Deciphering the structure and dynamics of non-canonical DNA implicated in cancer

项目总结 拟议中的研究将通过贡献新的研究成果来提高抗癌疗法的选择性和有效性。 关于非规范核酸结构、G-四链体(Gq)和I-基序的知识，以及它们的详细信息 与小分子配体的相互作用。生物信息学研究已确定700,000个序列具有GQ- 在人类基因组中形成潜力。富含C的相反链被建议形成I-基序。现在有了 令人信服的生物学证据表明GQ和I-基序在体内形成，并且这些结构相互补充 其他在调节与癌症相关的各种生物过程方面也是如此。GQ核酸一直坚定地 被确立为癌症的重要治疗靶点。同样的证据也证明了i-Motif是稳定的 不断积累。已经鉴定出选择性结合Gq DNA和RNA以及I基序的小分子， 一些已经被证明可以抑制肿瘤细胞的生长；然而，这种抑制的确切机制 都是未知的。此外，选择性I基序配体的数量很少。这样的配体最终可能会成为 用于癌症干预的先导化合物优于传统的突变疗法。 以核酸为中心的药物发现计划受到GQS和I基序结构信息有限的影响， 尤其是在配体存在的情况下。到目前为止，还没有关于I基序配体复合体的结构的报道。 GQ和I-主题的高度结构多样性使情况变得更加复杂，它们的矛盾 生物功能，以及我们针对特定折叠拓扑(例如，平行与反平行)的有限能力 GQ)。 为了应对这些挑战，我们建议对端粒进行全面的结晶学研究。 以及癌基因启动子GQS和I-基序，无论是单独的还是与新颖的和商业上可用的复合体 选择性小分子配体。为GQ和I-基序提供稳定性的相互作用的多样性将是 下定决心。配体结合部位的详细信息，以及配体的化学和结构特征 它们的亲和力和选择性将被确定。这项工作将由光谱学和 配基结合热力学参数的量热研究。对于GQ DNA来说，这要多得多 在探索中，结构研究将得到配体辅助的GQ折叠的严格动力学探索的补充。 动力学信息可以帮助我们确定GQ形成的时间尺度，从而确定可以 被这些结构的存在所影响。总的来说，拟议的工作将增进我们的理解 GQ和I-Motif结构可塑性的研究，为药物发现平台提供坐标，揭示了 对特定DNA或RNA靶标的配基选择性，并同时指导新的抗癌疗法的设计 为斯沃斯莫尔大学的本科生提供变革性培训。

PROJECT SUMMARY The proposed research will improve the selectivity and efficacy of anticancer therapies by contributing new knowledge about non-canonical nucleic acid structures, G-quadruplexes (GQ) and i-motifs, and details of their interactions with small-molecule ligands. Bioinformatics studies have identified 700,000 sequences with GQ- forming potential in the human genome. The C-rich opposite strands are proposed to form i-motifs. There is now convincing biological evidence that GQs and i-motifs form in vivo and that these structures complement each other in regulating a variety of cancer-related biological processes. GQ nucleic acids have been firmly established as an important therapeutic target for cancer. The same evidence for i-motifs is steadily accumulating. Small molecules that bind selectively to GQ DNA and RNA and to i-motifs have been identified, and some have been shown to inhibit tumor cells growth; however, exact mechanisms underlying this inhibition are not known. Additionally, the number of selective i-motif ligands is low. Such ligands may ultimately become lead compounds for cancer intervention superior to conventional mutagenetic therapies. Nucleic acid-centered drug discovery programs suffer from limited structural information for GQs and i-motifs, especially in the presence of ligands. As of now, no structure of an i-motif-ligand complex has been reported. The situation is further complicated by high structural diversity of both GQs and i-motifs, their contradictory biological functions, and our limited ability to target their specific folding topology (e.g., parallel vs antiparallel GQs). To address these challenges, we propose to perform comprehensive crystallographic investigation of telomeric and oncogene promoter GQs and i-motifs, both alone and in complex with novel and commercially available selective small-molecule ligands. The diversity of interactions which provide stability to GQs and i-motifs will be determined. The details of ligand binding sites, as well as chemical and structural features of ligands essential for their affinity and selectivity will be identified. This work will be complemented by spectroscopic and calorimetric studies of the thermodynamic parameters of ligand binding. For GQ DNA, that is much more explored, structural studies will be complemented by rigorous kinetic exploration of ligand-assisted GQ folding. Kinetic information can help us identify the timescale of GQ formation and, thus, biological processes that can be affected by the presence of these structures. Collectively, the proposed work will enhance our understanding of GQ and i-motif structural plasticity, supply coordinates for drug discovery platforms, shed light on the origin of ligand selectivity for a specific DNA or RNA target, and guide the design of novel anticancer therapies all while providing transformative training to Swarthmore undergraduates.