Computational Design of Fusion Inhibitors Targeting Drug-resistant HIVgp41

描述（由申请人提供）：对靶向HIVgp41的病毒进入融合抑制剂耐药的分子机制尚不清楚。在驱动结合的能量和结构相互作用的知识方面的根本差距阻碍了开发具有改善的耐药性谱的新药的长期目标。本申请的总体目标是（1）开发计算结构模型以定量已知gp41融合抑制剂（肽和小分子）的结合，（2）表征对当前抑制剂的耐药谱的起源，以及（3）发现新的小分子药物先导。基于强有力的初步结果，中心假设是gp41上保守的疏水口袋内的特异性相互作用，目前唯一可用的抗融合药物（肽抑制剂T20）没有利用，赋予下一代肽抑制剂改善的耐药性，并驱动小分子抑制剂的结合。拟议研究的基本原理是，强大的计算模型允许在原子水平上充分表征药物结合，这将使开发具有良好耐药性的HIV药物成为可能。因此，建议的工作是直接相关的国家卫生研究院计划的基础和应用研究，以发现和开发新的代理商和治疗策略，直接针对病毒的因素参与艾滋病毒的复制和持久性。这项工作采用全原子计算机模拟（分子动力学和对接），结合详细的能量和结构分析，以测试中心假设并实现每个具体目标中提出的目标。目的#1将确定对gp41的当前肽融合抑制剂的抗性的分子基础，以检验对T20的结合亲和力主要由与沿着结合界面的突变倾向区域沿着的相互作用驱动的假设。目的#2将表征所报道的gp41小分子抑制剂的作用机制，我们假设这是由于保守口袋内调节的特定能量和结构相互作用。目标#3将使用虚拟高通量筛选结合实验验证来识别新的有机小分子，其特异性地结合到gp41口袋。活性化合物将使用NMR和X射线晶体学进行结构表征并进一步开发。该提案的贡献是重要的，因为详细的结合模型和计算机模拟的结果将允许识别的分子基础被描绘，这将使改进的融合抑制剂的开发，保持对临床相关的HIV逃逸突变的活性。 公共卫生相关性：拟议研究的结果将用于揭示原子水平的结构和能量决定因素，这些决定因素描述了膜融合抑制剂与介导HIV感染的病毒进入蛋白gp41的结合。该提案旨在了解对gp41抑制剂耐药性的起源，并开发具有改善耐药性的新化合物，因此该发现预计将与公共卫生直接相关。

DESCRIPTION (provided by applicant): The molecular mechanisms of resistance to viral entry fusion inhibitors targeting HIVgp41 are not well-understood. Fundamental gaps in knowledge of the energetic and structural interactions which drive binding hamper the long-term goal of development of new drugs with improved resistance profiles. The overall objective of this application is to (1) develop computational structural models to quantify binding for known gp41 fusion inhibitors (both peptides and small molecules), (2) characterize origins of resistance profiles to current inhibitors, and (3) discover new small molecule drug-leads. Based on strong preliminary results, the central hypothesis is that specific interactions within a conserved hydrophobic pocket on gp41, not exploited by the only currently available anti-fusion drug (peptide inhibitor T20), confer improved resistance profiles to next-generation peptide inhibitors and drive binding for small molecule inhibitors. The rationale for the proposed research is that robust computational models allow drug binding to be fully characterized at the atomic level, and this will enable development of HIV drugs with favorable resistance profiles. Thus, the work proposed is directly relevant to the NIH plan for basic and applied research towards discovery and development of novel agents and therapeutic strategies directed against viral factors involved in HIV replication and persistence. The work employs all-atom computer simulations (molecular dynamics and docking), in conjunction with detailed energetic and structural analysis, to test the central hypothesis and accomplish the goals set forth in each specific aim. Aim #1 will determine the molecular basis of resistance to current peptide fusion inhibitors of gp41 to test the hypothesis that binding affinity for T20 is driven primarily by interactions with mutation-prone regions along the binding interface. Aim #2 will characterize the mechanism of action for reported small molecule inhibitors of gp41 which we postulate are due to specific energetic and structural interactions modulated within the conserved pocket. Aim #3 will identify new small organic molecules, which bind specifically to the gp41 pocket, using virtual-high-throughput-screening in conjunction with experimental validation. Active compounds will be characterized structurally using NMR and X-ray crystallography and developed further. The proposal's contributions are significant because results from detailed binding models and computer simulations will allow the molecular basis of recognition to be delineated, which will enable development of improved fusion inhibitors that maintain activity against clinically relevant HIV escape mutations. PUBLIC HEALTH RELEVANCE: Results from the proposed research will be used to uncover the atomic-level structural and energetic determinates which describe binding of membrane fusion inhibitors with the viral entry protein gp41 which mediates HIV infection. The proposal seeks to understand the origins of resistance to gp41 inhibitors, and develop new compounds with improved resistance profiles, thus the finding are expected to be of direct relevance to public health.