The slow but steady rise of binding free energy calculations in drug discovery

Xu Huafeng

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The slow but steady rise of binding free energy calculations in drug discovery

机译：药物发现中结合自由能计算的缓慢但稳步上升

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摘要

Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affinities and to prioritize candidate drug molecules accordingly. It has taken decades of collective effort to transform this academic concept into a technology adopted by the pharmaceutical and biotech industry. Having personally witnessed and taken part in this transformation, here I recount the (incomplete) list of problems that had to be solved to make this computational tool practical and suggest areas of future development.

机译：结合自由能计算越来越多地用于药物发现研究，以预测蛋白质-配体结合亲和力，并相应地确定候选药物分子的优先级。经过数十年的共同努力，将这一学术概念转化为制药和生物技术行业采用的技术。在亲眼目睹并参与了这一转变之后，我在这里叙述了为使这种计算工具实用而必须解决的（不完整的）问题清单，并提出了未来发展的领域。

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来源
《Journal of Computer-Aided Molecular Design》 |2023年第2期|67-74|共8页
作者
Xu Huafeng;
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作者单位

Roivant Discovery;

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原文格式 PDF
正文语种英语
中图分类电子计算机在化学中的应用;结构化学;
关键词
Binding free energy; Free energy perturbation; Simulations; Computational drug discovery; COMPUTATIONALLY-GUIDED OPTIMIZATION; PERTURBATION; INHIBITORS; MOLECULE; DESIGN; WATER; SIMULATIONS; ACCURATE; FLEXIBILITY; PREDICTIONS;

机译：结合自由能;自由能扰动;模拟;计算药物发现;计算引导优化;扰动;抑制剂;分子;设计;水;模拟;准确;灵活性;预测;

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1. Binding Free Energy-Based Footprint Pharmacophore Model to Enhance Virtual Screening and Drug Discovery: A Case on Glycosidases as Anti-influenza Drug Targets [J] . Mhlongo Ndumiso N., Soliman Mahmoud E. S. Letters in drug design & discovery . 2016,第10期

机译：Binding Free Energy-Based Footprint Pharmacophore Model to Enhance Virtual Screening and Drug Discovery: A Case on Glycosidases as Anti-influenza Drug Targets
2. Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations [J] . Chen Wei, Cui Di, Jerome Steven V.Michino MayakoLenselink Eelke B.Huggins David J.Beautrait AlexandreVendome JeremieAbel RobertFriesner Richard A.Wang Lingle Journal of chemical information and modeling . 2023,第10期

机译：Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations
3. Discovery of novel inhibitors of CDK2 using docking and physics‐based binding free energy calculation [J] . Lei Zheng, Yunpeng Yang, Jingxiao BaoLiping HeYifei QiJohn Z. H. Zhang Chemical biology and drug design . 2022,第5期

机译：Discovery of novel inhibitors of CDK2 using docking and physics‐based binding free energy calculation
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机译：(Battery Division Student Research Award Sponsored by Mercedes-Benz Research Development) Sustainable High-Performance Lithium-Ion Batteries: Aqueous Processing of Cobalt-Free High-Energy Cathodes
5. Membrane Permeability Prediction of Drug-like Molecules with Molecular Dynamics and Free Energy Calculations =基於分子動力學和自由能計算的藥物分子膜滲透性預測 [D] . Tse, Chi Hang. 2020

机译：Membrane Permeability Prediction of Drug-like Molecules with Molecular Dynamics and Free Energy Calculations =基于分子动力学和自由能计算的药物分子膜渗透性预测
6. MORPHEEINS – A NEW PATHWAY FOR ALLOSTERIC DRUG DISCOVERY [O] . EILEEN K. JAFFE -1

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7. Exploring the Proton Conductance and Drug Resistance of BM2 Channel through Molecular Dynamics Simulations and Free Energy Calculations at Different pH Conditions [O] . Zhang Yuxin, Shen Hujun, Zhang Mingbo, 2013

机译：Exploring the proton Conductance and Drug Resistance of Bm2 Channel through molecular Dynamics simulations and Free Energy Calculations at Different pH Conditions
8. A = 4 0 exp + - 1 exp + Binding-Energy Difference [R] . Gibson, B. F., Lehman, D. R. 1982

机译：a = 4 0 exp + - 1 exp + Binding-Energy Difference

The slow but steady rise of binding free energy calculations in drug discovery

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