In silico design and molecular docking study of CDK2 inhibitors with potent cytotoxic activity against HCT116 colorectal cancer cell line

Colorectal Cancer

J Genet Eng Biotechnol. 2020 Sep 15;18(1):51. doi: 10.1186/s43141-020-00066-2.


BACKGROUND: Colorectal cancer is common to both sexes; third in terms of morbidity and second in terms of mortality, accounting for 10% and 9.2% of cancer cases in men and women globally. Although drugs such as bevacizumab, Camptosar, and cetuximab are being used to manage colorectal cancer, the efficacy of the drugs has been reported to vary from patient to patient. These drugs have also been reported to have varying degrees of side effects; thus, the need for novel drug therapies with better efficacy and lesser side effects. In silico drugs design methods provide a faster and cost-effect method for lead identification and optimization. The aim of this study, therefore, was to design novel imidazol-5-ones via in silico design methods.

RESULTS: A QSAR model was built using the genetic function algorithm method to model the cytotoxicity of the compounds against the HCT116 colorectal cancer cell line. The built model had statistical parameters; R2 = 0.7397, R2adj = 0.6712, Q2cv = 0.5547, and R2ext. = 0.7202 and revealed the cytotoxic activity of the compounds to be dependent on the molecular descriptors nS, GATS5s, VR1_Dze, ETA_dBetaP, and L3i. These molecular descriptors were poorly correlated (VIF < 4.0) and made unique contributions to the built model. The model was used to design a novel set of derivatives via the ligand-based drug design approach. Compounds e, h, j, and l showed significantly better cytotoxicity (IC50 < 5.0 μM) compared to the template. The interaction of the compounds with the CDK2 enzyme (PDB ID: 6GUE) was investigated via molecular docking study. The compounds were potent inhibitors of the enzyme having binding affinity of range -10.8 to -11.0 kcal/mol and primarily formed hydrogen bond interaction with lysine, aspartic acid, leucine, and histidine amino acid residues of the enzyme.

CONCLUSION: The QSAR model built was stable, robust, and had a good predicting ability. Thus, predictions made by the model were reliably employed in further in silico studies. The compounds designed were more active than the template and showed better inhibition of the CDK2 enzyme compared to the standard drugs sorafenib and kenpaullone.