Subscribe to RSS
DOI: 10.1055/a-2793-9663
Intramolecular Interactions of Twenty-Eight Amide Derivatives with the C-ALB Kinase using a Theoretical Model as a Therapeutic Alternative to Treat Cancer
Authors
Abstract
Background
Several studies have shown that some drugs can slow the growth of cancer cells by inhibiting the c-Abl kinase. However, some of these drugs can cause side effects such as gynecomastia, pulmonary toxicity, and lentiginosis, among others. In the search for a therapeutic alternative, some amide derivatives have been developed to treat cancer. However, their interaction with the c-Abl kinase is not clear.
Objective
The aim of this study was to evaluate the interaction of 28 amide derivatives with the c-Abl kinase as a therapeutic alternative to treat cancer cells.
Methods
The theoretical interaction of amide derivatives with the c-Abl kinase was carried out using the 1iep protein as a theoretical model. Besides, bosutinib, dasatinib, imatinib, nilotinib, and radotinib were used as controls in the DockingServer program.
Results
The results displayed different types of aminoacid residues involved in the interaction of amide derivatives with the 1iep protein surface compared to the controls. In addition, the inhibition constant (Ki) was lower for compounds 15, 16, and 18 compared to radotinib. Finally, the Ki for amide derivatives 1, 19, and 21 were lower compared with bosutinib, dasatinib, imatinib, and nilotinib.
Conclusions
Theoretical data indicate that amide derivatives such as 1, 15, 16, 18, 19, and 21 might have a higher affinity for the 1iep protein surface. This phenomenon could be translated as c-Abl kinase inhibition, resulting in a decrease in cancer cell growth.
Publication History
Received: 06 December 2025
Accepted after revision: 20 January 2026
Article published online:
03 February 2026
© 2026. Thieme. All rights reserved.
Georg Thieme Verlag KG
Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany
-
References
- 1 Augustin H, Koh G. A systems view of the vascular endothelium in health and disease. Cell 2024; 187 (18) 4833-4858
- 2 Limbu S, McCloskey K. An endothelial cell is not simply an endothelial cell. Stem Cells Develop 2024; 3 (19/20) 517-527
- 3 Cheng C, Huang Y. Vascular endothelium: The interface for multiplex signal transduction. J Mol Cell Cardiol 2024; 195: 97-102
- 4 Ajoolabady A, Pratico D, Ren J. Endothelial dysfunction: mechanisms and contribution to diseases. Acta Pharmacol Sinica 2024; 45 (10) 2023-2031
- 5 Ge L, Xun C, Li W. et al. Extracellular vesicles derived from hypoxiapreconditioned olfactory mucosa mesenchymal stem cells enhance angiogenesis via miR-612. J Nanobiotech 2021; 19: 1-23
- 6 Lee H, Xu Y, He L. et al. Role of venous endothelial cells in developmental and pathologic angiogenesis. Circulation 2021; 144: 1308-1322
- 7 Kazemi S, Wenzel D, Kolossov E. et al. Differential role of bFGF and VEGF for vasculogenesis. Cell Physiolo Biochem 2002; 12 (2/3) 55-62
- 8 Przybylski M. A review of the current research on the role of bFGF and VEGF in angiogenesis. J Wound Care 2009; 18 (12) 516-519 https://www.mdpi.com/2072-6694/13/6/1422#
- 9 Shao R, Yan W, Pazik B, Pendergast A, Wang X. Cytoplasmic tyrosine kinase c-Abl is required for bFGF but not VEGF-induced tumor angiogenesis. Cancer Res 2006; 66 (08) 615
- 10 Yan W, Bentley B, Shao R. Distinct angiogenic mediators are required for basic fibroblast growth factor–and vascular endothelial growth factor-induced angiogenesis: the role of cytoplasmic tyrosine kinase c-Abl in tumor angiogenesis. Mol Biol Cell 2008; 19 (05) 2278-2288
- 11 Lin J, Arlinghaus R. Activated c-Abl tyrosine kinase in malignant solid tumors. Oncogene 2008; 27 (32) 4385-4391
- 12 Zhao H, Chen M, Lo Y. et al. The Ron receptor tyrosine kinase activates c-Abl to promote cell proliferation through tyrosine phosphorylation of PCNA in breast cancer. Oncogene 2014; 33 (11) 1429-1437
