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Deubiquitinase Screening Libraries

Deubiquitinating enzymes (DUBs), also known as deubiquitinating peptidases or ubiquitin proteases, ubiquitin hydrolases, represent a large group of proteases that cleave monoubiquitin and polyubiquitin chains from proteins [1]. This enzyme family contains about 100 proteins and can be subdivided into two main classes: cysteine proteases and metalloproteases. Deubiquitylating enzymes have been implicated in several human diseases, including cancer, chronic inflammation, autoimmune disorders, and neurodegenerative diseases [4].

Usually, a single ubiquitin protein or chains of ubiquitin are added to lysine residues of a substrate protein in order to activate and inactivate proteins, regulate the degradation of proteins via the proteasome and lysosome, as well as modulate protein-protein interactions. These post-translational modifications are added to proteins by the ubiquitination machinery: ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3) [3]. DUBs play an essential role in the ubiquitin pathway as they can reverse these effects by the removal of post-translational modifications. Their catalytic activity includes thiol-dependent hydrolysis of ester, thioester, amide, peptide, and isopeptide bonds formed by the C-terminal Gly of ubiquitin [1,2]. Deubiquitinases are attractive targets for small-molecule drug discovery, as they contain a well-defined active site, and the majority of them have a catalytic cysteine.

At Life Chemicals, we have developed two deubiquitinase-focused screening sets of over 18,000 drug-like screening compounds selected with both ligand-based and structure-based approaches to boost DUB drug discovery:

The compound selection can be customized based on your requirements, cherry picking is available.

Please, contact us at orders@lifechemicals.com for any additional information and price quotations.

For a pre plated set based on this Screening Library, please explore our Pre-plated Focused Libraries.

Take advantage of our related products to make your search even more rewarding:
 

Deubiquitinase Focused Library

A reference set of over 25,500 bioactive compounds with reported DUB inhibitor activity was prepared based on the data from the ChEMBL database. Then the Life Chemicals HTS Compound Collection was screened against it using a 2D fingerprint similarity search (85 % Tanimoto similarity cut-off). The PAINS filter together with our in-house developed toxicophore and undesired functionalities filters were also applied.

As a result, a screening set of over 15,300 structurally-diverse molecules with potential deubiquitinase inhibitory activity against different DUB-related targets, focusing mostly on two deubiquitinating enzymes, ubiquitin carboxyl-terminal hydrolases UCH1 and UCH2, has been obtained.

In addition, a Diversity Screening Set of over 3,900 structurally-diverse deubiquitinase-targeting screening compounds was added as a convenient starting point for DUB-focused drug discovery.

Representative compounds from the Deubiquitinase-focused Diversity Screening Set

Deubiquitinase Targeted Library

Our Deubiquitinase-targeted Library of over 3,300 structurally-diverse molecules for biological screening has been designed, employing structure-based and ligand-based approaches.

Our cheminformatics team has focused on the first pair of representatives (USP1/USP2) of the ubiquitin-specific protease superfamily and UBA5 of the E1 class to prepare the docking-based screening set presented here. The proprietary in silico screening platform was used to predict new types of bioactive compounds. All supporting data were taken from the ChEMBL DB and RCSB Protein Data Bank.

Docking of the entire Life Chemicals HTS Compound Collection in the active site of E1 activating protein was performed with the Glide from Schrödinger Suite (Fig. 1-2). A set of constraints was defined to improve docking result quality. The resulting Deubiquitinase E1 Targeted Library includes 2,200 in-stock drug-like screening compounds with potential E1 enzyme activity.

Pharmacophore modeling was applied to search for DUB-specific screening compounds with the aid of both Cresset and Schrödinger modules (Fig. 3). As a result, over 1,100 potential small-molecule inhibitors of ubiquitin-specific proteases (USP1, 2) were identified for the Deubiquitinase USP1, 2 Focused Screening Set.

Glide docking procedure for E1 crystal structures, based on the positions and orientations of reference molecules in the active site.

Figure 1. Glide docking procedure for E1 crystal structures, based on the positions and orientations of reference molecules in the active site. H-bond forming residues are marked with sticks, the hydrophobic core is red, and spheres of steric barrier (exclusion volumes) are gray. As required for screening, one obligatory hydrophobic core and three constraints from five possible H-bonds were set.

The example of the docking binding mode of potential inhibitors from the Life Chemicals Library.

Figure 2. The example of the docking binding mode of potential inhibitors from the Life Chemicals Library.

A. K-mean clustering method was implemented to select the best cluster by its total activity (colored 3D diagram is a visualized distribution of 150 clusters). B. QSAR field-based analysis for 3D bioactive structure prediction by conformer search and cross-alignment of reference compounds. C. Pharmacophore-based search of compounds against USP.

Figure 3. A. K-mean clustering method was applied to select the best cluster by its total activity (colored 3D diagram is a visualized distribution of 150 clusters). B. QSAR field-based analysis for 3D bioactive structure prediction by conformer search and cross-alignment of reference compounds. C. Pharmacophore-based search of compounds against USP.

References:

  1. Lopez-Castejon G, Edelmann MJ. Deubiquitinases: Novel Therapeutic Targets in Immune Surveillance. Mediators Inflamm. 2016:3481371. doi:10.1155/2016/3481371.
  2. Callis J. The ubiquitination machinery of the ubiquitin system. Arabidopsis Book. 2014;12:e0174. Published 2014 Oct 6. doi:10.1199/tab.0174.
  3. Song L, Luo ZQ. Post-translational regulation of ubiquitin signaling. J Cell Biol. 2019;218(6):1776-1786. doi:10.1083/jcb.201902074.
  4. Harrigan, J., Jacq, X., Martin, N. et al. Deubiquitylating enzymes and drug discovery: emerging opportunities. Nat Rev Drug Discov 17, 57–78 (2018). https://doi.org/10.1038/nrd.2017.152
 
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