Identification of novel PI3Kδ inhibitors by docking, ADMET prediction and molecular dynamics simulations

Background Phosphoinositide-3-kinase Delta (PI3K delta) plays a key role in B-cell signal transduction and inhibition of PI3K delta is confirmed to have clinical benefit in certain types of activation of B-cell malignancies. Virtual screening techniques have been used to discover new molecules for developing novel PI3K delta inhibitors with little side effects. Method: Computer aided drug design method were used to rapidly screen optimal PI3K delta inhibitors from the Asinex database. Virtual screening based molecular docking was performed to find novel and potential lead compound targeting PI3K delta, at first. Subsequently, drug likeness studies were carried out on the retrieved hits to evaluate and analyze their drug like properties such as absorption, distribution, metabolism, excretion, and toxicity (ADMET) for toxicity prediction. Three least toxic compounds were selected for the molecular dynamics (MD) simulations for 30 ns in order to validate its stability inside the active site of PI3K delta receptor. Results: Based on the present in silico analysis, two molecules have been identified which occupied the same binding pocket confirming the selection of active site. ASN 16296138 (Glide score: - 12.175 kcal/mol, cdocker binding energy: - 42.975 kcal/mol and Delta G(bind) value: - 90.457 kcal/mol) and HAS 00227397 (Glide score: - 10.988 kcal/mol, cdocker binding energy: - 39.3376 kcal/mol and Delta G(bind) value: - 81.953 kcal/mol) showed docking affinities comparatively much stronger than those of already reported known inhibitors against PI3K delta. These two ligand's behaviors also showed consistency during the simulation of protein-ligand complexes for 30000 ps respectively, which is indicative of its stability in the receptor pocket. Conclusion: Compound ASN 16296138 and BAS 00227397 are potential candidates for experimental validation of biological activity against PI3K delta in future drug discovery studies. This study smoothes the path for the development of novel leads with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of cancer.