- 13 Zhao H, Ou-Yang F, Chen I. et al. Enhanced resistance to tamoxifen by the c-ABL proto-oncogene in breast cancer. Neoplasia 2010; 12 (03) 214-IN3
- 14 Srinivasan D, Plattner R. Activation of Abl tyrosine kinases promotes invasion of aggressive breast cancer cells. Cancer Res 2006; 66 (11) 5648-5655
- 15 Sirvent A, Boureux A, Simon V, Leroy C, Roche S. The tyrosine kinase Abl is required for Src-transforming activity in mouse fibroblasts and human breast cancer cells. Oncogene 2007; 26 (52) 7313-7323
- 16 Zhou S, Tang L, Wang H. et al. Overexpression of c-Abl predicts unfavorable outcome in epithelial ovarian cancer. Gynecol Oncol 2013; 131 (01) 69-76
- 17 Schmandt R, Broaddus R, Lu K. et al. Expression of c-ABL, c-KIT, and platelet-derived growth factor receptor-β in ovarian serous carcinoma and normal ovarian surface epithelium. Interd Int J Am Cancer Soc 2003; 98 (04) 758-764
- 18 Lin K, Glenn M, Harris R. et al. c-Abl expression in chronic lymphocytic leukemia cells: clinical and therapeutic implications. Cancer Res 2006; 66 (15) 7801-7809
- 19 Allen J, Talab F, Zuzel M, Lin K, Slupsky J. c-Abl regulates Mcl-1 gene expression in chronic lymphocytic leukemia cells. Blood, J Am Soc Hematol 2011; 117 (08) 2414-2422
- 20 Nagar B. c-Abl tyrosine kinase and inhibition by the cancer drug imatinib (Gleevec/STI-571). J Nutrition 2007; 137 (06) 1518S-1523S
- 21 Keller G, Schafhausen P. Brümmendorf T. Bosutinib. Small Molecules in Oncology. Springer; 2009: 119-127
- 22 Remsing L, Rix U, Colinge J. et al. Global target profile of the kinase inhibitor bosutinib in primary chronic myeloid leukemia cells. Leukemia 2009; 23 (03) 477-485
- 23 Lindauer M, Hochhaus A. Dasatinib. Small Molecules in Hematology. Springer; 2018: 29-68
- 24 Amrein P. The potential for dasatinib in treating chronic lymphocytic leukemia, acute myeloid leukemia, and myeloproliferative neoplasms. Leukemia Lymph 2011; 52 (05) 754-763
- 25 Hegedűs C, Ozvegy-Laczka C, Apati A. et al. Interaction of nilotinib, dasatinib and bosutinib with ABCB1 and ABCG2: implications for altered anti-cancer effects and pharmacological properties. British J Pharmacol 2009; 158 (04) 1153-1164
- 26 Blanchard Z, Mullins N, Ellipeddi P. et al. Geminin overexpression promotes imatinib sensitive breast cancer: a novel treatment approach for aggressive breast cancers, including a subset of triple negative. PLoS One 2014; 9 (04) e95663
- 27 Heo S, Noh E, Kim J. et al. The c-Abl inhibitor, radotinib induces apoptosis in multiple myeloma cells via mitochondrial-dependent pathway. Sci Rep 2021; 11 (01) 13198
- 28 Kostryukov S, Belyakova O, Mishkin D, Stulnikov D, Dektyarev A. BCR-ABL Inhibitors in the Targeted Therapy of Chronic Myeloid Leukemia. Russian J Bioorg Chem 2025; 51 (04) 1471-1488
- 29 Hochhaus A, Larson R, Guilhot F. et al. Long-term outcomes of imatinib treatment for chronic myeloid leukemia. New England. J Med 2017; 376 (10) 917-927
- 30 Apperley J, Cortes J, Kim D. et al. Dasatinib in the treatment of chronic myeloid leukemia in accelerated phase after imatinib failure: the START a trial. J Clin Oncol 2009; 27 (21) 3472-3479
- 31 Campone M, Bondarenko I, Brinca S. et al. Phase II study of single-agent bosutinib, a Src/Abl tyrosine kinase inhibitor, in patients with locally advanced or metastatic breast cancer pretreated with chemotherapy. Annals Oncol 2012; 23 (03) 610-617
- 32 Masarova L, Cortes J, Patel K. et al. Long-term results of a phase 2 trial of nilotinib 400 mg twice daily in newly diagnosed patients with chronic-phase chronic myeloid leukemia. Cancer 2020; 126 (07) 1448-1459
- 33 Kim H, Chang H, Ryu M. et al. Concurrent male gynecomastia and testicular hydrocele after imatinib mesylate treatment of a gastrointestinal stromal tumor. J Korean Med Sci 2005; 20 (03) 512-515
