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Functional Dynamics of Cytochrome P4503A4

细胞色素 P4503A4 的功能动力学

基本信息

批准号：
10205098
负责人：
WILLIAM M ATKINS
金额：
$ 41.47万
依托单位：
UNIVERSITY OF WASHINGTON
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：
2018-09-18 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10205098
关键词：
Active Sites Affinity Anaerobic Bacteria Behavior Binding Binding Sites Biochemical Biochemistry Biophysics Bromocriptine CYP3A4 gene Catalysis Cessation of life Characteristics Clinical Research Competence Complex Crystallization Cytochromes Data Deuterium Drug Design Drug Interactions Drug Targeting Equilibrium Exhibits Face Fluconazole Frequencies Heme Hepatic Human Hydrogen Hydrogen Bonding Hydrogen Peroxide In Vitro Kinetics Knowledge Ligand Binding Ligands Link Lipid Bilayers Lipids Maps Mass Spectrum Analysis Measures Mechanics Membrane Membrane Lipids Methods Midazolam Modeling Molecular Molecular Conformation Monitor Motion Optics Oxidation-Reduction Pathway interactions Pharmaceutical Preparations Pharmacology Play Process Proline Property Protein Dynamics Protein Isoforms Reaction Recording of previous events Regulation Resolution Role Source Specificity Structure Toxic effect Uncertainty Water Work Xenobiotics base cofactor detoxication drug clearance drug metabolism experimental study improved inhibitor/antagonist inter-individual variation interest molecular dynamics molecular mechanics nanodisk novel predictive modeling prevent quantum response side effect trait translational model

项目摘要

Project Summary The proposed work aims to clarify longstanding mechanistic uncertainties about drug metabolizing cytochrome P450s (CYPs). These CYPs are extraordinarily substrate promiscuous and they are major determinants of xenobiotic detoxication, drug metabolism and drug interactions. Because of their role in drug metabolism, they are also drug targets, wherein their pharmacological manipulation can afford control of therapy with other drugs. One focus here is the knowledge gap concerning the relationship between ligand-dependent heme spin state and catalytic properties. In the CYP canonical catalytic reaction cycle developed for substrate specific isoforms, the substrate displaces heme bound water and causes a shift from low spin to high spin heme with concomitant shift in the heme properties that facilitate reduction and progress through the catalytic cycle. In contrast, with drug metabolizing CYPs, many drugs cause no shift to high spin heme, but they are efficiently metabolized or cause hydrogen peroxide formation, both of which require progression through the catalytic cycle. Recent results demonstrate that many of these substrates hydrogen bond to the axial water, rather than displace it. The catalytic properties of these water-bridged complexes have not been determined. Therefore, the proposed work will determine for CYP3A4 the heme redox properties and the catalytic competence of water-bridged complexes, using computational approaches and advanced biochemical methods including spectropotentiometry and stopped-flow reaction kinetics. Computational approaches will also be employed to understand the effect of water-bridged complexes on heme reduction processes. A second focus of the proposed work aims to clarify the role of conformational dynamics in the complex allosteric behavior of CYPs and their remarkable substrate promiscuity. Both traits are linked to the protein dynamics, which remain poorly characterized, and unclarified by the available crystal structures. The allosteric properties confound prediction of drug clearance and drug interactions, so there is great interest in translational models that better predict drug interactions based on refined allosteric models. Here, the experimental methods of hydrogen-deuterium exchange mass spectrometry (H/DX) and pre-steady state ligand binding methods with CYP3A4 in lipid bilayer nanodiscs are combined with computational approaches such as accelerated Molecular Dynamics simulations (aMD) and steered molecular dynamics. The proposed studies fill a significant gap in understanding the, previously experimentally inaccessible, CYP dynamics in a lipid membrane and the role of conformational dynamics in achieving substrate promiscuity and allostery.

项目摘要拟议的工作旨在澄清长期存在的机制不确定性药物代谢细胞色素 P450（CYP）。这些CYP是非常底物混杂的，它们是细胞增殖的主要决定因素。异生物质解毒、药物代谢和药物相互作用。由于它们在药物代谢中的作用，也是药物靶点，其中它们的药理学操作可以提供对其他药物治疗的控制。这里的一个焦点是关于配体依赖的血红素自旋状态之间的关系的知识缺口和催化性能。在为底物特异性而开发的单正则催化反应循环中，异构体，底物置换血红素结合水，并导致从低自旋到高自旋血红素的转变，伴随的血红素性质的转变，促进还原和通过催化循环的进展。在相反，对于药物代谢CYP，许多药物不引起高自旋血红素的转变，但它们有效地代谢或导致过氧化氢的形成，这两者都需要通过催化剂的进展，周期最近的结果表明，许多这些基板氢键的轴向水，而不是这些水桥络合物的催化性能尚未确定。因此，我们认为，所提出的工作将确定CYP 3A 4的血红素氧化还原特性和催化能力，水桥复合物，使用计算方法和先进的生物化学方法，包括光谱电位法和停流反应动力学。还将采用计算方法，了解水桥复合物对血红素还原过程的影响。拟议工作的第二个重点是澄清复杂的构象动力学的作用 CYP的变构行为及其显著的底物混杂性。这两个特征都与蛋白质有关动力学，这仍然是不好的特点，并通过可用的晶体结构不明确。变构性质混淆了药物清除和药物相互作用的预测，因此对翻译的兴趣很大。基于精细变构模型更好地预测药物相互作用。在这里，实验氢-氘交换质谱（H/DX）和预稳态配体结合的方法脂质双层纳米盘中的CYP 3A 4方法与计算方法相结合，加速分子动力学模拟（aMD）和操纵分子动力学。建议的研究填补在理解以前实验上无法实现的脂质中的脂质动力学方面存在重大差距，膜和构象动力学在实现底物混杂和变构中的作用。

项目成果

期刊论文数量（4）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection.

DOI：
10.1016/j.abb.2021.109064
发表时间：
2021-12-15
期刊：
Archives of biochemistry and biophysics
影响因子：
3.9
作者：
Redhair M;Atkins WM
通讯作者：
Atkins WM

CW EPR parameters reveal cytochrome P450 ligand binding modes.

DOI：
10.1016/j.jinorgbio.2018.02.021
发表时间：
2018-06
期刊：
Journal of inorganic biochemistry
影响因子：
3.9
作者：
Lockart MM;Rodriguez CA;Atkins WM;Bowman MK
通讯作者：
Bowman MK

Low molecular weight ligands bind to CYP3A4 via a branched induced fit mechanism: Implications for O2 binding.

低分子量配体通过分支诱导拟合机制与 CYP3A4 结合：对 O2 结合的影响。

DOI：
10.1016/j.abb.2023.109582
发表时间：
2023
期刊：
Archives of biochemistry and biophysics
影响因子：
3.9
作者：
Redhair,Michelle;Nath,Abhinav;Hackett,JohnC;Atkins,WilliamM
通讯作者：
Atkins,WilliamM

Multiple drug binding modes in Mycobacterium tuberculosis CYP51B1.

结核分枝杆菌 CYP51B1 中的多种药物结合模式。

DOI：
10.1016/j.jinorgbio.2020.110994
发表时间：
2020
期刊：
Journal of inorganic biochemistry
影响因子：
3.9
作者：
Lockart,MollyM;Butler,JosephT;Mize,CarsonJ;Fair,MorganN;Cruce,AlexA;Conner,KipP;Atkins,WilliamM;Bowman,MichaelK
通讯作者：
Bowman,MichaelK