Molecular Dynamics Conformation Of Opioid Peptides

阿片肽的分子动力学构象

• 批准号: 7007485
• 负责人: LAWRENCE H LAZARUS
• 金额: --
• 依托单位: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7007485
• 关键词: X ray crystallography; binding sites; chemical models; computer simulation; conformation; endogenous opioid; mathematical model; model design /development; molecular dynamics; nuclear magnetic resonance spectroscopy; opioid receptor; peptide structure; piperazines; protein structure function; receptor binding

Summary: Molecular modeling methodologies (molecular dynamics, conformational searching, Monte Carlo) used data from the crystallized structure of bovine rhodopsin (excluding the intracellular and extracellular domains), which is the only 7-transmembrane receptor crystallized to date, in order to develop a model of the delta-opioid receptor by in silico methods; i.e., computer-directed mutagenesis to ensure that the sequence of the rhodopsin format coincided with that of the delta-opioid receptor by exchanging specific amino acids. A variety of delta agonists and antagonists based on the Dmt-Tic pharmacophore derived from X-ray diffraction analyses of three selective compounds with different specificities (delta- and mu-opioid receptor selective, and non-selective), as well as specific mu-opioid receptor agonists, which should have very low affinity with the delta-opioid receptor, were docked into the proposed binding pocket. The ligand-binding domain was initially determined from data on site-directed mutagenesis obtained from the literature. The minimized molecular models of the ligands reflected their known biological activities and receptor affinities and conformational changes in the peptides were initially examined by 1-H NMR (COSY, NOESY, HOHAHA, ROESY, DQF-COSY experiments), CD under varying solvent and temperature conditions. In terms of the ligands, the aromatic ring distance may be a singularly important characteristic which distinguishes delta-opioid receptor antagonists and agonists for both mu- and delta-opioid receptors providing a presumptive "receptor-bound conformation" in spite of the inherent flexibility of the peptide. As anticipated, mu-opioid receptor agonists exhibited a poor fit in the delta receptor pocket region, confirming the application of this methodology. The topographical features observed with the Dmt-Tic pharmacophore differentiate it from all other peptides and its interaction with select side-chains in the receptor pocket. The data suggest that the presumed receptor-bound conformation of the peptide ligand and receptor involves stacking between aromatic rings and hydrogen bonding and that mu-opioid agonists poorly interacted with those residues specific for delta ligands. Furthermore, there appeared to be two regions in which agonists and antagonists interact, one of which is shared by these compounds. Thus, intra-ring distance of delta-opioid receptor antagonists may portend biological differences due to its fit within its receptor. Peptide analogues with dual receptor binding characteristics or selectivity for the mu-opioid receptor equally assisted in the application of molecular modeling in a predictive mode. Thus, model of the delta receptor and our delta- and mu-opioid antagonist and agonist pharmacophores will serve as scaffolds in the design of new potent ligands.

摘要：分子建模方法(分子动力学、构象搜索、蒙特卡罗)利用牛视紫质的结晶结构数据(不包括细胞内和胞外结构域)，以建立一个通过计算机控制的突变方法，通过交换特定的氨基酸来确保视紫红质的形式与三角洲-阿片受体的序列一致。基于DMT-Tic药效团的各种Delta激动剂和拮抗剂，以及与Delta-阿片受体亲和力非常低的特定mu阿片受体激动剂，被对接到拟议的结合口袋中，所述DMT-Tic药效基团来自于三种不同特异性的选择性化合物(Delta和u阿片受体选择性和非选择性)。配基结合结构域最初是从文献中获得的定点突变数据确定的。通过1-H核磁共振(COSY、NOESY、HOHAHA、ROESY、DQF-COSY实验)、CD等方法初步考察了不同溶剂和温度条件下多肽的构象变化。就配基而言，芳环距离可能是一个非常重要的特征，它区分了Delta-阿片受体拮抗剂和Mu-和Delta-阿片受体激动剂，尽管多肽具有固有的灵活性，但它提供了一种假定的“受体结合构象”。正如预期的那样，Mu-阿片受体激动剂在Delta受体口袋区域表现出较差的适合性，证实了这一方法的应用。用DMT-Tic药效团观察到的地形特征使其有别于所有其他多肽，以及它与受体口袋中选定的侧链的相互作用。这些数据表明，多肽配体和受体的假定受体结合构象涉及芳环和氢键之间的堆积，并且Mu-阿片激动剂与那些针对Delta配体的残基相互作用很差。此外，似乎存在两个激动剂和拮抗剂相互作用的区域，其中一个区域由这些化合物共享。因此，β-阿片受体拮抗剂的环内距离可能预示着生物差异，因为它与其受体相匹配。具有双受体结合特性或对Mu-阿片受体具有选择性的多肽类似物同样有助于以预测模式应用分子建模。因此，Delta受体的模型和我们的Delta-和Mu-阿片拮抗剂和激动剂药效载体将作为设计新的有效配体的支架。