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通过在显式溶剂中的快速增长计算类药物分子的溶剂化自由能:对AM1-BCC、RESP/HF/6-31G*、RESP-QM/MM和ABCG2固定电荷方法的评估

Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.

作者信息

Orlandi Matteo, Geng Yiqi, Macchiagodena Marina, Pagliai Marco, Procacci Piero

机构信息

Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.

Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy.

出版信息

J Chem Theory Comput. 2025 Aug 26;21(16):7977-7990. doi: 10.1021/acs.jctc.5c00749. Epub 2025 Aug 11.

Abstract

We assess the performance of the nonequilibrium alchemical fast-growth method in calculating water and 1-octanol solvation free energies, comparing the recently proposed ABCG2 model with other empirical and quantum mechanics (QM)-based approaches for modeling electrostatic interactions in condensed phases using fixed atomic charges. The fixed-charge protocols are tested on the challenging set of drug-like polyfunctional molecules previously used by Vassetti et al., , , 1983-1995, broadly spanning the chemical space and often exhibiting complex conformational landscapes. We find that the cost-effective empirical ABCG2 protocol consistently outperforms the AM1/BCC precursor model and the widely used HF/6-31G* charge derivation method, achieving solvation free energy accuracy comparable to an expensive QM/MM-based methodology for atomic fixed charge determination. For water-octanol transfer free energies, ABCG2 benefits from systematic error cancellation, yielding remarkable agreement with experimental data, exhibiting excellent Pearson and Kendall rank coefficients and a mean unsigned error below 1 kcal/mol, matching the performance of the costly QM/MM approach. These results suggest that the ABCG2 protocol holds great promise for the high-throughput in silico prediction of ligand-protein binding free energies in drug discovery projects.

摘要

我们评估了非平衡炼金术快速增长方法在计算水和1-辛醇溶剂化自由能方面的性能,将最近提出的ABCG2模型与其他基于经验和量子力学(QM)的方法进行了比较,这些方法使用固定原子电荷来模拟凝聚相中的静电相互作用。在Vassetti等人(1983 - 1995年)之前使用的具有挑战性的类药物多官能团分子集上测试了固定电荷协议,这些分子广泛涵盖化学空间,并且常常展现出复杂的构象景观。我们发现,具有成本效益的经验性ABCG2协议始终优于AM1/BCC前体模型和广泛使用的HF/6 - 31G*电荷推导方法,在确定原子固定电荷时,其实现的溶剂化自由能精度与基于昂贵的QM/MM方法相当。对于水 - 辛醇转移自由能,ABCG2受益于系统误差消除,与实验数据达成显著一致,展现出出色的皮尔逊和肯德尔等级系数,平均无符号误差低于1 kcal/mol,与昂贵的QM/MM方法的性能相当。这些结果表明,ABCG2协议在药物发现项目中高通量计算机模拟预测配体 - 蛋白质结合自由能方面具有巨大潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/562c/12392459/299b10057330/ct5c00749_0002.jpg

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