Covalent Profiling of RNA Targets and Off-targets
RNA 靶标和脱靶的共价分析
基本信息
- 批准号:10294248
- 负责人:
- 金额:$ 37.6万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2019
- 资助国家:美国
- 起止时间:2019-01-10 至 2022-11-30
- 项目状态:已结题
- 来源:
- 关键词:AcylationAffectAlkylationAntibioticsBindingBinding ProteinsBinding SitesBiologicalBiologyBiopsy SpecimenCUG repeatCellsChemicalsClinicalDataDevelopmentDiseaseDoseDrug InteractionsDrug TargetingFutureGenomicsHealthHumanIn VitroLigand BindingLigandsLinkMalignant NeoplasmsMeasurementMeasuresMethodologyMethodsModificationMolecularMolecular ProbesMyotonic DystrophyNucleotidesPathway interactionsPermeabilityPharmaceutical PreparationsProteinsRNARNA ProbesRNA analysisRNA chemical synthesisRNA-Protein InteractionReagentResearchResolutionSpecificityStructureTechnologyToxic effectTranscriptUntranslated RNAWorkanalytical methodanticancer researchbaseclinically relevantdesignexperimental studyimprovedin vivoinnovationkinase inhibitorlaboratory experimentnext generation sequencingnoveloff-target siteprogramsscaffoldscreeningsmall moleculetooltranscriptometranscriptome sequencingunpublished works
项目摘要
Recent work from many labs has underlined the critical importance of RNA-controlled cellular pathways, and
clinically relevant connections of specific RNAs to human health. As a result, the development of small-
molecule ligands for RNAs, in contrast to traditional protein targets, is now offering a promising approach for
future targeting of diseases. In addition to this designed approach, it seems likely that many current protein-
targeted drugs may well bind to RNAs off-target and cause unintended biological effects there. Thus, the
analysis of RNA-small molecule interactions transcriptome-wide is critical. Unfortunately, methods for
analyzing RNA-ligand interactions directly in the cell lag far behind those for protein-ligand binding analysis.
Preliminary experiments from this laboratory have established multiple new molecular tools for analysis of
biologically and clinically relevant RNAs. New RNA Seq-based approaches have been developed for
identifying RNA base modifications directly. Central to this new project was the recent development of the
first cell-permeable RNA acylating agents, based on a nicotinyl scaffold, that react with accessible 2'-OH
groups transcriptome-wide. This allows unprecedented measurement of RNA structure and protein-RNA
interactions in vivo at nucleotide resolution. In very recent work, new acylating reagents that can polyacylate
RNAs in vitro, temporarily inactivating the RNA have been developed. These groups can then be removed
chemically or photochemically to control RNA activity temporally or locally. Overall, this recent new work
suggests a suite of new molecular reagents, tools and sequencing methods that can be used directly in cells
to analyze ligand-RNA interactions for the whole transcriptome in one experiment.
The proposed project will develop a new set of functionalized RNA-reactive reagents, including acylating
and alkylating species, that can enter cells and provide specific, quantitative information about ligand binding
in the transcriptome. Combined with next-gen sequencing, the methods will pinpoint binding sites in specific
transcripts. These methodologies, together termed Reactivity-Based RNA Profiling (RBRP), will be applied to
analyzing off-target binding by known drugs with clinically limiting toxicity. Further, new reactivity-based
approaches - involving reactive druglike fragments – will be used to identify ligands for cancer-related RNAs.
This work is significant because it will develop enabling molecular technologies that will greatly enhance
the study of RNA biology and biomedicine, analyzing drug interactions transcriptome-wide and directly in the
cell. In addition, it will outline how serious is the phenomenon of protein-targeted drugs binding off target to
RNAs. The research program is innovative because it develops a suite of new molecular probes and novel
molecular strategies, making use of RNA reactivity. It will develop unprecedented data regarding existing
clinically useful but toxic drugs. It will also develop novel cell-permeable ligands for RNAs upregulated in
cancer, which can be broadly useful as molecular tools for cancer research.
