K-RasG12D has an allosteric small molecule binding site

• Published in: Biochemistry (Easton) Vol. 58; no. 21; pp. 2542 - 2554
• Main Authors: Feng, Huizhong, Zhang, Yan, Bos, Pieter H., Chambers, Jennifer M., Dupont, Marcel M., Stockwell, Brent R.
• Format: Journal Article
• Language: English
• Published: 14.05.2019
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/acs.biochem.8b01300

KRAS is the most commonly mutated oncogene in human cancer, with particularly high mutation frequencies in pancreatic cancers, colorectal cancers and lung cancers 1 . The high prevalence of KRAS mutations and its essential role in many cancers makes it a potentially attractive drug target; however, it has been difficult to create small molecule inhibitors of mutant K-Ras proteins. Here, we identified a small molecule binding site on K-Ras G12D using computational analyses of the protein structure, and then used a combination of computational and biochemical approaches to discover small molecules that bind to this pocket, which we have termed the P110 site, due to its adjacency to proline-110. We determined that one compound, named K -Ras A llosteric L igand KAL-21404358, bound to K-Ras G12D , as measured by microscale thermophoresis (MST), thermal shift assay (TSA), and nuclear magnetic resonance (NMR) spectroscopy. This compound impaired the K-Ras G12D interaction with B-Raf, and disrupted the RAF-MEK-ERK and the PI3K-AKT signaling pathway. We synthesized additional compounds, based on the KAL-21404358 scaffold with more potent binding and greater aqueous solubility. In summary, these findings suggest that the P110 site is a promising pocket for binding of small molecule allosteric inhibitors of K-Ras G12D .