Pharmacological inhibition of cathepsin C (CatC) as a potential approach for cancer therapeutics

References

• Arbyn, M., Weiderpass, E., Bruni, L., de Sanjosé, S., Saraiya, M., Ferlay, J., & Bray, F. (2020). Estimates of incidence and mortality of cervical cancer in 2018: a worldwide analysis. The Lancet Global Health, 8(2), e191–e203. https://doi.org/10.1016/S2214-109X(19)30482-6
   PubMed Web of Science ®Google Scholar
• Case, D. A., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., Cheatham, T. E., III, Darden, T. A., Duke, R. E., Gohlke, H., others. (2014). The FF14SB Force Field. Amber, 14, 29–31.
   Google Scholar
• Case, D. A., Belfon, K., Ben-Shalom, I., Brozell, S. R., Cerutti, D., Cheatham, T., Cruzeiro, V. W. D., Darden, T., Duke, R. E., Giambasu, G., others. (2020). Amber, 2020.
   Google Scholar
• Cianni, L., Feldmann, C. W., Gilberg, E., Gütschow, M., Juliano, L., Leitão, A., Bajorath, J., & Montanari, C. A. (2019). Can cysteine protease cross-class inhibitors achieve selectivity? Journal of Medicinal Chemistry, 62(23), 10497–10525.
   PubMed Web of Science ®Google Scholar
• Conus, S., & Simon, H. (2010). Cathepsins and their involvement in immune responses. Swiss Medical Weekly. https://doi.org/10.4414/smw.2010.13042
   Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(January), 42717–42713. https://doi.org/10.1038/srep42717
   PubMedGoogle Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Chemical biology (pp. 243–250). Springer.
   Google Scholar
• Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules (Basel, Switzerland), 20(7), 13384–13421.
   PubMed Web of Science ®Google Scholar
• Genheden, S., Kuhn, O., Mikulskis, P., Hoffmann, D., & Ryde, U. (2012). The normal-mode entropy in the MM/GBSA method: Effect of system truncation, buffer region, and dielectric constant. Journal of Chemical Information and Modeling, 52(8), 2079–2088.
   PubMed Web of Science ®Google Scholar
• Halgren, T. a. (1996). Merck molecular force field. Journal of Computational Chemistry, 17(5–6), 490–519. https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6 < 520::AID-JCC2 > 3.0.CO;2-W
   Web of Science ®Google Scholar
• Hansson, T., Oostenbrink, C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190–196. https://doi.org/10.1016/s0959-440x(02)00308-1
   PubMed Web of Science ®Google Scholar
• Hubeau, C., Rocks, N., & Cataldo, D. (2020). ADAM28: Another ambivalent protease in cancer. Cancer Letters, 494, 18–26.
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38.
   PubMedGoogle Scholar
• Izaguirre, J. A., Catarello, D. P., Wozniak, J. M., & Skeel, R. D. (2001). Langevin stabilization of molecular dynamics. The Journal of Chemical Physics, 114(5), 2090–2098. https://doi.org/10.1063/1.1332996
   Web of Science ®Google Scholar
• Ketterer, S., Mitschke, J., Ketscher, A., Schlimpert, M., Reichardt, W., Baeuerle, N., Hess, M. E., Metzger, P., Boerries, M., Peters, C., Kammerer, B., Brummer, T., Steinberg, F., Reinheckel, T &., others. (2020). Cathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling. Nature Communications, 11(1), 1–18. https://doi.org/10.1038/s41467-020-18935-2
   PubMed Web of Science ®Google Scholar
• Kettritz, R. (2016). Neutral serine proteases of neutrophils. Immunological Reviews, 273(1), 232–248. https://doi.org/10.1111/imr.12441
   PubMed Web of Science ®Google Scholar
• Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews Drug Discovery, 3(11), 935–949. https://doi.org/10.1038/nrd1549
   PubMed Web of Science ®Google Scholar
• Korkmaz, B., Caughey, G. H., Chapple, I., Gauthier, F., Hirschfeld, J., Jenne, D. E., Kettritz, R., Lalmanach, G., Lamort, A.-S., Lauritzen, C., Łȩgowska, M., Lesner, A., Marchand-Adam, S., McKaig, S. J., Moss, C., Pedersen, J., Roberts, H., Schreiber, A., Seren, S., Thakker, N. S &., others. (2018). Therapeutic targeting of cathepsin C: From pathophysiology to treatment. Pharmacology & Therapeutics, 190, 202–236.
