MOLECULAR MODELLING--ANTI-HIV DRUG STEPWISE DESIGN

本文所描述的抗HIV-1药物的设计基础 项目是HIV-1独特的药物受体核糖核酸 酸。HIV-1具有高度折叠的单链RNA基因组，即RNA-DNA 杂交体，以及在宿主细胞中短暂存在的DNA双链 细胞质。在这个项目的头两年，我们发现 第一个与RNA强结合的简单有机分子 与DNA的弱结合，以及与DNA-RNA杂交物选择性结合的分子 双面的。这项提案中的抗HIV-1药物建立在这些药物的基础上 发现。HIV-1关键基因控制区的RNA具有双链结构 具有碱基凸起、环和碱基对错配的构象 基因表达中的顺式作用元件，对HIV-1是必不可少的 复制。HIV-1RNA的折叠区与DNA有几个不同之处 特征：RNA在小凹槽中有一个2‘-OH基团， 提供氢键的可能性；分子的静电势 RNA主槽的负压性明显大于 DNA；而RNA凹槽的立体特征是非常 与DNA的不同。基于RNA相互作用的知识， 在这项提案的头两年中获得的收益，我们设计了 利用所有这些功能的分子 与RNA的选择性相互作用将抑制HIV-1复制。一个 例如，羧基苯基菲啶化合物结合 在生理条件下对DNA无关紧要，但可强烈结合 致RNA。大量的实验证据表明，这种分子 高选择性地结合到与碱基凸起相邻的双链区域 例如在HIV-1RNA基因控制区(例如，TAR和RRE)。 发现几个未熔融的芳香族阳离子与 核糖核酸和脱氧核糖核酸，并提出了新的分子也将结合 对RNA作用强，对DNA作用弱。设计方法是循序渐进的。 一类新的抗HIV-1药物，RNA特异性有机抑制物 (RASORS)，这将抑制HIV-1基因的表达和复制。这个 RASORS组合了双工识别单元，例如上述那些， 以及与未配对的RNA碱基结合的单位，例如存在于 底部凸起或循环。这些单元由链接器连接，这些链接器还增强了 RNA结合。RASORS的双工单元将插入TAR或RRE中 靠近底座凸起或环状，并放置未配对的底座识别 RASORS单元，位于与未配对对象交互的最佳位置 本垒打。在优化RNA相互作用后，将有更多基团 添加到碱性RASORS中，选择性地水解HIV-1RNA。我们有 设计了这样一种带有能氢键的羧基的催化剃须刀 到HIV RNA 2‘-OH，并瞬时地从2’-OH中除去氢。 该分子具有阳离子吡啶基官能团(用于质子捐赠) 与相同位置的磷酸盐相邻，这样RNA就可以被水解 在核糖核酸酶型机制中。这种水解对RNA是有选择性的 而且不能发生在DNA上。Rasor结合将引导催化剂 HIV-1RNA中所需特定部位的活性。

The basis for the design of the anti-HIV-1 drugs described in this project is the unique drug receptor characteristics of HIV-1 nucleic acids. HIV-1 has a highly folded single-stranded RNA genome, an RNA-DNA hybrid, and a DNA duplex that exist transiently in the host cell cytoplasm. In the first two years of this project, we have discovered the first simple organic molecules that bind strongly to RNA but very weakly to DNA, and molecules that bind selectivity to DNA-RNA hybrid duplexes. The anti-HIV-1 drugs in this proposal build on those discoveries. The HIV-1 RNA in critical gene control regions has duplex conformations with base bulges, loops and base-pair mismatches that are cis-acting elements in gene expression and are essential for HIV-1 replication. The folded regions of HIV-1 RNA differ from DNA in several characteristics: the RNA has a 2'-OH group in the minor groove that offers hydrogen bonding possibilities; the electrostatic potential of the RNA major groove is significantly more negative than either groove in DNA; and the steric characteristics of the RNA grooves are very different from those of DNA. Based on knowledge of RNA interactions, gained during the first two years of this proposal, we have designed molecules to take to take advantage of all of these features for selective interactions with RNA that will inhibit HIV-1 replication. A carboxyphenylphenanthridinium compound, for examples, binds insignificantly to DNA under physiological conditions but binds strongly to RNA. Considerable experimental evidence suggests that this molecule binds with high selectivity to duplex regions adjacent to base bulges such as those in HIV-1 RNA gene control regions (eg. TAR and RRE). Several unfused aromatic cations were found to bind quite strongly to both RNA and DNA, and new molecules are proposed that will also bind strongly to RNA but weakly to DNA. The design methods proceed stepwise to a new class of anti-HIV-1 drugs, RNA specific organic repressors (RASORS), that will inhibit HIV-1 gene expression and replication. The RASORS combine a duplex recognition unit, such as those described above, and a unit that binds to unpaired RNA bases such as those that exist at base bulges or loops. These units are joined by linkers that also enhance RNA binding. The duplex unit of RASORS will intercalate in TAR or RRE adjacent to base bulges or loops and place the unpaired base recognition unit of RASORS at an optimum position to interact with the unpaired bases. After the RNA interactions are optimized, additional groups will be added to the basic RASORS to selectively hydrolyze HIV-1 RNA. We have designed such a catalytic RASOR with a carboxyl that can hydrogen bond to an HIV RNA 2'-OH and transiently remove the hydrogen from the 2'-OH. The molecule has a cationic pyridyl function (for proton donation) adjacent to the phosphate at the same site so that RNA can be hydrolyzed in a ribonuclease type mechanism. This hydrolysis is selective for RNA and cannot occur with DNA. RASOR binding will direct the catalytic activity to the desired specific sites in HIV-1 RNA.