许多实验室最近的工作强调了 RNA 控制的细胞途径的至关重要性,并且
特定 RNA 与人类健康的临床相关联系。其结果是,小型化的发展
与传统的蛋白质靶标相比,RNA 的分子配体现在为
未来针对疾病的目标。除了这种设计方法之外,目前许多蛋白质-
靶向药物很可能与脱靶的 RNA 结合,并在那里引起意想不到的生物效应。因此,
转录组范围内 RNA-小分子相互作用的分析至关重要。不幸的是,方法
直接在细胞中分析 RNA-配体相互作用远远落后于蛋白质-配体结合分析。
该实验室的初步实验已经建立了多种新的分子工具来分析
生物学和临床相关的RNA。新的基于 RNA Seq 的方法已经开发出来
直接识别RNA碱基修饰。这个新项目的核心是最近的发展
第一种可渗透细胞的 RNA 酰化剂,基于烟酰基支架,可与可接近的 2'-OH 发生反应
转录组范围内的群体。这使得对 RNA 结构和蛋白质-RNA 的前所未有的测量成为可能
核苷酸分辨率下的体内相互作用。在最近的工作中,可以聚酰化的新酰化试剂
已经开发出体外RNA,暂时使RNA失活。然后可以删除这些组
化学或光化学来暂时或局部控制RNA活性。总的来说,这部近期的新作
提出了一套可直接在细胞中使用的新分子试剂、工具和测序方法
在一项实验中分析整个转录组的配体-RNA 相互作用。
拟议的项目将开发一套新的功能化 RNA 反应试剂,包括酰化试剂
和烷基化物质,可以进入细胞并提供有关配体结合的特定定量信息
在转录组中。与下一代测序相结合,这些方法将精确定位特定的结合位点
成绩单。这些方法统称为基于反应性的 RNA 分析 (RBRP),将应用于
分析具有临床限制毒性的已知药物的脱靶结合。此外,新的基于反应性的
涉及反应性药物样片段的方法将用于识别癌症相关 RNA 的配体。
这项工作意义重大,因为它将开发使能分子技术,从而大大增强
RNA生物学和生物医学的研究,分析转录组范围内的药物相互作用并直接在
细胞。此外,还将概述蛋白质靶向药物脱靶结合的现象有多严重。
RNA。该研究计划具有创新性,因为它开发了一套新的分子探针和新颖的
分子策略,利用 RNA 反应性。它将开发有关现有数据的前所未有的数据
临床上有用但有毒的药物。它还将开发新的细胞渗透性配体,用于在
癌症,可作为癌症研究的分子工具广泛使用。
项目成果
期刊论文数量(8)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA.
- DOI:10.1002/anie.202112106
- 发表时间:2021-12-13
- 期刊:
- 影响因子:0
- 作者:Xiao L;Jun YW;Kool ET
- 通讯作者:Kool ET
Conjugation of RNA via 2'-OH acylation: Mechanisms determining nucleotide reactivity.
- DOI:10.1039/d2cc00660j
- 发表时间:2022-03-15
- 期刊:
- 影响因子:4.9
- 作者:Jash, Biswarup;Kool, Eric T.
- 通讯作者:Kool, Eric T.
Aqueous Activation of RNA 2'-OH for Conjugation with Amines and Thiols.
RNA 2-OH 的水活化用于与胺和硫醇的缀合。
- DOI:10.1021/acs.bioconjchem.3c00370
- 发表时间:2024
- 期刊:
- 影响因子:4.7
- 作者:Shioi,Ryuta;Xiao,Lu;Kool,EricT
- 通讯作者:Kool,EricT
Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity.
- DOI:10.1016/j.chembiol.2022.05.005
- 发表时间:2022-08-18
- 期刊:
- 影响因子:8.6
- 作者:Xiao, Lu;Fang, Linglan;Kool, Eric T.
- 通讯作者:Kool, Eric T.
The chemistry and applications of RNA 2'-OH acylation.
- DOI:10.1038/s41570-019-0147-6
- 发表时间:2020-01
- 期刊:
- 影响因子:0
- 作者:Velema WA;Kool ET
- 通讯作者:Kool ET
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ERIC T. KOOL其他文献
ERIC T. KOOL的其他文献
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{{ truncateString('ERIC T. KOOL', 18)}}的其他基金
Transcriptome Analysis with RNA-Reactive Probes
使用 RNA 反应探针进行转录组分析
- 批准号:
10406530 - 财政年份:2022
- 资助金额:
$ 37.6万 - 项目类别:
Transcriptome Analysis with RNA-Reactive Probes
使用 RNA 反应探针进行转录组分析
- 批准号:
10793323 - 财政年份:2022
- 资助金额:
$ 37.6万 - 项目类别:
Transcriptome Analysis with RNA-Reactive Probes
使用 RNA 反应探针进行转录组分析
- 批准号:
10602470 - 财政年份:2022
- 资助金额:
$ 37.6万 - 项目类别:
Covalent Profiling of RNA Targets and Off-targets
RNA 靶标和脱靶的共价分析
- 批准号:
10061624 - 财政年份:2019
- 资助金额:
$ 37.6万 - 项目类别:
Probing the Transcriptome with Multifunctional Acylation Chemistry
用多功能酰化化学探索转录组
- 批准号:
9926279 - 财政年份:2018
- 资助金额:
$ 37.6万 - 项目类别:
Probing the Transcriptome with Multifunctional Acylation Chemistry
用多功能酰化化学探索转录组
- 批准号:
9494223 - 财政年份:2018
- 资助金额:
$ 37.6万 - 项目类别:
Measuring and Modulating Oxidative DNA Damage Surveillance Pathways
测量和调节氧化 DNA 损伤监测途径
- 批准号:
9287818 - 财政年份:2017
- 资助金额:
$ 37.6万 - 项目类别:
Measuring and Modulating Oxidative DNA Damage Surveillance Pathways
测量和调节氧化 DNA 损伤监测途径
- 批准号:
9924487 - 财政年份:2017
- 资助金额:
$ 37.6万 - 项目类别:
Measuring and Modulating DNA Damage Surveillance Pathways
测量和调节 DNA 损伤监测途径
- 批准号:
10617737 - 财政年份:2017
- 资助金额:
$ 37.6万 - 项目类别:
Measuring and Modulating DNA Damage Surveillance Pathways
测量和调节 DNA 损伤监测途径
- 批准号:
10396578 - 财政年份:2017
- 资助金额:
$ 37.6万 - 项目类别:
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