基于片段设计的YTHDF2配体的发现

IF 4.3 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Annalisa Invernizzi, Francesco Nai, Rajiv Kumar Bedi, Pablo Andrés Vargas-Rosales, Yaozong Li, Elena Bochenkova, Marcin Herok, František Zálešák and Amedeo Caflisch*, 
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引用次数: 0

摘要

n6 -腺苷甲基化是mRNA最丰富的修饰。YTH结构域家族蛋白的三个成员(YTHDF1-3)在细胞质中识别m6A-RNA修饰。我们通过与YTHDF2对接,筛选了约50万个片段(即含有11-20个非氢原子的分子),在体外测试的47个片段中鉴定出6个活性化合物(命中率为13%)。获得对接命中的28个类似物提供了额外的10个活性化合物(IC50 < 100 μM)。在蛋白质晶体学指导下,通过合成32个衍生物对配体高效片段进行优化,最终得到一系列YTHDF2配体,通过荧光偏振(FP)测定和均匀时间分辨荧光(htf)测定,这些配体具有低微摩尔亲和力。该系列具有非常好的配体效率(每个非氢原子约0.3-0.4千卡/摩尔)。结果表明,化合物23与YTHDF2结合的Kd值为1.3 μM, IC50值为11 μM,对其他所有YTH读取器蛋白均有选择性。该系列的一些化合物与三种YTHDF蛋白结合具有相似的低微摩尔亲和力,而它们对YTHDC1和YTHDC2的作用较弱。相比之下,化合物17和30也与YTHDC2结合,Kd分别为6.3和4.9 μM。我们还通过对接鉴定的片段揭示了YTHDF2复合物中的6个晶体结构。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Discovery of YTHDF2 Ligands by Fragment-Based Design

N6-Adenosine methylation is the most abundant modification of mRNA. The three members of the YTH domain family proteins (YTHDF1–3) recognize in the cytoplasm the m6A-RNA modification. We screened a library of about 500,000 fragments (i.e., molecules with 11–20 non-hydrogen atoms) by docking into YTHDF2, which resulted in the identification of six active compounds among 47 tested in vitro (hit rate of 13%). The acquisition of 28 analogues of the docking hits provided an additional set of 10 active compounds (IC50 < 100 μM). Protein crystallography-guided optimization of a ligand-efficient fragment by the synthesis of 32 derivatives culminated in a series of YTHDF2 ligands, which show low-micromolar affinity measured by a fluorescence polarization (FP) assay and a homogeneous time-resolved fluorescence-based (HTRF) assay. The series is characterized by very favorable ligand efficiency (of about 0.3–0.4 kcal/mol per non-hydrogen atom). Compound 23 binds to YTHDF2 according to the FP and HTRF assays with a Kd value of 1.3 μM and an IC50 value of 11 μM, respectively, and it is selective against all of the other YTH reader proteins. Several compounds of the series bind to the three YTHDF proteins with similar low-micromolar affinity, while they are less potent for YTHDC1 and YTHDC2. In contrast, compounds 17 and 30 bind also to YTHDC2, with Kd of 6.3 and 4.9 μM, respectively. We also disclose six crystal structures of YTHDF2 in the complex with the fragments identified by docking.

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来源期刊
ACS Bio & Med Chem Au
ACS Bio & Med Chem Au 药物、生物、化学-
CiteScore
4.10
自引率
0.00%
发文量
0
期刊介绍: ACS Bio & Med Chem Au is a broad scope open access journal which publishes short letters comprehensive articles reviews and perspectives in all aspects of biological and medicinal chemistry. Studies providing fundamental insights or describing novel syntheses as well as clinical or other applications-based work are welcomed.This broad scope includes experimental and theoretical studies on the chemical physical mechanistic and/or structural basis of biological or cell function in all domains of life. It encompasses the fields of chemical biology synthetic biology disease biology cell biology agriculture and food natural products research nucleic acid biology neuroscience structural biology and biophysics.The journal publishes studies that pertain to a broad range of medicinal chemistry including compound design and optimization biological evaluation molecular mechanistic understanding of drug delivery and drug delivery systems imaging agents and pharmacology and translational science of both small and large bioactive molecules. Novel computational cheminformatics and structural studies for the identification (or structure-activity relationship analysis) of bioactive molecules ligands and their targets are also welcome. The journal will consider computational studies applying established computational methods but only in combination with novel and original experimental data (e.g. in cases where new compounds have been designed and tested).Also included in the scope of the journal are articles relating to infectious diseases research on pathogens host-pathogen interactions therapeutics diagnostics vaccines drug-delivery systems and other biomedical technology development pertaining to infectious diseases.
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