Annalisa Invernizzi, Francesco Nai, Rajiv Kumar Bedi, Pablo Andrés Vargas-Rosales, Yaozong Li, Elena Bochenkova, Marcin Herok, František Zálešák and Amedeo Caflisch*,
{"title":"基于片段设计的YTHDF2配体的发现","authors":"Annalisa Invernizzi, Francesco Nai, Rajiv Kumar Bedi, Pablo Andrés Vargas-Rosales, Yaozong Li, Elena Bochenkova, Marcin Herok, František Zálešák and Amedeo Caflisch*, ","doi":"10.1021/acsbiomedchemau.5c00099","DOIUrl":null,"url":null,"abstract":"<p ><i>N</i><sup>6</sup>-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 m<sup>6</sup>A-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 (IC<sub>50</sub> < 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 <b>23</b> binds to YTHDF2 according to the FP and HTRF assays with a <i>K</i><sub>d</sub> value of 1.3 μM and an IC<sub>50</sub> 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 <b>17</b> and <b>30</b> bind also to YTHDC2, with <i>K</i><sub>d</sub> 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.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"753–765"},"PeriodicalIF":4.3000,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00099","citationCount":"0","resultStr":"{\"title\":\"Discovery of YTHDF2 Ligands by Fragment-Based Design\",\"authors\":\"Annalisa Invernizzi, Francesco Nai, Rajiv Kumar Bedi, Pablo Andrés Vargas-Rosales, Yaozong Li, Elena Bochenkova, Marcin Herok, František Zálešák and Amedeo Caflisch*, \",\"doi\":\"10.1021/acsbiomedchemau.5c00099\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p ><i>N</i><sup>6</sup>-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 m<sup>6</sup>A-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 (IC<sub>50</sub> < 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 <b>23</b> binds to YTHDF2 according to the FP and HTRF assays with a <i>K</i><sub>d</sub> value of 1.3 μM and an IC<sub>50</sub> 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 <b>17</b> and <b>30</b> bind also to YTHDC2, with <i>K</i><sub>d</sub> 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.</p>\",\"PeriodicalId\":29802,\"journal\":{\"name\":\"ACS Bio & Med Chem Au\",\"volume\":\"5 4\",\"pages\":\"753–765\"},\"PeriodicalIF\":4.3000,\"publicationDate\":\"2025-06-27\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00099\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACS Bio & Med Chem Au\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://pubs.acs.org/doi/10.1021/acsbiomedchemau.5c00099\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Bio & Med Chem Au","FirstCategoryId":"1085","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acsbiomedchemau.5c00099","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
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.
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.