PROTAC R&D Service platform
PROTACs (Proteolysis Targeting Chimeras) are a novel chemical biology technology that uses bifunctional small molecules to bind target proteins and E3 ubiquitin ligases. This binding induces the target protein to be ubiquitylated and then degraded by the proteasome. PROTACs offer a fast and reversible chemical knock-down approach to control protein function. They have the potential to overcome most of the limitations of small molecule inhibitors and target the “undruggable” proteome.
PROTACs are heterobifunctional molecules that consist of three components:
A ligand of an E3 ubiquitin ligase
A ligand that targets the protein of interest (POI)
A linker connecting both moieties
GENERATING A CHEMICAL TOOLBOX TO SUPPORT PROTACs R&D
PROTACs: great opportunities for academia and industry
TARGETED PROTEIN DEGRADATION
PROteolysis TArgeting Chimeras (PROTACs) have become a promising and appealing technology for modulating a protein of interest (POI) by degradation. Targeted protein degradation is a novel strategy that uses small molecules to hijack endogenous proteolysis systems to degrade disease-relevant proteins. PROTACs have been proven to show better selectivity compared to classic inhibitors. PROTACs can be described as a chemical knockdown approach with rapidity and reversibility, which presents new and different biology compared to other gene-editing tools by avoiding misinterpretations that arise from potential genetic compensation and/or spontaneous mutations. PRTOACs have been widely explored throughout the world and have outperformed not only in cancer diseases, but also in immune disorders, viral infections and neurodegenerative diseases.
PROTACs are heterobifunctional molecules that connect a POI ligand containing a target-binding warhead on one end to an E3 ubiquitin ligase (E3) recruiting ligand with an optimal linker. Degradation is initiated when PROTACs promote the POI and E3 to form a ternary complex. After that, subsequent POI ubiquitination happened when the ubiquitination machinery is brought in close proximity and then the ubiquitinated POI was recognized and degraded by the 26S proteasome, which is part of the ubiquitinproteasome system (UPS) in eukaryotic cells. (Fig. 1)
Figure 1. Targeted protein degradation mechanism of action
COMPARISON OF MOLECULAR GLUES AND PROTACs
Although molecular glues and PROTACs are both bifunctional protein degraders, they have distinct mechanisms of action and structural features. Molecular glues are small molecular degraders that mainly induce or stabilize PPI between a E3 ligase and a target protein to form a ternary complex, leading to protein ubiquitination and subsequent proteasomal degradation. (Figure 2a) In contrast, PROTACs are heterobifunctional degraders with a warhead that binds to an E3 ligase, a ligand that binds to a target protein of interest, and a linker to connect the warhead and ligand. (Figure 2b)
Notably, molecular glues can also be used as warheads in PROTACs design.23 For example, thalidomide analogs have been widely used as ligands to the E3 ligase cereblon (CRBN) and have generated numerous potent protein degraders (e.g., dBET124 in Figure 2).9 The transformation of a molecular glue into a PROTACs warhead depends on its ligase binding mode and potency of the ligase.
Figure 2.Ligand–linker conjugates
Mode of action and structural features of molecular glue and PROTAC. (a) Molecular glue acts as a PPI inducer to enhance or induce interactions between E3 ligase and the target protein and thereby trigger ubiquitination and degradation. The structural characteristics of molecular glue are exemplified by pomalidomide. (b) PROTAC is a heterobifunctional compound containing an E3 ligase-binding warhead, a linker, and a ligand of a target protein. The structural characteristics of PROTAC are exemplified by BET degrader dBET1 with a CRBN E3 ligase binder (pomalidomide derivative, colored orange), an amide linker (colored purple) and a BET ligand (colored green).
LET US HELP YOU BUILD YOUR DEGRADER LIBRARY BASED ON WHAT IS MOST IMPORTANT TO YOU.
Reach out to your Innatura technical specialist for a sortable list or structure data file of all synthesis products, including ligand–linker conjugates, heterobifunctional linkers, ligands, and related probe compounds.
STREAMLINED SYNTHESIS OF HETEROBIFUNCTIONAL DEGRADER LIBRARIES
Our protein degrader building blocks are the easiest way to generate heterobifunctional degrader screening libraries from one starting target ligand to expedite degrader hit discovery. Within this building block collection that comprises all the components to construct degraders, our ligand–linker conjugates eliminate upfront synthetic steps, requiring only the chemistry to link a target ligand on the terminal functional group (Figure 3). Moreover, if the same terminal chemistry is selected, a chemist can simultaneously react various ligand–linker conjugates with one starting target ligand in parallel to generate an initial screening library.
DIVERSITY OF THE LIGAND-LINKER CONJUGATES
Our suite of ligand–linker conjugates contains strategic combinations of E3 ligands, exit vectors, linkers, and terminal chemistry.
E3 ligase recruiters and ligands: While more E3 ligases are being researched for targeted protein degradation, a handful are used most often in the development of protein degraders.7 Our conjugates include ligands and varied exit vectors for the validated E3 ligases CRBN, VHL, IAP, and RNF4 (Figure 4).
Linkers: Alkyl and PEG linkers are excellent starters to sample a range of hydrophobicity, flexibility, and lengths. In addition, we offer many “mixed”8 and rigid9–11 linkers to achieve diverse linker properties in your library (Figure 3).
Terminal chemistry: A variety of popular functional groups are available for linking the target warhead; our largest group includes terminal amines (Figure 3).
Synthetic time-saver: Ligand–linker conjugates simplify the synthesis of single degraders and parallel synthesis for library construction
Molecule design: Permutations of highest-interest E3 ligands, exit vectors, and linkers within the conjugates ease upfront combinatorial library design
Compatibility: Linkers conjugate to common functional groups present on target ligands
SAR: Strategic component variation built into the ligand–linker conjugates provides an upfront glimpse at SAR for informed optimization
Figure 4.E3 Ligase ligands featured in conjugates
Innatura chemical development team developed a process for the VHL1 and VHL2 and we can prepare at gram scale.
We can prepare various linkers (PEG linkers and C linkers) with varying linker sizes (3 to 6 for PEG linkers and 3 to 14 for C linkers and with different functional groups (NH2, COOH, Cl).