- 34 Nekoukar Z, Moghimi M, Salehifar E. A narrative review on adverse effects of dasatinib with a focus on pharmacotherapy of dasatinib-induced pulmonary toxicities. Blood Res 2021; 56 (04) 229-242
- 35 Won K, Jo S, Lee Y, Chang S. Radotinib-induced lentiginosis: a report of an adverse cutaneous reaction associated with a tyrosine kinase inhibitor. Clin Exp Dermatol 2016; 41 (02) 162-165
- 36 Nagar B, Bornmann W, Pellicena P. et al. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res 2002; 62 (15) 4236-4243
- 37 Halgren T. Merck molecular force field. I. Basis, form, scope, parametrization, and performance of MMFF94. J Comp Chem 1998; 17 (5/6) 490-519
- 38 Morris G, Goodsell D. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem 1998; 19 (14) 1639-1662
- 39 Solis F, Wets R. Minimization by Random Search Techniques. Math Oper Res 1981; 6 (01) 19-30
- 40 Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017; 7: 42717
- 41 Azzam K. SwissADME and pkCSM webservers predictors: An integrated online platform for accurate and comprehensive predictions for in silico ADME/T properties of artemisinin and its derivatives. Kompl Ispol Mineral Syra 2023; 325 (02) 14-21
- 42 Askerova U. Prediction of acute toxicity for (Z)-3-(2-phenylhydrazinylidene) benzofuran-2 (3H)-one and its derivatives for rats using GUSAR program. New Mat Comp Appl 2023; 7 (01) 50-56
- 43 Li S, Yao Z, Zhao Y. et al. Design, synthesis and biological evaluation of novel acrylamide analogues as inhibitors of BCR–ABL kinase. Bioorg Med Chem Lett 2012; 22 (16) 5279-5282
- 44 Wang X, Xu Z, Feng J. et al. Synthesis and biological evaluation of novel aromatic amide derivatives as potential BCR-ABL inhibitors. Bioorg Med Chem Lett 2023; 81: 129144
- 45 Alshehr M, Kumar N, Kuthi N. et al. Computer-aided drug discovery of c-Abl kinase inhibitors from plant compounds against chronic myeloid leukemia. J Biomol Struct Dyn 2025; 43 (14) 7712-7732
- 46 Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl allosteric inhibitors: where we are and where we are going to. Molecules 2020; 25 (18) 4210
- 47 Manetti F, Locatelli G, Maga G. et al. A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors. J Med Chem 2006; 49 (11) 3278-3286
- 48 Cao R, Wang Y, Huang N. Discovery of 2-acylaminothiophene-3-carboxamides as multitarget inhibitors for BCR-ABL kinase and microtubules. J Chem Inf Model 2015; 55 (11) 2435-2442
- 49 Fallacara A, Tintori C, Radi M, Schenone S, Botta M. Insight into the allosteric inhibition of Abl kinase. J Chem Inf Model 2014; 54 (05) 1325-1338
- 50 Pereira E, Moreira M, Caffarena E. Molecular interactions of c-ABL mutants in complex with imatinib/nilotinib: a computational study using linear interaction energy (LIE) calculations. J Mol Model 2012; 18 (09) 4333-4341
- 51 Kiesel B, Guo J, Bakkenist C, Beumer J. Non-linear absorption pharmacokinetics (PK) of the ATR inhibitor AZD6738 in mice. Cancer Res 2020; 80 (16) 3019-3019
- 52 Iliadis A, Brown A, Huggins M. APIS: a software for model identification, simulation and dosage regimen calculations in clinical and experimental pharmacokinetics. Computer Meth Prog Biomed 1992; 38 (04) 227-239
- 53 Dedík L, Ďurišová M. CXT-MAIN: a software package for determination of the analytical form of the pharmacokinetic system weighting function. Computer Meth Prog Biomed 1996; 51 (03) 183-192
- 54 Dix D, Houck K, Martin M, Richard A, Setzer R, Kavlock R. The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol Sci 2007; 95 (01) 5-12
- 55 Klopman G, Rosenkranz H. Toxicity estimation by chemical structure analysis: the TOX II program. Toxicol Lett 1995; 79 (1/3) 145-155
- 56 Waters M, Auletta A. The GENE-TOX program: genetic activity evaluation. J Chem Inf Comp Sci 1981; 21 (01) 35-38
