Jameel Froze, Stein Matthias
Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
Phys Chem Chem Phys. 2024 Aug 7;26(31):21197-21203. doi: 10.1039/d4cp01529k.
Calculating the Gibbs energies of binding of ligand-receptor systems with a thermochemical accuracy of ± 1 kcal mol is a challenge to computational approaches. After exploration of the conformational space of the host, ligand and their resulting complexes upon coordination by semi-empirical GFN2 MD and -MD simulations, the systematic refinement through a multi-level improvement of binding modes in terms of electronic energies and solvation is able to give Gibbs energies of binding of drug molecules to CB[8] and β-CD macrocyclic receptors with such an accuracy. The accurate treatment of a small number of structures outperforms system-specific force-matching and alchemical transfer model approaches without an extensive sampling and integration.
以±1千卡/摩尔的热化学精度计算配体-受体系统的结合吉布斯能,对计算方法来说是一项挑战。通过半经验GFN2分子动力学(MD)和 -MD模拟探索主体、配体及其配位后形成的复合物的构象空间后,通过在电子能量和溶剂化方面对结合模式进行多级改进的系统优化,能够以这样的精度给出药物分子与CB[8]和β-环糊精大环受体的结合吉布斯能。对少量结构的精确处理优于没有广泛采样和积分的系统特定力匹配和炼金术转移模型方法。