COMPUTER-AIDED DRUG DESIGN MINICORE FACILITY PROJECT

该项目由计算机辅助药物设计MiniCore设施负责人Marc C. Nicklaus博士领导，主要目的是阐明HIV-1整合酶蛋白与DNA和/或抑制剂复合物的结构，并利用由此获得的结构知识设计更好的该酶抑制剂，以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。HIV生命周期中的这一步对病毒复制至关重要。抑制整合被认为是开发抗艾滋病治疗的一个有吸引力的靶点，因为没有已知的in的细胞同源物，从而提高了开发有效的低毒性抗in药物的希望。在使用蛋白酶和逆转录酶（RT）抑制剂的混合物期间出现的多重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32kDa蛋白，是病毒颗粒中包含的gag-pol融合蛋白前体的产物。在RT完成原病毒DNA合成后，IN从每个病毒DNA末端切割两个核苷酸（3'-加工）。在随后迁移到宿主细胞核后，IN催化在3‘加工步骤中产生的嵌入的3’末端插入到宿主DNA的一条链中。这种反应被称为3'端连接（也称为整合或链转移），并同时发生在病毒DNA的两端。随后的间隙连接由细胞DNA修复酶进行，以产生完全整合的原病毒DNA。先前的工作主要基于NCI数据库中的3d药效团搜索，已经获得了许多in抑制剂。随着更多、更好的HIV-1 IN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，现在有可能尝试对全长蛋白质的更大结构（高达多聚体单元）进行建模。然后这些模型可以与病毒DNA和/或抑制剂混合。分子动力学模拟和其他计算化学研究正在进行中，其目标是将各种片段和其他实验信息结合起来，以获得一个模型结构，该模型结构将允许开发针对HIV-1 IN的靶向抑制剂。

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 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 is now possible to attempt modeling of larger structures, up to multimeric units, of the full-length protein. These models can then be complexed with the viral DNA and/or inhibitors. Molecular dynamics simulations and other computational chemistry studies are ongoing with the goal of combining the various fragments and other experimental pieces of information to obtain a modeled structure that will allow targeted inhibitor development against HIV-1 IN.