ELIOT: A platform to navigate the E3 pocketome and aid the design of new PROTACs. (27th July 2022)

• Record Type: Journal Article
• Authors: Palomba, Tommaso; Baroni, Massimo; Cross, Simon; Cruciani, Gabriele; Siragusa, Lydia
• Is Part Of: Chemical biology & drug design. Volume 101:Number 1(2023)
• Page Start: 69
• Page End: 86
• Publication Date: 2022-07-27
• Subjects: cancer -- E3 ligase -- PROTACs -- protein degradation -- ubiquitin–proteasome system; Drugs -- Design -- Periodicals; Pharmaceutical chemistry -- Periodicals; Biochemistry -- Periodicals; 615.19005
• DOI: 10.1111/cbdd.14123
• Languages: English
• ISSNs: 1747-0277

Abstract

Abstract: Proteolysis‐targeting chimeras (PROTACs) are novel therapeutics for the treatment of human disease. They exploit the enormous potential of the E3 ligases, a class of proteins that mark a target protein for degradation via the ubiquitin–proteasome system. Despite the existence of several E3 ligase‐related databases, the choice of the functioning ligase is limited to only 1.6% of those available, probably due to the fragmentary understanding of their structures and their known ligands; in fact, none of the existing databases report detailed studies covering their 3D structure or their pockets. Here, we report ELIOT (E3 LIgase pocketOme navigaTor), an accurate and complete platform containing the E3 ligase pocketome to enable navigation and selection of new E3 ligases and new ligands for the design of new PROTACs. All E3 ligase pockets were characterized with innovative 3D descriptors including their PROTAC‐ability score, and similarity analyses between E3 pockets are presented. Tissue specificity and their degree of involvement in patients with specific cancer types are also annotated for each E3 ligase, enabling appropriate selection for the design of a PROTAC with improved specificity. All data are available at https://eliot.moldiscovery.com . Abstract : E3 ligase pocketome feature representation.