SEQUENCE-SPECIFIC RECOGNITION OF DNA BY DIMER MOTIFS

二聚体基序对 DNA 的序列特异性识别

• 批准号: 6872685
• 负责人: W David Wilson
• 金额: $ 27.65万
• 依托单位: GEORGIA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-07-01 至 2009-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6872685
• 关键词: DNA binding protein; DNA footprinting; X ray crystallography; benzimidazoles; biophysics; cations; chemical structure function; chemical synthesis; combinatorial chemistry; covalent bond; dimer; drug design /synthesis /production; drug discovery /isolation; heterocyclic compounds; inhibitor /antagonist; intermolecular interaction; model design /development; molecular dynamics; nuclear magnetic resonance spectroscopy; nucleic acid sequence; nucleic acid structure; oncoproteins; physical model; structural biology; transcription factor

DESCRIPTION (provided by applicant): Continuation funds are requested for a project that has been funded for three+ years and that supports collaborating laboratories in nucleic acid targeted drug design and synthesis and in the biophysical chemistry of nucleic acid complexes. Based on results obtained under initial funding, it is clear that stacked-dimers of heterocyclic cations represent a powerful new motif for specific, strong recognition of mixed base pair DNA sequences and inhibition of protein-DNA complexes. The compounds have low toxicity with excellent biological activity and a compound from this class is set to enter Phase III clinical trials. Since the two strands of the double helix contain different chemical information, compounds that recognize DNA can do so with the highest specificity if they read both strands. Based on these observations our hypothesis is that stacked dimer recognition of DNA by designed heterocyclic cations offers unique opportunities for development of new classes of drugs for broad-based selective molecular recognition of the duplex and inhibition of DNA-protein complexes. Such dimers have significant potential for development as new types of therapeutics, for reagents in biotechnology, as agents for control of cellular gene expression, and for inhibition of specific protein-DNA complexes. We have designed and are studying two dimer-stacking motifs that recognize the minor groove in new and different ways. One system is being developed to inhibit bZlP transcription factors such as the Fos/Jun oncoproteins, while the second system will target the minor groove HMGA oncoproteins. We will prepare and study compounds that (i) increase the sequence recognition capability of the dimer systems by using a variety of heterocycles; (ii) extend the length of the base sequence that is read by extending the length of the dimers; (iii) enhance the affinity and specificity of binding by preparation of covalent dimers. The compound-DNA complexes will be characterized with a powerful array of biophysical methods including NMR and x-ray; enzymatic and chemical footprinting; biosensor-SPR and ITC. At the most fundamental level, the heterocyclic dimer systems will provide significant new understanding of the molecular basis of DNA recognition and how it is affected by the local interplay of base pair chemistry, solvent and ligand properties. The heterocyclic system is the only motif for targeting mixed sequences of DNA with clinically useful and cell permeable agents.

描述（由申请人提供）：为已资助三年以上的项目申请持续资金，该项目支持核酸靶向药物设计和合成以及核酸复合物生物物理化学方面的合作实验室。根据初始资助下获得的结果，很明显，杂环阳离子的堆叠二聚体代表了一种强大的新基序，可特异性、强烈地识别混合碱基对 DNA 序列并抑制蛋白质-DNA 复合物。该类化合物毒性低，生物活性优异，该类化合物即将进入Ⅲ期临床试验。由于双螺旋的两条链包含不同的化学信息，因此识别 DNA 的化合物如果能够读取两条链，就能以最高的特异性进行识别。基于这些观察，我们的假设是，设计的杂环阳离子对 DNA 的堆叠二聚体识别为开发新型药物提供了独特的机会，用于双链体的广泛选择性分子识别和 DNA-蛋白质复合物的抑制。此类二聚体具有作为新型治疗剂、生物技术试剂、细胞基因表达控制剂以及特定蛋白质-DNA复合物抑制剂的巨大开发潜力。我们已经设计并正在研究两种二聚体堆积基序，它们以新的不同方式识别小沟。正在开发一种系统来抑制 bZIP 转录因子，例如 Fos/Jun 癌蛋白，而第二种系统将针对小沟 HMGA 癌蛋白。我们将制备和研究以下化合物：（i）通过使用各种杂环来提高二聚体系统的序列识别能力； (ii)通过延长二聚体的长度来延长所读取的碱基序列的长度； (iii)通过制备共价二聚体来增强结合的亲和力和特异性。化合物-DNA 复合物将通过一系列强大的生物物理方法（包括 NMR 和 X 射线）进行表征；酶足迹和化学足迹；生物传感器-SPR和ITC。在最基本的层面上，杂环二聚体系统将为 DNA 识别的分子基础以及碱基对化学、溶剂和配体特性的局部相互作用如何影响它提供重要的新理解。杂环系统是用临床有用的细胞渗透剂靶向 DNA 混合序列的唯一基序。