PROTAC-mediated protein degradation is UPS-dependent, and the formation of the POI-PROTAC-E3 ternary complex is a prerequisite for the successful degradation of the target protein. Currently, the "bell" model is commonly used to describe the formation of ternary complexes. The hook effect often mentioned in the literature can also be explained by this model, i.e., the formation of POI-PROTAC and E3-PROTAC binary complexes is preferred at higher concentrations of PROTAC, which affects the formation of ternary complexes, so the degradation activity of PROTAC is not strictly concentration-dependent, and the degradation activity decreases at higher concentrations.
The formation of ternary complexes is not strictly positively correlated with the affinity of PROTAC, as it is also affected by PPI (protein-protein interaction). The synergistic effect is often used to describe the effect of the interaction between POI and E3 on the stability of the ternary complex.
In 2017, the crystal structure of the first ternary complex BRD4-MZ1-VHL was resolved for the first time by Ciulli's group, which reveals the interaction between BRD4 and VHL as well as between the linker of PROTAC and BRD4. Furthermore, the positive synergistic effect of PPI was investigated using a variety of biophysical approaches, and it was found that this positive synergistic effect was responsible for PROTAC's ability to promote selective and efficient degradation of BRD family proteins.
Design of PROTAC
PROTAC has acquired a lot of attention because of its inherent advantages and mechanism of action. The key priority for new drug research is to build and identify efficient PROTAC through an efficient assessment mechanism. Despite the fact that PROTAC has been extensively investigated and that several targets are involved, the conformational links are still unclear. From the structural characteristics of PROTAC, the main considerations for its design are as follows.
POI ligands are often inhibitors with specific activity that are available on the market or have been documented in the literature. Reversible inhibitors, covalent irreversible inhibitors, and covalent reversible inhibitors all can establish a covalent link. It can be classified as an ATP competitive inhibitor or an allosteric inhibitor based on the distinct binding pockets.
* Selection of E3 ligases and their ligands
The main E3 ligases reported in the literature for use in PROTAC are CRBN, VHL, cIAP, and MDM2, with CRBN and VHL being the most efficacious and widely employed. Among them, the ligands of CRBN are mainly lenalidomide, pomalidomide and their analogues, and the ligands of VHL are mainly VHL-L.
* Linker selection
Linker can be characterized as an alkyl chain or a PEG chain depending on its composition, and there is also literature that uses a more rigid alkynyl bipiperidine ring, a spiro ring with a nitrogen atom, or a bridge ring as linker to limit the flexibility and freedom of the PROTAC molecule. The length of the linker has been shown to alter the degrading activity of PROTAC in the literature, and the most widely employed lengths are in the range of 4 to 15 carbon atoms (or heteroatoms). The has varying effects on the degrading activity depending on the target site.
* Selection and composition of connection sites
In addition to the linker composition and length, the location of the linker connection has an influence on degrading activity and even selectivity. The POI ligand and E3 ligase ligand are usually connected in the area where the ligand is exposed to the solvent. The connection site is usually connected by an amide bond, a carbon atom, or a heteroatom (O, N, or others), and the connection is achieved via a condensation process or a nucleophilic substitution reaction. Michael D. Burkart et al. just published an article in J Med Chem detailing how joint design plays a role in PROTAC.
PROTAC, a breakthrough technology, has undergone 20 years of development, particularly in the last five years, and has emerged as a new avenue for drug research and development. The range of tasks that may be achieved with this technology is extensive, the market is enormous, and the future looks bright.
