Heterocycle Cation Recognition of the DNA Minor Groove.

描述(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，但治疗这些疾病的安全、可靠的药物或正在开发中的药物不足。该领域受到新细胞受体或药物类型的想法的限制。这项建议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一个独特的细胞靶点，即数千个富含AT的DNA微环，这些微环互锁在寄生虫线粒体动泡体基因组中。我们的提案计划采用创新的方法来抑制与打开、复制和重组子代/亲代动粒相关的微环的复杂复制反应。我们将从根本上解决这个问题，并将设计和合成新类型的化合物来干扰动泡膜的复制。我们将使用创新的新化合物对模型和动泡体DNA进行生物物理研究，结果将与公认的寄生虫生物学家合作小组所做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，这些新方向主要基于受资助项目的发现。我们的总体假设是：我们可以为设计具有治疗潜力的新型化合物奠定基本基础，这些化合物是由于对动泡膜的非标准DNA序列和结构的协同作用而产生的。为了进行这项研究，两个合作小组将进行有重点的化合物合成以及DNA复合体的生物物理表征，以回答用其他方法很难回答的具体问题。在目标1下，我们建立在一项发现的基础上，该发现表明，经典的微小沟槽结合模型过于有限，线性化合物可以通过使用界面水与DNA强烈和特异地结合。我们将探索线性化合物结合的极限，并确定结合水的络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导致DNA显著弯曲。一组使用两个连接的AT位点结合单元和短接头将螺旋弯曲到小凹槽中。另一组使用强结合的次要凹槽基序，带有部分嵌入的楔形物，将DNA弯曲到主要凹槽中。这种对结构的影响应该在寄生虫的动泡体上特别明显。在目标3中，我们利用了这样一个事实，即动殖体富含AT，但它们的AT序列被分解成小单位，这些小单位通常被一个或两个GC碱基对分开。我们提出了具有强结合AT基序的化合物，这些基序与特定识别介入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，将为动泡体DNA中相当常见的位点提供高度特异性。我们有一个独特的、合作的研究团队，他们改写了小分子-小沟槽复合体形成的机制，并为DNA治疗设计了化合物，来开展这项研究。 与公共健康相关：不断发现新药对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“可用药”的靶点。因此，识别其他药物受体是至关重要的，例如DNA，特别是允许选择性靶向的DNA结构。获得对小分子DNA相互作用的更好的基础理解对于开发这些新的靶标至关重要。临床上有用的喹诺酮类抗生素、四链选择剂和二胺类抗寄生虫药物的发现证实了这一方法。

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.