Pharmacophore-based drug design and synthesis of potential CDK2 inhibitors as anticancer entities

The transformation of a normal cell into a tumor cell is one of the initial steps in cell cycle deregulation. The cell cycle is regulated by cyclin-dependent kinases (CDKs) that belong to the protein kinase family. CDK2 is an enchanting target for specific genotype tumors since cyclin E is selective for CDK2 and the deregulation of specific cancer forms. Thus, CDKs inhibitor specifically CDK2/cyclin A-E has the potential to be a valid cancer target as per the currently undergoing clinical trials. A series of 1-phenylpyrazole as core structure and the hybrids molecules of aniline and hydrazides (1a-1g) & (3a-3e) were synthesized and screened for inhibition of CDK2/ cyclin A/E using computational tools. The cytotoxicity of these compounds was screened against MCF-7 (human breast cancer cells) cell lines at a concentration of 40 ppm using an MTT assay. Molecular docking of the compounds with PDB ID:1VYZ was performed using Auto-dock, the results indicated all compounds exhibited good binding interaction with CDK2. The binding affinity of the co-crystalline ligand was found to be -6.5 Kcal/mol whereas the binding affinity of the synthesized compounds was in the range of 7.0 to 7.7 Kcal/mol. Compound 1e and 3d substituted with 2-nitrophenyl and 4-chlorobenzoyl group respectively showed good activity with the highest % cytotoxicity in MCF-7 cell line studies. The computational and cytotoxicity data indicated 3d to be very good and can be used as a lead compound for the development of CDK2 inhibitors as anticancer agents.