Multiassay Profiling of a Focused Small Molecule Library Reveals Predictive Bidirectional Modulation of the lncRNA MALAT1 Triplex Stability In Vitro.
Multiassay Profiling of a Focused Small Molecule Library Reveals Predictive Bidirectional Modulation of the lncRNA MALAT1 Triplex Stability In Vitro.
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DOI：
10.1021/acschembio.2c00124
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发表时间：
2022-09-16
影响因子：
4
通讯作者：
Hargrove AE
中科院分区：
文献类型：
--
作者：
Zafferani M;Martyr JG;Muralidharan D;Montalvan NI;Cai Z;Hargrove AE
RNA三级结构的快速表征揭示了它们在人类疾病中的普遍性和积极作用。小分子介导的RNA三级结构调控为开发治疗靶向和/或揭示与这些RNA基序相关的途径提供了一个有吸引力的途径。通过靶向非编码RNA MALAT1的3‘端的三螺旋来强调这种潜力，MALAT1是一种与几种人类疾病有关的转录本。据报道，这种三联体可以降低转录本对降解的敏感性，并促进其在细胞内的积累。虽然小分子已被证明与MALAT1三螺旋结合并影响其稳定性，但导致这些结构调制的小分子特性尚不清楚。我们设计了一个以MALAT1三螺旋为靶点的文库，利用尚未被探索但在核酸结合方面有先例的Dinazene支架。我们使用多种分析方法来综合评估哪些参数(如果有的话)可以预测小分子亲和力和对三链稳定性的影响。我们设计和/或优化了竞争、量热和热位移分析以及酶降解分析，后者导致在支架中心文库中发现了三螺旋稳定性的双向调节剂。定量结构-活性关系的确定为基于亲和力和稳定性的分析提供了预测模型。这项工作建立了一套用于评估小分子的强大的正交生物物理工具：RNA三链相互作用，可以生成预测模型，并将允许小分子询问与疾病相关的RNA三螺旋的不断增长的身体。
The rapidly accelerating characterization of RNA tertiary structures has revealed their pervasiveness and active roles in human diseases. Small molecule-mediated modulation of RNA tertiary structures constitutes an attractive avenue for the development of tools for therapeutically targeting and/or uncovering the pathways associated with these RNA motifs. This potential has been highlighted by targeting of the triple helix present at the 3′-end of the noncoding RNA MALAT1, a transcript implicated in several human diseases. This triplex has been reported to decrease the susceptibility of the transcript to degradation and promote its cellular accumulation. While small molecules have been shown to bind to and impact the stability of the MALAT1 triple helix, the small molecule properties that lead to these structural modulations are not well understood. We designed a library utilizing the diminazene scaffold, which is underexplored but precedented for nucleic acid binding, to target the MALAT1 triple helix. We employed multiple assays to holistically assess what parameters, if any, could predict the small molecule affinity and effect on triplex stability. We designed and/or optimized competition, calorimetry, and thermal shift assays as well as an enzymatic degradation assay, the latter of which led to the discovery of bidirectional modulators of triple helix stability within the scaffold-centric library. Determination of quantitative structure–activity relationships afforded predictive models for both affinity- and stability-based assays. This work establishes a suite of powerful orthogonal biophysical tools for the evaluation of small molecule:RNA triplex interactions that generate predictive models and will allow small molecule interrogation of the growing body of disease-associated RNA triple helices.
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影响因子：
16.6
作者：
Donlic, Anita;Morgan, Brittany S.;Hargrove, Amanda E.
通讯作者：
Hargrove, Amanda E.
影响因子：
2.9
作者：
Cuchillo, Claudi M.;Victoria Nogues, M.;Raines, Ronald T.
通讯作者：
Raines, Ronald T.
影响因子：
14.8
作者：
Fedorova O;Jagdmann GE Jr;Adams RL;Yuan L;Van Zandt MC;Pyle AM
通讯作者：
Pyle AM
影响因子：
16.8
作者：
Brown JA;Bulkley D;Wang J;Valenstein ML;Yario TA;Steitz TA;Steitz JA
通讯作者：
Steitz JA
影响因子：
1.8
作者：
Aryani A;Denecke B
通讯作者：
Denecke B