The PROTACtable genome

Proteolysis-targeting chimeras (PROTACs) are an emerging drug modality that may offer new opportunities to circumvent some of the limitations associated with traditional small-molecule therapeutics. By analogy with the concept of the 'druggable genome', the question arises as to which potential drug targets might PROTAC-mediated protein degradation be most applicable. Here, they present a systematic approach to the assessment of the PROTAC tractability (PROTACtability) of protein targets using a series of criteria based on data and information from a diverse range of relevant publicly available resources. Our approach could support decision-making on whether a particular target may be amenable to modulation using a PROTAC. Using our approach, they identified 1,067 proteins of the human proteome that have not yet been described in the literature as PROTAC targets that offer potential opportunities for future PROTAC-based efforts.

Proteolysis-targeting chimera (PROTAC) molecules are bifunctional: one end binds to a protein of interest (POI) and the other end binds to an E3 ligase to form a ternary complex. The recruited E3 ligase then mediates the transfer of ubiquitin from an E2 enzyme to the POI. After dissociation of the ternary complex the ubiquitylated POI is removed by the proteasome degradation machinery. The PROTAC is then available to bind to another POI (assuming the interaction with the POI is non-covalent). The part of the PROTAC that binds to the POI does not have to affect the function of the POI, as illustrated by the orthosteric and allosteric binding options. Also shown are the two PROTAC molecules in clinical trials for which structures have been disclosed; ARV-110 is an androgen receptor degrader whereas ARV-471 targets the oestrogen receptor (see main text for more details). Mr, relative molecular mass.

A new approach to disease modulation via targeted protein degradation is gaining momentum in drug discovery. The best-known technology within this field at present is based on heterobifunctional molecules termed proteolysis-targeting chimeras (PROTACs). First described in 2001, PROTACs are designed to degrade target proteins by redirecting the ubiquitin–proteasome system. Ubiquitin-directed degradation involves two broad steps: tagging the target protein via covalent attachment of several ubiquitin molecules (polyubiquitylation), and then subsequent recognition and degradation of the tagged protein by the proteasome. During tagging (also called conjugation), an E3 ubiquitin ligase transfers ubiquitin from a recruited E2 ubiquitin-conjugating enzyme to a lysine residue on the target protein via an isopeptide bond. Subsequent rounds of ubiquitylation result in the formation of a polyubiquitin chain. There are several ways that the linkages of such polyubiquitin chains can be formed, with Lys48-linked and to a lesser extent Lys11-linked chains known to be recognized by the proteasome. The key role of a PROTAC molecule is to drive the formation of the ternary complex (protein target–PROTAC–E3 ligase) by bringing a specific E3 ligase (encoded by one of the more than 600 E3 ligase human genes)into proximity to the defined target protein, thus catalysing the ubiquitylation process.

PROTACs may represent a powerful tool to extend druggable space to new target types previously considered intractable or undruggable. Examples include targets such as disease-relevant scaffolding proteins, subunits of larger functional complexes and other non-enzymatic proteins such as transcription factors or RNA-binding proteins. In contrast to traditional small-molecule-mediated pharmacology, PROTACs effectively act as catalysts, accelerating the ubiquitylation and proteasomal degradation processes of the target protein, which in turn may result in different pharmacodynamic consequences compared with traditional inhibition. Furthermore, despite the fact that PROTACs are usually larger than drug-like small molecules, they can show good tissue penetration, and based on the limited evidence available to date, it seems that in vivo activity and oral bioavailability of such molecules could be more attainable than might be initially anticipated from strict application of the rule-of-five criteria for physicochemical characteristics.

In view of the growing interest in PROTACs both as potential therapeutics and as chemical biology tools, they explore here the question of which potential drug targets may be most amenable to this new modality. Inspired by the concept of the ‘druggable genome’ they refer to this set of targets as the ‘PROTACtable genome’. The approach they take is to examine the factors that would make a potential protein amenable to the PROTAC approach, and to integrate information from various publicly available data sources to deliver a genome-wide analysis to the wider community. Overall, the approach provides a practical tool that can be used in combination with other evidence to help drug discovery researchers with target analysis, prioritization and decision-making.

a | Protein targets are assigned to buckets based on whether they meet particular criteria, and a given protein may be present in multiple buckets. Buckets 1–3 correspond to proteins for which proteolysis-targeting chimeras (PROTACs) have entered clinical development. Bucket 4 is for proteins with a literature report of a PROTAC. Buckets 5 and 6 relate to whether the protein has a reported ubiquitylation site. Bucket 7 relates to the availability of experimental data on the half-life of the protein, and bucket 8 is for proteins for which a small-molecule binder with sufficient affinity is available. Finally, each target is assigned a score based on its cellular location and the confidence with which this is known, as indicated. b | The overlap of targets present in the three different resources used for assignment to bucket 6 (PhosphoSitePlus, mUbiSiDa and diglycine proteomics). A more detailed explanation of the different buckets and assignment rules is provided in the main text.

a | Numbers of targets assigned to each of the proteolysis-targeting chimera (PROTAC) buckets. Note that a target can be assigned to more than one bucket. b | Numbers of targets in four PROTACtability categories, counting each target once in its highest tractability category. The categories are defined as follows: targets in any of buckets 1–3 are assigned to the clinical precedence category; targets in bucket 4 are assigned to the literature precedence category; targets that meet defined conditions described in the main text with regard to the other buckets are assigned to the discovery opportunity category; and all other targets are assigned to the incomplete evidence category. Based on this categorization, 1,336 targets are currently considered PROTACtable. c | Overlap of targets assigned to PROTAC buckets relating to literature precedence (bucket 4) and ubiquitylation site information (buckets 5 and 6). d | Overlap of targets assigned to PROTAC buckets relating to literature precedence (bucket 4), half-life data (bucket 7) and known small-molecule binder (bucket 8).

Schneider, M., Radoux, C.J., Hercules, A. et al. The PROTACtable genome. Nat Rev Drug Discov (2021). https://doi.org/10.1038/s41573-021-00245-x