Ensemble Docking Interrogates Structural Determinants of Ligand-Protein Interactions

在化学和生物学的界面上，使用小分子文库来询问蛋白质，以推断底物识别的结构决定因素，结构/活性关系（SAR）的基本原理或调节机制。我们的假设是，如果同时确定了相互作用的能量学和结构-活性关系，可以提高小分子-蛋白质对接的准确性。这种方法将抵消比较模型的不准确性。因此，本提案的目标是开发一种算法“ROSETTALIGANDENSEMBLE”，该算法将具有已知亲和力/活性的小分子集合对接到膜蛋白的比较模型中。我们将应用该方法鉴定ADP受体P2Y12的拮抗和逆拮抗配体特性所需的结构决定因素。进一步，该算法将用于研究神经肽Y4受体的变构调节机制。这两种GPCR系统都被选为研究小分子-GPCR相互作用的模型情景，因为不仅有已知生物活性的小分子集中文库，而且已经建立了一个即时的实验反馈回路来测试新的配体，而且还使用受体变体来确定相互作用位点。

At the interface of chemistry and biology proteins are interrogated using libraries of small molecules to deduce structural determinants of substrate recognition, the fundamentals of structure/activity relationship (SAR), or the mechanism of modulation. It is our hypothesis that accuracy of small molecule-protein docking can be improved if simultaneously the energetics of the interaction and the structure-activity relations are identified. This approach will counter-balance the inaccuracy of the comparative model. It is therefore the objective of the present proposal to develop an algorithm ‘ROSETTALIGANDENSEMBLE’ that docks an ensemble of small molecules with known affinities/activities into a comparative model of the membrane protein. We will apply the method to the identification of structural determinants required for agonistic and inverse agonistic ligand properties at the ADP receptor P2Y12. Further, the algorithm will be employed to study the mechanism of allosteric modulation of the neuropeptide Y4 receptor. Both GPCR systems have been selected as model scenarios to study small molecule-GPCR interaction as not only focused libraries of small molecules with known biological activities are available but an immediate experimental feedback loop has been setup to test novel ligands but also use receptor variants to determine interaction sites.