Molecular modeling of G protein-coupled receptors

G 蛋白偶联受体的分子建模

• 批准号: 7967134
• 负责人: Stefano Costanzi
• 金额: $ 67.65万
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7967134
• 关键词: 11 cis Retinal; 3-Dimensional; Adenosine; Adenosine A2A Receptor; Adrenergic Receptor; Affinity; Agonist; Arrhythmia; Asthma; Binding; Bioinformatics; Biological; Blood Platelets; Blood Vessels; C-terminal; Cattle; Cell membrane; Chemicals; Classification; Collaborations; Complex; Computer Assisted; Computing Methodologies; Crystallization; Databases; Development; Diabetes Mellitus; Discipline; Docking; Evaluation; Family Study; Fibrinolytic Agents; Freedom; G-Protein-Coupled Receptors; Goals; Heart; Homology Modeling; Hormones; Human body; Laboratories; Lead; Ligands; Light; Lung; Marketing; Mediating; Membrane Proteins; Metabolism; Modeling; Modification; Molecular; Molecular Models; Molecular Weight; Motion; Mutagenesis; Names; National Institute of Diabetes and Digestive and Kidney Diseases; Nature; Nonesterified Fatty Acids; North Carolina; Nucleotides; Organ; Pharmaceutical Preparations; Pharmacologic Substance; Phylogenetic Analysis; Physiological; Physiology; Play; Positioning Attribute; Process; Proteins; Publishing; Purinergic P1 Receptors; Quantitative Structure-Activity Relationship; Receptor Activation; Recording of previous events; Regulation; Research; Resources; Retinal; Rhodopsin; Rodent; Role; Running; Screening procedure; Series; Site-Directed Mutagenesis; Smooth Muscle; Solutions; Stimulus; Structure; Structure-Activity Relationship; Techniques; Testing; Thyrotropin; Thyrotropin-Releasing Hormone; Thyrotropin-Releasing Hormone Receptors; Time; Transmembrane Domain; Universities; Water; Work; analog; base; beta-adrenergic receptor; blind; blood glucose regulation; cheminformatics; computer studies; design; drug discovery; extracellular; flexibility; human ADORA2A protein; hypertension treatment; improved; interest; member; molecular dynamics; molecular modeling; molecular recognition; novel; polypeptide; purinoceptor P2Y1; receptor; research study; virtual

Adenosine receptors.The adenosine receptors are widely expressed in several organs of the human body, and mediate important physiological functions in the heart, lungs, blood vessels, and platelets. The crystal structure of the A2A subtype of the adenosine receptor has been recently crystallized in complex with the potent antagonist ZM241385. In coordination with the solution of the A2A structure, a blind assessment of GPCR structure modeling and docking has been organized by the same authors, who asked modelers from all around the world to submit their prediction of the A2A receptor in complex with ZM241385. Among all those submitted, my models resulted to be the most accurate, with very low RMSDs between experimental and predicted structures for both protein and ligand. In line with what was published by me last year, this experiment demonstrated that homology modeling and molecular docking can be effectively used to study the interactions of GPCRs with their ligands. The results have recently been published in Nature Reviews Drug Discovery. Beta-adrenergic receptors. The beta-adrenergic receptors (beta-ARs) reside predominantly in smooth muscles and play crucial roles in the physiology of heart and airways. Antagonists of the beta-ARs are widely used for various indications, particularly the treatment of hypertension and cardiac arrhythmias. Agonists of the beta2-AR are clinically used in the treatment of asthma. With rhodopsin, the beta-ARs are the most studied GPCRs and constitute an ideal platform for the development of computational methodologies subsequently applicable to the whole superfamily. In the course of this fiscal year, we published the development of a series of regression models that combine ligand-based and structure-based techniques for the prediction of ligand-receptor affinities, applicable to virtual screenings aimed at identifying new active molecules and to the design of more potent analogs. We are currently running a series of controlled, a posteriori, virtual screenings using the crystal structure as well as homology models of the beta2-AR. The