Technical Background
Chemical proteomic technology emerges as a beacon of change, steering drug discovery away from purified proteins and towards the realm of living cells.
Chemical proteomic technology serves as a robust drug discovery platform, characterized by the investigation of small molecule-protein interactions within living cells. One of our covalent drug discovery platforms is designed to discover covalent binders that engage protein targets through the covalent reactions with the thiol group of cysteine residues. Unlike traditional single-target screening strategies, the chemical proteomics platform enables quantitative analysis of interactions between electrophilic fragments and nearly all proteins in living cells with the resolution of amino acid residue. It boasts coverage across more than 10,000 proteins and～40,000 cysteine sites(potential drug binding sites)from several mammalian cell lines.
Workflow
The workflow for discovery of covalent compounds targeting binding sites*on proteins, based on the DIA-ABPP (Data-Independent Acquisition-Activity-Based Protein Profiling) patent (A covalent binding site is an amino acid that can be labeled by chemical probes, thereby enabling ligandability)
Technical Advantages
Feature 1
Cysteine-targeted covalent library
The cysteine-targeted covalent library contains representative mild electrophilic “warheads”, such as acrylamides and chloroacetamides. The “drug-like” library contains ~ 3000 compounds, with more than 80% exhibiting a molecular weight of 300-500 Da. For most compounds, the Tanimoto similarity index is around 0.3 for every two members, indicating a high degree of diversity.
Feature 2
Protein target library
Currently, the library of protein targets captured by the thiol-specific chemical probe covers 39962 cysteine sites from 12421 proteins, including kinase, phosphatase, ligases, and transcription factors.
Case Study
DCAF1 serves as a substrate receptor for two distinct E3 ligases (CRL4DCAF1 and EDVP), playing a critical physiological role in protein degradation. Several covalent and noncovalent binders targeting the WDR domain of DCAF1 have been developed to support targeted degradation applications (Targeted Protein Degradation by Electrophilic PROTACs that Stereoselectively and Site-Specifically Engage DCAF1. J. Am. Chem. Soc. 2022, 144, 40, 18688–18699. DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance. Nat. Commun. 2024, 15, 275).
We discovered for the first time that Mol-380 covalently engages with DCAF1_C69, highlighting it as a potential druggable site for TPD applications, separate from the WDR domain. Our findings highlight the ChomiX automated chemical proteomic platform's significant value in discovering new ligands for undruggable targets in living cells, including transcriptional factors and membrane proteins, underscoring its potential impact in drug development and functional exploration.
Structurally, the binding site of C69 lies adjacent to the validated pocket on WD40 domain, as indicated by the complex model, offering a novel site for PROTACs development.