Akkus E, Tayfuroglu O, Yildiz M, Kocak A. Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant.
J Phys Chem B 2023;
127:4415-4429. [PMID:
37171911 DOI:
10.1021/acs.jpcb.3c00834]
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Abstract
Here, we report the accuracy improvements of molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations by adoption of ANI-ML potentials in replacement of MM terms, the use of solvent-accessible surface area (SASA) and volume (SAV) values from the Monte Carlo sampling of the probe, and introducing two different interior dielectric constants for electrostatic interactions of protein-ligand (P-L) and polar solvation term in the MMPBSA calculations. Our results show that the Pearson correlation coefficients of MMPBSA-calculated values with respect to experimental binding free energies can be drastically improved from 0.48 to 0.90 by adoption of ANI-ML potentials in replacement of MM energy terms in the equation, referred to as ANI-PBSA. Moreover, we show that the SASA/SAV-combined equation in the scaled particle theory (SPT) can be a better choice to model nonpolar solvation term, reaching nearly the same accuracy by ANI-PBSA calculations. Finally, we introduce two different values of interior dielectric constants, which could be an alternative strategy between the single and variable constant definitions.
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