Drug leads via flexible-receptor docking: application to an RNA cancer target

通过柔性受体对接的药物先导：应用于 RNA 癌症靶点

• 批准号: 7482561
• 负责人: Jay F. Stearns
• 金额: $ 18.98万
• 依托单位: CONTOUR MOLECULAR, LLC
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-03-17 至 2008-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7482561
• 关键词: 2-cyclopentyl-5-(5-isoquinolylsulfonyl)-6-nitro-1H-benzo(D)imidazole; Accounting; Address; Affinity; Antineoplastic Agents; Binding; Binding Sites; Biological Assay; California; Cells; Characteristics; Class; Clinical; Complex; Computer Simulation; Computer software; Data; Databases; Development; Disease regression; Docking; Drug Delivery Systems; Drug Design; Drug usage; Enzyme Inhibition; Epitopes; Explosion; Gel; Goals; Human; Inhibitory Concentration 50; Lead; Ligands; Malignant Neoplasms; Maps; Measures; Molecular; Molecular Weight; Monitor; New Agents; Oral; Pharmaceutical Preparations; Phase; Pliability; Principal Investigator; Proteins; Protocols documentation; Public Health; RNA; Ribonucleoproteins; Rodent Model; San Francisco; Score; Shapes; Site; Small Business Funding Mechanisms; Small Business Innovation Research Grant; Specificity; Structure; Telomerase; Telomerase Inhibitor; Telomerase RNA Component; Testing; Therapeutic Agents; Time; Universities; Zinc; base; cost; design; improved; inhibitor/antagonist; novel; programs; receptor; small molecule; software development; three dimensional structure; tool; tumor; 2-cyclopentyl-5-(5-isoquinolylsulfonyl)-6-nitro-1H-benzo(D)imidazole; Accounting; Address; Affinity; Antineoplastic Agents; Binding; Binding Sites; Biological Assay; California; Cells; Characteristics; Class; Clinical; Complex; Computer Simulation; Computer software; Data; Databases; Development; Disease regression; Docking; Drug Delivery Systems; Drug Design; Drug usage; Enzyme Inhibition; Epitopes; Explosion; Gel; Goals; Human; Inhibitory Concentration 50; Lead; Ligands; Malignant Neoplasms; Maps; Measures; Molecular; Molecular Weight; Monitor; New Agents; Oral; Pharmaceutical Preparations; Phase; Pliability; Principal Investigator; Proteins; Protocols documentation; Public Health; RNA; Ribonucleoproteins; Rodent Model; San Francisco; Score; Shapes; Site; Small Business Funding Mechanisms; Small Business Innovation Research Grant; Specificity; Structure; Telomerase; Telomerase Inhibitor; Telomerase RNA Component; Testing; Therapeutic Agents; Time; Universities; Zinc; base; cost; design; improved; inhibitor/antagonist; novel; programs; receptor; small molecule; software development; three dimensional structure; tool; tumor

