【Liman’s “Protein Degradation Drug Product Portfolio”】Officially Launched!

The LIMAN Bio team has extensive expertise in the development of proteolysis-targeting drugs, offering end-to-end services spanning target identification and validation, lead compound discovery and optimization, mechanism-of-action (MOA) studies, and pharmacokinetic/pharmacodynamic (PK/PD) investigations. LIMAN provides high-throughput gene-editing products—knockout and knock-in cell lines—along with complementary mass-spectrometry–based assay reagents and customized services to streamline and accelerate these research workflows. Through a comprehensive portfolio of offerings in this field, we deliver integrated, end-to-end solutions for both pharmaceutical clients and basic research institutions.

Figure 1: Liman’s Product and Service Portfolio in the TPD Field

1. Protein ubiquitination and ubiquitome profiling to elucidate the mechanism of action (MOA) of proteolysis-targeting drugs

Ubiquitination of proteins is a post-translational modification mediated by E3 ubiquitin ligases that targets proteins for degradation via the ubiquitin–proteasome system (UPS), thereby maintaining cellular homeostasis. In recent years, this critical biological process has been harnessed through small-molecule compounds—such as PROTACs and molecular glues—to promote interactions between E3 ubiquitin ligases and disease-associated protein targets (POIs), thereby inducing ubiquitination and selective degradation of these disease-driving proteins to achieve therapeutic effects. As an increasing number of proteolysis-targeting drugs advance into preclinical and clinical development, ubiquitination-modification omics, by specifically identifying and quantifying POI ubiquitination, provides crucial insights into the extent and dynamic changes of ubiquitination. This knowledge facilitates our understanding of the mechanisms of action and efficacy of these compounds and offers direct data support for optimizing structure–activity relationships (SAR). Moreover, ubiquitination-modification omics can analyze ubiquitination patterns in cellular or tissue samples to identify potential off-target effects of targeted protein degraders, thereby reducing the risk of clinical adverse events arising from such off-target effects.

Figure 2: Mechanism of Action of PROTAC Degraders

2. K-diGly antibody independently developed by Leman

Ubiquitination refers to the covalent linkage formed when the ε-amino group of a lysine (K) residue in a substrate protein reacts with the carboxyl group of the C-terminal glycine in the di-glycine (diGly) motif of a ubiquitin molecule, thereby generating an amide bond. Following trypsin cleavage at arginine (R) and lysine (K), the characteristic K-GG sequence is generated. Given that ubiquitination modifications typically occur at low stoichiometric levels and exhibit a broad dynamic range, it is necessary to enrich the modified peptides prior to mass spectrometric analysis to facilitate their identification. To this end, we first generated an animal-derived antibody against ubiquitinated peptides and successfully obtained the ELEMAb™ K-ε-GG Antibody, which specifically recognizes ubiquitination modifications. Subsequently, we evaluated the enrichment efficiency for standardized ubiquitinated peptides using the SpikeMix™ PTM-Kit 47-Lys(GG).

3. High-Throughput Ubiquitination Modification Omics

More than 96.54% of ubiquitinated proteins and 93.51% of ubiquitinated peptides were repeatedly identified, demonstrating that the ELEMAb™ K-ε-GG Antibody exhibits excellent reproducibility in the identification of ubiquitination modifications. These results underscore the antibody’s reliability and stability in recognizing and enriching ubiquitinated modifications, thereby providing a robust foundation for subsequent research.

Figure 5: Repeatability Evaluation of ELEMAb™ K-ε-GG Antibody Identification

4. Ubiquitination-based proteomics confirms the mechanism of action of the degrader

Lenalidomide is a drug with remarkable clinical efficacy against multiple myeloma and other B-cell malignancies. To gain deeper insight into its mechanism of action, researchers employed ubiquitination-modification omics and found that lenalidomide increases the ubiquitination levels of IKZF1 and IKZF3. Furthermore, whole-proteome analysis revealed that lenalidomide reduces the abundance of IKZF1 and IKZF3. As key transcription factors in multiple myeloma, these findings elucidate the mechanism by which lenalidomide exerts its antitumor effects through the regulation of the ubiquitination and degradation of these transcription factors.

Figure 6. Ubiquitination-based proteomics reveals the mechanism of action of lenalidomide.

References

1. Targeted protein degradation mechanisms. Drug Discov Today Technol. 2019 Apr;31:53-60.

2. Lenalidomide induces selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science. 2014 Jan 17;343(6168):301–5.