Overcoming ALK resistance with covalent cysteine-reactive inhibitors

The current standard of care for ALK rearranged non-small cell lung cancer (NSCLC) is targeted therapy with ALK tyrosine kinase inhibitors (TKIs) which bind within the kinase domain of ALK. Due to the development of ALK resistance mutations or bypass activation of parallel or downstream signal pathways, patients inevitably relapse. Even with the introduction of second or third generation TKIs, median overall survival has been estimated to be 6.8 years . Recent advances in immunotherapy have demonstrated progress in lung cancer treatment. However, a majority of ALK positive NSCLC patients have yet to realize the benefits from checkpoint inhibitors or CAR-T cell therapies due to primary resistance or toxicity. Therefore, the development of new treatments for ALK-rearranged NSCLC is an area of critical need. We believe that an effective assault on ALK-driven tumors requires the implementation of creative strategies that allow us to expand our arsenal of drugs to target ALK beyond its kinase domain. To meet this challenge, we have developed and employed cysteine druggability mapping (CDM), a method to define the landscape of inhibitor-protein interactions in a cancer cell. CDM identifies cysteines that can bind to covalent drug-like molecules which serve as early prototypes on which to base cancer drug development programs.
Cysteine-reactive covalent inhibitors have already emerged as an effective approach to targeting protein kinases. Osimertinib, a third-generation epidermal growth factor receptor (EGFR) TKI covalent inhibitor, overcomes EGFR T790M resistance mutations following treatment with EGFR TKI, demonstrating significant improvements over standard EGFR TKIs when used as first line therapy. Importantly, targeting cysteines with covalent inhibitors massively expands the number of proteins which are targetable with small molecule inhibitors, including many targets previously considered undruggable.

We will use ALK fusion positive cancer cell lines, together with tumor tissues from patients who developed resistance mechanisms, to generate druggable cysteine profiles by CDM. Druggable proteins specific to ALK fusion positive samples, including EML4-ALK itself, will be prioritized in our screening for protein degraders from a library of over 2,500 advanced cysteine reactive compounds. After screening, we will assess the specificity of the compound hits and validate their anti-tumor activity using ALK fusion positive cell lines and patient derived ALK TKI-resistant cell lines. We consider the use of the novel, cutting-edge cysteine targeting technology to screen for potent therapeutic compounds as a valuable proposition to improve management of patients with ALK positive lung cancer, with the goal of transforming this cancer into a chronic condition.