Computer-Aided Drug Design (CADD) Group Project: HIV Int

该项目的主要目标是阐明HIV-1整合酶蛋白与DNA和/或抑制剂的复合体的结构，并利用由此获得的结构知识来设计更好的这种酶的抑制剂，从而开发新的抗艾滋病药物。 HIV整合酶(IN)是病毒编码的酶，负责将逆转录病毒DNA整合到宿主基因组中。艾滋病毒生命周期中的这一步对病毒复制至关重要。抑制整合被认为是抗艾滋病治疗的一个有吸引力的靶点，因为目前还不知道IN的细胞同源物，从而增加了开发有效的、低毒的抗IN药物的希望。在给予蛋白酶和逆转录酶(RT)抑制剂的鸡尾酒疗法期间出现多药耐药病毒表型，进一步突出了替代治疗方法的必要性。 In是一种32 kDa的蛋白质，是病毒颗粒中包含的Gag-Poll融合蛋白前体的产物。在RT完成前病毒DNA合成后，IN从病毒DNA末端各切割两个核苷酸(“3‘-加工”)。在随后迁移到宿主细胞核后，IN催化将在3‘-处理步骤中产生的凹陷的3’末端插入宿主DNA的一条链中。这种反应称为3‘末端连接(也称为整合或链转移)，在病毒DNA的两端同时发生。随后的缝隙连接被认为是由细胞DNA修复酶执行的，以产生完全整合的前病毒DNA。 以前的工作，主要是基于NCI数据库中的3D药效团搜索，已经产生了一些IN的抑制剂。随着HIV-1 IN更多更好的实验结构(X射线晶体和核磁共振结构)以及密切相关的酶(如ASV整合酶)的出现，对更大的结构进行建模已成为可能，最高可达全长蛋白质的多聚体单元。这些模型已经与病毒DNA(末端)复合，已知的抑制剂与这种蛋白质-DNA复合体的对接已经开始。分子动力学模拟和其他计算化学研究正在进行中，目的是改进建模结构，使我们能够有针对性地开发更好的HIV-1 IN抑制剂。

The principal objective of this project, headed by Dr. Marc C. Nicklaus, Head, Computer-Aided Drug Design MiniCore Facility, is to elucidate the structure of the HIV-1 integrase protein, complexed with DNA and/or inhibitors, and to use the structural knowledge thus obtained to design better inhibitors of this enzyme with the goal of developing new anti-AIDS drugs. HIV integrase (IN) is the virally encoded enzyme responsible for integration of the retroviral DNA into the host genome. This step in the life cycle of HIV is essential for viral replication. Inhibition of integration is seen as an attractive target in the development of anti-AIDS therapies because no cellular homologue to IN is known, thus raising the hope that effective anti-IN based drugs with low-toxicity can be developed. The emergence of multidrug-resistant virus phenotypes during administration of cocktails of protease and reverse transcriptase (RT) inhibitors has further highlighted the need for alternative therapeutic approaches. IN is a 32kDa protein that is a product of the gag-pol fusion protein precursor contained in the virus particle. Upon completion of proviral DNA synthesis by RT, IN cleaves two nucleotides from each viral DNA end ("3'-processing"). After subsequent migration to the host cell's nucleus, IN catalyzes the insertion of the recessed 3'-terminus, generated during the 3'-processing step, into one strand of the host DNA. This reaction is termed 3' end joining (also known as integration or strand transfer) and occurs for both ends of the viral DNA simultaneously. The subsequent gap-joining is presumed to be performed by cellular DNA repair enzymes to yield a fully integrated proviral DNA. Previous work, mainly based on 3D-pharmacophore searches in the NCI database, had yielded a number of inhibitors of IN. With the advent of more, and better, experimental structures (X-ray crystal and NMR structures) of HIV-1 IN as well as closely related enzymes such as ASV integrase, it has become possible to model larger structures, up to multimeric units of the full-length protein. These models have been complexed with (the ends of) the viral DNA, and docking of known inhibitors into this protein-DNA complex has begun. Molecular dynamics simulations and other computational chemistry studies are ongoing with the goal of improving the modeled structures to allow us targeted development of better HIV-1 IN inhibitors.