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

基本信息

批准号：
7733068
负责人：
MARC NICKLAUS
金额：
$ 20.03万
依托单位：
DIVISION OF BASIC SCIENCES - NCI
依托单位国家：
美国
项目类别：
财政年份：
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/7733068
关键词：
AIDS therapy Acids Active Sites Annual Reports Anti-HIV Agents Binding Catalytic Domain Cell Nucleus Chimeric Proteins Cleaved cell Clinical Trials Complex Computer Assisted Computer Simulation Computing Methodologies Custom DNA DNA Repair Enzymes DNA biosynthesis DNA chemical synthesis Databases Development Docking Drug Delivery Systems Drug Design Drug toxicity Endopeptidases Enzyme Inhibitor Drugs Enzyme Inhibitors Enzymes Gagging Genome Goals HIV HIV Integrase HIV Integrase Inhibitors HIV-1 Homologous Gene Homology Modeling Human Integrase Integrase Inhibitors Ions Knowledge Legal patent Length Libraries Life Cycle Stages Ligands Metals Methods Modeling Multi-Drug Resistance Nucleotides Numbers Patients Peptide Hydrolases Perception Pharmaceutical Preparations Phase Phenotype Process Protein Precursors Proteins PubMed Publishing RNA-Directed DNA Polymerase Reaction Replication-Associated Process Resources Reverse Transcriptase Inhibitors Sampling Screening procedure Series Services Site Structural Models Structure System Techniques Therapeutic Toxic effect United States Food and Drug Administration Viral Virion Virus Work X-Ray Crystallography abstracting base design enzyme model in vivo inhibitor/antagonist migration molecular modeling novel pharmacophore pol genes prevent success viral DNA

项目摘要

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&db=PubMed&list_uids=9083480&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&db=pubmed&dopt=Abstract&list_uids=16075307&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&db=PubMed&list_uids=12920196&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&Cmd=ShowDetailView&TermToSearch=17719223&ordinalpos=1&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 effort 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, not IN-related patent-covered, compounds 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 about 70 has been chosen and submitted for purchase.

该项目的主要目标是阐明与 DNA 和/或抑制剂复合的 HIV-1 整合酶蛋白的结构，利用由此获得的结构知识设计更好的该酶抑制剂，目标是开发新的抗 HIV 药物药物，并应用任何其他可能有助于识别新的、有前途的 HIV-1 整合酶抑制剂的计算机辅助药物设计方法。 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骤对于病毒复制至关重要。整合的抑制被视为抗艾滋病疗法开发中有吸引力的目标，因为尚无与IN同源的细胞，因此提高了开发有效的低毒性抗IN药物的希望。在施用蛋白酶和逆转录酶（RT）抑制剂混合物期间出现的多重耐药病毒表型进一步凸显了对替代治疗方法的需求。 IN是一种32kDa的蛋白质，是病毒颗粒中含有的gag-pol融合蛋白前体的产物。通过 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”）。随后迁移至宿主细胞核后，IN 催化将 3' 加工步骤中产生的凹进 3' 末端插入宿主 DNA 的一条链中。该反应称为 3' 末端连接（也称为整合或链转移），并且病毒 DNA 的两端同时发生。据推测，随后的间隙连接是由细胞 DNA 修复酶进行的，以产生完全整合的原病毒 DNA。 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9083480&dopt=Abstract) 之前的工作主要基于 NCI 数据库中的 3D 药效团搜索，已得出一些结果IN抑制剂。随着更多、更好的 HIV-1 IN 实验结构（通过 X 射线晶体学和 NMR）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，包括多聚体模型已成为可能。全长蛋白质，目前尚无其实验结构。我们利用所有可用的实验证据，通过分子建模技术生成了这样的结构。特别强调获得酶活性位点的模型以及与其相连的病毒 DNA，因为它可能是在 3' 处理之后但在链转移之前，如 (http://www.ncbi.nlm.nih. gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16075307&query_hl=1) Karki 等人， 2004。该模型可用于保留体内活性的基于结构的抑制剂设计。我们（http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12920196&dopt=Abstract）利用这些结构模型来研究各种二酮酸的潜在结合模式HIV-1 IN 抑制剂，尚无可用的实验复合结构。结果表明，二酮酸IN抑制剂可能会螯合催化位点的金属离子，并且还可以防止病毒DNA的3'加工末端暴露于人类DNA。这些模型 (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17719223&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum) 成功完全用于抑制剂开发，利用资源，包括我们中描述的资源(http://ccrintra.cancer.gov/cms/annual_reports/projects/printer_Friendly_report.asp?ProjID=6190) 数据库项目特别是通过对超过 2600 万个可购买筛查样本的数据库进行计算机筛选。目前的工作重点是基于配体的抑制剂设计，利用来自少数分子的结构信息，这些分子已进入后期临床试验或被批准作为抗艾滋病毒药物。基于这些结构基序，设计了一系列新颖的、不涉及 IN 相关专利的化合物，并通过新实施的 (http://www.chemnavigator.com/cnc/services/SCSORS_Overview.asp) 提交合成报价。）中提到的半定制在线综合请求系统（SCSORS） (http://ccrintra.cancer.gov/cms/annual_reports/Projects/printer_Friendly_report.asp?ProjID=6864) 数据库项目。从全球 10 多家不同供应商报价的 8,000 多种化合物中，我们选择了一组约 70 种化合物并提交购买。