Structure-based rational design of oligonucleotide-mediated chemical ribonucleases

非科学总结：合成的、强大的催化分子的高度特异性作用，可以切割和加工核酸，不仅是细胞生命的本质和个体遗传信息转化为其物理构成的基础，而且还提供了现代化学生物学的很大一部分工具。模仿一些能够破坏信使RNA的天然酶的活性中心的新型人造化合物的发展为产生新的有用的现代化学生物学工具，甚至可能是药物，影响特定的信使RNA和病毒遗传物质提供了基础。最近，人们在化学核糖核酸酶的创造上做出了相当大的努力，这种催化分子能够在所需的位置上不可逆地破坏RNA分子。这些化合物可能适用于生物医学领域和公共卫生领域的一系列问题，也适用于生命科学和化学生物学的各个领域。然而，无金属化学核糖核酸酶生物性能不理想的问题仍未得到解决。最近，在我们与一个俄罗斯研究小组合作的过程中，发现了一种新型的化学核酸酶，它具有非常不同寻常的生物学特性。这些新化合物是由合成的短蛋白质样分子与合成的DNA片段化学融合而成的。这些新型催化分子最显著的特点是，短DNA片段极大地增强了以前无活性的蛋白质样分子的生物活性。我们的初步研究表明，这两种化学实体的合并似乎产生了一种新的杂交类型的分子，它可以协同结合两种成分的单个特性，从而产生一种新的、不寻常的生物能力。类dna成分似乎诱导了类蛋白质片段的“活性”结构，从而显著增强了其催化性能。然而，这一不寻常发现背后的基本过程从未被研究过。因此，巨大的挑战是在分子水平上理解这些功能重要的实体（即短合成蛋白质样分子和短DNA片段）如何相互作用并相互改变其功能。因此，本提案的目的是确定控制这些新型合成催化剂生物活性的结构规则和分子机制，并控制这些分子是否能够识别和特异性切割另一个分子。这一领域的成功将为我们提供一种化学手段来开发化学生物学的新工具，例如与天然酶相比，具有更高活性、改变特异性和改善储存性能的催化剂。我们已经获得了实验证据，我们正在设计的分子可以提供特定和有效的切割，但现在我们需要了解管理这些过程的精细分子机制。为了实现这一目标，我们必须通过高分辨率的结构研究和高水平的计算方法，将这项研究建立在坚实的实验基础上。

Non-scientific Summary:The highly specific action of synthetic, robust catalytic molecules that can cleave and process nucleic acids not only underlies the essence of cellular life and the translation of the genetic message of an individual into their physical make-up, but also provides a substantial portion of the tools of modern chemical biology. The development of novel man-made chemical compounds imitating the active centre of some natural enzymes that are capable of damaging messenger RNA provides a basis for generating new useful tools of modern chemical biology, perhaps even drugs, affecting specific messenger RNAs and viral genetic material. Recently a considerable effort has been made in the creation of chemical ribonucleases, catalytic molecules capable of damaging RNA molecules irreversibly at desired positions. These compounds can potentially be applicable to a range of problems in biomedical areas and public healthcare and also in various areas of life sciences and chemical biology. However, the problem of unsatisfactory biological performance of metal-free chemical ribonucleases remains unsolved. Recently, in the frame of our collaborative work with a Russian research group, a new type of chemical nuclease, showing very unusual biological properties, was discovered. These novel compounds were constructed by chemical fusion of short, synthetic protein-like molecules with synthetic DNA fragments. The most remarkable feature of these novel catalytic molecules was that the short DNA fragment enormously enhanced the biological activity of a previously inactive protein-like molecule. Our preliminary study showed that the merger of these two chemical entities seems to produce a new, hybrid type of molecule that can synergistically combine the individual properties of the two components to yield a new and unusual biological ability. The DNA-like component seems to induce an `active` structure of the protein-like fragment and hence significantly enhance its catalytic performance. However, the basic, fundamental processes behind this unusual discovery have never been studied. The great challenge is therefore to provide an understanding at the molecular level of how these functionally significant entities (i.e. the short synthetic protein-like molecule and the short DNA fragment) interact with each other and mutually change their functions. The aim of this proposal is therefore to determine the structural rules and molecular mechanisms which govern biological activity of these novel synthetic catalysts and control whether these molecules can recognize and specifically cleave another molecule. Success in this area will provide us with a chemical means to develop novel tools for chemical biology, such as catalysts with increased activity, altered specificity and improved storage properties compared to natural enzymes. We already have obtained experimental evidence that the molecules we are designing can provide specific and efficient cleavage, but now we need to understand the fine molecular mechanisms managing these processes. To achieve this we have to put this research onto a solid experimental basis through high resolution structural studies and a high-level computational approach.