Like other post-translational modifications, ubiquitination is reversible and can be reversed by a large group of proteases called deubiquitinating enzymes (DUBs). DUBs play crucial roles in the ubiquitin pathway by removing monoubiquitin and polyubiquitin chains from proteins. Their catalytic activity includes thiol-dependent hydrolysis of esters, thioesters, amides, peptides and isopeptide bonds formed by the C-terminal Gly of ubiquitin. Typically, individual ubiquitin proteins or chains are added to the lysine residues of the substrate protein. These post-translational modifications are added to proteins through a ubiquitination mechanism: ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3).
Mechanism of action of deubiquitinating enzymes
- Generation of free ubiquitin molecules from newly transcribed ubiquitin precursor proteins
- Rescue of ubiquitin-tagged proteins, thereby escaping proteasomal or lysosomal degradation and acting to stabilize the target protein
- Removal of non-degraded ubiquitin signals
- Recycling of ubiquitin molecules shed from degraded target proteins
- Shear the ubiquitin chain and edit the ubiquitin modifications
Figure 1. Protein ubiquitination and deubiquitination. (Cai, J.; et al. 2019)
Library Design
BOC Sciences focuses on the first pair of representatives of the major ubiquitin-specific protease superfamily (USP1/USP2) and UBA5 of the E1 class to design and prepare our Deubiquitinase screening library
a. Firstly, we used Schrödinger Suit to perform docking against the compounds from the entire BOC Sciences HTS compound collection of in the active site of E1 activating proteins
- The gliding docking of the E1 crystal structure is developed based on the position and orientation of the reference molecule in the active site
- We set an obligatory hydrophobic core and three constraints from five possible H-bonds depending on the need of the screening
b. Then, a set of constraints is well defined to improve the quality of the docking results, and the resulting Deubiquitinase E1 targeted library includes 2,200 drug-like screening compounds with potential E1 enzyme activity
c. Pharmacophore modeling is performed to search for DUB-specific screening compounds, which helps to identify over 1,100 potential small molecule inhibitors of ubiquitin-specific protease (USP1, 2) for the Deubiquitinase USP1, 2 focused screening set
- We apply the K-means clustering method to select the best clusters by total activity
- QSAR field-based analysis is also available for 3D bioactive structure prediction by conformation search and cross-alignment of reference compounds
- BOC Sciences also supports pharmacophore-based search of compound against USP
Deubiquitinase Screening Library Characteristics
- Structure-based and ligand-based approaches are employed to design Deubiquitinase screening library
- This proprietary in silico screening platform is suitable for predicting novel active compounds
- All supporting data are drawn from widely sourced commercial protein databases
- Our Deubiquitinase-focused library contains more than 3,300 structurally diverse molecules for biological screening campaigns
- No PAINS or toxic substances/unwanted functions: filtered by strict ‘Ro5-like’ physicochemical and most stringent in-house structural filters
- All PAIN and reactive compounds are excluded from selection by internal filter applications
- Confirmed bioactivity and safety via preclinical studies and clinical trials
- Structural diversity, significant efficacy, and cellular penetration
- Structural document, IC50, and other chemical and biological data are provided
- All compounds are continually updated
- Compound cherry-picking service is provided
What We Deliver
- Delivered within 2 weeks in any customer-preferred format
- Powders, dry films or DMSO solutions formatted in vials, 96 or 384-well plates
- All compounds have a minimum purity of 90% assessed by 1H NMR and HPLC
- Analytical data is provided
BOC Sciences provides professional, rapid and high-quality services of Deubiquitinase Screening Library design at competitive prices for global customers. Personalized and customized services of Deubiquitinase Screening Library design can satisfy any innovative scientific study demands. Our clients have direct access to our staff and prompt feedback to their inquiries. If you are interested in our services, please contact us immediately!
Reference
- Cai, J.; et al. The role of ubiquitination and deubiquitination in the regulation of cell junctions. Protein & Cell. 2017. 9(9): 754-769.
