AUTHOR=Wang Shiyu , Sun Xiaolin , Cui Wenqiang , Yuan Shuguang TITLE=MM/PB(GB)SA benchmarks on soluble proteins and membrane proteins JOURNAL=Frontiers in Pharmacology VOLUME=13 YEAR=2022 URL=https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2022.1018351 DOI=10.3389/fphar.2022.1018351 ISSN=1663-9812 ABSTRACT=

Predicting protein-ligand binding free energy rapidly and accurately remains a challenging question in modern drug discovery. Molecular mechanics/Poisson-Boltzmann (Generalized Born) surface area (MM/PB(GB)SA) has emerged as an essential tool for accelerating cost-efficient binding free energy calculation. This study presents benchmarks with three membrane-bound protein systems and six soluble protein systems. Different parameters were sampled for different benchmarks to explore the highest accuracy. These include ligand charges, protein force fields, extra points, GB models, nonpolar optimization methods, internal dielectric constants and membrane dielectric constants. Comparisons of accuracy were made between MM/PB(GB)SA, docking and free energy perturbation (FEP). The results reveal a competitive performance between MM/PB(GB)SA and FEP. In summary, MM/PB(GB)SA is a powerful approach to predict ligand binding free energy rapidly and accurately. Parameters of MM/PB(GB)SA calculations, such as the GB models and membrane dielectric constants, need to be optimized for different systems. This method can be served as a powerful tool for drug design.