   PubMed Web of Science ®Google Scholar
• Korkmaz, B., Lamort, A.-S., Domain, R., Beauvillain, C., Gieldon, A., Yildirim, A. Ö., Stathopoulos, G. T., Rhimi, M., Jenne, D. E., & Kettritz, R. (2021). Cathepsin C inhibition as a potential treatment strategy in cancer. Biochemical Pharmacology, 194, 114803.
   PubMed Web of Science ®Google Scholar
• Korkmaz, B., Lesner, A., Marchand-Adam, S., Moss, C., & Jenne, D. E. (2020). Lung protection by cathepsin C inhibition: A new hope for COVID-19 and ARDS? Miniperspective. Journal of Medicinal Chemistry, 63(22), 13258–13265. https://doi.org/10.1021/acs.jmedchem.0c00776
   PubMed Web of Science ®Google Scholar
• Kräutler, V., van Gunsteren, W. F., & Hünenberger, P. H. (2001). A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of Computational Chemistry, 22(5), 501–508. https://doi.org/10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V
   Web of Science ®Google Scholar
• Lyu, C., Chen, T., Qiang, B., Liu, N., Wang, H., Zhang, L., & Liu, Z. (2021). CMNPD: A comprehensive marine natural products database towards facilitating drug discovery from the ocean. Nucleic Acids Research, 49(D1), D509–D515.
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Petersen, H. G. (1995). Accuracy and efficiency of the particle mesh Ewald method. The Journal of Chemical Physics, 103(9), 3668–3679. https://doi.org/10.1063/1.470043
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. III, (2013). PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095.
   PubMed Web of Science ®Google Scholar
• Rudin, C. M., Brambilla, E., Faivre-Finn, C., & Sage, J. (2021). Small-cell lung cancer. Nature Reviews Disease Primers, 7(1), 1–20. https://doi.org/10.1038/s41572-020-00235-0
   PubMed Web of Science ®Google Scholar
• Rudzinska-Radecka, M., Frolova, A. S., Balakireva, A. V., Gorokhovets, N. V., Pokrovsky, V. S., Sokolova, D. V., Korolev, D. O., Potoldykova, N. V., Vinarov, A. Z., Parodi, A., & Zamyatnin, A. A. (2022). In silico, in vitro, and clinical investigations of cathepsin B and stefin A mRNA expression and a correlation analysis in kidney cancer. Cells, 11(9), 1455. https://doi.org/10.3390/cells11091455
   PubMed Web of Science ®Google Scholar
• Schafmeister, C., Ross, W. S., & Romanovski, V. (1995). The leap module of AMBER. University of California.
   Google Scholar
• Shen, X. B., Chen, X., Zhang, Z. Y., Wu, F. F., & Liu, X. H. (2021). Cathepsin C inhibitors as anti-inflammatory drug discovery: Challenges and opportunities. European Journal of Medicinal Chemistry, 225, 113818.
   PubMed Web of Science ®Google Scholar
• Sprenger, K. G., Jaeger, V. W., & Pfaendtner, J. (2015). The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids. The Journal of Physical Chemistry. B, 119(18), 5882–5895.
   PubMed Web of Science ®Google Scholar
• Sussman, J. L., Lin, D., Jiang, J., Manning, N. O., Prilusky, J., Ritter, O., & Abola, E. E. (1998). Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules. Acta Crystallographica Section D Biological Crystallography, 54(6), 1078–1084. https://doi.org/10.1107/S0907444998009378
   PubMedGoogle Scholar
• Turner, P. J. (2005). XMGRACE, Version 5.1. 19. Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology.
   Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H. Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Whitty, A. (2011). Growing PAINS in academic drug discovery. Future Medicinal Chemistry, 3(7), 797–801. https://doi.org/10.4155/fmc.11.44
   PubMed Web of Science ®Google Scholar
• Woods, C. J., Malaisree, M., Hannongbua, S., & Mulholland, A. J. (2011). A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies. Journal of Chemical Physics, 134(5). https://doi.org/10.1063/1.3519057
   Google Scholar
• Woods, C. J., Malaisree, M., Michel, J., Long, B., McIntosh-Smith, S., & Mulholland, A. J. (2014). Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water. Faraday Discussions, 169, 477–499. https://doi.org/10.1039/c3fd00125c
   PubMed Web of Science ®Google Scholar