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

基本信息

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
项目类别：
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

项目摘要

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方案，用于生成 RNA 药物靶标的特异性、高亲和力、小分子配体。在第一阶段，我们将使用端粒酶核糖核蛋白的 RNA 部分上的一个新位点来创建人类端粒酶抑制剂，这是一种经过验证的抗癌靶点。尽管经过了二十年的发展，分子对接软件仍无法实现药物分子与其靶标 RNA 的诱导拟合。 MORDOR 是加州大学旧金山分校最近开发的一个软件程序，它允许配体和受体具有灵活性，从而首次实现了 RNA 靶标的诱导拟合和计算机配体设计的实用化。大量数据表明，人端粒酶 RNA (hTR) 上各个保守位点的配体应该会导致酶抑制并最终导致肿瘤消退。 P2b 结构域代表这些保守的 hTR 位点之一，因为它涉及关键的分子开关。我们将测试以下假设：诱导拟合对接可用于设计 hTR-P2b 结合物，从而设计端粒酶抑制剂，并且通过串联对接和实验方法，我们可以成功提高 RNA 配体的亲和力和特异性。我们期望实现以下第一阶段目标：目标 1A。从包含 130,000 种药物样化合物的 NCI 数据库中选择与 MORDOR 一起使用的化合物，并将其中 35,000-50,000 个结构对接至我们的 hTR-P2b 构建体中。相似性搜索、对接和 NMR 测试之后的方法迭代将增强结合物库。目标 1B。使用 MORDOR 筛选 ZINC 数据库的 49,000 个片段子集。目标 2. 使用 NMR 筛选最佳计算“命中”结合，绘制目标 hTR 上的结合位点，确定配体的结合表位，并使用两个对照 RNA 测量最佳命中的 KD 值以确定选择性。目标 3. 设计新配体，其亲和力比从目标 1 化合物获得的起始结构至少增加五倍，并且对对照 RNA 有选择性。目标 4. 使用基于凝胶的 P2b-P3 竞争测定或基于细胞的 TRAP 测定或两者来测试最佳化合物的活性。在该项目第一阶段结束时，我们将验证灵活受体的配体设计方案，并合成一些早期端粒酶抑制剂先导化合物以进行优化。公共健康相关性：使用计算机模型发现药物已经取得了一定的成功，部分原因是药物靶标（蛋白质和 RNA）在药物结合时会改变形状（通常是适度的）。我们开发的软件考虑了蛋白质和 RNA 药物靶点的灵活性以及假定抑制剂的灵活性。我们建议使用该软件来寻找端粒酶的抑制剂，端粒酶是一种复杂的核糖核蛋白，是已知的抗癌药物靶标。具体来说，我们将使用初始结合物来设计和合成端粒酶关键 RNA 成分的抑制剂。