PROTAC

Elements of PROTAC Design

(1) Selection of POI ligands
POI ligands are generally selected from listed or literature-reported inhibitors with certain activity, which can be divided into reversible inhibitors, covalent irreversible inhibitors and covalent reversible inhibitors according to whether the inhibitors can form covalent bonds. Depending on the binding pocket, they can be further classified into ATP-competitive inhibitors and metastable inhibitors. In order to obtain PROTAC with intellectual property, certain structural derivatization of the inhibitor is often done first, and the optimized inhibitor is used as a ligand for POI.

(2) Selection of E3 ligases and their ligands
The main E3 ligases reported in the literature for application to PROTAC are CRBN, VHL, cIAP and MDM2, among which the more effective and most frequently used are CRBN and VHL. Among them, the ligands of CRBN are mainly lenalidomide, pomalidomide and their analogues, and the ligands of VHL are mainly VHL-L.

(3) Selection of Linker
Alkyl, PEG, and extended glycol chains are by far the most common linker motifs appearing in published degrader structures. It has been reported in the literature that the length of the linker also affects the PROTAC degradation activity, and the commonly used linker lengths are generally in the range of 4-15 carbon atoms (or heteroatoms). Depending on the target site, the length of the linker has different effects on the degradation activity. In addition, Click chemistry is often applied among the linkers of PROTAC molecules for linking the two ends of the molecules due to milder reaction conditions and higher efficiency.

(4) Selection of linker sites and composition of linker sites
PROTAC is structurally linked to two ligands by a linker. in addition to the composition and length of the linker, the site of linker connection also affects the degradation activity and even the selectivity. the linking site of POI ligand and E3 ligase ligand is generally in the region where the ligand is exposed to the solvent. The linkage sites are generally linked by amide bonds, carbon atoms or heteroatoms (e.g. O, N, etc.), by condensation reactions or nucleophilic substitution reactions, etc. The role of junction design in PROTAC was recently described in an article published in J Med Chem by Michael D. Burkart et al.

PROTAC vs. Traditional Small-Molecule Drugs: Advantages

 

Wider range of action, higher activity, and the ability to target undruggable targets

Traditional small molecules and antibodies inhibit the function of target proteins through an "occupancy-driven" pharmacology model, which requires high concentrations of the inhibitor or monoclonal antibody to occupy the active site of the target and block downstream signaling pathways. In contrast, PROTAC is "event-driven", not affecting the function of the protein, but mediating the degradation of the disease-causing target protein. As long as PROTAC mediates the formation of the ternary complex and ubiquitinates target protein, it is theoretically recyclable and therefore can be used repeatedly in catalytic amounts.

 

Improved selectivity, activity and safety

Compared to traditional small molecule inhibitors, PROTAC can achieve selectivity at certain targets that is difficult to achieve with small molecules. For example, the multi-targeted tyrosine kinase inhibitor (TKI) Foretinib can bind more than 130 kinases. The results showed that compound 1 and compound 2 could only degrade 36 and 62 proteins, respectively, and only 12 were degraded by both.

PROTAC technology can not only achieve selectivity that is difficult to achieve with small molecule inhibitors, but also has very significant advantages in enhancing activity. Taking BET (BRD2/3/4), the earliest target applied by PROTAC technology, as an example, QCA570, discovered by Qin Chong et al, showed significantly better cellular anti-proliferative activity than inhibitors such as JQ1, whose activity was mostly at nanomolar level, while QCA570 increased its activity by three orders of magnitude, reaching an amazing picomolar level. Based on the excellent in vitro cellular anti-proliferative activity, the degraders also showed potent anti-tumor activity in vivo and exhibited low dose and low frequency of administration as well.

 

Overcome drug resistance

Small molecule inhibitors or antagonists are inevitably subject to acquired drug resistance during clinical use, such as EGFR-T790M and C797S resistance. Although resistance can be addressed by developing new generations of inhibitors, such as third- and fourth-generation EGFR, new resistance will emerge with the use of new generations of drugs.PROTAC technology has shown some advantages in overcoming drug resistance. Groups such as Crews, Jian Jin, Sanqi Zhang and Gray have related EGFR-PROTACs studies aiming to overcome drug resistance mutations through protein degradation pathways or find breakthrough inhibitors for protein degradation therapies. It can be seen that the first, second, third and fourth generation inhibitors have been applied to the design of PROTACs as ligands for binding the target protein EGFR. Among them, Gray's group has also applied metamorphic inhibitors to PROTAC with good results, selectively degrading different EGFR mutants while circumventing the degradation of wild type. This selectivity was further validated by in vitro anti-proliferative activity.

Major Trends In The Future Development Of Protac