Identification of Ligand‐binding Hotspot Residues of CDK4 Using Molecular Docking and Molecular Dynamics Simulation

Abstract

Cyclin‐dependent protein kinases (CDKs) are serine/threonine kinases of the CMGC family. The cyclin D/CDK4 complex plays an important role in cell proliferation. Deregulation of the CDK4‐cyclin D pathway leads to uncontrolled cell proliferation, causing various tumors and cancers in humans. CDK4 overexpression is widely observed in colorectal and uterine cervical carcinomas, liposarcomas, osteosarcomas, and breast cancer. CDK4 is extensively studied as a therapeutic target in breast cancer. Hence, the identification of the binding modes of inhibitors and important active‐site residues is crucial. However, an experimentally determined crystal structure of ligand‐bound CDK4 kinase has not been reported to date. Thus, this study aimed to identify hotspot residues in the ligand‐binding interface of CDK4. Three compounds exhibiting very high inhibitory activity against CDK4 (Cpd03, Cpd13, and Cpd14) were selected as potent antagonists in this study. Molecular docking and molecular dynamics simulation were carried out to identify the binding modes and crucial residues. For validation, we calculated total binding free energy and energy decomposition, which identified residues Ala151, Ala30, Asp152, His89, Ile9, Leu141, Phe87, Val17, and Val90 are the highest‐energy contributors important for inhibitor binding. The results of our study provide insights in the binding patterns of CDK4 inhibitors and reveal key residues in the ligand‐binding interface.