HIV Integrase Modeling and Computer-Aided Inhibitor Development

HIV 整合酶建模和计算机辅助抑制剂开发

• 批准号: 8157333
• 负责人: MARC NICKLAUS
• 金额: $ 14.25万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 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/8157333
• 关键词: Computer Assisted; Development; HIV Integrase; Modeling; inhibitor/antagonist

The principal objective of this project is to elucidate the structure of the HIV-1 integrase protein, complexed with DNA and/or inhibitors, to use the structural knowledge thus obtained to design better inhibitors of this enzyme with the goal of developing new anti-HIV drugs, and to apply any other computer-aided drug design method that may be helpful in identifying new, promising HIV-1 integrase inhibitors. 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. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve and db=PubMed and list_uids=9083480 and dopt=Abstract 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 (by X-ray crystallography and NMR) of HIV-1 IN as well as of closely related enzymes such as ASV integrase, it has become possible to model larger structures including multimeric models of the full-length protein, for which experimental structures are not available as of yet. We have generated such structures by means of molecular modeling techniques using all available experimental evidence. Special emphasis was placed on obtaining a model of the enzyme's active site with the viral DNA apposed to it as it might be after 3'-processing but before strand transfer, as described in "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve and db=pubmed and dopt=Abstract and list_uids=16075307 and query_hl=1" Karki et al., 2004. This model is useful for structure-based inhibitor design of inhibitors which retain activity in vivo. We have made http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve and db=PubMed and list_uids=12920196 and dopt=Abstract use of these structural models to study the potential binding modes of various diketo-acid HIV-1 IN inhibitors for which no experimental complexed structures are available. The results indicate that the diketo-acid IN inhibitors probably chelate the metal ion in the catalytic site and also prevents the exposure of the 3'-processed end of the viral DNA to human DNA. These models were "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed and Cmd=ShowDetailView and TermToSearch=17719223 and ordinalpos=1 and itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum" success fully used for inhibitor development, utilizing resources including those described in our "http://ccrintra.cancer.gov/cms/annual_reports/projects/printer_friendly_report.asp?ProjID=6190" database project, in particular through in silico screening of a database of more than 26 million purchasable screening samples. Current efforts have been focusing on ligand-based inhibitor design, making use of the structural information coming from those few molecules that have made it into late-phase clinical trials or been approved as anti-HIV drug. Based on these structural motifs, a series of novel compounds not covered by IN-related patents were designed and submitted for quotation for synthesis via the newly implemented "http://www.chemnavigator.com/cnc/services/SCSORS_Overview.asp" Semi-Custom Online Synthesis Request System (SCSORS) mentioned in the "http://ccrintra.cancer.gov/cms/annual_reports/Projects/printer_friendly_report.asp?ProjID=6864" Database project. From the more than 8,000 compounds quoted by more than 10 different suppliers world-wide, a set of nearly 100 has been chosen and submitted for purchase. Several compounds have been obtained so far from this set, with weak anti-IN activity exhibited by a few. Compound synthesizability and stability issues are currently being studied.

该项目的主要目的是阐明HIV-1整合酶蛋白与DNA和/或抑制剂复合的结构，使用由此获得的结构知识来设计更好的这种酶的抑制剂，以开发新的抗HIV药物，并应用任何其他计算机辅助药物设计方法，可能有助于识别新的，有前途的HIV-1整合酶抑制剂。HIV整合酶（IN）是负责将逆转录病毒DNA整合到宿主基因组中的病毒编码酶。HIV生命周期中的这一步对于病毒复制至关重要。整合的抑制被认为是抗AIDS疗法开发中的有吸引力的靶点，因为没有已知的IN的细胞同源物，从而提高了可以开发具有低毒性的有效的基于抗IN的药物的希望。在蛋白酶和逆转录酶（RT）抑制剂的鸡尾酒管理过程中出现的多重耐药病毒表型，进一步强调了替代治疗方法的需要。IN是一种32kDa的蛋白质，它是病毒颗粒中含有的gag-pol融合蛋白前体的产物。在通过RT完成前病毒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的细胞核后，IN催化在3'-加工步骤期间产生的凹陷的3'-末端插入宿主DNA的一条链中。该反应被称为3 '端连接（也称为整合或链转移），并且在病毒DNA的两端同时发生。推测随后的缺口连接是通过细胞DNA修复酶进行的，以产生完全整合的前病毒DNA。http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd = C10和db = PubMed和list_uids = 9083480和dopt = Abstract先前的工作，主要基于在NCI数据库中的3D药效团搜索，已经产生了许多IN抑制剂。随着HIV-1 IN以及密切相关的酶如ASV整合酶的更多和更好的实验结构（通过X射线晶体学和NMR）的出现，已经有可能模拟更大的结构，包括全长蛋白质的多聚体模型，其实验结构尚未可用。我们已经产生了这样的结构，通过分子建模技术，使用所有可用的实验证据。特别强调的是获得酶的活性位点的模型，其中病毒DNA与其并列，因为它可能在3 ′-加工之后但在链转移之前，如"www.example.com cmd = pmd和db = pubmed和dopt = Abstract和list_uids = 16075307和query_hl = 1 "Karki等人，2004.该模型可用于基于结构的抑制剂设计的抑制剂，保留在体内的活性。我们已经建立了www.example.com cmd = C1111和db = PubMed和list_uids = 12920196和dopt = Abstract使用这些结构模型来研究各种二酮酸HIV-1 IN抑制剂的潜在结合模式，对于这些抑制剂，没有实验复合结构可用。结果表明，二酮酸IN抑制剂可能螯合催化位点的金属离子，并阻止病毒DNA的3 '-加工末端暴露于人DNA。 这些模型是"www.example.com Db = pubmed和Cmd = ShowDetailView和TermToSearch = 17719223和ordinalpos = 1和itool = pixzSystem2.pixz.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum "成功完全用于抑制剂开发，利用资源，包括我们的" www.example.com ProjID = 6190 "数据库项目，特别是通过对超过2600万个采购筛选样本的数据库进行计算机筛选。 目前的努力一直集中在基于配体的抑制剂设计上，利用来自那些已经进入后期临床试验或被批准为抗HIV药物的少数分子的结构信息。基于这些结构基序，设计了一系列未被IN相关专利覆盖的新化合物，并通过"www.example.com"中提到的新实施的"www.example.com"半定制在线合成请求系统（SCSORS）提交用于合成的报价ProjID = 6864 "数据库项目。从全球10多家不同供应商提供的8，000多种化合物中，选择了近100种化合物并提交采购。到目前为止，已经从这组化合物中获得了几种化合物，其中一些化合物表现出弱的抗IN活性。目前正在研究化合物的合成性和稳定性问题。