Identification of IL-2 inducible tyrosine kinase inhibitors by quantum mechanics and ligand based virtual screening approaches

References

• Abdel-Wahab, N., Shah, M., Lopez-Olivo, M. A., & Suarez-Almazor, M. E. (2018). Use of immune checkpoint inhibitors in the treatment of patients with cancer and preexisting autoimmune disease: A systematic review. Annals of Internal Medicine, 168(2), 121–130. https://doi.org/10.7326/M17-2073
   PubMed Web of Science ®Google Scholar
• Bhullar, K. S., Lagarón, N. O., McGowan, E. M., Parmar, I., Jha, A., Hubbard, B. P., & Rupasinghe, H. P. V. (2018). Kinase-targeted cancer therapies: Progress, challenges and future directions. Molecular Cancer, 17(1), 1–20. https://doi.org/10.1186/s12943-018-0804-2
   PubMedGoogle Scholar
• Bryan, M. C., & Rajapaksa, N. S. (2018). Kinase inhibitors for the treatment of immunological disorders: Recent advances. Journal of Medicinal Chemistry, 61(20), 9030–9058. https://doi.org/10.1021/ACS.JMEDCHEM.8B00667/ASSET/IMAGES/LARGE/JM-2018-00667B_0028.JPEG
   PubMed Web of Science ®Google Scholar
• Ćetković, H., Halasz, M., & Herak Bosnar, M. (2018). Sponges: A reservoir of genes implicated in human cancer. Marine Drugs, 16(1), 20. https://doi.org/10.3390/md16010020
   PubMed Web of Science ®Google Scholar
• Gomez-Rodriguez, J., Meylan, F., Handon, R., Hayes, E. T., Anderson, S. M., Kirby, M. R., Siegel, R. M., & Schwartzberg, P. L. (2016). Itk is required for Th9 differentiation via TCR-mediated induction of IL-2 and IRF4. Nature Communications, 7(1), 10857. https://doi.org/10.1038/ncomms10857
   PubMedGoogle Scholar
• Hussain, A., Yu, L., Faryal, R., Mohammad, D. K., Mohamed, A. J., & Smith, C. I. E. (2011). TEC family kinases in health and disease – loss-of-function of BTK and ITK and the gain-of-function fusions ITK–SYK and BTK–SYK. The FEBS Journal, 278(12), 2001–2010. https://doi.org/10.1111/J.1742-4658.2011.08134.X
   PubMed Web of Science ®Google Scholar
• Inácio, D. P., Amado, T., Silva-Santos, B., & Gomes, A. Q. (2018). Control of T cell effector functions by miRNAs. Cancer Letters, 427, 63–73. https://doi.org/10.1016/J.CANLET.2018.04.011
   PubMed Web of Science ®Google Scholar
• Kaur, M., Bahia, M. S., & Silakari, O. (2012). Inhibitors of interleukin-2 inducible T-cell kinase as potential therapeutic candidates for the treatment of various inflammatory disease conditions. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences, 47(3), 574–588. https://doi.org/10.1016/J.EJPS.2012.07.013
   PubMed Web of Science ®Google Scholar
• Khajehzadeh, M., & Sadeghi, N. (2018). Molecular structure, the effect of solvent on UV–vis and NMR, FT–IR and FT–Raman spectra, NBO, frontier molecular orbital analysis of Mitomycin anticancer drug. Journal of Molecular Liquids, 256, 238–246. https://doi.org/10.1016/j.molliq.2018.01.099
   Web of Science ®Google Scholar
• Kurochkina, N., & Guha, U. (2013). SH3 domains: Modules of protein–protein interactions. Biophysical Reviews, 5(1), 29–39. https://doi.org/10.1007/S12551-012-0081-Z
   PubMedGoogle Scholar
• Lechner, K. S., Neurath, M. F., & Weigmann, B. (2020). Role of the IL-2 inducible tyrosine kinase ITK and its inhibitors in disease pathogenesis. Journal of Molecular Medicine (Berlin, Germany), 98(10), 1385–1395. https://doi.org/10.1007/S00109-020-01958-Z/TABLES/1
   PubMed Web of Science ®Google Scholar
• Liang, W., Li, K., Zhang, Q., Li, K., Ai, K., Zhang, J., Jiao, X., Li, J., Wei, X., & Yang, J. (2022). Interleukin-2 inducible T cell kinase (ITK) may participate in the anti-bacterial immune response of Nile tilapia via regulating T-cell activation. Fish & Shellfish Immunology, 127, 419–426. https://doi.org/10.1016/J.FSI.2022.06.044
   PubMed Web of Science ®Google Scholar
