Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
Garrett L Lindsey, Thomas K Hockley, Alejandro Villa Gomez, Andrew C Marshall, William R Brothers, Colin T Finney, Jacob Gross, Archa H Fox, Gene W Yeo, Bruno Melillo, Charles S Bond, Benjamin F Cravatt
Cell chemical biology · 2026 · Vol. 33 (2) · pp. 256-267.e11
Abstract
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We previously described a chloroacetamide compound (R)-SKBG-1 that covalently binds the RBP NONO and stabilizes its interactions with mRNAs, leading to transcriptional remodeling and suppression of cancer cell growth. Here, we report the crystal structure of an (R)-SKBG-1:NONO complex, which confirms covalent modification of cysteine-145 at a pocket proximal to the RNA-binding interface of the protein. We show that this pocket can also be targeted by a lower reactivity chlorofluoroacetamide analog (R, R)-GL-373, which retains the pharmacological properties of (R)-SKBG-1, including blockade of estrogen receptor expression in breast cancer cells, while displaying much greater proteome-wide selectivity. Our findings thus show that NONO can be targeted by covalent ligands with high specificity to pharmacologically suppress pro-tumorigenic gene products in cancer cells.
Linked datasets 1
Transcriptome changes in MCF7 cells after treatment with NONO ligands and controls
Homo sapiens
60 data files
| File | Type | Size |
|---|---|---|
| 1-sgC-373_R1_001.fastq.gz | RNA-Seq | 2.6 GB |
| 1-sgC-374_R1_001.fastq.gz | RNA-Seq | 2.7 GB |
| 1-sgC-DMSO_R1_001.fastq.gz | RNA-Seq | 3.0 GB |
| 1-sgC-R_R1_001.fastq.gz | RNA-Seq | 2.8 GB |
| 1-sgC-S_R1_001.fastq.gz | RNA-Seq | 3.3 GB |
| 1-sgN-373_R1_001.fastq.gz | RNA-Seq | 3.2 GB |
| 1-sgN-374_R1_001.fastq.gz | RNA-Seq | 3.6 GB |
| 1-sgN-R_R1_001.fastq.gz | RNA-Seq | 3.4 GB |
| 1-sgN-S_R1_001.fastq.gz | RNA-Seq | 2.9 GB |
| 2-sgC-373_R1_001.fastq.gz | RNA-Seq | 2.8 GB |
| 2-sgC-R_R1_001.fastq.gz | RNA-Seq | 3.5 GB |
| 2-sgC-S_R1_001.fastq.gz | RNA-Seq | 2.9 GB |
| 2-sgN-373_R1_001.fastq.gz | RNA-Seq | 3.0 GB |
| 2-sgN-374_R1_001.fastq.gz | RNA-Seq | 3.3 GB |
| 2-sgN-DMSO_R1_001.fastq.gz | RNA-Seq | 3.2 GB |
| 2-sgN-R_R1_001.fastq.gz | RNA-Seq | 3.3 GB |
| 2-sgN-S_R1_001.fastq.gz | RNA-Seq | 2.8 GB |
| 3-sgC-373_R1_001.fastq.gz | RNA-Seq | 3.3 GB |
| 3-sgC-374_R1_001.fastq.gz | RNA-Seq | 3.4 GB |
| 3-sgC-DMSO_R1_001.fastq.gz | RNA-Seq | 2.4 GB |
| 3-sgC-R_R1_001.fastq.gz | RNA-Seq | 2.9 GB |
| 3-sgC-S_R1_001.fastq.gz | RNA-Seq | 2.4 GB |
| 3-sgN-373_R1_001.fastq.gz | RNA-Seq | 3.7 GB |
| 3-sgN-R_R1_001.fastq.gz | RNA-Seq | 2.4 GB |
| SRR33873308_GSM9032936 | RNA-Seq | 2.6 GB |
| SRR33873308.lite | RNA-Seq | 2.6 GB |
| SRR33873309_GSM9032935 | RNA-Seq | 2.8 GB |
| SRR33873310_GSM9032934 | RNA-Seq | 2.9 GB |
| SRR33873311_GSM9032933 | RNA-Seq | 2.4 GB |
| SRR33873312_GSM9032932 | RNA-Seq | 3.3 GB |
| SRR33873313_GSM9032931 | RNA-Seq | 3.4 GB |
| SRR33873314_GSM9032930 | RNA-Seq | 3.0 GB |
| SRR33873314.lite | RNA-Seq | 3.0 GB |
| SRR33873315_GSM9032929 | RNA-Seq | 3.2 GB |
| SRR33873316_GSM9032928 | RNA-Seq | 2.7 GB |
| SRR33873316.lite | RNA-Seq | 2.7 GB |
| SRR33873317_GSM9032927 | RNA-Seq | 2.9 GB |
| SRR33873317.lite | RNA-Seq | 2.9 GB |
| SRR33873318_GSM9032926 | RNA-Seq | 3.3 GB |
| SRR33873319_GSM9032925 | RNA-Seq | 3.6 GB |
| SRR33873320_GSM9032924 | RNA-Seq | 3.7 GB |
| SRR33873321_GSM9032923 | RNA-Seq | 3.0 GB |
| SRR33873322_GSM9032922 | RNA-Seq | 3.2 GB |
| SRR33873323_GSM9032921 | RNA-Seq | 2.4 GB |
| SRR33873324_GSM9032920 | RNA-Seq | 2.9 GB |
| SRR33873325_GSM9032919 | RNA-Seq | 3.3 GB |
| SRR33873326_GSM9032918 | RNA-Seq | 2.9 GB |
| SRR33873327_GSM9032917 | RNA-Seq | 3.5 GB |
| SRR33873328_GSM9032916 | RNA-Seq | 2.8 GB |
| SRR33873329_GSM9032915 | RNA-Seq | 2.4 GB |
| SRR33873330_GSM9032914 | RNA-Seq | 2.9 GB |
| SRR33873330.lite | RNA-Seq | 2.9 GB |
| SRR33873331_GSM9032913 | RNA-Seq | 3.0 GB |
| SRR33873332_GSM9032912 | RNA-Seq | 3.4 GB |
| SRR33873333_GSM9032911 | RNA-Seq | 2.7 GB |
| SRR33873333.lite | RNA-Seq | 2.7 GB |
| SRR33873334_GSM9032910 | RNA-Seq | 2.7 GB |
| SRR33873335_GSM9032909 | RNA-Seq | 3.3 GB |
| SRR33873336_GSM9032908 | RNA-Seq | 2.8 GB |
| SRR33873337_GSM9032907 | RNA-Seq | 2.6 GB |
Potentially related datasets 2
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
Analysis pipelines 1
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE299099 Data Processing geo_data_processing | — | 3 | GSE299099 |
Funding 3 grants
| Grant | Funder |
|---|---|
| OT2 CA278692 | NCI NIH HHS (United States) |
| R01 CA238249 | NCI NIH HHS (United States) |
| R35 CA231991 | NCI NIH HHS (United States) |