Chemoproteomics-based Off-Target Screening of Small Molecule Drugs

The selection of technology needs to be comprehensively judged in combination with sample type, target characteristics and research stage:

Dynamic analysis of living cells: CETSA or click chemistry technology is preferred because it can directly detect protein-drug interactions under physiological conditions (such as the verification of TNP-470 off-target effects in the case).

Membrane protein or post-translational modification research: Affinity-based chemical proteomics is recommended, and its probes can penetrate the cell membrane to capture membrane-bound proteins (such as fluoroquinolone drug mitochondrial damage research).

Early drug screening: The covalent drug platform is combined with quantitative chemical proteomics to achieve target verification and off-target warning at the same time (such as the off-target discovery of HDAC inhibitor MBLAC2).

Achieve early warning through multi-dimensional data integration:

Target network map construction: Use quantitative chemical proteomics to draw drug-protein interaction networks and identify high-abundance binding proteins (such as BACE inhibitors using TPP technology to discover cathepsin D off-target).

Dynamic modification monitoring: ABPP combined with metabolic labeling probes to track the effect of drugs on enzyme activity in real time (such as monitoring the activity of CRBN complexes in the study of thalidomide teratogenicity).

Targeted optimization of probe design and detection methods is required:

Probe penetration improvement: development of lipid-soluble photoaffinity probes (such as CiproP1 probes that penetrate bacterial membranes to locate mitochondrial proteins).

Membrane protein stabilization technology: combined with Nanodisc technology to maintain the native conformation of membrane proteins and improve the accuracy of CETSA detection (such as off-target research plans for GPCR drugs).

Cryo-electron microscopy: verification of probe labeling sites through structural biology (such as analysis of PROTAC degraders and target protein complexes).

It has been extended to the analysis of pollutant toxicity mechanisms and ecological evaluation of new drugs:

Heavy metal toxicity research: Use metal reaction probes to label metal enzymes (such as the mechanism of glutathione peroxidase inactivation caused by cadmium pollution).

Antibiotic ecological impact assessment: Use LIP-MS technology to detect the damage of antibiotics to the stability of soil microbial proteins (such as the proteolytic effect of holomycin on soil actinomycetes).

Nanoparticle toxicity screening: Develop oxidative stress response probes to evaluate protein oxidative damage induced by nanomaterials (such as titanium dioxide nanoparticle pulmonary toxicity research).

Standardized analysis processes and interdisciplinary collaboration need to be established:

Bioinformatics tools: Use MaxQuant+PDBE database to visualize protein interaction networks (such as HDAC inhibitor target map generation).

Multi-omics data integration: Combine transcriptome and metabolome data to verify off-target effects (such as multi-omics verification of mitochondrial damage of fluoroquinolones).

Clinical relevance assessment: Establish a causal association model between off-target proteins and adverse reactions (such as dose-effect analysis of MBLAC2 off-target and neurotoxicity).