Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs.

Abstract

Protein three-dimensional (3D) structure prediction is one of the most challenging issues in the field of computational biochemistry, which has overwhelmed scientists for almost half a century. A significant breakthrough in structural biology has been established by developing the artificial intelligence (AI) system AlphaFold2 (AF2). The AF2 system provides a state-of-the-art prediction of protein structures from nearly all known protein sequences with high accuracy. This study examined the reliability of AF2 models compared to the experimental structures in drug discovery, focusing on one of the most common protein drug-targeted classes known as G protein-coupled receptors (GPCRs) class A. A total of 32 representative protein targets were selected, including experimental structures of X-ray crystallographic and Cryo-EM structures and their corresponding AF2 models. The quality of AF2 models was assessed using different structure validation tools, including the pLDDT score, RMSD value, MolProbity score, percentage of Ramachandran favored, QMEAN Z-score, and QMEANDisCo Global. The molecular docking was performed using the Genetic Optimization for Ligand Docking (GOLD) software. The AF2 models' reliability in virtual drug screening was determined by their ability to predict the ligand binding poses closest to the native binding pose by assessing the Root Mean Square Deviation (RMSD) metric and docking scoring function. The quality of the docking and scoring function was evaluated using the enrichment factor (EF). Furthermore, the capability of using AF2 models in molecular docking to identify hits with key protein-ligand interactions was analyzed. The posing power results showed that the AF2 models successfully predicted ligand binding poses (RMSD < 2 Å). However, they exhibited lower screening power, with average EF values of 2.24, 2.42, and 1.82 for X-ray, Cryo-EM, and AF2 structures, respectively. Moreover, our study revealed that molecular docking using AF2 models can identify competitive inhibitors. In conclusion, this study found that AF2 models provided docking results comparable to experimental structures, particularly for certain GPCR targets, and could potentially significantly impact drug discovery.