Cruz Alejandro, Warshel Arieh
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States.
Department of Chemical Engineering-ETSEIB, Universitat Politècnica de Catalunya, Barcelona, 08028 Spain.
J Chem Inf Model. 2025 Aug 25;65(16):8637-8652. doi: 10.1021/acs.jcim.5c01163. Epub 2025 Aug 4.
G-protein-coupled receptors (GPCRs) constitute the largest superfamily of integral membrane proteins in the human genome that mediate most transmembrane signaling processes. Malfunction of these signaling processes is related to many human pathologies (Parkinson's, heart diseases, etc.), causing GPCRs to be the largest family of druggable proteins. Traditionally, GPCRs were targeted by orthosteric ligands. However, this regulation usually causes side effects, provoking many GPCRs-associated pathologies to remain without an effective treatment. Allosteric regulation offers a promising alternative to circumvent this problem, and consequently, comprehending its details is of utmost importance. For this reason, we developed in the present work a methodology to study the allosteric modulation in a comprehensive way. Specifically, this methodology allows calculating the free energy profiles (Δ) for activation processes of GPCRs and their derived complexes combining the usage of targeted molecular dynamics (TMD) simulations to generate the intermediate structures of a given activation process, with the protein-dipole Langevin-dipole (PDLD) method within the linear response approximation (LRA) framework (PDLD/S-LRA-2000) and our refined coarse-grained (CG) model for GPCRs to calculate the binding and conformational free energy contributions (Δ, Δ), respectively, which take into account the cellular membrane effects by an implicit membrane. Sphingosine 1-phosphate receptor 1 (S1PR1) has been chosen as a case study due to its available data for benchmark purposes. Apart from validating our developed methodology, the conducted S1PR1 study has partially filled its knowledge gap regarding allosteric modulation and has allowed rational design of a de novo pure positive allosteric modulator for one of its prospective allosteric cavities according to our calculations. The methodology presented in this paper provides a very useful tool to study the GPCRs allosteric modulation, and the GPCRs activation processes in general, which will hopefully encourage a more thorough exploration of the topic.
G蛋白偶联受体（GPCRs）是人类基因组中最大的整合膜蛋白超家族，介导大多数跨膜信号传导过程。这些信号传导过程的功能异常与许多人类疾病（帕金森病、心脏病等）相关，使得GPCRs成为最大的可成药蛋白家族。传统上，GPCRs由正构配体作为靶点。然而，这种调节通常会引起副作用，导致许多与GPCRs相关的疾病仍然没有有效的治疗方法。变构调节为解决这个问题提供了一个有前景的替代方案，因此，了解其细节至关重要。出于这个原因，我们在目前的工作中开发了一种全面研究变构调节的方法。具体而言，该方法允许结合使用靶向分子动力学（TMD）模拟来生成给定激活过程的中间结构，以及在线性响应近似（LRA）框架（PDLD/S-LRA-2000）内的蛋白质偶极朗之万偶极（PDLD）方法和我们改进的GPCRs粗粒度（CG）模型，来计算GPCRs及其衍生复合物激活过程的自由能分布（Δ），分别计算结合自由能和构象自由能贡献（Δ，Δ），其中通过隐式膜考虑细胞膜效应。由于其有用于基准测试的可用数据，鞘氨醇-1-磷酸受体1（S1PR1）被选作案例研究。除了验证我们开发的方法外，所进行的S1PR1研究部分填补了其在变构调节方面的知识空白，并根据我们的计算允许为其一个潜在的变构腔合理设计一种全新的纯正变构调节剂。本文提出的方法为研究GPCRs变构调节以及一般的GPCRs激活过程提供了一个非常有用的工具，有望鼓励对该主题进行更深入的探索。
