KRAS G12C fragment screening renders new binding pockets

ABSTRACT

KRAS genes belong to the most frequently mutated family of oncogenes in cancer. The G12C mutation, found in a third of lung, half of colorectal and pancreatic cancer cases, is believed to be responsible for a substantial number of cancer deaths. For 30 years, KRAS has been the subject of extensive drug-targeting efforts aimed at targeting KRAS protein itself, but also its post-translational modifications, membrane localization, protein–protein interactions and downstream signalling pathways. So far, most KRAS targeting strategies have failed, and there are no KRAS-specific drugs available. However, clinical candidates targeting the KRAS G12C protein have recently been developed. MRTX849 and recently approved Sotorasib are covalent binders targeting the mutated cysteine 12, occupying Switch II pocket.

Herein, we describe two fragment screening drug discovery campaigns that led to the identification of binding pockets on the KRAS G12C surface that have not previously been described. One screen focused on non-covalent binders to KRAS G12C, the other on covalent binders.

KEYWORDS:

• KRAS
• fragment screening
• covalent inhibitor
• induced binding pocket

Acknowledgments

We thank Dr Kwame Amaning for critical reading of the manuscript. We thank Dr Andreas Karlsson for preparing analysis of the non-covalent fragment library. We thank Dr Eiso AB and Dr Gregg Seagal from ZOBIO for providing incredible PO-NMR support in the project and great collaboration spirit. ESRF and Soleil synchrotrons staffs are acknowledged for assisting in the x-ray data collection.

Author Contributions

M. Mathieu: x-ray crystallography, management, paper writing

V. Steier: protein biochemistry and crystallization

F. Fassy: mass spectrometry and biochemistry experiments, paper writing

C. Delorme: protein biochemistry

D. Papin: in-silico modelling

B. Genet: mass spectrometry experiments

F. Duffieux: recombinant protein design and production

T.Bertrand: x-ray crystallography, paper writing

L. Delarbre: SPR experiments design and analysis, paper writing

H. Le Borgne: Mass spectrometry experiments

A. Parent: NMR experiments

P. Didier: protein biochemistry

J.P. Marquette: DSF experiments

M. Lowinski: SPR experiments.

J. Houtmann: DSF experiments

A. Lamberton: SPR experiments

L. Debussche: designed and coordinated research

A.Rak: project strategy, data analysis and interpretation, management, paper writing and submission

Competing Interest Statement

All authors: No competing interests besides Sanofi employee (or retired from Sanofi employment) and Sanofi shareholder