Abstract 3884: Artificial intelligence (AI)-enabled discovery of GLX1546, a novel and potent inhibitor of ULK1/2 kinases and autophagy
Authors: Cui Guonan , Sun Xulun , Zhu Wenyu , Wang Qi , Li Jinchen , Pan Zhongzong , Li Chengtao 
Published: March 2024

Background: Autophagy is an evolutionarily conserved process, critical for the recycling of damaged or excess cellular components, which promotes cell survival and growth under stress conditions. Cancer cells, especially those with RAS mutations, can activate the ULK1/2 (UNC-51-like kinase 1/2)-initiated autophagy pathway for survival and diminish RAS pathway inhibitors’ efficacy. The combination of RAS pathway and ULK1/2 kinase inhibitors may provide synergistic or additive effects for RAS mutated solid tumors. We have identified a structurally small molecule, GLX1546, which shows strong inhibition against ULK1/2, as well as autophagy induced by RAS pathway inhibitors in cells.

Methods: Multiple dual-target activity predictive models were constructed and trained using extensive protein-ligand interaction data. These models, in conjunction with in-house built physicochemical property predictive models, were integrated into an AI-driven computational pipeline to perform the in silico screening on both ULK1/2 inhibitory activities and drug-like properties. ULK1/2 in vitro activities were assessed by enzymatic assays and cellular assays based on the phosphorylation of ULK substrate. The in vivo anti-tumor efficacy of GLX1546 was evaluated in A549 CDX mouse model both as monotherapy and in combination with trametinib.

Results: An AI-driven high-throughput virtual screening strategy using deep learning models was implemented for the discovery of novel and potent ULK1/2 small-molecule inhibitors. GLX1546 was developed as a potent ULK1/2 inhibitor with IC50 values of 1.13 nM for ULK1 and 4.75 nM for ULK2. Moreover, to address trametinib-induced activation of ULK1/2 in KRAS and BRAF mutated solid tumors, GLX1546 provided IC50 values of 54 nM in A549, 21 nM in HCT 116, 67 nM in MIA PaCa-2, and 76 nM in A375 cells against both basal and trametinib-induced pATG13. Furthermore, GLX1546 exhibited good exposure, sound safety, and high oral bioavailability (~100%) in mice. The combination of trametinib (PO, QD) with GLX1546 (PO, BID) in 21-day cycles also led to inhibition of ATG13 phosphorylation and greater tumor growth inhibition than trametinib alone in A549 CDX mouse model.

Conclusions: These results indicate that GLX1546 can inhibit ULK-mediated autophagy induced by trametinib. The combination of GLX1546 with RAS pathway inhibitors may offer a novel cancer therapy for RAS mutated cancers, highlighting AI as an effective tool for drug discovery.

Keywords: AI-driven drug discovery, autophagy, small-molecule inhibitors, ULK

Citation Format: Guonan Cui, Xulun Sun, Wenyu Zhu, Qi Wang, Jinchen Li, Zhongzong Pan, Chengtao Li. Artificial intelligence (AI)-enabled discovery of GLX1546, a novel and potent inhibitor of ULK1/2 kinases and autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3884.