Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge

Future Medicinal Chemistry
Cheng PengWeiliang Zhu

Abstract

Aim: It is a challenge to predict binding-free energy (ΔG) accurately. Methodology/results: For accurate ΔG prediction, a new strategy combining solvated interaction energy (SIE) or molecular mechanics/generalized Born surface area (MM/GBSA) approach with the Coulson charge of both protein and ligand calculated by semiempirical quantum mechanics (SQM), named SIE-SQMPC or MM/GBSA-SQMPC approach, was developed and tested on 50 protein-ligand complexes. Both approaches achieved higher correlation (R2) between experimental and predicted ΔG than that with Amber-ff03 charge, even for ligands with highly different scaffolds. But, SIE-SQMPC is computationally much faster than MM/GBSA-SQMPC. Conclusion: SIE-SQMPC provided an effective alternative to predict ΔG of protein-ligand binding (R2 = 0.66-0.94 for SIE-AM1; R2 = 0.59-0.98 for SIE-PM7), which has the potential of high-throughput processing for molecular docking and drug design.

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Citations

Mar 11, 2020·Journal of Biomolecular Structure & Dynamics·Renganathan SenthilSingaravelu Usha
Jan 3, 2021·BMC Complementary Medicine and Therapies·Rishab MarahathaNiranjan Parajuli
Feb 3, 2021·Journal of Biomolecular Structure & Dynamics·Elton José Ferreira ChavesGerd Bruno Rocha
Apr 4, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Leonor ContrerasRoberto Rozas
May 4, 2021·Journal of Chemical Information and Modeling·Yan-Jing ShengHong-Ming Ding

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Methods Mentioned

BETA
X-ray

Software Mentioned

Amber
MOPAC2016
AM1
mach Stichprobe mit Selektion ( MSMS )
QMPC PM7
AMOEBA
QMPC
antechamber
Modeller
sietraj

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