At a scientific level the work was distributed to three scientific work packages each with their unique focus on specific aspects in the ubiquitin system.
Overview of results:
One work package focused on the unique SLiM discovery tool pipeline allowing large scale discovery of motifs and integrating this with bioinformatic approaches as well as mass spectrometry-based approaches. During UBIMOTIF hundreds of protein domains from ubiquitin ligases and DUBs where screened which returned numerous novel motifs. Several computational platforms were developed suited for investigating SLiMs and have been made available to the research community. For a number of novel SLiMs the network analyzed these in a cellular context to elucidate their function in depth using dedicated cellular model systems.
To harness the new knowledge of SLiMs for therapeutic approaches several projects focused on small molecule development. Through evaluation of expression data specific members of the Cul3 ubiquitin ligases were identified as relevant targets for small molecule discovery and PROTAC development. Expression protocols for targets were developed and subsequently screened in fragment-based screening assays leading to hits that were further validated. Novel tool compounds for a Cul3 member have also been developed and characterized which constitutes an important step towards developing novel PROTACs.
A large effort of the network focused on understanding the cellular functions of SLiMs in the ubiquitin system. The focus has been on specific ubiquitin ligases and chain types. Novel insights into substrate recognition by Cul3 complexes and the hGID complex has been obtained hereby providing insight into how they regulate cellular processes. A unique system for ubiquitin replacement has also been established to understand how different ubiquitin chain types contribute to specificity in the system.
Exploitation of results:
The ubiquitin system is viewed as a highly relevant biological system for drug targeting. Particular the emergence of PROTACs, also known as molecular glues, constitute an important area of research with important clinical implications. An important unique element of the UBIMOTIF network was that SLiM binding pockets could constitute ideal targets for small molecule development that could be further developed into PROTACs. The establishment of expression and purification protocols for a large number of ubiquitin ligases and DUBs and the identification of SLiMs binding to these domains constitute an important resource for the scientific community that will allow exploitation of the ubiquitin system in the future for medical applications. The UBIMOTIF has already exploited this by developing small molecule compounds that bind to Cul3 family members, important ubiquitin ligases in the cell, that constitute an important first step in developing PROTACs.
Dissemination of results:
One of the main channels for dissemination has been through presentation at scientific meetings and through departmental seminars. The ESRs and their PIs have participated in more than 100 relevant meetings and presented their work either in the form of posters or through oral presentations with the target audience being the scientific community. All ESRs have also presented their work at departmental seminars at their institutes and at UBIMOTIF annual meetings. At annual meetings we have invited relevant researchers in the field so they became aware of the work in UBIMOTIF. The work on curating motifs as part of ESR journal clubs is integrated into the ProViz webpage (
http://slim.icr.ac.uk/proviz/(opens in new window)) making this available to researchers across the world. As specific projects have finalized, they have been published in relevant journals making the results available to the scientific community and public. Computational tools such as FaSTPACE and xProtCAS that have been developed by UBIMOTIF are freely available to download.
