Deciphering the structure and dynamics of quadruplex DNA and DNA-ligand complexes

破译四链体 DNA 和 DNA-配体复合物的结构和动力学

基本信息

批准号：
9304843
负责人：
Liliya A Yatsunyk
金额：
$ 41.05万
依托单位：
SWARTHMORE COLLEGE
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-06-01 至 2020-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9304843
关键词：
Address Advanced Development Adverse effects Affect Affinity Amination Amines Antineoplastic Agents Architecture Area BCL2 gene Binding Binding Sites Bioinformatics Biological Biological Process Biological Testing Cancer Intervention Cessation of life Charge Chemicals Chemistry Complement Complex Crystallization DNA DNA Damage DNA Repair DNA Structure Data Disease Epigenetic Process G-Quartets Gene Expression Regulation Generations Genomics Goals Human Human Genome In Vitro Investigation KRAS2 gene Kinetics Knowledge Lead Ligand Binding Ligands Light Malignant Neoplasms Metals Modification Molecular Molecular Conformation Neoplasm Metastasis Oncogenes Oncoproteins Outcome Porphyrins Probability Propionic Acids Recovery Regulation Research Resolution Roentgen Rays Side Structure Telomere Maintenance Telomere Maintenance Gene Testing Thermodynamics Training Vascular Endothelial Growth Factors Work anti-cancer therapeutic biophysical properties c-myc Genes cancer therapy cell growth design driving force drug candidate drug discovery flexibility improved in vivo interest mesoporphyrin IX neoplastic cell novel preference programs promoter quadruplex DNA scaffold small molecule stoichiometry targeted treatment telomere therapeutic target three dimensional structure tumor growth undergraduate student

项目摘要

PROJECT SUMMARY The proposed research will improve the selectivity and efficacy of anticancer therapies by contributing new knowledge about non-canonical G-quadruplex (GQ) DNA structure, and the interactions of GQs with small- molecule ligands. Bioinformatics studies have identified 370,000 sequences with G-quadruplex-forming potential in the human genome. There is now convincing biological evidence that GQs form in vivo and that these structures regulate a variety of cancer-related biological processes, such as telomere protection, oncogene expression, epigenetic modification, and DNA repair. Thus, GQ DNA has been firmly established as an important therapeutic target for cancer. Small molecules that bind selectively to GQ DNA have been identified, and some have been shown to inhibit tumor cells growth; however, exact mechanisms underlying this inhibition are not known. Such small-molecule ligands may ultimately become lead compounds for the generation of novel selective cancer drugs superior to conventional mutagenetic therapies. Unfortunately, DNA-centered drug discovery programs suffer from limited structural information available for GQs, especially in the presence of ligands. The situation is further complicated by high structural diversity of GQs, their contradictory biological functions, and our limited ability to target a specific GQ folding topology. To address these challenges, we propose to perform comprehensive crystallographic investigations focused on telomeric and oncogene promoter G-quadruplexes, both alone and in complex with a variety of small-molecule ligands. This work will be accompanied by spectroscopic and calorimetric studies of the thermodynamic parameters of ligand binding to GQ DNA (e.g., stoichiometry, affinity, selectivity, driving forces). The static structural view of GQs and GQ-ligand complexes will be complemented by rigorous kinetics studies of ligand-assisted GQ folding and structural rearrangements. Kinetic information can help us identify the timescale of G-quadruplex formation and thus biological processes that can be affected by the presence of these structures. Chemical and structural features of ligands essential for G-quadruplex binding or structural rearrangements will be identified from kinetics and structural studies. Furthermore, we propose chemical modification to the scaffold of N-methylmesoporphyrin IX (NMM), which we showed displays unprecedented selectivity for a parallel GQ fold, yet has modest binding affinity. The modifications should lead to new ligands that retain this selectivity but have improved binding affinity. Ligands that display selective GQ interactions in vitro will be tested in vivo for their biological effects, and genomic targets will be identified. Collectively, the proposed work will enhance our understanding of GQ structural plasticity, supply coordinates for drug discovery platforms, shed light on the origin of ligand selectivity for a specific DNA target, and guide the design of novel highly selective anticancer therapies while providing transformative training to Swarthmore undergraduate students.

项目摘要拟议的研究将通过贡献新的研究来提高抗癌疗法的选择性和效率关于非经典G-四链体（GQ）DNA结构的知识，以及GQ与小的相互作用分子配体。生物信息学研究已经确定了370,000个序列，并通过G四链体形成人类基因组的潜力。现在有令人信服的生物学证据表明，GQ在体内形成，并且这些结构调节了各种与癌症相关的生物学过程，例如端粒保护，癌基因表达，表观遗传修饰和DNA修复。那是GQ DNA首先被确定为癌症的重要治疗靶点。选择性结合与GQ DNA的小分子已经鉴定出来，有些已显示出抑制肿瘤细胞生长的抑制。但是，确切的机制这种抑制尚不清楚。如此小的分子配体可能最终成为新型选择性癌症药物的产生优于常规诱变疗法。很遗憾，以DNA为中心的药物发现计划遭受了GQ可用的结构信息有限，尤其是在配体的情况下。由于GQ的高结构多样性，它们的情况更加复杂矛盾的生物学功能以及我们针对特定GQ折叠拓扑的有限能力。为了应对这些挑战，我们建议进行全面的晶体学调查专注于单独和复杂的远程和癌基因启动子G四链体小分子配体。这项工作将通过光谱学和Calolimetric研究来完成配体与GQ DNA结合的热力学参数（例如，化学计量，亲和力，选择性，驾驶力量）。严格的动力学将完成GQ和GQ配体配合物的静态结构视图配体辅助GQ折叠和结构重排的研究。动力学信息可以帮助我们识别 G-四链体形成的时间尺度，因此可能受到存在的生物过程这些结构。 G-四链体结合或结构性必不可少的配体的化学和结构特征将从动力学和结构研究中确定重排。此外，我们建议化学修改了N-甲基甲氧甲林IX（NMM）的支架，我们显示了表现前所未有的对并行GQ折叠的选择性，但具有适度的绑定亲和力。修改应导致新的配体保留了这种选择性，但有改善的结合亲和力。在中显示选择性GQ相互作用的配体体内将测试体外的生物学作用，并确定基因组靶标。集体，拟议的工作将增强我们对GQ结构可塑性的理解，提供药物的坐标发现平台，阐明了特定DNA目标配体选择性的起源，并指导设计新型高度选择性的抗癌疗法，同时为Swarthmore提供变革性训练本科生。