Targeting oncogenes with allosteric inhibitors and engineered monobody proteins

Over the past two decades, more than 70 ATP-competitive kinase inhibitors were approved for the treatment of patients with haematological and solid tumors. Despite this remarkable progress, the development of drug resistance severely blunted initial clinical responses. An alternative strategy is the identification and targeting of allosteric sites that are critical for oncogenicity. This could decrease drug resistance, as the allosteric site could be targeted alternatingly or simultaneously. The BCR-ABL fusion tyrosine kinase is the driving mutation of chronic myelogenous leukemia (CML) and some acute lymphoblastic leukemias. Our detailed studies of the structure and regulation of BCR-ABL have led to the identification of the allosteric myristoyl binding pocket that is critical for BCR-ABL-dependent oncogenic transformation. I will present how based on these insights, small-molecule myristoyl pocket inhibitors were developed, of which asciminib was recently approved for the treatment of CML patients.



In the second part of my presentation, I will present how monobodies can be used to target protein-protein interactions of key oncogenes. Monobodies are synthetic in vitro-evolved binders built on the fibronectin type III (FN3) domain. They are only ~10kDa in size, lack cysteine residues and can bind their target proteins with low nanomolar affinity. We extensively use monobodies to target key nodes of oncogenic signaling networks: These include BCR-ABL, the oncogenic SHP2 and SHP1 tyrosine phosphatase, the SH2 domains of Src family kinases, the transcription factors STAT3 and STAT5 and the E3 ubiquitin ligase c-Cbl. I will focus on our efforts in converting monobodies from potent pre-clinical target validation tools to next-generation protein-based therapeutics by developing approaches to deliver monobody proteins to cells and to engineer mirror-image D-monobodies.