Identification and characterization of binders to a cryptic and functional pocket in KRAS

RAS proteins control cell proliferation and activating mutations are collectively the most frequent oncogenic event observed in cancer patients, justifying investments into multiple drug discovery efforts. While RAS-directed therapeutic agents targeting either the inactive GDP-bound or the active GTP-bound state have entered the clinic, invariably resistance is observed. Mutations at drug binding sites represent a common resistance mechanism indicating the need to discover new targetable pockets in RAS. Such efforts are hindered by the small globular size of the protein, for long considered undruggable. Here we perform macrocyclic peptides mRNA and nanobody yeast display screens and discover a targetable ligand-induced pocket in RAS. In vitro and cellular experiments with the KM12 and KM12-AM nanobodies show RAS inhibition via displacement of cRAF, by affecting their protein-protein interaction via the less studied cRAF CRD domain. Further, we provide orthogonal functional validation for the discovered binding pocket via mutagenesis experiments. Notably, the discovered RAS-targeting approach enables simultaneous targeting of both GTP-bound active and GDP-bound inactive states and leaves the SwII pocket unaltered, opening possibilities of combinatorial approaches with clinically approved SwII pocket inhibitors.

Authors

Institutions

Publication Details

Journal
Nature Communications
Published
2025-12-02
DOI
https://doi.org/10.1038/s41467-025-65844-3
Citations
3
Primary Topic
Protein Kinase Regulation and GTPase Signaling
Type
article
Field-Weighted Citation Impact
2.42
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Identification and characterization of binders to a cryptic and functional pocket in KRAS

Giorgio Giacomo Galli, Saskia M. Brachmann, Christoph E. Dumelin, Andreas L. Marzinzik et al.
3 citations
Nature Communications
Protein Kinase Regulation and GTPase Signaling
2.42
article

Identification and characterization of binders to a cryptic and functional pocket in KRAS

Giorgio Giacomo Galli, Saskia M. Brachmann, Christoph E. Dumelin, Andreas L. Marzinzik, Kim S. Beyer, Wassim Abdul Rahman, Lukas Leder, Marc Hattenberger, Luca Tordella, Mylene Lanter, Régis Cèbe, Jessica Desogus, Florence Zink, Wolfgang Jahnke, Nils Ostermann, Kathrin Müller, Simona Cotesta, Sauveur-Michel Maira, Daniel Guthy, Sol Katz, Melusine Bleu, Oliver Esser, Jessica Klein, Lionel Muller, Damiano Borrello, Patrick Welker, Kerstin Pollehn, Aurélie Gluck-Gadé
article en
3 citations

Abstract

RAS proteins control cell proliferation and activating mutations are collectively the most frequent oncogenic event observed in cancer patients, justifying investments into multiple drug discovery efforts. While RAS-directed therapeutic agents targeting either the inactive GDP-bound or the active GTP-bound state have entered the clinic, invariably resistance is observed. Mutations at drug binding sites represent a common resistance mechanism indicating the need to discover new targetable pockets in RAS. Such efforts are hindered by the small globular size of the protein, for long considered undruggable. Here we perform macrocyclic peptides mRNA and nanobody yeast display screens and discover a targetable ligand-induced pocket in RAS. In vitro and cellular experiments with the KM12 and KM12-AM nanobodies show RAS inhibition via displacement of cRAF, by affecting their protein-protein interaction via the less studied cRAF CRD domain. Further, we provide orthogonal functional validation for the discovered binding pocket via mutagenesis experiments. Notably, the discovered RAS-targeting approach enables simultaneous targeting of both GTP-bound active and GDP-bound inactive states and leaves the SwII pocket unaltered, opening possibilities of combinatorial approaches with clinically approved SwII pocket inhibitors.

Nature CommunicationsVol. 16(1)
Novartis (Switzerland) (CH), Procter & Gamble (Belgium) (BE)
Openalex Percentile: Top 10%
Protein Kinase Regulation and GTPase Signaling
2.42
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.