Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans
Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans
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DOI：
10.1093/nar/gkaa585
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发表时间：
2020-08-20
影响因子：
14.9
通讯作者：
Hargrove, Amanda E.
中科院分区：
文献类型：
--
作者：
Donlic, Anita;Zafferani, Martina;Hargrove, Amanda E.
基于小分子的长非编码RNA转移相关肺腺癌转录物1（MALAT 1）中的三螺旋的调节已被提出作为用于癌症治疗的有吸引力的途径和用于理解小分子：RNA识别的模型系统。为了阐明基本的识别原理和结构-功能关系，我们设计并合成了9种基于二苯基呋喃的小分子DPFp 8的新型类似物，DPFp 8是先前确定的MALAT 1的铅结合剂。我们研究了识别模式在结合中的作用，并沿着了三螺旋的亲和力、稳定性和体外酶促降解之间的关系。具体而言，分子对接研究确定了驱动亲和力和选择性的模式，包括有限的配体灵活性，如通过配体预组织和结合口袋的3D形状互补性所观察到的。差示扫描荧光法的使用允许快速评价配体诱导的三螺旋热稳定性，这与RNA酶R外切核酸酶体外降解该结构的降低相关。稳定的大小与三螺旋和其前体茎环结构之间的结合模式和选择性有关。总之，这项工作表明了基于支架的库在揭示识别原理和提高广泛适用的策略，包括功能测定，小分子RNA靶向方面的价值。
Small molecule-based modulation of a triple helix in the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been proposed as an attractive avenue for cancer treatment and a model system for understanding small molecule:RNA recognition. To elucidate fundamental recognition principles and structure-function relationships, we designed and synthesized nine novel analogs of a diphenylfuran-based small molecule DPFp8, a previously identified lead binder of MALAT1. We investigated the role of recognition modalities in binding and in silico studies along with the relationship between affinity, stability and in vitro enzymatic degradation of the triple helix. Specifically, molecular docking studies identified patterns driving affinity and selectivity, including limited ligand flexibility, as observed by ligand preorganization and 3D shape complementarity for the binding pocket. The use of differential scanning fluorimetry allowed rapid evaluation of ligand-induced thermal stabilization of the triple helix, which correlated with decreased in vitro degradation of this structure by the RNase R exonuclease. The magnitude of stabilization was related to binding mode and selectivity between the triple helix and its precursor stem loop structure. Together, this work demonstrates the value of scaffold based libraries in revealing recognition principles and of raising broadly applicable strategies, including functional assays, for small molecule-RNA targeting.