results indicate that, molecular docking is very effective in prioritizing true binders versus non-binders, not only with the crystal structure, but also when using homology models. We are currently studying the possibility of incorporating the flexibility of the receptor into the virtual screening process. Rhodopsin. Rhodopsin is a GPCR activated by light, which causes the isomerization of the covalently bound 11-cis-retinal to all-trans-retinal, consequently triggering the activation of the receptor. As stated, rhodopsin, together with the adrenergic receptors, is the most well characterized GPCR. In the course of this fiscal year, we worked on a review entitled "Rhodopsin and the others: a historical perspective on structural studies of G protein-coupled receptors". This unique article covers in a systematic manner over a century of history, illustrating the amount of structural information that, since the late eighteen hundreds, has been accumulated for rhodopsin, providing a platform for the study of the structure-function relationships of the whole superfamily. Moreover, we continued our molecular dynamics simulations intended to uncover the structure-function relationships of rhodopsin, this time concentrating on the role of water molecules in the activation process. Preliminary results suggest a functional role of water molecules in the conformational changes that lead from the inactive to the active state of the receptor. P2Y receptors. P2Y receptors are GPCRs activated by extracellular nucleotides. Of particular interest are P2Y1 antagonists, which have shown the potential of being developed into novel potent antithrombotic agents. In collaboration with the laboratories of Drs. Kenneth Jacobson (NIDDK) and Kendall Harden (University of North Carolina), for the past few years I have been conducting bioinformatics and molecular modeling studies intended to shed light onto the structure-function relationships of the P2Y receptors. In the course of this fiscal year, as a result of a virtual screening conducted by us, we identified novel diverse ligands of the P2Y1 receptor. We are currently designing analogs of these hits, with the aim of improving their affinity of the receptor. Moreover, molecular docking of novel analogs, combined with NMR experiments, allowed us to further understand the process of molecular recognition for this receptor, in particular with regard to the conformational requirements. Work in this direction is still in progress. FFAR1 (a.k.a. GPR40). FFAR1 (a.k.a. GPR40) is a GPCR activated by long chain free fatty acids (FFAs), which is involved in the regulation of metabolic processes and glucose homeostasis. In particular, FFAR1 is considered an appealing target for the treatment of type two diabetes. Our research, in collaboration with the laboratory of Dr. Marvin Gershengorn (NIDDK), is intended for the elucidation of the structure-function relationships of FFAR1 and for the discovery of novel ligands. In the course of this fiscal year, we published the identification of two potential ionic locks between the second extracellular loop and the transmembrane domain, the disruption of which possibly triggers the activation of the receptor. These results are very much in line with the above mentioned observations concerning the requirement of freedom of motion of the second extracellular loop for the activation of the adrenergic receptors, suggesting that a common activation mechanism might be shared by several members of the GPCR superfamily. TRH-Rs. Thyrotropin-releasing hormone (THR) is a tripeptide hormone which stimulates the release of thyrotropin by activating specific GPCRs known as thyrotropin-releasing hormone receptors (TRH-Rs). Two different TRH-R subtypes have been identified in rodents. The goal of our research, in collaboration with the laboratory of Dr. Marvin Gershengorn (NIDDK), is the elucidation of the structure-function relationships of the two subtypes and the identification of novel ligands able to discriminate against them. Combining molecular modeling with site-directed mutagenesis experiments, we are currently investigating the functional role of the C-terminal domain of the receptor.

