,
doi:10.1042/bj20130101Montopoli, Zumerle, Vettor, Rugge, Zorzi et al., Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (N = 4532), Ann. Oncol,
doi:10.1016/j.annonc.2020.04.479Olsson, Sondergaard, Rostkowski, Jensen, PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions, J. Chem. Theory Comput,
doi:10.1021/ct100578zPartridge, Choy, Silva-Garcia, Yu, Li et al., Structures of full-length plasma kallikrein bound to highly specific inhibitors describe a new mode of targeted inhibition, J. Struct. Biol,
doi:10.1016/j.jsb.2019.03.001Pászti-Gere, Czimmermann, Ujhelyi, Balla, Maiwald et al., In vitro characterization of TMPRSS2 inhibition in IPEC-J2 cells, J. Enzyme Inhib. Med. Chem,
doi:10.1080/14756366.2016.1193732Sanchez-Martin, Moroni, Ferraro, Laquatra, Cannino et al., Rational design of allosteric and selective inhibitors of the molecular chaperone TRAP1, Cell Rep,
doi:10.1016/j.celrep.2020.107531Sgrignani, Bon, Colombo, Magistrato, Computational approaches elucidate the allosteric mechanism of human aromatase inhibition: a novel possible route to small-molecule regulation of CYP450s activities?, J. Chem. Inf. Mod,
doi:10.1021/ci500425ySgrignani, Bonaccini, Grazioso, Chioccioli, Cavalli et al., Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations, J. Comput. Chem,
doi:10.1002/jcc.21251Sgrignani, Garofalo, Matkovic, Merulla, Catapano et al., Structural biology of STAT3 and its implications for anticancer therapies development, Int. J. Mol. Sci,
doi:10.3390/ijms19061591Shen, Mao, Wu, Tanaka, Zhang, TMPRSS2: a potential target for treatment of influenza virus and coronavirus infections, Biochimie,
doi:10.1016/j.biochi.2017.07.016Sherman, Day, Jacobson, Friesner, Farid, Novel procedure for modeling ligand/receptor induced fit effects, J. Med. Chem,
doi:10.1021/jm050540cShrimp, Kales, Sanderson, Simeonov, Shen et al., An enzymatic TMPRSS2 assay for assessment of clinical candidates and discovery of inhibitors as potential treatment of COVID-19, ACS Pharmacol. Transl. Sci,
doi:10.1021/acsptsci.0c00106Singh, Decroly, Khatib, Villoutreix, Structurebased drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages, Eur. J. Pharm. Sci,
doi:10.1016/j.ejps.2020.105495Stubbs, Renatus, Bode, An active zymogen: unravelling the mystery of tissue-type plasminogen activator, Biol. Chem
Sungnak, Huang, Becavin, Berg, Queen et al., SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes, Nat. Med,
doi:10.1038/s41591-020-0868-6Szabo, Wu, Dickson, Netzel-Arnett, Antalis et al., Type II transmembrane serine proteases, Thromb. Haemost,
doi:10.1160/th03-02-0071Tibshirani, Walther, Hastie, Estimating the number of clusters in a data set via the gap statistic, R. Stat. Soc,
doi:10.1111/1467-9868.00293Tubiana, Carvaillo, Boulard, Bressanelli, TTClust: a versatile molecular simulation trajectory clustering program with graphical summaries, J. Chem. Inform. Modell,
doi:10.1021/acs.jcim.8b00512Waterhouse, Bertoni, Bienert, Studer, Tauriello et al., SWISS-MODEL: homology modelling of protein structures and complexes, Nucleic Acids Res
Wiederstein, Sippl, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucl. Acids Res
Xu, Wang, Hu, Gao, Ma et al., CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction, Nucleic Acids Res
Yamamoto, Matsuyama, Li, Takeda, Kawaguchi et al., 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, Antimicrob. Agents Chemother,
doi:10.1128/aac.01043-16Yu, Zhou, Tanaka, Yao, Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere, Bioinformatics,
doi:10.1093/bioinformatics/btp599Zang, Gomez Castro, Mccune, Zeng, Rothlauf et al., TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes, Sci. Immunol,
doi:10.1126/sciimmunol.abc3582DOI record:
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