Heterocycle Binding and Biology in the DNA Minor Groove

描述（由申请人提供）：杂环阳离子，由我们的合作研究小组开发，特异性结合DNA小槽中的扩展AT序列。这些化合物已显示出对几种寄生微生物具有低人体毒性的临床生物活性，一种口服前药已通过针对几种寄生微生物的II期临床试验取得进展。该化合物计划于2004年10月开始针对人类锥虫病的III期试验。生物物理学和体内生物学研究清楚地表明，这些化合物的作用靶点是DNA，特别是着丝体微生物（如锥虫和利什曼原虫）的着丝体DNA （kDNA）。杂环阳离子在体内已经显示出阻断转录增强子与富含AT序列结合的能力，并重新分配拓扑异构酶II酶，这对于独特的kDNA系统复制到富含AT的区域至关重要。我们的假设是，这两种作用都需要在富含AT的kDNA中紧密结合的药物分子的协同作用。本课题的研究旨在通过更好地了解药物在寄生虫中的生物学作用的分子基础，开发新的dna靶向抗菌药物。我们将使用平行化学和组合化学方法来开发系统和合理的新化合物集，以解决有关杂环- dna复合物的具体问题。将使用一系列传统的以及新颖的生物物理方法来评估化合物与不同DNA序列的相互作用，例如它们在微生物中的目标DNA序列。我们特别关注化合物在紧密间隔的富含at的结合位点上的协同结合对DNA结构和蛋白质抑制的影响。将评估化合物对DNA结构和性质的长期和短期影响。我们将对选定的化合物进行详细的结构研究，我们认为这些化合物可以为分子识别机制提供基本的见解。我们将通过使用模型肽系统以及体内蛋白质抑制分析来测试化合物抑制选择性靶向AT丰富序列的转录增强子的能力。所有新化合物都将针对几种微生物进行测试，结果将与它们结合DNA和抑制蛋白质-DNA相互作用和功能的能力相关。

DESCRIPTION (provided by applicant): Heterocyclic cations, developed by our collaborative research groups, bind specifically to extended AT sequences in the DNA minor groove. These compounds have shown clinical biological activity with low human toxicity against several parasitic microorganisms, and an orally available prodrug has progressed through Phase II clinical trials against several parasitic organisms. The compound is scheduled to begin Phase III trials against human trypanosomiasis in October 2004. Biophysical and in vivo biological studies clearly suggest that the target of action of the compounds is DNA and, in particular, the kinetoplast DNA (kDNA) of kinetoplastid microorganisms, such as trypanosomes and leishmania. The heterocyclic cations have shown in vivo ability to block transcription enhancer binding to AT rich sequences and to redistribute the topoisomerase II enzyme, which is critical for replication of the unique kDNA system into AT rich regions. Our hypothesis is that both of these effects require synergistic action of closely bound drug molecules in the AT rich kDNA. The research in this proposal is designed to develop new DNA-targeted antimicrobial drugs by providing a better understanding of the molecular basis of the biological action of the dications in parasites. We will use both parallel and combinatorial chemistry approaches to develop systematic and rational sets of new compounds to address specific questions about the heterocycle-DNA complexes. A battery of traditional, as well as novel biophysical methods, will be used to evaluate the interactions of the compounds with different DNA sequences, such as those that they target in the microorganisms. We are specifically focused on the effects on DNA structure and protein inhibition of cooperative binding of the compounds at closely spaced AT rich binding sites. Both long and short range effects of the compounds on DNA structure and properties will be evaluated. Detailed structural studies will be conducted with selected compounds that we feel can provide fundamental insight into the molecular recognition mechanisms. We will test the ability of the compounds to inhibit transcription enhancers that selectively target AT rich sequences by using model peptide systems, as well as in vivo analysis of protein inhibition. All new compounds will be tested against several microorganisms, and the results will be correlated with their ability to bind DNA and inhibit protein-DNA interactions and functions.