Abstract B075: Identifying functional allosteric binding sites using a systematic and scalable AMPS screening platform for drug discovery
Authors: Padyana Anil K , Schinzel Anna , Murray Gordon , LaPointe Joseph H , Selmer Kaitlyn , Pham Truc , Buskes Melissa J , Sengupta Shomit , Blanco Maria-Jesus , Roddy Thomas , Dorsch Marion 
Published: December 2023

Endogenous cellular metabolites have been shown to bind and regulate proteins involved in tumorigenesis. These low-affinity metabolite-protein interactions can modulate protein function through binding at allosteric sites. As an example, in normal cells, the ABL1 protein is regulated by N-terminal myristylation, which binds to a hydrophobic pocket in the C-terminal lobe of the kinase domain autoinhibiting its activity. Fusion of BCR to ABL1 leads to deletion of the N-terminal myristylation site activating BCR-ABL oncoprotein leading to chronic myeloid leukemia (CML). Similarly, autopalmitoylation of TEAD proteins regulates transcriptional output of Hippo signaling and tumorigenesis. Allosteric metabolite binding sites on these targets have been successfully used to generate new medicines (e.g.: Asciminib for BCR-ABL) and investigational cancer therapies (e.g.: IK-930, VT3989 for TEAD). However, there are limited approaches that can be broadly deployed to discover functional regulatory sites on precision oncology targets. Atavistik Bio has developed the AMPS (Atavistik Metabolite Protein Screening) platform that enables systematic and scalable screening of metabolites against proteins or protein complexes of interest. The AMPS platform technology integrates equilibrium dialysis with sensitive mass-spectrometry to screen a proprietary metabolite library. A state-of-the-art computational workflow coupled with deep mechanistic structure-function characterization enables us to discover novel functional allosteric modulators. To validate the platform, we have screened several precision oncology targets and characterized the AMPS metabolite hits with functional assays. For ABL1 tyrosine kinase, we have applied AMPS on distinct enzyme forms to probe the role of metabolite binding in the context of phosphorylation states and drug resistant T315I mutant forms. In addition, AMPS allows us to investigate novel metabolite sensitization of ABL1 in the presence of existing drugs Imatinib and Asciminib. Results from AMPS and follow up experiments highlight phosphorylation state dependency on myristate binding to ABL1. In conclusion, we demonstrate the AMPS platform can identify highly conserved allosteric protein-metabolite interactions to advance small molecule drug discovery efforts for new precision medicines.

Citation Format: Anil K Padyana, Anna Schinzel, Gordon Murray, Joseph H LaPointe, Kaitlyn Selmer, Truc Pham, Melissa J Buskes, Shomit Sengupta, Maria-Jesus Blanco, Thomas Roddy, Marion Dorsch. Identifying functional allosteric binding sites using a systematic and scalable AMPS screening platform for drug discovery [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B075.