Exploiting ELIOT for scaffold-repurposing opportunities: TRIM33 a possible novel E3 ligase to expand the toolbox for PROTAC design

DOI: 10.3390/ijms232214218

Authors: Tommaso Palomba (University of Perugia) , Giusy Tassone (University of Siena) , Carmine Vacca (University of Perugia) , Matteo Bartalucci (University of Perugia) , Aurora Valeri (Molecular Horizon srl) , Cecilia Pozzi (University of Siena) , Simon Cross (Molecular Discovery Ltd) , Lydia Siragusa (Molecular Horizon srl; Molecular Discovery Ltd) , Jenny Desantis (University of Perugia)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: International Journal Of Molecular Sciences , VOL 23

State: Published (Approved)
Published: November 2022
Diamond Proposal Number(s): 21741 , 29907

Abstract: The field of targeted protein degradation, through the control of the ubiquitin–proteasome system (UPS), is progressing considerably; to exploit this new therapeutic modality, the proteolysis targeting chimera (PROTAC) technology was born. The opportunity to use PROTACs engaging of new E3 ligases that can hijack and control the UPS system could greatly extend the applicability of degrading molecules. To this end, here we show a potential application of the ELIOT (E3 LIgase pocketOme navigaTor) platform, previously published by this group, for a scaffold-repurposing strategy to identify new ligands for a novel E3 ligase, such as TRIM33. Starting from ELIOT, a case study of the cross-relationship using GRID Molecular Interaction Field (MIF) similarities between TRIM24 and TRIM33 binding sites was selected. Based on the assumption that similar pockets could bind similar ligands and considering that TRIM24 has 12 known co-crystalised ligands, we applied a scaffold-repurposing strategy for the identification of TRIM33 ligands exploiting the scaffold of TRIM24 ligands. We performed a deeper computational analysis to identify pocket similarities and differences, followed by docking and water analysis; selected ligands were synthesised and subsequently tested against TRIM33 via HTRF binding assay, and we obtained the first-ever X-ray crystallographic complexes of TRIM33α with three of the selected compounds.

Journal Keywords: PROTAC; E3 ligase; scaffold-repurposing; BRD; TRIM33; TRIM24; targeted protein degradation; molecular interaction fields

Subject Areas: Biology and Bio-materials, Medicine


Instruments: I04-Macromolecular Crystallography

Added On: 24/11/2022 10:02

Documents:
ijms-23-14218-v3.pdf

Discipline Tags:

Health & Wellbeing Structural biology Drug Discovery Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)