AMINOGLYCOSIDE/RNA INTERACTIONS AND CORNEAL INFECTIONS

RNA分子能够形成精确的三维结构，可以作为有机小分子的结合位点。理解控制RNA/小分子识别过程规则的规则将使我们能够实现针对特定RNA结构的拮抗剂的重新设计的长期目标，就像为基于蛋白质的酶和受体设计抑制剂一样。设计用于抑制RNA分子的特定抑制剂可能在眼科和一般医学中引起极大的兴趣，例如，在设计中，可以专门干扰导致视网膜变性的突变蛋白的表达的小分子，以及在设计中可以对抗产生传染病的生物体的RNA分子。本提案描述了获得对某些天然存在的RNA拮抗剂（氨基糖苷类）被特定RNA分子识别的规则的理解的方法。通过柱法选择随机RNA分子，以高亲和力和特异性与含有抗生素的氨基糖苷结合。开发了新的定量荧光方法来确定抗生素与选定的RNA适体结合的亲和力和化学计量学。新的化学方法被开发出来，以揭示确定特定抗生素结合位点的适体区域。计划对高亲和力结合适配体进行高场核磁共振结构研究。这些识别特定氨基糖苷的特定RNA适体中的基序将被确定并用于指导未来设计针对天然存在的RNA分子的特定拮抗剂。在这种情况下，两个生物学上发生的RNA分子是原核16S rRNA解码区和HIV-RRE转录激活子区。对氨基糖苷与解码区和RRE区结合的定量结构-活性研究导致了包含1,3(2)-羟胺部分的新型氨基糖苷类多样性文库的设计。针对RNA解码区和RRE区的特异性拮抗剂将被制备和定量研究。这些拮抗剂有望成为设计治疗角膜感染药物的起点。总的来说，本文所述的研究将作为设计特异性RNA拮抗剂的一般程序的基础。

RNA molecules are able to form precise three-dimensional structures which can be binding-sites for small organic molecules. An understanding of the rules that govern RNA/small molecule recognition processes rules would allow for an approach to our long-term goal of the de novo design of antagonists directed at particular RNA structures, in much the same way that inhibitors are designed for protein-based enzymes and receptors. Specific inhibitors designed to inhibit RNA molecules could be of enormous interest in ophthalmology and generally in medicine, in the design, for example, of small-molecules that can specifically interfere with the expression of mutant proteins that can lead to retinal degeneration, and in the design of small molecules that can antagonize RNA molecules from infectious disease producing organisms. This proposal describes approaches to gaining an understanding of the rules by which certain classes of naturally occurring RNA antagonists, the aminoglycosides, are recognized by specific RNA molecules. Random RNA molecules are selected by column methods to bind to defined aminoglycoside containing antibiotics with high affinity and specificity. New quantitative fluorescence methods are developed to determine the affinities and stoichiometries of antibiotic binding to the selected RNA aptamers. Novel chemical approaches are developed to reveal the regions of the aptamers which define the binding-sites for the specific antibiotic. High field NMR structural studies on the high affinity binding aptamers are planned. Those motifs in the specific RNA aptamers which recognize particular aminoglycosides will be determined and used as a guide for the future design of specific antagonists directed against naturally occurring RNA molecules. Two biologically occurring RNA molecules of particular interest in this context are the procaryotic 16S rRNA decoding region and the HIV-RRE transcriptional activator region. Quantitative structure-activity studies on aminoglycoside binding to the decoding and RRE regions leads to the design of novel aminoglycosidemimetic diversity libraries containing l,3(2)-hydroxylamine moieties. Specific antagonists directed against the decoding and RRE regions of RNA will be prepared and studies quantitatively. These antagonists are expected to be starting points for the design of drugs useful in the treatment of corneal infections. Overall, the studies described herein will serve as the basis for a general program on the design of specific RNA antagonists.