Discovery of new classes of PARP-1 inhibitors for the treatment of cancer

描述（由申请人提供）：聚（adp -核糖）聚合酶-1 （PARP-1）是一种在细胞命运决定中起重要作用的酶，已被作为一种治疗靶点。PARP-1抑制剂在选择性杀死具有某些DNA修复缺陷（BRCA1/2阴性）的乳腺癌和卵巢癌方面显示出前景。难以治疗的癌症，如三阴性乳腺癌（TNBC）通常符合这一特征，显示出PARP-1抑制剂的巨大潜力和应用。这个例子为化疗引入了一种称为“合成致死”的新范式，即选择性地杀死具有遗传缺陷的癌细胞，对正常功能细胞产生轻微影响。目前的临床试验表明，同源重组缺陷患者对PARP-1抑制剂单药治疗和与传统化疗方案联合治疗均有积极反应。目前，只有一类PARP-1抑制剂已经成熟，尽管开发具有更高选择性的替代类是非常可取的。最近在复合体中关键PARP-1结构域的结构发现为如何开发更具选择性和有效性的新型PARP-1抑制剂提供了见解。本申请的目的是：(1)验证PARP-1的新药物靶点，(2)开发检测PARP-1变构机制的方法，(3)鉴定小分子支架作为新的PARP-1抑制剂。我们将采用基于结构的药物设计方法来验证PARP-1抑制剂的开发将减少与其他PARP异构体和NAD结合酶的交叉抑制的假设，提供新的工具，扩大我们对PARP-1与癌症的理解，并提供创新的癌症治疗方法。为了验证这一假设，需要测试的具体目标是：(1)评估PARP-1的Zn3结构域作为新的药物靶点，(2)开发能够检测DNA结合时PARP-1结构域之间通信的高通量分析，以及(3)确定PARP-1的adp核糖口袋中重要的结构相互作用，这些相互作用可以帮助在该位点进行合理的药物设计。计算建模和定点诱变的结合被用于验证新的药物靶点。此外，正在设计两种新的互补检测方法，可以检测激活后PARP-1的域间通信。配体晶体学是本研究计划的主要组成部分，加速了基于结构的药物设计方法。从这项工作中鉴定出的抑制剂可能在PARP亚型中具有选择性，从而允许研究PARP-1特异性抑制而不是“多PARP”抑制。长期目标包括开发具有翻译潜力的新的PARP-1抑制剂候选物，这些候选物将无毒且有效地治疗BRCA1/2和/或其他DNA修复缺陷的癌症。

DESCRIPTION (provided by applicant): Poly(ADP-ribose) polymerase-1 (PARP-1) is an enzyme that has important roles in cell fate determination, and has been pursued as a therapeutic target. PARP-1 inhibitors have shown promise in selectively killing breast and ovarian cancers with certain DNA repair defects (BRCA1/2 negative). Difficult to treat cancers such as triple-negative breast cancer (TNBC) commonly fit this profile, presenting a significant potential and application of PARP-1 inhibitors. This example has introduced a new paradigm in chemotherapy termed "synthetic lethality", where cancer cells with genetic defects are selectively killed with inconsequential effects on normal functioning cells. Current clinical trial are showing that patients with homologous recombination defects respond positively to PARP-1 inhibitors in monotherapy and in combination with traditional chemotherapeutic regimens. Currently, only one class of PARP-1 inhibitors has matured, although the development of alternative classes with improved selectivity is highly desirable. The recent structure discovery of key PARP-1 domains in complex with duplex DNA provides insights on how to develop new classes of PARP-1 inhibitors that can be more selective and effective. The objectives of this application are to (1) validate a new drug target site of PARP-1, (2) develop methods of detecting PARP-1 allosteric mechanisms and (3) identify small molecule scaffolds as new classes of PARP-1 inhibitors. A structure based drug design approach will be undertaken to test the hypothesis that development of alternative classes of PARP-1 inhibitors will diminish cross inhibition with other PARP isoforms and NAD binding enzymes, providing new tools that will broaden our understanding of PARP-1 with cancer and offer innovative cancer therapies. To test this hypothesis, the specific aims to be tested are (1) evaluation of the Zn3 domain of PARP-1 as a new drug target site, (2) development of high-throughput assays that are capable of detecting communication between PARP-1 domains upon DNA binding, and (3) to determine important structural interactions in the ADP-ribose pocket of PARP-1 that can assist a rational drug based design at this site. A combination of computational modeling and site-directed mutagenesis are being used to validate new drug target sites. In addition, two novel, complementary assays that can detect PARP-1 inter-domain communication upon activation are being designed. Crystallography with ligands constitutes a major component of this research plan, accelerating a structure based drug design approach. Identified inhibitors from this work are likely to be selective among PARP isoforms, allowing PARP-1 specific inhibition to be studied over "multi-PARP" inhibition. Long-term goals encompass development of new PARP-1 inhibitor candidates with translational potential that will be non-toxic and effective in treating cancers with BRCA1/2 and/or other DNA repair deficiencies.