Inhibition and Catalytic Degradation of Promutagenic DNA Deaminases

促诱变 DNA 脱氨酶的抑制和催化降解

基本信息

批准号：
10729968
负责人：
Rahul Manu Kohli
金额：
$ 18.99万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-06 至 2025-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10729968
关键词：
Address Binding Biology Breathing Catalogs Cell Line Cell Nucleus Cells Characteristics Chemicals Chimera organism Clinical Cyclization Cytidine Deaminase Cytoplasm Cytosine DNA DNA Damage DNA biosynthesis Deaminase Deamination Dinucleoside Phosphates Disease Distant Engineering Enzymes Exonuclease Family Family member Frequencies Future Genome Genomics Goals HIV Host Defense Immune In Vitro Knowledge Ligands Link Malignant - descriptor Malignant Neoplasms Mediating Molecular Molecular Probes Mutagenesis Mutate Mutation Nature Outcome Pathogenesis Pathologic Pathologic Mutagenesis Physiological Play Positioning Attribute Process Proteins Proteolysis Resistance Retroelements Retroviridae Risk Role Route Shapes Single-Stranded DNA Somatic Mutation Specificity Structural Models Structure Structure-Activity Relationship Technology Testing Therapeutic Time Ubiquitination Uracil Viral Virus Work Zebularine amino group antagonist base cancer cell cancer genome cancer initiation cancer type cellular engineering cytosine analog density design genetic approach improved inhibitor insight interest member meter mimicry multicatalytic endopeptidase complex nanomolar novel novel strategies nucleic acid delivery nucleic acid inhibitor preference protein degradation recruit response small molecule stem therapeutic target tool tumor tumor initiation tumor progression ubiquitin-protein ligase whole genome

项目摘要

PROJECT SUMMARY This proposal aims to develop the first potent and specific antagonists of the pro-mutagenic effects of APOBEC DNA deaminase enzymes in cells. Access to whole genome sequences has helped reveal common mutational signatures across various cancers. One such prominent mutational signature, termed SBS2, includes hypermutated clusters containing a high density of C to T/G substitutions on the same strand, a phenomenon known as kataegis. These features, in addition to the enrichment of the mutations in 5’-TC motifs, point to a causative role for APOBEC3 (A3) family enzymes. While these enzymes normally mutate and restrict retroviruses or retroelements, studies have confirmed that two family members, APOBEC3A (A3A) and APOBEC3B (A3B), have a prominent role in pathological mutagenesis targeting the host genome. The relative contributions of each enzyme remain a matter of vigorous debate, as genetic approaches specifically targeting A3A or A3B are limited by their high homology to one another and juxtaposition on the genome. Furthermore, no molecular tools currently exist that can disrupt A3 function. There is therefore a pressing need for molecular probes that can either inhibit or deplete A3 enzymes from cells. This proposal builds on the hypothesis that insights into the mechanism and substrate selectivity of A3 enzymes can be leveraged to design potent and specific antagonists. Specifically, we have demonstrated that mechanism-based inhibitor moieties can be presented in preferred secondary structures and engineered into exonuclease-resistant DNA molecules to yield potent nanomolar inhibitors of A3A. These molecules present the opportunity for facile functionalization, which can be utilized to convert classical inhibitors into molecules capable of inducing the catalytic degradation of the target APOBEC enzymes in cells, via an unprecedented combination of nucleic acid inhibitors and proteasome targeting (PROTAC) technology. Taken together, this proposal aims to fill a critical gap in the field by introducing tools to perturb APOBEC function in cells in order to reveal their underlying biology and offer a roadmap for potential therapeutics.

项目概要该提案旨在开发第一个有效且特异性的 APOBEC 促突变作用拮抗剂细胞中的 DNA 脱氨酶有助于揭示常见的突变。一种名为 SBS2 的显着突变特征包括同一条链上含有高密度 C 到 T/G 取代的超突变簇，这是一种现象这些特征，除了 5’-TC 基序突变的富集之外，还指向一个 APOBEC3 (A3) 家族酶的致病作用，而这些酶通常会发生突变和限制。逆转录病毒或逆转录元件，研究已证实两个家族成员 APOBEC3A (A3A) 和 APOBEC3B (A3B) 在针对宿主基因组的病理诱变中发挥着重要作用。每种酶的贡献仍然是一个激烈争论的问题，因为遗传方法专门针对 A3A 或 A3B 受到彼此高度同源性和基因组并置的限制。目前不存在可以破坏 A3 功能的分子工具，因此迫切需要分子工具。可以抑制或消耗细胞中 A3 酶的探针该提议建立在以下假设之上。对 A3 酶的机制和底物选择性的深入了解可用于设计有效的、具体来说，我们已经证明基于机制的抑制剂部分可以是以优选的二级结构呈现，并被改造为耐外切核酸酶的 DNA 分子，以产生这些分子为 A3A 的有效纳摩尔抑制剂提供了简便的功能化机会。可用于将经典抑制剂转化为能够诱导催化降解的分子通过核酸抑制剂和蛋白酶体的前所未有的组合，靶向细胞中的 APOBEC 酶综上所述，该提案旨在通过引入靶向（PROTAC）技术来填补该领域的关键空白。扰乱细胞中 APOBEC 功能的工具，以揭示其基础生物学并提供路线图潜在的治疗方法。