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Entropy for End-Point and FFT-Based Binding Free Energy Calculations

用于端点和基于 FFT 的结合自由能计算的熵

基本信息

批准号：
10204042
负责人：
David Do Le Minh
金额：
$ 33.48万
依托单位：
ILLINOIS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-08-01 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10204042
关键词：
Accounting Affinity Algorithms Amino Acids Antibiotics Bacteria Benchmarking Binding Binding Proteins Biochemical Biological Biological Assay Biological Process Blinded Charge Chemistry Code Communities Complex Computer Assisted Computer software Computers Computing Methodologies Crystallization Data Set Docking Drug Design Drug Screening Endocrine Disruptors Entropy Enzymes Fourier Transform Free Energy Genetic Variation Human Life Ligands Measures Metabolic Methods Missense Mutation Molecular Molecular Conformation Mutation Occupations Pathway interactions Performance Pharmaceutical Preparations Proteins Research Sampling Science Solvents Statistical Mechanics Structure System TP53 gene Techniques Testing Translations base data resource drug discovery exhaustion flexibility follow-up gain of function improved insight mutant open source physical separation prospective protein complex protein structure prediction restraint simulation small molecule libraries tumor growth virtual

项目摘要

Project Summary Computers are often used to predict how tightly two molecules associate, their binding free energy. These predictions are helpful for designing drugs, predicting the consequences of genetic variation, and understanding how molecules interact to sustain life. Unfortunately, currently available methods are either fast or accurate, but not both. In general, fast methods do a poor job accounting for entropy, which is an important part of the free energy. The main objective of this project is to develop better ways to account for entropy in two popular techniques for studying molecular interactions: “end-point” simulations of the bound complexes and their unbound counterparts; and molecular docking based on the Fast Fourier Transform. Speciﬁcally, new ways to analyze calculation results will be derived, implemented, assessed, and optimized. Additionally, the methods will be combined with enhanced sampling techniques. Our new end-point and FFT-based methods will be assessed by their ability to reproduce benchmark results from slower but more accurate computational methods, as well as experimental results. The benchmark dataset will include protein-ligand complexes and protein-protein complexes with known binding afﬁnities and crystal structures, as well as protein-protein complexes for which the effect of missense mutations on binding have been measured. We will also perform benchmark calculations on mutants of the tumor suppressor p53 that gain the ability to activate new proteins and promote tumor growth. In addition to serving as benchmarks, these calculations may provide mechanistic insight into how proteins bind various ligands and how p53 mutants gain new binding partners. Our new methods will also be tested in recurring community challenges: the “Drug Design Data Resource” (D3R) grand challenge to predict protein-ligand complex structures and afﬁnities and the “Critical Assessment of PRediction of Interactions” (CAPRI) challenge for protein-protein structure prediction. These blinded challenges will allow for an unbiased comparison of our methods to those from other research groups. Finally, we will assess our methods in a drug discovery project. We will use established methods and our new methods to virtually screen a chemical library against a pair of structurally similar bacterial metabolic enzymes. One enzyme is relevant to active and the other to dormant bacteria. Compounds predicted to selectively bind the bacterial (opposed to human) enzymes will be experimentally tested in biochemical assays. We anticipate that our improved methods will be signiﬁcantly more accurate than established approaches, advancing research ranging from interactome prediction to drug discovery.

项目摘要计算机经常被用来预测两个分子的结合自由能有多紧密。这些预测有助于设计药物，预测基因变异的后果，以及理解分子如何相互作用来维持生命。不幸的是，目前可用的方法要么快速要么准确，但不能两者兼而有之。总体而言，快速方法不能很好地计算熵，而熵是自由能。这个项目的主要目标是开发更好的方法来解释两个流行的研究分子相互作用的技术：结合络合物及其相互作用的“终点”模拟基于快速傅立叶变换的分子对接。SpeciiﬁCally，新方法分析计算结果将被派生、实施、评估和优化。此外，这些方法将与增强的采样技术相结合。我们的新端点和基于FFT的方法将根据它们再现基准结果的能力进行评估来自速度较慢但更准确的计算方法以及实验结果。基准数据集将包括蛋白质-配体复合体和已知结合了ﬁ离子和晶体的蛋白质-蛋白质复合体结构以及错义突变对结合的影响具有的蛋白质-蛋白质复合体被测量过了。我们还将对肿瘤抑制基因p53的突变体进行基准计算，激活新蛋白质并促进肿瘤生长的能力。除了作为基准，这些计算可能为了解蛋白质如何与各种配体结合以及p53突变体如何获得新的有约束力的伙伴。我们的新方法还将在反复出现的社区挑战中进行测试：“药物设计数据资源” (D3R)预测蛋白质-配体复杂结构和Afﬁ的重大挑战和“关键评估相互作用的预测“(CAPRI)对蛋白质-蛋白质结构预测的挑战。这些盲目的挑战将允许将我们的方法与其他研究小组的方法进行公正的比较。最后，我们将在一个药物发现项目中评估我们的方法。我们将使用现有的方法和我们的新方法方法针对一对结构相似的细菌代谢酶虚拟筛选化学文库。一种酶与活跃的细菌有关，另一种与休眠细菌有关。预测将选择性结合的化合物细菌(而不是人类)的酶将在生化分析中进行实验测试。我们期待着我们改进的方法将明显比现有的方法更准确，从而推动研究从交互作用组预测到药物发现。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

A Structural Model for Bax∆2-Mediated Activation of Caspase 8-Dependent Apoptosis.

Bax-2 介导的 Caspase 8 依赖性细胞凋亡激活的结构模型。

DOI：
10.3390/ijms21155476
发表时间：
2020
期刊：
International journal of molecular sciences
影响因子：
5.6
作者：
Xie,Bing;Yao,Qi;Xiang,Jialing;Minh,DavidDL
通讯作者：
Minh,DavidDL

Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR.

DOI：
10.1002/prot.26158
发表时间：
2021-10
期刊：
Proteins
影响因子：
2.9
作者：
Willow SY;Yuan M;Juárez O;Minh DDL
通讯作者：
Minh DDL

Role of Subunit D in Ubiquinone-Binding Site of Vibrio cholerae NQR: Pocket Flexibility and Inhibitor Resistance.

亚基 D 在霍乱弧菌 NQR 泛醌结合位点中的作用：口袋灵活性和抑制剂抗性。

DOI：
10.1021/acsomega.9b02707
发表时间：
2019
期刊：
ACS omega
影响因子：
4.1
作者：
Raba,DanielA;Yuan,Ming;Fang,Xuan;Menzer,WilliamM;Xie,Bing;Liang,Pingdong;Tuz,Karina;Minh,DavidDL;Juárez,Oscar
通讯作者：
Juárez,Oscar

Simple Entropy Terms for End-Point Binding Free Energy Calculations.