DESCRIPTION (provided by applicant): The goal of this SBIR project is to develop a general protocol for generating specific, high affinity, small molecule ligands for RNA drug targets. In Phase 1, we will create inhibitors to human telomerase, a validated anti-cancer target, using a novel site on the RNA moiety of the telomerase ribonucleoprotein. Despite two decades of development, molecular docking software cannot allow for induced fit of a drug molecule to its target RNA. MORDOR, a software program recently developed at the University of California San Francisco, permits both ligand and receptor flexibility, enabling induced fitting and making in silico ligand design for RNA targets practical for the first time. A wealth of data suggests that ligands for various conserved loci on human telomerase RNA (hTR) should lead to enzyme inhibition and ultimately tumor regression. The P2b domain represents one of these conserved hTR loci, as it is involved in a crucial molecular switch. We will test the hypothesis that induced-fit docking can be used to design hTR- P2b binders and consequently telomerase inhibitors and that through a tandem docking and experimental approach, we can successfully improve affinity and specificity of RNA ligands. We expect to achieve the following Phase 1 aims: Aim 1A. Select compounds from the NCI database of 130,000 drug-like compounds for use with MORDOR, and dock 35,000-50,000 of these structures to our hTR-P2b construct. Iteration of the approach followed similarity searching, docking, and NMR testing will enhance the pool of binders. Aim 1B. Use MORDOR to screen the 49,000- fragment subset of the ZINC database. Aim 2. Use NMR to screen top computational "hits" for binding, map the binding site on the target hTR, determine binding epitope for the ligand and measure KD values for the best hits using two control RNAs to determine selectivity. Aim 3. Design new ligands with at least a five-fold increase in affinity over a starting structure obtained from Aim 1 compounds and that are selective for control RNAs. Aim 4. Test the best compounds for activity using a gel-based P2b-P3 competition assay or a cell-based TRAP assay or both. At the end of Phase I of this project, we will have validated our ligand design protocol for flexible receptors and synthesized some early telomerase inhibitor leads for optimization. PUBLIC HEALTH RELEVANCE: Discovering drugs using computer models has been marginally successful, in part because the drug targets - proteins and RNA - change shape (usually modestly) when a drug is bound. We have developed software that takes the flexibility of the protein and RNA drug targets into account as well as the flexibility of the putative inhibitors. We propose to use this software to find inhibitors of telomerase, a complex ribonucleoprotein which is a known anti-cancer drug target. Specifically, we will use the initial binders to design and synthesize inhibitors of a crucial RNA component of telomerase.

描述（由申请人提供）：该SBIR项目的目标是开发一种通用协议，用于生成针对RNA药物靶标的特定，高亲和力，小分子配体。在第1阶段，我们将使用端粒酶核糖核蛋白的RNA部分上的新位点对人端粒酶（一种经过验证的抗癌靶标的抑制剂）创建抑制剂。尽管开发了二十年，但分子对接软件仍无法允许药物分子与其靶RNA的拟合拟合。最近在加利福尼亚大学旧金山分校开发的软件计划Mordor允许配体和受体灵活性，可以首次实用的RNA靶标的诱导配件和制造硅配体设计。大量数据表明，人类端粒酶RNA（HTR）的各种保守基因座的配体应导致酶抑制并最终导致肿瘤回归。 P2B结构域代表了这些保守的HTR基因座之一，因为它参与了关键的分子开关。我们将检验以下假设：诱导的对接可以用于设计Htr-P2B粘合剂和端粒酶抑制剂，并且通过串联对接和实验方法，我们可以成功地提高RNA配体的亲和力和特异性。我们希望实现以下第1阶段目标：目标1A。从NCI数据库中选择130,000种类似药物的化合物，可与Mordor一起使用，将这些结构中的35,000-50,000座停靠在我们的HTR-P2B构建体中。该方法的迭代遵循相似性搜索，对接和NMR测试将增强粘合剂的池。目标1B。使用mordor筛选锌数据库的49,000个片段子集。 AIM 2。使用NMR筛选顶部计算“命中”以进行绑定，绘制目标HTR上的结合位点，确定配体的结合表位，并使用两个控制RNA确定选择性，并测量最佳命中的KD值以确定选择性。 AIM 3。设计新的配体，与从AIM 1化合物获得的起始结构相比，亲和力至少增加了五倍，并且对控制RNA具有选择性。 AIM 4。使用基于凝胶的P2B-P3竞赛测定法或基于细胞的陷阱测定法或两者兼而有之的最佳化合物。在该项目的第一阶段结束时，我们将验证我们针对柔性受体的配体设计方案，并合成了一些早期的端粒酶抑制剂铅进行优化。 公共卫生相关性：使用计算机模型发现药物的成功，部分原因是药物靶标 - 蛋白质和RNA-在药物结合时（通常是适度）的形状（通常是适度）。我们开发了将蛋白质和RNA药物靶标的灵活性以及推定抑制剂的灵活性考虑的软件。我们建议使用该软件来查找端粒酶的抑制剂，端粒酶是一种复杂的核糖核蛋白，是已知的抗癌药物靶标。具体而言，我们将使用初始粘合剂来设计和合成端粒酶至关重要的RNA成分的抑制剂。