• Manoj, K. P., Elangovan, N., & Chandrasekar, S. (2022). Synthesis, XRD, Hirshfeld surface analysis, ESP, HOMO-LUMO, quantum chemical modeling and anticancer activity of di(p-methyl benzyl)(dibromo)(1,10-phenanthroline) tin(IV) complex. Inorganic Chemistry Communications, 139, 109324. https://doi.org/10.1016/j.inoche.2022.109324
   Web of Science ®Google Scholar
• Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of useful decoys, enhanced (DUD-E): Better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. https://doi.org/10.1021/JM300687E/SUPPL_FILE/JM300687E_SI_004.TXT
   PubMed Web of Science ®Google Scholar
• Nair, A., Chauhan, P., Saha, B., & Kubatzky, K. F. (2019). Conceptual evolution of cell signaling. International Journal of Molecular Sciences, 20(13), 3292. https://doi.org/10.3390/ijms20133292
   PubMed Web of Science ®Google Scholar
• Pais, T.F., Ali, H., Moreira da Silva, J., Duarte, N., Neres, R., Chhatbar, C., Acúrcio, R.C., Guedes, R.C., Strano Moraes, M.C., Costa-Silva, B. and Kalinke, U. (2022). Brain endothelial ST ING1 activation by Plasmodium-sequestered heme promotes cerebral malaria via type I IFN response. Proceedings of the National Academy of Sciences, 119(36), e2206327119.
   Google Scholar
• Ponader, S., & Burger, J. A. (2014). Bruton’s tyrosine kinase: From X-linked agammaglobulinemia toward targeted therapy for B-cell malignancies. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology, 32(17), 1830–1839. https://doi.org/10.1200/JCO.2013.53.1046
   PubMed Web of Science ®Google Scholar
• Roskoski, R. (2016). Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes. Pharmacological Research, 103, 26–48. https://doi.org/10.1016/j.phrs.2015.10.021
   PubMed Web of Science ®Google Scholar
• Roskoski, R. (2020). Properties of FDA-approved small molecule protein kinase inhibitors: A 2020 update. Pharmacological Research, 152, 104609. https://doi.org/10.1016/J.PHRS.2019.104609
   PubMed Web of Science ®Google Scholar
• Schwartz, D. M., Kanno, Y., Villarino, A., Ward, M., Gadina, M., & O'Shea, J. J. (2017). JAK inhibition as a therapeutic strategy for immune and inflammatory diseases. Nature Reviews. Drug Discovery, 16(12), 843–862. https://doi.org/10.1038/nrd.2017.201
   PubMed Web of Science ®Google Scholar
• Seda, V., Mraz, M., & Marek Mraz, C. (2015). B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. European Journal of Haematology, 94(3), 193–205. https://doi.org/10.1111/EJH.12427
   PubMed Web of Science ®Google Scholar
• Seok, S.-H., & Gianni, S. (2021). Structural insights into protein regulation by phosphorylation and substrate recognition of protein kinases/phosphatases. Life, 11(9), 957. https://doi.org/10.3390/life11090957
   PubMedGoogle Scholar
• Shah, K., Al-Haidari, A., Sun, J., & Kazi, J. U. (2021). T cell receptor (TCR) signaling in health and disease. Signal Transduction and Targeted Therapy, 6(1), 1–26. https://doi.org/10.1038/s41392-021-00823-w
   PubMed Web of Science ®Google Scholar
• Sheng, Y., Watanabe, H., Maruyama, K., Watanabe, C., Okiyama, Y., Honma, T., Fukuzawa, K., & Tanaka, S. (2018). Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase. Computational and Structural Biotechnology Journal, 16, 421–434. https://doi.org/10.1016/J.CSBJ.2018.10.003
   PubMed Web of Science ®Google Scholar
• Sipeki, S., Koprivanacz, K., Takács, T., Kurilla, A., László, L., Vas, V., & Buday, L. (2021). Novel roles of SH2 and SH3 domains in lipid binding. Cells, 10(5), 1191. https://doi.org/10.3390/cells10051191
   PubMed Web of Science ®Google Scholar
