Identification of Therapeutic Compounds Targeting Phosphatidylinositol 3-Kinase (PI3K) Through Molecular Docking, Dynamics Simulation, and DFT Calculations

Abstract

Cancer is one of the leading causes of death worldwide and characterized by uncontrolled cell proliferation. The phosphatidylinositol 3-kinase (PI3K) is an enzyme, which is essential for regulating cell growth and survival, is often dysregulated in tumors. Currently available PI3K inhibitors (like Duvelisib) have significant side effects, highlighting the need for safer therapeutics. Gallic acid, a natural phenolic compound with remarkable antineoplastic properties, showcases a promising scaffold for drug development. The aim of this study is to identify potential PI3K inhibitors from gallic acid derivatives using advanced computational techniques such as PASS prediction, molecular docking, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analysis, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Five derivatives 21, 37, 44, 68 and 75 were selected based on their predicted antineoplastic activity among 90 derivatives, as well as the control drug Duvelisib. Compound 68 proved to be the most promising candidate, exhibiting strong binding affinity to the PI3K receptor, forming multiple hydrogen bonds with key residues, and showing stable interactions over 500 ns MD simulation. ADMET analysis revealed that compound 68 had favorable pharmacokinetic properties. Compound 21 also showed strong binding affinity but exhibited limitations in its pharmacokinetic profile. This study aims to improve our understanding of ligand-protein dynamics in PI3K inhibition and highlight the potential of gallic acid derivatives in developing safer and more effective PI3K inhibitors for cancer therapy. Our results support further experimental validation of compound 68 and suggest that gallic acid derivatives could contribute to the development of safer therapies.

Keywords: ADMET; Gallic Acid; MD Simulation; Molecular Docking; Phosphatidylinositol 3-kinase (PI3K).