MOLECULAR DYNAMICS STUDIES OF MUTANT HIV GP120 ENVELOP PROTEINS WITH BOUND HIV

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 朱迪思·拉朗德，布林莫尔学院：利用基于ROCS形状的匹配算法和gp120包膜蛋白的分子动力学研究开发新型HIV进入抑制剂这一计算项目的关键目标是合理地设计小分子拮抗剂，阻断人类CD4细胞表面受体和HIV-1的gp120包膜蛋白之间的相互作用，作为治疗艾滋病的潜在疗法。病毒被膜蛋白gp120在与细胞内的CD4受体结合后会发生很大的构象变化，从而允许随后与趋化因子受体结合以及病毒-宿主细胞融合(1)。NIH PO1 GM 56550项目团队(基于结构的HIV-1包膜功能在细胞进入中的拮抗作用)已经合成并分析了一系列NBD化合物类似物(2)(图1，B)。这些化合物与CD4与gp120的结合竞争，并增强了CD4：gp120与趋化因子受体CCR5的结合。Schon等人(2)通过ITC对NBD化合物的热力学性质的解释表明，这类化合物诱导gp120以类似于CD4结合的方式形成结构。这些化合物在与细胞受体结合之前增强了病毒的失活。通过使用Glide(3，4)的计算对接研究，预测了这类化合物的结合模式。对带有关键结合位点残基的一系列NBD化合物的突变分析表明，某些化合物和突变增加了结合亲和力并增强了病毒的感染力(10)。这些突变数据提供了导致化合物激动性的关键蛋白质相互作用的信息。在目前的分配过程中，我构建了一个包含800万个类药物化合物的锌集合(11)的构象数据库，并使用基于ROCs(12-14)形状的虚拟筛选方法开发了新的活性类似物HIV gp120-CD4结合。如在Amber(5)中实现的那样，分子动力学已经被用来探索与野生型结合的抑制剂NBD556的动态波动以及gp120包膜的各种突变。Gp120包膜蛋白与各种小分子络合，完成了100皮秒的分子动力学轨迹。在模拟过程中对蛋白质-配体相互作用的定性观察表明，哌啶环上的四甲基取代是不对称的相互作用。野生型和突变型蛋白质-配体复合体的轨迹也被用来预测结合亲和力，使用在琥珀公司实施的MM/PBSA方法(9)。基于ROC的虚拟筛选和MD模拟将在下一个分配期(4-1-10至3-31-11)继续进行。匹兹堡超级计算中心的沃霍尔和索尔克将分配110,000个SU的资源，并在更新可用时为PVM的实施和算法优化提供高级技术支持。持续、快速地利用PSC资源将进一步加强基于结构的艾滋病毒进入抑制剂的发现。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Judith LaLonde, Bryn Mawr College: Development of Novel HIV Entry Inhibitors Using the ROCS Shaped Based Matching Algorithm and Molecular Dynamics Studies of gp120 Envelop Proteins The key objective of this computational project is to rationally design small-molecule antagonists that block the interaction between the human CD4 cell-surface receptor and the gp120 envelop protein of HIV-1 as potential therapeutics for the treatment of AIDS. The viral envelop protein, gp120, undergoes a large conformational change upon binding to the cellular CD4 receptor allowing subsequent binding to the chemokine receptor and viral-host cell fusion (1). The NIH PO1 GM 56550 project team (Structure-Based Antagonism of HIV-1 Envelope Function in Cell Entry) has synthesized and assayed a series of NBD compound analogs (2) (Figure 1, B). These compounds compete with CD4 binding to gp120 and enhance binding of CD4:gp120 to the chemokine receptor CCR5. Elucidation of the thermodynamic properties of NBD compounds via ITC by Schon et al (2) indicates that this compound class induces the structuring of gp120 in a manor similar to CD4 binding. These compounds enhance inactive the virus prior to binding to the cellular receptor. A predicted binding mode for this class of compounds has been produced from computational docking studies using Glide (3, 4). Mutational analysis of the series of NBD compounds with key binding site residues has shown certain compounds and mutations increase binding affinity and enhance viral infectivity (10). This mutational data provides information of key protein interactions responsible for the agonistic properties of the compounds. Over the course of the current allocation I have constructed a conformer data base of the Zinc collection (11) of 8 million drug-like compounds and used the ROCS (12-14) shaped based virtual screening methods to develop new active analogues HIV gp120-CD4 binding. Molecular dynamics as implemented in AMBER (5) has been used to explore the dynamic fluctuations of the inhibitor NBD556 bound to wild type and various mutations of the gp120 envelope. Molecular dynamics 100 pico-second trajectories have been completed with over 64 gp120 envelop proteins complexed with various small molecules. A qualitative view of protein-ligand interactions during the simulation indicates an asymmetrical interaction of the tetramethyl substitutions on the piperadine ring. The trajectories of the wild-type and mutant proteins-ligand complexes are also being used to predict binding affinity using the MM/PBSA methodology (9) as implemented in Amber. Both ROCS based virtual screening and MD simulations will be continued during the next allocation period (4-1-10 to 3-31-11) A resource of 110,000 SU split between Warhol and Salk at the Pittsburgh Super Computing Center as well as Advanced Technical Support for implementation of PVM and optimization of algorithms when updates are available. Continued, rapid turn-over using the PSC resources will further enhance the structure-based discovery of HIV entry inhibitors.