Mass spectrometry Studies on Radical Reactions of DNA

描述（由申请人提供）：许多非水解性DNA切割剂的作用被认为是基于活性苯基自由基，它从DNA中的脱氧核糖中提取氢原子。与此过程相关的各种问题，包括药物在DNA上的结合位点、自由基形成的机制、药物对不同DNA位点的可及性以及产生的DNA自由基的命运，正在被科学家们解决，以促进更好的抗肿瘤和抗病毒药物的合理设计。然而，该过程的关键部分，即自由基中间体与DNA的反应，仍未被探索。尽管药物设计迫切需要有关控制该反应的因素的信息，但由于研究这种高活性物种的实验困难，人们对药物形成的自由基中间体几乎一无所知。我们的目标是学习如何通过结构变化来控制自由基战斗部的反应性和内在选择性。我们开发了一种新的基于质谱的实验方法来研究生物相关的自由基反应。该方法涉及将带电基团连接到感兴趣的自由基上，以便在FT-ICR质谱仪中进行操作，其中通过激光诱导声解吸引入小的中性生物分子。该提案是一个为期四年的项目的延续，包括1)购买和设置必要的仪器，2)证明该方法的可行性，3)检查已知系统，以表明该方法产生与中性自由基和溶液条件相关的数据，以及4)收集动力学反应性数据，以提供几种新的结构/反应性关系，以促进更好的非水解DNA切割器的设计。目前提出的工作中最重要的领域包括：(1)发展更复杂系统的结构/反应性关系，(2)探索不同自由基对寡核苷酸不同位点的选择性，(3)检查自由基攻击肽的倾向以模拟蛋白质损伤，以及(4)基于在上述研究中获得的见解，开发提供一般预测能力的反应性范式。这一范式将用于设计针对特定目标的基战斗部和前药。Rick Borch教授（普渡大学药物化学和分子药理学）是癌症药物设计和机制方面的专家，Mark Lipton教授（普渡大学有机化学）是双基前体药物合成方面的专家，他们将指导这项研究，并帮助找到将知识融入新药设计和测试的最佳途径。

DESCRIPTION (provided by applicant): The action of many non-hydrolytic DNA cleaving agents is believed to be based on reactive phenyl radicals that abstract hydrogen atoms from deoxyribose in DNA. Various issues relating to this process, including the drug's binding site on DNA, the mechanism of radical formation, its accessibility to various DNA sites, and the fate of the resulting DNA radicals, are being addressed by scientists to advance the rational design of better antitumor and antiviral drugs. However, the key part of the process, the reaction of the radical intermediate with DNA, remains unexplored. Although information on the factors that control this reaction is critically needed for drug design, nearly nothing is known about the radical intermediates formed from drugs because of severe experimental difficulties in studying such highly reactive species. Our goal is to learn how to control the reactivity and intrinsic selectivity of a radical warhead by structural changes. We have developed a novel experimental approach based on mass spectrometry to study biologically relevant radical reactions. The method involves attaching a charged group to a radical of interest for manipulation in an FT-ICR mass spectrometer wherein small neutral biomolecules are introduced by laser-induced acoustic desorption. This proposal presents a continuation of a four-year project that involved 1) purchase and set-up of the necessary instrumentation, 2) demonstration of the feasibility of the approach, 3) examination of known systems to show that the method yields data relevant to neutral radicals and solution conditions, and 4) collection of kinetic reactivity data to provide several novel structure/reactivity relationships for advancement of the design of better non-hydrolytic DNA cleavers. The most important areas of the currently proposed work include (1) development of structure/reactivity relationships for more complex systems, (2) exploration of the selectivity of different radicals toward different sites in oligonucleotides, (3) examination of the propensity of the radicals to attack peptides to model protein damage, and (4) based on the insights gained in the above studies, development of a reactivity paradigm that provides general predictive power. (5) This paradigm will be used to design target-specific radical warheads and prodrugs. Professors Rick Borch (Medicinal Chemistry and Molecular Pharmacology, Purdue), a specialist in cancer drug design and mechanisms,and Mark Lipton (Organic Chemistry, Purdue), an expert in synthesis of biradical producing prodrugs, will guide the research and help in finding the best way to incorporate knowledge into the design and testing of novel drugs.