Evaluation of Benzamide-Chalcone Derivatives as EGFR/CDK2 Inhibitor: Synthesis, In-Vitro Inhibition, and Molecular Modeling Studies

Abstract

Background: EGFR (Epidermal Growth Factor Receptor) and CDK2 (Cyclin Dependent Kinase 2) are important targets in the treatment of many solid tumors and different ligands of these receptors share many common structural features. Objective: The study involved synthesis of benzamide-substituted chalcones and determination of their antiproliferative activity as well as preliminary evaluation of EGFR and CDK2 inhibitory potential using both receptor binding and computational methods. Methods: We synthesized 13 benzamide-substituted chalcone derivatives and tested their antiproliferative activity against MCF-7, HT-29 and U373MG cell-lines using Sulforhodamine B Assay. Four compounds were examined for activity against EGFR and CDK2 kinase. The compounds were docked into both EGFR and CDK2 using Glide software. The stability of the interactions for most active compound was evaluated by Molecular Dynamics Simulation using Desmond software. Molecular Docking studies on mutant EGFR (T790M, T790M/L858R, and T790M/C797S) were also carried out. Results: From the SRB assay, we concluded that compounds 1g, and 1k were effective in inhibiting the growth of MCF-7 cell line whereas the other compounds were moderately active. Most compounds were either moderately active or inactive on U373 MG and HT-29 cell line. Compounds 1g and 1k showed good inhibitory activity against CDK2 kinase while 1d and 1f were moderately active. Compounds 1d, 1f, 1g, and 1k were moderately active against EGFR kinase. Molecular docking reveals involvement of one hydrogen bond with Met793 in binding with EGFR however; it was not stable during simulation and these compounds bind to the receptor mainly via hydrophobic contacts. This fact also points towards a different orientation of the inhibitor within the active site of EGFR kinase. Binding mode analysis for CDK2 inhibition studies indicate that hydrogen bonding interaction with Lys 33 and Leu83 are important for the activity. These interactions were found to be stable throughout the simulation. Considering the results for wild-type EGFR inhibition, the docking studies on mutants were performed and which indicate that the compounds bind to the mutant EGFR but the amino acid residues involved are similar to the wild-type EGFR and therefore, the selectivity seems to be limited. Conclusion: These benzamide-substituted chalcone derivatives will be useful as lead molecules for the further development of newer inhibitors of EGFR and/or CDK2 kinases.

Cinnamamide-chalcone derivatives as CDK2 inhibitors: synthesis, pharmacological evaluation, and molecular modelling study

“…The pi-pi stacking with Phe80 seems to be an important but not a compulsory interaction for the compounds to be active as it was not observed in case of all compounds. The interactions observed in this study are consistent with some of the other reported studies [13,32,[33][34][35][36][37].…”

“…Using the relative light units [RLUs] in the presence of drug at three different concentration levels, the percentage enzyme activity was calculated at each concentration of the compound tested. The IC 50 values were calculated from a plot of the percentage enzyme activity vs. log concentration of the compounds [32,45].…”

Design, synthesis and molecular docking of new fused 1H-pyrroles, pyrrolo[3,2-d]pyrimidines and pyrrolo[3,2-e][1, 4]diazepine derivatives as potent EGFR/CDK2 inhibitors

“…cinobufagin 30 . In addition, biological and computational evidence supported that anticancer agents such as benzamide-substituted chalcones exerted their anti-proliferative effects via dual EGFR/CDK2 inhibitory activities 31 .…”

Synthesis and biological evaluation of benzamide‐chalcone hybrids as potential c‐Met kinase and COX‐2 inhibitors

“…We have previously worked on benzamide‐chalcone hybrids for epidermal growth factor receptor and cyclin‐dependent kinase 2 (CDK2) inhibition. [ 31 ] Various chalcone‐benzamide hybrids have been explored as curcumin analogs for cytotoxicity and antiangiogenic activity. [ 32 ] Asymmetric indole curcumin analogs have been evaluated as anti‐inflammatory agents with the potential to inhibit COX‐2, tumor necrosis factor‐α (TNF‐α), and interleukin‐6 (IL‐6), trypsin, and β‐glucuronidase.…”