Is there a common allosteric binding site for all GPCRs?

所有 GPCR 是否都有一个共同的变构结合位点？

基本信息

批准号：
10690270
负责人：
Zhijun Li
金额：
$ 10万
依托单位：
SAINT JOSEPH'S UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-15 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10690270
关键词：
Accounting Address Affinity Agonist Allosteric Regulation Allosteric Site Binding Binding Sites Biological CCR9 gene Cells Complex Cryoelectron Microscopy Databases Disease Docking Drug Design Drug Screening Drug Targeting Event G-Protein-Coupled Receptors GTP-Binding Protein alpha Subunits, Gs GTP-Binding Proteins Homologous Gene Human Individual Libraries Ligands Location Membrane Molecular Conformation Peptides Pharmaceutical Preparations Pharmacologic Substance Proteins Proteome Receptor Mediated Signal Transduction Reporting Research Research Design Running Signal Transduction Site Site-Directed Mutagenesis Stimulus Structure Testing Therapeutic Time Transmembrane Domain Work antagonist base chemokine receptor combinatorial computer studies design drug development drug discovery extracellular improved in silico in vitro Assay in vitro activity in vitro testing interest macromolecule member molecular dynamics monocyte chemoattractant protein 1 receptor novel novel strategies positive allosteric modulator screening simulation small molecule success tool virtual

项目摘要

Project Summary G-protein coupled receptors (GPCRs) represent the largest superfamily of human proteome with more than 800 members. Given the key role of GPCRs in signal transduction across membranes, GPCRs are the number one drug target, accounting for approximately 25% of the current drugs in the market. Despite significant progresses in drug discovery targeting GPCRs, many pharmaceutically important GPCRs remain elusive. In recent years, a novel venue has been reported to exploit the allosteric sites on them for the development of drugs to treat various diseases. Identifying the allosteric sites on GPCRs, however, remains a challenge. This proposal aims to explore the existence of a common allosteric site below the middle of the transmembrane domain that spatially overlaps with the G-protein binding site for all human GPCRs. The long- term objective of this project is to understand the mechanism of allosteric regulations in GPCRs. For this proposal, proposed works will include two specific Aims. Aim I is to identify allosteric antagonists and agonists of eight representative GPCRs from Class A, B, C and F that bind to the proposed common allosteric site on these GPCRs through in silico screening and in vitro test. For this aim, two GPCRs with known structure, one in its inactive conformation and one in its active conformation, will be chosen from each of the four non-sensory GPCR Classes, A, B, C and F. Then in silico screening against ZINC database will be performed using each structure. For top-ranked compounds, their binding stability and binding affinity in the binding site will be computationally studied using molecular dynamics simulations. Finally, for those top-ranked antagonists and agonists, in vitro activity studies and site-specific mutagenesis studies will be carried out. Aim II is to improve the selectivity and potency of the identified GLP-1R allosteric agonist through structure-based molecule design and experimental test. This aim will be carried out by: 1) obtain the active structure of both GLP-1R and GCGR and run molecular dynamics simulations; 2) compare the conformation snapshots from GLP-1R simulations with those of GCGR and identify one conformation of GLP-1R that have the largest structural difference at the proposed allosteric site from all GCGR conformations; 3) dock the GLP-1R allosteric agonist to the allosteric site in the identified GLP-1R conformation from las step and perform in virtual combinatorial library design to generate optimized compounds; 4) re-dock the top-ranked compounds from last step to the same allosteric site on the GCGR conformation most similar to GLP-1R conformation; and 5) in vitro assay test the lowest ranked compounds from last step. Given the strategic location of this common binding site, the success of this proposal could provide a useful venue for biological studies and therapeutic discovery targeting various GPCRs.

项目摘要 G蛋白偶联受体（GPCR）代表了人类的最大超家族具有800多名成员的蛋白质组。鉴于GPCR在信号中的关键作用跨膜的转导，GPCR是第一名的药物目标目前大约25％的市场药物。尽管取得了重大进展靶向GPCR的药物发现，仍然存在许多重要的GPCR 难以捉摸。近年来，据报道，一个新颖的场地可以利用变构站点在他们身上开发药物以治疗各种疾病。识别变构但是，GPCR上的站点仍然是一个挑战。该建议旨在探索在跨膜结构域中间的中间存在一个常见的变构位点这在空间上与所有人类GPCR的G蛋白结合位点重叠。长期该项目的术语目标是了解变构法规的机制 GPCR。对于此提案，拟议的作品将包括两个具体目标。目的我要确定来自A，B，C类的八个代表性GPCR的变构拮抗剂和激动剂 F与硅中的这些GPCR上提出的常见变构位点结合的F 筛查和体外测试。为此，两个具有已知结构的GPCR，其中一个将从每个四个非感官GPCR类，A，B，C和F。数据库将使用每个结构进行。对于排名最高的化合物，他们结合位点中的结合稳定性和结合亲和力将进行计算研究使用分子动力学模拟。最后，对于那些排名最高的对手和激动剂将进行体外活性研究和位点特异性诱变研究。 AIM II是提高已鉴定的GLP-1R变构激动剂的选择性和效力通过基于结构的分子设计和实验测试。这个目标将被携带出局：1）获得GLP-1R和GCGR的活性结构并运行分子动力学模拟； 2）比较GLP-1R模拟的构象快照与GCGR的那些，并确定一个具有最大的GLP-1R的构象所有GCGR构象所提出的变构位点的结构差异； 3）将GLP-1R变构激动剂扩展到已确定的GLP-1R中的变构位点 LAS步骤的构象并在虚拟组合库设计中执行以生成优化化合物； 4）从最后一步重新涂上排名最高的化合物 GCGR构象上的变构位点与GLP-1R构象最相似； 5）体外测定测试上一步的最低化合物。鉴于这个共同绑定站点的战略位置，该提案的成功可以为生物学研究和治疗发现靶向提供有用的场所各种GPCR。