Partial PROTACs for Targeted Protein Degradation

Targeted Protein Degradation

An emerging strategy in drug discovery to access difficult-to-treat diseases is targeted protein degradation. While traditional small-molecule or antibody drugs may only allow access to ~20% of the proteome, degradation techniques may open the door to the other 80%.1 The molecules used in these approaches are often called proteolysis targeting chimeras (PROTACs), bifunctional molecules that eliminate target proteins from cells (Figure 1).1-5

Targeted protein degradation via proteolysis-targeting chimeras (PROTACs)

Targeted protein degradation via proteolysis-targeting chimeras (PROTACs)

Figure 1. Targeted protein degradation via proteolysis-targeting chimeras (PROTACs)

 

PROTACs are designed with three primary components:

  1. A ligand at one end that targets the protein of interest (POI)
  2. A second ligand at the opposite end that binds an E3 ligase
  3. A crosslinker in the middle that joins the two ends (Figure 2).

The simultaneous PROTAC binding of two proteins brings the POI in close enough proximity for polyubiquitination by the E2 enzyme associated to the E3 ligase, which flags the POI for degradation through the proteasome.1-5

Partial PROTACs for Target Degradation

The design of small molecules for target degradation is not trivial since even slight alterations in ligands and crosslinkers can affect binding to the POI or E3 ligase or the formation of the ternary complex.3-5 Thus, many analogs are synthesized – varying each structure slightly – and screened in cells to discover the optimal PROTAC for target degradation. To streamline this synthesis, the Partial PROTACs are a collection of crosslinker-E3 ligase ligand conjugates with a pendant functional group for covalent linkage to a target ligand (Figure 2). Furthermore, because the same functional group is present across a series, one target ligand can be conjugated to several Partial PROTACs in parallel for facile library generation and subsequent screening (Figure 3).

Partial PROTACs are permutations of the following components:

  • Ligands targeting the E3 ligase Cereblon (CRBN) or von Hippel–Lindau (VHL)
  • Crosslinkers with varied lengths and compositions
  • Conjugation sites with reactivity for common functional groups

Primary components of PROTAC

Figure 2. Primary components of PROTAC

Advantages

  • Compatibility: Linkers conjugate to common functional groups present on target ligands.
  • Molecule design: Strategic variety encompassed in the combinations of linkers and ligands aids the design of target degraders.
  • Synthetic time-saver: The E3 ligand-crosslinker conjugates decrease the amount of time spent on PROTACs synthesis.
  • Library generation: Using Partial PROTACs with the same conjugation site enables the simultaneous generation of several PROTACs via parallel synthesis.
Partial PROTACs simplify the synthesis of PROTACs.
Use of a set of Partial PROTACs with the same conjugation site streamlines the synthesis of libraries.

Figure 3. PROTAC Synthesis and PROTAC Library Generation

 

Ligands for CRBN
 
Ligands for VHL
 

Partial PROTACs for CRBN
P=Pomalidomide
 

Partial PROTACs for VHL
A=(S,R,S)-AHPC
 

Figure 4. Abbreviated product structures

 

Materials

Catalog Number Products for CRBN Catalog Number Products for VHL
P0018 Pomalidomide 901490 (S,R,S)-AHPC hydrochloride
901494 N-Methylated Pomalidomide 901487 (S,S,S)-AHPC hydrochloride
901500 Pomalidomide-C3-CO2H 901518 (S,R,S)-AHPC-C3-CO2H
901496 Pomalidomide-C6-CO2H 901534 (S,R,S)-AHPC-C6-CO2H
901525 Pomalidomide-C9-CO2H 901535 (S,R,S)-AHPC-C9-CO2H
901527 Pomalidomide-PEG1-CO2H 901512 (S,R,S)-AHPC-PEG1-CO2H
901526 Pomalidomide-PEG2-CO2H 901491 (S,R,S)-AHPC-PEG2-CO2H
901504 Pomalidomide-PEG3-CO2H 901519 (S,R,S)-AHPC-PEG3-CO2H
901824 Pomalidomide-PEG4-CO2H 901856 (S,R,S)-AHPC-PEG4-CO2H
901828 Pomalidomide-PEG5-CO2H 901858 (S,R,S)-AHPC-PEG5-CO2H
901829 Pomalidomide-PEG6-CO2H 901859 (S,R,S)-AHPC-PEG6-CO2H
901516 Pomalidomide-PEG1-NH2 HCl 901493 (S,R,S)-AHPC-PEG1-NH2 HCl
901513 Pomalidomide-PEG2-NH2 HCl 901488 (S,R,S)-AHPC-PEG2-NH2 HCl
901495 Pomalidomide-PEG3-NH2 HCl 901511 (S,R,S)-AHPC-PEG3-NH2 HCl
901830 Pomalidomide-PEG4-NH2 HCl 901848 (S,R,S)-AHPC-PEG4-NH2 HCl
901831 Pomalidomide-PEG5-NH2 HCl 901850 (S,R,S)-AHPC-PEG5-NH2 HCl
901832 Pomalidomide-PEG6-NH2 HCl 901860 (S,R,S)-AHPC-PEG6-NH2 HCl
901523 Pomalidomide-PEG1-Alkyne 901503 (S,R,S)-AHPC-PEG1-Alkyne
901529 Pomalidomide-PEG2-Alkyne 901517 (S,R,S)-AHPC-PEG2-Alkyne
901531 Pomalidomide-PEG3-Alkyne 901533 (S,R,S)-AHPC-PEG3-Alkyne
901833 Pomalidomide-PEG4-Alkyne 901851 (S,R,S)-AHPC-PEG4-Alkyne
901834 Pomalidomide-PEG5-Alkyne 901855 (S,R,S)-AHPC-PEG5-Alkyne
901835 Pomalidomide-PEG6-Alkyne 901873 (S,R,S)-AHPC-PEG6-Alkyne
901558 Lenalidomide