Dynamics of Ligand Binding and Protein Kinase Regulation

配体结合动力学和蛋白激酶调节

基本信息

批准号：
10625416
负责人：
Markus A Seeliger
金额：
$ 40.77万
依托单位：
STATE UNIVERSITY NEW YORK STONY BROOK
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-07-15 至 2026-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10625416
关键词：
Affect Affinity Binding Biological Assay Biological Process Biology Catalytic Domain Cells Chemicals Clinical Collaborations Computer Models Computing Methodologies Conserved Sequence Cyclic AMP-Dependent Protein Kinases Data Data Set Development Disease Dissociation Drug Modelings Drug resistance Enzymes Family Foundations Goals Health Human In Vitro Kinetics Knowledge Ligand Binding Malignant Neoplasms Medicine Molecular Molecular Conformation Mutation Pharmaceutical Preparations Phenotype Phosphotransferases Process Productivity Protein Engineering Protein Kinase Protein Tyrosine Kinase Proteins Public Health Regulation Research Roentgen Rays Role Signal Pathway Signal Transduction Specificity Testing design inhibitor kinase inhibitor pharmacokinetics and pharmacodynamics pressure protein structure resistance mechanism resistance mutation src-Family Kinases therapeutic target

项目摘要

PROJECT SUMMARY. Protein kinases are a large family of ubiquitous signaling enzymes in human cells. Their dysregulation often underlies diseases such as cancer, making them excellent therapeutic targets. However, the high structural and sequence conservation of the protein kinase catalytic domains has complicated the development of specific inhibitors. Many clinically-successful kinase inhibitors achieve specificity in part by binding only to distinct kinase conformations. While the analysis of thousands of X-ray crystal structures of protein kinases has shown that a single kinase domain can access different active and inactive conformations, little is known about how kinases interconvert between the conformations. The rationale of this proposal is that a quantitative understanding of the stability of these conformations and the dynamics of their interconversion are key to understanding kinase activity, regulation, ligand binding and drug resistance in health and disease states. The objective of this project is to obtain a comprehensive understanding of the role of conformational dynamics in kinase function, regulation and drug resistance through altered drug dissociation rates. This proposal is part of a continuum of research centered around three questions: Q1: How do regulatory domains, interacting proteins and disease-relevant mutations affect the conformational dynamics of tyrosine kinases? Our goal is to determine how the solution dynamics of Src kinase domain responds to these biologically important perturbations. Q2: What are the molecular and cellular determinants of ligand-binding kinetics? We will test our computational model for the drug binding process experimentally, both in vitro and in cells, by assessing drug affinities and binding and dissociation kinetics. Our goal is to determine quantitative parameters for the drug binding process and how the alteration of these parameters by mutation underlies drug resistance. Q3: How can phenotypic clustering of inhibition data be used to reveal hidden kinase features? Our goal is to mine kinome-wide inhibition datasets to group kinases by their inhibition phenotype, which reflects on the evolutionary pressure and adaption that other biological functions impose on kinases. We will use structural approaches (X-ray and NMR), cellular drug binding and activity assays, ligand binding kinetics, protein engineering, chemical biology and diverse computational methods. A network of productive collaborations supports this project. The impact of this project is to provide clinicians with the mechanism of resistance mutations, medicinal chemists with kinase inhibitor pharmacodynamics and pharmacokinetics and cell biologists with parameters to understand kinase signaling. The long-term goal is to lay the foundation for the design of safe, effective, and sufficiently specific inhibitors of disease-associated protein kinases.

项目摘要。蛋白激酶是人类细胞中普遍存在的信号传导酶的大家族。他们的失调通常是癌症等疾病的基础，使其成为出色的治疗靶点。但是，蛋白激酶催化结构域的高结构和序列保存使特定抑制剂的发展。许多临床成功的激酶抑制剂部分获得了特异性仅与不同的激酶构象结合。而分析数千个X射线晶体结构蛋白激酶已经表明，单个激酶结构域可以访问不同的活性和非活动构象，关于激酶如何在构象之间相互互换的知之甚少。该提议的理由是对这些构象的稳定性及其互连动态的定量理解是了解健康和疾病状态中的激酶活性，调节，配体结合和耐药性的关键。该项目的目的是获得对构象动态作用的全面理解在激酶功能中，通过改变的药物解离率改变了调节和耐药性。该建议是一部分一系列研究集中在三个问题上：问题1：调节域，相互作用的蛋白质和与疾病相关的突变如何影响构象酪氨酸激酶的动力学？我们的目标是确定SRC激酶域的溶液动力学如何响应这些在生物学上重要的扰动。 Q2：配体结合动力学的分子和细胞决定因素是什么？我们将测试我们的计算通过评估药物亲和力和细胞中的药物结合过程模型结合和解离动力学。我们的目标是确定药物结合过程的定量参数以及这些参数通过突变的改变是耐药性的基础。 Q3：如何使用抑制数据的表型聚类来揭示隐藏的激酶特征？我们的目标是通过其抑制激酶的抑制作用表型，对激酶进行分组的抑制数据集，这反映了其他生物学功能对激酶施加的进化压力和适应性。我们将使用结构方法（X射线和NMR），细胞药物结合和活性测定，配体结合动力学，蛋白质工程，化学生物学和多种计算方法。生产力网络合作支持该项目。该项目的影响是为临床医生提供抗性突变，具有激酶抑制剂药效学和药代动力学的药物学家以及具有参数的细胞生物学家了解激酶信号传导。长期目标是为设计与疾病相关蛋白激酶的安全，有效和足够特异性抑制剂的设计。

项目成果

期刊论文数量（20）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk.

DOI：
10.1021/acs.biochem.2c00685
发表时间：
2023-03-21
期刊：
BIOCHEMISTRY
影响因子：
2.9
作者：
Kan, Yagmur;Paung, YiTing;Kim, Yunyoung;Seeliger, Markus A.;Miller, W. Todd
通讯作者：
Miller, W. Todd

Probing conformational dynamics to understand kinase inhibition.

DOI：
10.7554/elife.92753
发表时间：
2023-10-18
期刊：
eLife
影响因子：
7.7
作者：
Outhwaite IR;Seeliger MA
通讯作者：
Seeliger MA

A Novel In Vitro CypD-Mediated p53 Aggregation Assay Suggests a Model for Mitochondrial Permeability Transition by Chaperone Systems.

DOI：
10.1016/j.jmb.2016.08.001
发表时间：
2016-10-09
期刊：
Journal of molecular biology
影响因子：
5.6
作者：
Lebedev I;Nemajerova A;Foda ZH;Kornaj M;Tong M;Moll UM;Seeliger MA
通讯作者：
Seeliger MA

Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites.

DOI：
10.1038/s41467-017-02240-6
发表时间：
2017-12-18
期刊：
Nature communications
影响因子：
16.6
作者：
Tong M;Pelton JG;Gill ML;Zhang W;Picart F;Seeliger MA
通讯作者：
Seeliger MA

Targeting the Hemopexin-like Domain of Latent Matrix Metalloproteinase-9 (proMMP-9) with a Small Molecule Inhibitor Prevents the Formation of Focal Adhesion Junctions.

DOI：
10.1021/acschembio.7b00758
发表时间：
2017-11-17
期刊：
ACS chemical biology
影响因子：
4
作者：
Alford VM;Kamath A;Ren X;Kumar K;Gan Q;Awwa M;Tong M;Seeliger MA;Cao J;Ojima I;Sampson NS
通讯作者：
Sampson NS