Identification of a Highly Cooperative PROTAC Degrader Targeting GTP-Loaded KRAS(On) Alleles

  • J Am Chem Soc. 2025 Nov 12;147(45):41367-41378. doi: 10.1021/jacs.5c10354.
Vesna Vetma  1  2 ,  Ilaria Puoti  1 ,  Natalia K Karolak  1 ,  Sohini Chakraborti  1  2 ,  Emelyne Diers  2 ,  Enrico Girardi  3 ,  Shakil Khan  1  2 ,  Giorgia Kidd  1  2 ,  Katrin G Kropatsch  3 ,  Ross Mclennan  1  2 ,  Suzanne O'Connor  1  2 ,  Matthias Samwer  3 ,  Nicole Trainor  2 ,  Claire Whitworth  2 ,  Andre J Wijaya  1  2 ,  Jeff Y F Wong  1  2 ,  David Zollman  1  2 ,  William Farnaby  1  2 ,  Johannes Popow  3 ,  Alessio Ciulli  1  2 ,  Peter Ettmayer  3 ,  Kirsten McAulay  1
Affiliations
  • 1. Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K.
  • 2. Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, DD1 5EH Dundee, Scotland, U.K.
  • 3. Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria.
PMID: 41166656 DOI: 10.1021/jacs.5c10354
Abstract

Kirsten rat sarcoma viral oncogene homologue (KRAS) is a frequently mutated oncogene in multiple types of Cancer and is a high priority target for oncology drug development. There are many different KRAS mutations, including mutations that favor the GTP-loaded hydrolysis-incompetent "active" state of KRAS, KRAS(on), that can lead to tumorigenesis. However, small molecule interventions thus far have predominantly targeted single mutations of "inactive" GDP-loaded KRAS, KRAS(off), such as KRASG12C. Here, we address this gap through the development of heterobifunctional VHL-based PROTACs capable of engaging and degrading KRAS(on), thus addressing a wider range of KRAS mutations. By studying ternary complex affinity, stability, and binding modes using SPR and X-ray cocrystal structures, we identified PROTACs that exhibit high positive cooperativity in forming ternary complexes with VHL and GCP-loaded KRAS as representative of KRAS(on) variants. Degrader activity profiling in relevant Cancer cells supported the discovery of ACBI4, a PROTAC which forms a highly stable and cooperative ternary complex between VHL and GTP-bound KRAS and which potently degrades KRASG12R, leading to antiproliferative effect in KRAS mutant-driven Cancer cells. ACBI4 provides a new chemical tool for studying the impact of degrading KRAS(on) mutants, which is not possible with current pan-KRAS inhibitors or degraders.

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