The 3D Structure of Human DP Prostaglandin G-Protein-Coupled Receptor Bound to Cyclopentanoindole Antagonist, Predicted Using the DuplexBiHelix Modification of the GEnSeMBLE Method

Prostaglandins play a critical physiological
role in both cardiovascular and immune systems, acting through their
interactions with 9 prostanoid G protein-coupled receptors (GPCRs).
These receptors are important therapeutic targets for a variety of
diseases including arthritis, allergies, type 2 diabetes, and cancer.
The DP prostaglandin receptor is of interest because it has unique
structural and physiological properties. Most notably, DP does not
have the 3–6 ionic lock common to Class A GPCRs. However, the
lack of X-ray structures for any of the 9 prostaglandin GPCRs hampers
the application of structure-based drug design methods to develop
more selective and active medications to specific receptors. We predict
here 3D structures for the DP prostaglandin GPCR, based on the GEnSeMBLE
complete sampling with hierarchical scoring (CS-HS) methodology. This
involves evaluating the energy of 13 trillion packings to finally
select the best 20 that are stable enough to be relevant for binding
to antagonists, agonists, and modulators. To validate the predicted
structures, we predict the binding site for the Merck cyclopentanoindole
(CPI) selective antagonist docked to DP. We find that the CPI binds
vertically in the 1–2–7 binding pocket, interacting
favorably with residues R3107.40 and K762.54 with additional interactions with S3137.43, S3167.46, S191.35, etc. This binding site differs significantly
from that of antagonists to known Class A GPCRs where the ligand binds
in the 3–4–5–6 region. We find that the predicted
binding site leads to reasonable agreement with experimental Structure–Activity
Relationship (SAR). We suggest additional mutation experiments including
K762.54, E1293.49, L1233.43, M2706.40, F2746.44 to further validate the structure,
function, and activation mechanism of receptors in the prostaglandin
family. Our structures and binding sites are largely consistent and
improve upon the predictions by Li et al. (J. Am. Chem. Soc. 2007, 129 (35), 10720) that used our earlier MembStruk prediction methodology.

前列腺素（Prostaglandins）在心血管系统与免疫系统中均发挥关键生理作用，通过与9种前列腺素类G蛋白偶联受体（GPCRs）相互结合实现生理功能。此类受体是关节炎、过敏、2型糖尿病及癌症等多种疾病的重要治疗靶点。其中DP前列腺素受体因其独特的结构与生理特性受到广泛关注，最显著的特征是其并不具备A类G蛋白偶联受体共有的3-6离子锁结构。然而，目前9种前列腺素GPCRs均缺乏X射线晶体结构，这极大阻碍了基于结构的药物设计方法的应用，难以开发出针对特定受体的高选择性、高活性药物。本研究基于GEnSeMBLE完整采样分层打分（CS-HS）方法，对DP前列腺素GPCR的三维结构进行了预测：该方法需评估13万亿种构象堆积的能量，最终筛选出稳定性足以用于结合拮抗剂、激动剂与调节剂的最优20种结构。为验证所预测的结构，本研究对结合于DP受体的默克（Merck）环戊基吲哚（CPI）选择性拮抗剂开展了结合位点预测，结果发现CPI以垂直方式结合于1-2-7结合口袋，可与残基R3107.40与K762.54形成稳定相互作用，并额外与S3137.43、S3167.46、S1913.35等残基产生相互作用。该结合位点与已知A类GPCR拮抗剂的结合位点存在显著差异，后者的配体通常结合于3-4-5-6区域。本研究预测的结合位点与实验构效关系（SAR）结果具有合理的一致性。我们建议开展包括K762.54、E1293.49、L1233.43、M2706.40、F2746.44在内的额外突变实验，以进一步验证前列腺素家族受体的结构、功能及激活机制。本研究预测的结构与结合位点整体一致性良好，且相较于Li等人（J. Am. Chem. Soc. 2007, 129 (35), 10720）采用早期MembStruk预测方法得到的结果有所改进。