腺苷受体。腺苷受体广泛表达于人体的多个器官中，并介导心脏、肺、血管和血小板中的重要生理功能。 腺苷受体A2A亚型的晶体结构最近已与强效拮抗剂ZM241385形成复合物结晶。 配合A2A结构的解决，同一作者组织了GPCR结构建模和对接的盲评估，他们要求来自世界各地的建模者提交他们对与ZM241385复合物的A2A受体的预测。在所有提交的模型中，我的模型是最准确的，蛋白质和配体的实验结构和预测结构之间的 RMSD 非常低。与我去年发表的内容一致，这个实验证明同源建模和分子对接可以有效地用于研究 GPCR 与其配体的相互作用。该结果最近发表在《自然评论药物发现》上。 β-肾上腺素能受体。 β-肾上腺素能受体（β-AR）主要存在于平滑肌中，在心脏和气道的生理学中发挥着至关重要的作用。 β-AR 拮抗剂广泛用于各种适应症，特别是高血压和心律失常的治疗。 β2-AR激动剂在临床上用于治疗哮喘。对于视紫红质，β-AR 是研究最多的 GPCR，并构成了开发随后适用于整个超家族的计算方法的理想平台。 在本财年中，我们发布了一系列回归模型的开发，这些模型结合了基于配体和基于结构的技术来预测配体-受体亲和力，适用于旨在识别新活性分子的虚拟筛选以及更有效的类似物的设计。 我们目前正在使用 beta2-AR 的晶体结构和同源模型进行一系列受控的后验虚拟筛选。结果表明，分子对接对于区分真正的结合物与非结合物的优先顺序非常有效，不仅在晶体结构方面，而且在使用同源模型时也是如此。我们目前正在研究将受体的灵活性纳入虚拟筛选过程的可能性。 视紫质。视紫红质是一种被光激活的 GPCR，它会导致共价结合的 11-顺式-视黄醛异构化为全反式-视黄醛，从而触发受体的激活。 如前所述，视紫红质与肾上腺素能受体一起是特征最明确的 GPCR。在本财年中，我们进行了一篇题为“视紫红质和其他：G 蛋白偶联受体结构研究的历史视角”的综述。这篇独特的文章系统地涵盖了一个多世纪的历史，说明了自十八世纪末以来，视紫红质积累的大量结构信息，为研究整个超家族的结构与功能关系提供了平台。 此外，我们继续进行分子动力学模拟，旨在揭示视紫红质的结构与功能关系，这次重点关注水分子在活化过程中的作用。初步结果表明水分子在导致受体从非活性状态变为活性状态的构象变化中发挥功能性作用。 P2Y 受体。 P2Y 受体是由细胞外核苷酸激活的 GPCR。特别令人感兴趣的是 P2Y1 拮抗剂，它已显示出开发成新型有效抗血栓药物的潜力。与博士实验室合作。 Kenneth Jacobson (NIDDK) 和 Kendall Harden（北卡罗来纳大学）在过去几年中一直在进行生物信息学和分子建模研究，旨在阐明 P2Y 受体的结构与功能关系。 在本财年中，根据我们进行的虚拟筛选，我们发现了 P2Y1 受体的新型多样化配体。我们目前正在设计这些命中的类似物，目的是提高它们与受体的亲和力。 此外，新型类似物的分子对接结合核磁共振实验，使我们能够进一步了解该受体的分子识别过程，特别是构象要求。这个方向的工作仍在进行中。 FFAR1（又名 GPR40）。 FFAR1（又名 GPR40）是一种由长链游离脂肪酸 (FFA) 激活的 GPCR，参与代谢过程和葡萄糖稳态的调节。特别是，FFAR1 被认为是治疗二型糖尿病的一个有吸引力的靶点。我们与 Marvin Gershengorn 博士 (NIDDK) 实验室合作进行的研究旨在阐明 FFAR1 的结构-功能关系并发现新型配体。 在本财年中，我们发表了对第二个细胞外环和跨膜结构域之间两个潜在离子锁的鉴定，其破坏可能会触发受体的激活。这些结果与上述关于肾上腺素能受体激活需要第二细胞外环运动自由的观察结果非常一致，表明GPCR超家族的几个成员可能共享共同的激活机制。 TRH-R。促甲状腺素释放激素 (THR) 是一种三肽激素，通过激活称为促甲状腺素释放激素受体 (TRH-R) 的特定 GPCR 来刺激促甲状腺素的释放。已在啮齿类动物中鉴定出两种不同的 TRH-R 亚型。我们与 Marvin Gershengorn 博士 (NIDDK) 实验室合作的研究目标是阐明这两种亚型的结构功能关系，并鉴定能够区分它们的新型配体。结合分子建模与定点诱变实验，我们目前正在研究受体 C 末端结构域的功能作用。