Heterocycle Cation Recognition of the DNA Minor Groove.

DNA 小沟的杂环阳离子识别。

• 批准号: 8035391
• 负责人: W David Wilson
• 金额: $ 35.76万
• 依托单位: GEORGIA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-02-01 至 2015-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8035391
• 关键词: Accounting; Address; Affinity; Africa; African Trypanosomiasis; Amino Acid Motifs; Antiparasitic Agents; Area; Base Pairing; Binding; Binding Sites; Biological; Biological Testing; Cations; Cells; Chagas Disease; Circular DNA; Clinical; Collaborations; Complex; Coupled; Crystallography; DB75; DNA; DNA Sequence; DNA Structure; Daughter; Development; Diamidine; Disease; Drug Receptors; Eukaryotic Cell; Exhibits; Funding; Genome; Genomics; Goals; Grant; Human; Infection; Kinetoplast DNA; Knowledge; Letters; Libraries; Link; London; Maintenance; Major Groove; Methods; Minor Groove; Mitochondria; Modeling; Molecular; New Agents; Parasites; Parasitic Diseases; Parents; Patients; Pharmaceutical Preparations; Phase III Clinical Trials; Population; Prodrugs; Proteome; Public Health; Quinolone Antibiotic; Reaction; Research; Research Design; Risk; Site; Specificity; Structure; Testing; Therapeutic; Thermodynamics; Toxic effect; Trypanosoma; Trypanosoma brucei brucei; Trypanosoma cruzi; Trypanosomiasis; Water; Work; base; cellular targeting; design; drug development; flexibility; improved; innovation; interfacial; kDNA Minicircles; microorganism; news; novel; public health relevance; receptor; small molecule; uptake

DESCRIPTION (provided by applicant): Although about 40% of the world population is at risk of deadly parasitic disease infections, there are insufficient safe, reliable drugs for treatment of or under development for these diseases. The field is limited by ideas for novel cellular receptors or types of drugs. The research in this proposal is focused on methods to address both problems. We propose compounds that can selectively target a unique cellular target, the thousands of AT-rich, DNA minicircles that are interlocked into the parasite mitochondrial kinetoplast genome. Our proposal has plans for innovative approaches to inhibit the complex replication reactions of the minicircles involved with opening, copying and restructuring daughter/parent kinetoplasts. We will approach the problem from a fundamental basis and will design and synthesize new types of compounds to interfere with kinetoplast replication. We will conduct biophysical studies on both model and kinetoplast DNAs with the innovative new compounds and the results will be correlated with cell uptake and distribution studies that are done by collaborating groups of recognized parasite biologists. Three specific aims describe new directions in our research that are largely based on discoveries from the funded project. Our general hypothesis is: we can establish a fundamental basis for the design of new types of compounds that have therapeutic potential as a result of synergistic effects on the nonstandard DNA sequences and structures of the kinetoplast. To do this research two collaborating groups will conduct focused compound synthesis along with biophysical characterization of DNA complexes to answer specific questions that are very difficult to answer by other approaches. Under aim 1 we build on a discovery that shows the classical model for minor groove binding is too limited and that linear compounds can bind strongly and specifically to DNA by using interfacial water. We will explore the limits on linear compound binding and determine if there is a thermodynamic signature for complexes with a bound water. Under aim 2 we propose completely new types of compounds, which are designed to mimic protein motifs and cause significant bending of DNA. One set uses two connected AT site binding units with a short linker to bend the helix into the minor groove. The other set uses a strong binding minor groove motif with a partial intercalating wedge to bend DNA into the major groove. Such effects on structure should be particularly pronounced at the kinetoplast of parasites. Under aim 3 we use the fact that kinetoplasts are AT rich but their AT sequences are broken into small units that are typically separated by one or two GC base pairs. We propose compounds with strong-binding AT motifs that are linked with groups that specifically recognize intervening GC base pairs. This added GC selectivity, coupled to specific terminal AT recognizing motifs, will provide high specificity for sites that are quite common in kinetoplast DNA. We have a unique, collaborative research team, which has rewritten the mechanism for small molecule-minor groove complex formation and for design of compounds for DNA therapeutics, to carry out this research. PUBLIC HEALTH RELEVANCE: Continued discovery of new drugs is vital for maintenance of the public health. Despite the advances in genomics only a small percentage of the proteome provides "druggable" targets. It is, therefore, essential to identify other drug receptors such as DNA, particularly DNA structures that allow selective targeting. Acquiring an improved fundamental understanding of small molecule DNA interactions is crucial to development of these novel targets. Discovery of the clinically useful quinolone antibiotics, quadruplex selective agents and diamidine antiparasitic drugs validates this approach.

描述（由申请人提供）：尽管世界上约 40% 的人口面临致命寄生虫病感染的风险，但用于治疗这些疾病的安全、可靠的药物不足或正在开发中。该领域受到新型细胞受体或药物类型的想法的限制。本提案的研究重点是解决这两个问题的方法。我们提出的化合物可以选择性地靶向独特的细胞靶标，即与寄生虫线粒体动质体基因组互锁的数千个富含 AT 的 DNA 小环。我们的提案计划采用创新方法来抑制与打开、复制和重组子代/亲代动质体相关的小环的复杂复制反应。我们将从根本上解决这个问题，并设计和合成新型化合物来干扰动质体复制。我们将使用创新的新化合物对模型和动质体 DNA 进行生物物理学研究，并将结果与​​由公认的寄生虫生物学家合作小组完成的细胞摄取和分布研究相关联。三个具体目标描述了我们研究的新方向，这些方向主要基于资助项目的发现。我们的总体假设是：我们可以为设计新型化合物奠定基础，这些化合物由于对非标准 DNA 序列和动质体结构的协同作用而具有治疗潜力。为了进行这项研究，两个合作小组将进行有针对性的化合物合成以及 DNA 复合物的生物物理表征，以回答其他方法很难回答的特定问题。在目标 1 下，我们建立在一项发现的基础上，该发现表明小沟结合的经典模型过于有限，并且线性化合物可以通过使用界面水强烈且特异性地与 DNA 结合。我们将探索线性化合物结合的限制，并确定与结合水的复合物是否存在热力学特征。在目标 2 下，我们提出了全新类型的化合物，这些化合物旨在模仿蛋白质基序并引起 DNA 的显着弯曲。一组使用两个连接的 AT 位点结合单元和一个短接头，将螺旋弯曲到小沟中。另一组使用强结合小沟基序和部分嵌入楔形将 DNA 弯曲到大沟中。这种对结构的影响在寄生虫的动质体上尤其明显。在目标 3 下，我们利用这样一个事实：动质体富含 AT，但它们的 AT 序列被分解成小单元，这些单元通常由一两个 GC 碱基对分隔。我们提出了具有强结合 AT 基序的化合物，这些基序与特异性识别插入 GC 碱基对的基团相连。这种增加的 GC 选择性，与特定的末端 AT 识别基序相结合，将为动质体 DNA 中非常常见的位点提供高度特异性。我们拥有一个独特的协作研究团队来开展这项研究，该团队重写了小分子-小沟复合物形成的机制以及 DNA 治疗化合物的设计。 公共健康相关性：新药的持续发现对于维护公共健康至关重要。尽管基因组学取得了进步，但只有一小部分蛋白质组提供了“可成药”的靶标。因此，有必要识别其他药物受体，例如 DNA，特别是允许选择性靶向的 DNA 结构。加深对小分子 DNA 相互作用的基本了解对于开发这些新靶标至关重要。临床上有用的喹诺酮抗生素、四联选择剂和二脒抗寄生虫药的发现验证了这种方法。