Heterocycle Cation Recognition of the DNA Minor Groove.

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，但用于治疗或正在开发这些疾病的安全可靠的药物不足。该领域受到新的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一个独特的细胞靶标，数千个富含at的DNA微环，这些微环联锁在寄生虫线粒体着丝体基因组中。我们提出了一种创新的方法来抑制与子/亲本着丝体打开、复制和重组有关的小环的复杂复制反应。我们将从根本上解决这个问题，并将设计和合成新型化合物来干扰着丝体的复制。我们将利用创新的新化合物对模型和着丝体dna进行生物物理研究，结果将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。我们的一般假设是：由于对着丝体的非标准DNA序列和结构的协同作用，我们可以为设计具有治疗潜力的新型化合物奠定基础。为了进行这项研究，两个合作小组将进行重点化合物合成以及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中，我们建立在一个发现的基础上，该发现表明，小凹槽结合的经典模型过于有限，线性化合物可以通过使用界面水强烈而特异性地结合到DNA上。我们将探索线性化合物结合的限制，并确定是否存在与结合水的配合物的热力学特征。在目标2下，我们提出了全新类型的化合物，这些化合物被设计成模仿蛋白质基序并引起DNA的显著弯曲。一套使用两个连接的AT位点结合单元，用短接头将螺旋弯曲成小槽。另一组使用一个强结合的小槽基序与部分插入楔形弯曲DNA进入主槽。这种对结构的影响在寄生虫的着丝体中应该特别明显。在目标3中，我们使用的事实是，着丝体富含AT，但它们的AT序列被分解成小单元，通常由一个或两个GC碱基对分开。我们提出了具有强结合AT基序的化合物，这些基序与特异性识别中间GC碱基对的基团相连。这种增加的GC选择性，加上特定的末端AT识别基序，将为着丝质体DNA中相当常见的位点提供高特异性。我们有一个独特的合作研究团队，他们重写了小分子凹槽复合物形成的机制，并设计了用于DNA治疗的化合物，来进行这项研究。

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.