Genetic algorithm-de novo, molecular dynamics and MMGBSA based modelling of a novel Benz-pyrazole based anticancer ligand to functionally revert mutant P53 into wild type P53

Abstract

ABSTRACT Mutations in P53 cause a loop unfolding, resulting in loss of activity and finally leading to cancer. One strategically reported way to arrest such oncogenesis is the restoration of tertiary structure as well as the function of mutant P53. In this attempt, we have designed a benzo-pyrazole-based novel ligand starting from a carbazole compound (EYB or PK9324) reported earlier to reinstate such function in mutant P53 (Y220C mutant, PDB: 6GGD). Assuming PK9324 as the template scaffold, de novo technique (Genetic algorithm, eLEA3D) was adopted within the binding pocket of 6GGD and our ligand DLIG1 was designed after several rounds of mutations. Docking and molecular dynamics (MD) simulation revealed significant interactions with key amino acid residues such as Cys220, Asp228, Leu145, Trp146, Val147, Thr150, Pro151, Pro152, Pro222, Pro223, Asp228, and Thr230. Along with sufficient binding stability, the MMGBSA analysis revealed its comparable binding free energy with other reported reference ligands (i.e. PK9324 and PK9318). Similar to these reference ligands, DLIG1 exhibited specificity in binding towards the Y220C mutant rather than towards wild-type P53. Finally, DLIG1 displayed a reorientation of a hydrophobic cavity in Y220C that hinted restoration of electrostatic interactions within the key loops of P53 favoring regain of its function.