• Sun, Y., Peng, I., Webster, J. D., Suto, E., Lesch, J., Wu, X., Senger, K., Francis, G., Barrett, K., Collier, J. L., Burch, J. D., Zhou, M., Chen, Y., Chan, C., Eastham-Anderson, J., Ngu, H., Li, O., Staton, T., Havnar, C., … Zarrin, A. A. (2015). Inhibition of the kinase ITK in a mouse model of asthma reduces cell death and fails to inhibit the inflammatory response. Science Signaling, 8(405), ra122. https://doi.org/10.1126/SCISIGNAL.AAB0949/SUPPL_FILE/8_RA122_SM.PDF
   PubMed Web of Science ®Google Scholar
• Szilveszter, K. P., Németh, T., & Mócsai, A. (2019). Tyrosine kinases in autoimmune and inflammatory skin diseases. Frontiers in Immunology, 10(AUG), 1862. https://doi.org/10.3389/FIMMU.2019.01862/BIBTEX
   PubMedGoogle Scholar
• Tan, F. H., Putoczki, T. L., Stylli, S. S., & Luwor, R. B. (2019). Ponatinib: A novel multi-tyrosine kinase inhibitor against human malignancies. OncoTargets and Therapy, 12, 635–645. https://doi.org/10.2147/OTT.S189391
   PubMed Web of Science ®Google Scholar
• Torke, S., & Weber, M. S. (2020). Inhibition of Bruton’s tyrosine kinase as a novel therapeutic approach in multiple sclerosis. Expert Opinion on Investigational Drugs, 29(10), 1143–1150. https://doi.org/10.1080/13543784.2020.1807934
   PubMed Web of Science ®Google Scholar
• Vargas, L., Hamasy, A., Nore, B. F., & Smith, C. I. E. (2013). Inhibitors of BTK and ITK: State of the new drugs for cancer, autoimmunity and inflammatory diseases. Scandinavian Journal of Immunology, 78(2), 130–139. https://doi.org/10.1111/SJI.12069
   PubMed Web of Science ®Google Scholar
• Velloso, F. J., Bianco, A. F. R., Farias, J. O., Torres, N. E. C., Ferruzo, P. Y. M., Anschau, V., Jesus-Ferreira, H. C., Chang, T. H. T., Sogayar, M. C., Zerbini, L. F., & Correa, R. G. (2017). The crossroads of breast cancer progression: Insights into the modulation of major signaling pathways. OncoTargets and Therapy, 10, 5491–5524. https://doi.org/10.2147/OTT.S142154
   PubMed Web of Science ®Google Scholar
• Von Bonin, A., Rausch, A., Mengel, A., Hitchcock, M., Krüger, M., Von Ahsen, O., Merz, C., Röse, L., Stock, C., Martin, S. F., Leder, G., Döcke, W. D., Asadullah, K., & Zügel, U. (2011). Inhibition of the IL-2-inducible tyrosine kinase (Itk) activity: A new concept for the therapy of inflammatory skin diseases. Experimental Dermatology, 20(1), 41–47. https://doi.org/10.1111/J.1600-0625.2010.01198.X
   PubMed Web of Science ®Google Scholar
• Weiss, F., Lauffenburger, D., & Friedl, P. (2022). Towards targeting of shared mechanisms of cancer metastasis and therapy resistance. Nature Reviews. Cancer, 22(3), 157–173. https://doi.org/10.1038/s41568-021-00427-0
   PubMed Web of Science ®Google Scholar
• Wolber, G., & Langer, T. (2005). LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. Journal of Chemical Information and Modeling, 45(1), 160–169. https://doi.org/10.1021/ci049885e
   PubMed Web of Science ®Google Scholar
• Yamaoka, T., Kusumoto, S., Ando, K., Ohba, M., & Ohmori, T. (2018). Receptor tyrosine kinase-targeted cancer therapy. International Journal of Molecular Sciences, 19(11), 3491. https://doi.org/10.3390/ijms19113491
   PubMed Web of Science ®Google Scholar
• Zapf, C. W., Gerstenberger, B. S., Xing, L., Limburg, D. C., Anderson, D. R., Caspers, N., Han, S., Aulabaugh, A., Kurumbail, R., Shakya, S., Li, X., Spaulding, V., Czerwinski, R. M., Seth, N., & Medley, Q. G. (2012). Covalent inhibitors of interleukin-2 inducible T cell kinase (ItK) with nanomolar potency in a whole-blood assay. Journal of Medicinal Chemistry, 55(22), 10047–10063. https://doi.org/10.1021/JM301190S/SUPPL_FILE/JM301190S_SI_001.PDF
   PubMed Web of Science ®Google Scholar
• Zarrin, A. A., Bao, K., Lupardus, P., & Vucic, D. (2021). Kinase inhibition in autoimmunity and inflammation. Nature Reviews. Drug Discovery, 20(1), 39–63. https://doi.org/10.1038/s41573-020-0082-8
   PubMed Web of Science ®Google Scholar