Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction.
Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction.
复制标题
DOI：
10.1021/acscentsci.1c00802
复制
发表时间：
2021-11-24
影响因子：
18.2
通讯作者：
Tikhonova IG
中科院分区：
文献类型：
--
作者：
Ciancetta A;Gill AK;Ding T;Karlov DS;Chalhoub G;McCormick PJ;Tikhonova IG
通过变构位点靶向G蛋白偶联受体（GPCR）在鉴定具有增加的选择性和潜在减少的副作用的药物方面提供优于正构位点的优势。在这项研究中，我们开发了一种探针限制的动态映射协议，允许在GPCR细胞外和细胞内侧，以及在受体-脂质界面的变构位点的预测。所施加的谐波壁电位增强了GPCR的选定区域中的探针分子的采样，同时防止了分子动力学模拟中的膜变形。与常用的共溶剂相比，来自GPCR变构配体结构的特异性探针在变构位点作图中表现更好。选择M2毒蕈碱受体、β2肾上腺素能受体和P2 Y1嘌呤能受体进行方案回顾性验证。接下来前瞻性验证该方案以定位[5-氟-4-（羟甲基）-2-甲氧基苯基]-（4-氟-1H-吲哚-1-基）甲酮在D2多巴胺受体上的结合位点，随后的诱变证实了该预测。该协议提供了对膜蛋白变构位点周围关键氨基酸残基的快速有效预测，并促进了变构调节剂的基于结构的设计。使用特定的探针从G蛋白偶联受体变构配体，我们的探针限制的动态映射优于标准的共溶剂和检测变构位点在细胞外/细胞内侧和脂质界面。
Targeting G protein-coupled receptors (GPCRs) through allosteric sites offers advantages over orthosteric sites in identifying drugs with increased selectivity and potentially reduced side effects. In this study, we developed a probe confined dynamic mapping protocol that allows the prediction of allosteric sites at both the GPCR extracellular and intracellular sides, as well as at the receptor–lipid interface. The applied harmonic wall potential enhanced sampling of probe molecules in a selected area of a GPCR while preventing membrane distortion in molecular dynamics simulations. The specific probes derived from GPCR allosteric ligand structures performed better in allosteric site mapping compared to commonly used cosolvents. The M2 muscarinic, β2 adrenergic, and P2Y1 purinergic receptors were selected for the protocol’s retrospective validation. The protocol was next validated prospectively to locate the binding site of [5-fluoro-4-(hydroxymethyl)-2-methoxyphenyl]-(4-fluoro-1H-indol-1-yl)methanone at the D2 dopamine receptor, and subsequent mutagenesis confirmed the prediction. The protocol provides fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins and facilitates the structure-based design of allosteric modulators. Using specific probes from G protein-coupled receptor allosteric ligands, our probe confined dynamic mapping outperforms standard cosolvents and detects allosteric sites at extra-/intracellular sides and the lipid interface.
登录
查看更多内容
影响因子：
3.6
作者：
Free, R. Benjamin;Chun, Lani S.;Sibley, David R.
通讯作者：
Sibley, David R.
影响因子：
64.8
作者：
Hollenstein, Kaspar;Kean, James;Marshall, Fiona H.
通讯作者：
Marshall, Fiona H.
影响因子：
3.3
作者：
Klauda, Jeffery B.;Venable, Richard M.;Freites, J. Alfredo;O'Connor, Joseph W.;Tobias, Douglas J.;Mondragon-Ramirez, Carlos;Vorobyov, Igor;MacKerell, Alexander D., Jr.;Pastor, Richard W.
通讯作者：
Pastor, Richard W.
影响因子：
7.3
作者：
Fyfe, Tim J.;Zarzycka, Barbara;Capuano, Ben
通讯作者：
Capuano, Ben
影响因子：
7.3
作者：
Alvarez-Garcia, Daniel;Barril, Xavier
通讯作者：
Barril, Xavier