Post-Translational Modifications in Drug Discovery

Protein post-translational modifications (PTMs) are critical regulatory mechanisms that control protein function and are involved in nearly all cellular processes, including signal transduction, gene expression, metabolic regulation, and immune responses. Dysregulation of PTMs is closely associated with the onset and progression of various diseases. As a result, PTM regulatory enzymes and their associated pathways have become important targets in drug discovery. With the rapid advancement of mass spectrometry–based proteomics, it is now possible to systematically analyze PTMs, providing powerful tools for drug target discovery, mechanism-of-action studies, and biomarker identification. The following sections highlight five major directions of PTM proteomics in drug research.

  Bobalova, J. et al. J Agric Food Chem. 2023.

Figure 1. Scheme of MS-based Proteomic Strategies for PTM Analysis

 

1. Phospho-proteomics in drug research

Phosphorylation is one of the most extensively studied PTMs and is involved in nearly all signaling pathways. Aberrant kinase activity can lead to cancer, immune disorders, and drug resistance. Phospho-proteomics, through mass spectrometry analysis, enables system-wide mapping of signaling changes before and after drug treatment, supporting:

• Target identification: Discovery of key pathogenic kinases such as BCR-ABL, EGFR, and BTK.
• Drug development: Successful kinase inhibitors include Imatinib, Gefitinib, and Ibrutinib.
• Resistance mechanisms: Elucidation of resistance caused by mutations or bypass signaling, guiding the design of second- and third-generation kinase inhibitors.

 

Phospho-proteomics has become a central tool in oncology and immunotherapy drug development.

 

2. Acetyl-proteomics in drug research

Acetylation plays a pivotal role in epigenetic regulation, particularly histone acetylation, which determines chromatin accessibility and directly influences gene expression. Acetyl-proteomics enables high-throughput mapping of global acetylation profiles, revealing chromatin modifications in response to drug treatment.

• Target identification: Histone deacetylases (HDACs) and histone acetyltransferases (HATs).
• Representative drugs: HDAC inhibitors such as Vorinostat and Romidepsin, both approved for cancer therapy.
• Research value: Acetyl-proteomics allows researchers to optimize drug specificity, evaluate global effects on gene expression networks, and identify acetylation sites associated with drug resistance.

 

3. Ubiquitinomics in drug research

Ubiquitination regulates protein degradation and is essential for maintaining protein homeostasis. Ubiquitinomics, powered by mass spectrometry, provides a global landscape of ubiquitination and supports the development of protein degradation–based therapeutics.

• Target identification: Proteasomes, E3 ligases, and deubiquitinating enzymes (DUBs).
• Representative drugs: Proteasome inhibitors such as Bortezomib and Carfilzomib, which are standard therapies for multiple myeloma.
• Novel strategies: E3 ligase–based targeted degradation approaches, including PROTACs and molecular glues, which are rapidly expanding the druggable proteome.

 

Ubiquitinomics supports traditional inhibitor development while driving the emergence of targeted protein degradation strategies.

 

4. Glyco-proteomics in drug research

Glycosylation is essential for protein folding, secretion, stability, and immune recognition. Glyco-proteomics enables precise analysis of glycan structures and glycosylation sites, providing unique advantages in drug development and quality control.

• Targets and applications: Glycosyltransferases and glycosidases are key drug targets. Aberrant glycosylation is closely linked to cancer metastasis, immune evasion, and metabolic diseases.
• Representative drugs: Miglustat, a glycosidase inhibitor, is approved for lysosomal storage disorders.
• Research value: In antibody drug and biopharmaceutical development, glycosylation analysis is crucial for consistency evaluation and for studying structure–function relationships.

 

Glyco-proteomics plays an important role in biopharmaceutical development, cancer biomarker discovery, and metabolic disease research.

 

5. Methyl-proteomics in drug research

Methylation, including lysine and arginine methylation, is widely distributed on histones and profoundly impacts gene expression and chromatin state. Methyl-proteomics provides system-wide insights into how drugs regulate epigenetic modifications.

•   Target identification: Histone methyltransferases (HMTs) and histone demethylases (HDMs).
• Representative drugs: Tazemetostat, an EZH2 inhibitor, has been approved for the treatment of certain lymphomas.
• Research value: Methyl-proteomics supports the assessment of drug specificity, investigation of off-target effects, and development of next-generation epigenetic modulators.

 

The rapid development of PTM proteomics has enabled drug discovery to investigate disease mechanisms and drug responses at a systems level. Whether phosphorylation, acetylation, ubiquitination, glycosylation, or methylation, PTM-focused proteomics has provided a solid foundation for target identification, mechanism elucidation, and biomarker discovery.