Targeting SH2 Domains as an Emerging Drug Discovery Strategy

Protein-protein interactions are physical contacts within a protein or between two or more proteins that regulate the function of one or more proteins, or which direct a protein to be localized to a specific region in the cell. These interactions play a major role in cell signaling by conveying a biochemical message from outside or inside the cell, and subsequently changing cellular processes in response to this message. New therapeutic approaches attempt to stop aberrant cellular signaling in disease states by blocking protein-protein interactions, thereby disrupting transmission of the signaling pathway’s message. On average, between 10 to 15% of phase I-III small molecule candidates at the 10 biggest pharmaceutical companies in 2023 were protein-protein interaction inhibitors (Brennan et al., 2024, Nat. Rev. Drug. Discov.). Examples of protein-protein interaction modules in proteins include SH2 domains, bromo domains, SH3 domains, PH domains, PTB domains and WW domains, among many others.

The Basics of SH2 Domains

SH2 domains are an emerging target of interest for the development of small molecules blocking protein-protein interactions; there are 120 SH2 domains annotated in the human genome, and these protein-protein interaction modules are found in multiple functional protein classes, including kinases, transcription factors, E3 ligases and adaptor proteins. Dysregulation of the biological function of SH2 domain-containing proteins, such as through mutation or overexpression of the target gene product, can lead to pathological states, such as cancer and chronic inflammation. SH2 domains act as protein-protein interaction domains through binding of phosphotyrosine residues on target proteins. The selectivity of the interaction is imparted by the flanking amino acids surrounding the phosphotyrosine residue on the recognized protein. The function of the SH2 domain is context dependent. For example, an SH2 domain can act as a regulatory module for protein catalysis in one protein, or as recruitment scaffold for other binding partners in another protein. Importantly, not all SH2 domain-containing proteins have enzymatic activity, and many of these proteins are emerging drug targets, such as transcription factors.

SH2 Domains Enable Alternative Targeting Strategies

Resistance mutations which cause decreased efficacy of existing kinase active site inhibitors has led to the search for alternative targeting strategies of these proteins which circumvent known clinical resistance mutations. Targeting SH2 domains in kinases has emerged as a potential means of modulating either kinase activity regulation or the recruitment of the kinase to molecular scaffolds, thereby interrupting cellular signaling pathways by indirect methods. In addition, many SH2 domain containing proteins lack a catalytic activity or have poorly defined binding pockets outside of the SH2 domain, and as such were considered challenging targets for drug discovery programs. The emergence of targeted protein degradation strategies and a resurgence in covalent inhibitor development has caused these targets to be given a second look in the development of new therapeutics.

Published studies have explored developing small molecule inhibitors of the SH2 domains of STAT transcription factors (Mandal et al., 2015, J. Med. Chem.; Elumalai et al., 2015, Angew. Chem. Int. Ed.; Krueger et al., 2015, Blood), as well as various kinases (Park et al., 2002, Bioorg. Med. Chem. Lett.; Singaram et al., 2023, Nat. Chem. Biol.; Visperas et al., 2017, SLAS Discov.). Furthermore, advances in the field of targeted protein degradation have resulted in the development of proteolysis targeting chimera (PROTAC) molecules capable of degrading STAT transcription factors via the proteosome-ubiquitination pathway through PROTAC engagement with the target protein via its SH2 domain (Kaneshige et al., 2023, Nat. Chem. Biol.; Bai et al., 2019, Cancer Cell; Kaneshige et al., 2024, J. Med. Chem.).

What’s Next for SH2 Domains in Drug Discovery

Ligand-SH2 domain interaction selectivity has previously been studied at scale across the target class for phosphopeptide ligands (Liu et al., 2010, Mol. Cell. Proteomics; Tinti et al., 2013, Cell Rep.; Machida et al., 2007, Mol. Cell; Jones et al., 2006, Nature). However, the assessment of binding selectivity of small molecule ligands across the SH2 target class to assess binding selectivity has yet to be performed. These studies will be needed to determine the selectivity of small molecule inhibitors and protein degrader molecular handles targeting SH2 domains for early clues of potential toxicity and/or polypharmacology. This information can then be used downstream to assess the functional consequences of identified off-target binding effects in orthogonal assays.