Aderibigbe AyoOluwa O, Pandey Pankaj, Doerksen Robert J
Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, USA.
National Center for Natural Products Research, University of Mississippi, University, Mississippi, USA.
J Biomol Struct Dyn. 2022 Aug;40(13):5729-5747. doi: 10.1080/07391102.2021.1873187. Epub 2021 Jan 22.
In October 2019, the first X-ray crystal structure of a ternary cannabinoid receptor 1 (CB1) complex (PDB ID: 6KQI) was published, including the well-known orthosteric agonist, CP55940, and the well-studied negative allosteric modulator, ORG27569. Prior to the release of 6KQI, we applied binding pocket analysis and molecular docking to carefully prepared computational models of the ternary CB1 complex, in order to predict the binding site for ORG27569 with the CP55940-bound CB1 receptor. We carefully studied the binding pose of agonist ligands in the CB1 orthosteric pocket, including CP55940. Our computational studies identified the most favorable binding site for ORG27569, in the CP55940-CB1 complex, to be at the intracellular end of the receptor. However, in the 6KQI structure, ORG27569 was found at an extrahelical, intramembrane site on the complex, a site that partially overlaps with the site predicted in our calculations to be second-best. We performed molecular dynamics simulations of the CP55940-bound CB1 complex with ORG27569 at different binding sites. Our analysis of the simulations indicated that ORG27569 bound favorably and stably in each simulation, but, as in the earlier calculations, bound best at the intracellular site, which is different than that found in the crystal structure. These results suggest that the intracellular site might serve as an alternative binding site in CB1. Our studies show that the computational techniques we used are valuable in identifying ligand-binding pockets in proteins, and could be useful for the study of the interaction mode of other allosteric modulators.
2019年10月，三元大麻素受体1（CB1）复合物的首个X射线晶体结构（PDB ID：6KQI）发表，其中包括著名的正构激动剂CP55940和经过充分研究的负变构调节剂ORG27569。在6KQI发布之前，我们对精心构建的三元CB1复合物计算模型进行了结合口袋分析和分子对接，以预测ORG27569与结合CP55940的CB1受体的结合位点。我们仔细研究了激动剂配体在CB1正构口袋中的结合姿态，包括CP55940。我们的计算研究确定，在CP55940-CB1复合物中，ORG27569最有利的结合位点位于受体的细胞内末端。然而，在6KQI结构中，ORG27569位于复合物的膜内螺旋外位点，该位点与我们计算预测的次优位点部分重叠。我们对结合CP55940的CB1复合物与ORG27569在不同结合位点进行了分子动力学模拟。我们对模拟结果的分析表明，ORG27569在每次模拟中都能良好且稳定地结合，但与早期计算结果一样，在细胞内位点结合最佳，这与晶体结构中发现的位点不同。这些结果表明，细胞内位点可能是CB1中的一个替代结合位点。我们的研究表明，我们使用的计算技术在识别蛋白质中的配体结合口袋方面很有价值，并且可能有助于研究其他变构调节剂的相互作用模式。
