Discovery of novel SOS1 inhibitors using machine learning

Duo, Lihui; Chen, Yi; Liu, Qiupei; Ma, Zhangyi; Farjudian, Amin; Yong Ho, Wan; Shin Low, Sze; Ren, Jianfeng; Hirst, Jonathan D.; Xie, Hua; Tang, Bencan

Abstract

Overactivation of the rat sarcoma virus (RAS) signaling is responsible for 30% of all human malignancies. Son of sevenless 1 (SOS1), a crucial node in the RAS signaling pathway, could modulate RAS activation, offering a promising therapeutic strategy for RAS-driven cancers. Applying machine learning (ML)-based virtual screening (VS) on small-molecule databases, we selected a random forest (RF) regressor for its robustness and performance. Screening was performed with the L-series and EGFR-related datasets, and was extended to the Chinese National Compound Library (CNCL) with more than 1.4 million compounds. In addition to a series of documented SOS1-related molecules, we uncovered nine compounds that have an unexplored chemical framework and displayed inhibitory activity, with the most potent achieving more than 50% inhibition rate in the KRAS G12C/SOS1 PPI assay and an IC50 value in the proximity of 20 μg mL−1. Compared with the manner that known inhibitory agents bind to the target, hit compounds represented by CL01545365 occupy a unique pocket in molecular docking. An in silico drug-likeness assessment suggested that the compound has moderately favorable drug-like properties and pharmacokinetic characteristics. Altogether, our findings strongly support that, characterized by the distinctive binding modes, the recognition of novel skeletons from the carboxylic acid series could be candidates for developing promising SOS1 inhibitors.

Citation

Duo, L., Chen, Y., Liu, Q., Ma, Z., Farjudian, A., Yong Ho, W., …Tang, B. (2024). Discovery of novel SOS1 inhibitors using machine learning. RSC Medicinal Chemistry, 15(4), 1392-1403. https://doi.org/10.1039/D4MD00063C

• Journal Article Type: Article
• Acceptance Date: Mar 14, 2024
• Online Publication Date: Mar 15, 2024
• Publication Date: Mar 15, 2024
• Deposit Date: Mar 30, 2024
• Publicly Available Date: Apr 8, 2024
• Journal: RSC Medicinal Chemistry
• Print ISSN: 2632-8682
• Electronic ISSN: 2632-8682
• Publisher: Royal Society of Chemistry
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Issue: 4
• Pages: 1392-1403
• DOI: https://doi.org/10.1039/D4MD00063C
• Public URL: https://nottingham-repository.worktribe.com/output/33027482
• Publisher URL: https://pubs.rsc.org/en/content/articlelanding/2024/md/d4md00063c