Quantum chemical optimization and residue-specific stabilization of CDK20 inhibitors in hepatocellular carcinoma.

Abstract

Cyclin-dependent kinase 20 (CDK20), also known as cell cycle-related kinase (CCRK), plays a pivotal role in hepatocellular carcinoma (HCC) progression by regulating β-catenin signaling and promoting uncontrolled proliferation. Despite its emerging significance, selective small-molecule inhibitors of CDK20 remain unexplored. In this study, a known CDK20 inhibitor, ISM042-2-048, was employed as a reference to retrieve structurally similar compounds from the PubChem database using an 85% similarity threshold. Out of 6,235 candidates, the top three compounds (153295720, 145037521, and 163292314) were shortlisted through MTiOpenScreen-based virtual screening. Geometry optimizations using density functional theory (B3LYP/cc-pVDZ) refined each ligand's electronic properties before re-docking against the AlphaFold-derived CDK20 structure. 153295720 exhibited the highest binding affinity (- 11.8 kcal/mol), engaging critical active-site residues such as Met⁸⁴, Lys³³, Ala¹³¹, and Asp¹⁴⁵ through polar and hydrophobic interactions. Molecular dynamics simulations (500 ns) confirmed the complex's structural stability, with 153295720 showing the lowest RMSD and RMSF fluctuations and highly persistent hydrogen bonding. MM/GBSA analysis further supported its superiority, revealing the most favorable binding energy (- 69.09 ± 8.29 kcal/mol), dominated by van der Waals and electrostatic interactions. Free energy landscape analysis revealed a single dominant basin, and superimposition of MD-derived minima with the docked pose yielded an RMSD of 1.464 Å, supporting pose fidelity. Comparatively, the reference compound displayed greater conformational drift and reduced energetic convergence. This integrative computational approach establishes 153295720 as a structurally and dynamically superior inhibitor, capable of stabilizing key catalytic residues of CDK20. These findings provide a rational basis for the biochemical targeting of CDK20 in HCC and highlight residues essential for selective inhibition, paving the way for experimental validation and lead optimization.