Catalytic in vivo protein knockdown by small-molecule PROTACs

By changing ubiquitin ligase selectivity, these compounds redirect the ligase to carry out repeated rounds of target ubiquitination catalytically.

“By reprogramming ubiquitin ligase selectivity, these molecules divert the ligase to drive multiple rounds of target ubiquitination in a catalytic manner16.”

A single degrader molecule can degrade multiple protein molecules, a mechanism referred to as event-driven pharmacology, which may increase efficacy.

“A key promise of TPD is the prospect of increased efficacy due to a single degrader molecule being able to degrade multiple protein molecules, this unique mechanism of action is referred to as event-driven pharmacology (Bondeson et al., 2015).”

The discovery of small-molecule mimetics of the HIF1α peptide opened the door to the rational design of PROTACs based wholly on small molecular structures - for example, the first PROTACs based on the bromodomain protein inhibitor JQ1 that recruited VHL to degrade bromodomain-containing protein 4 (BRD4).

“The discovery of small-molecule mimetics of the HIF1α peptide20,21 opened the door to the rational design of PROTACs based wholly on small molecular structures — for example, the first PROTACs based on the bromodomain protein inhibitor JQ1 that recruited VHL to degrade bromodomain-containing protein 4 (BRD4)22,23.”

Incorporating a ligand into a PROTAC allows the POI to be degraded without requiring a large excess of drug, resulting in more complete target blockade and a wider therapeutic window.

“By incorporating the ligand into a PROTAC, which often acts in an iterative or ‘pseudo-catalytic’ fashion by binding and facilitating the interaction of its ligase and POI targets, the POI can be degraded without requiring a large excess of drug, thereby resulting in more complete target blockade and a wider therapeutic window22,48.”

Disruption of CRL4CRBN components and the associated cullin-RING ligase machinery results in resistance to lenalidomide in multiple myeloma and lymphoma cells.

“In genome-wide genetic screens of MM cells and lymphoma cells, disruption of CRL4CRBN components and the associated cullin-RING ligase machinery was found to result in resistance to lenalidomide143–145.”

VHL PROTACs targeting ERRα or RIPK2 achieved efficient degradation of both proteins at doses ranging from 3 nM (RIPK2) to 100 nM (ERRα).

“Using a warhead targeting either the estrogen-related receptor alpha (ERRα) [91] or the serine threonine kinase RIPK2, efficient degradation of both proteins could be achieved with doses ranging from 3 nM (RIPK2) to 100 nM (ERRα) [20].”

PROTACs with even moderate E3 ligase affinity have proven capable of directing efficient degradation.

“We address features of E3 ligase ligandability, but note that PROTACs with even moderate E3 ligase affinity have proven capable of directing efficient degradation 14 .”

PROTACs can achieve high cellular potency due to their catalytic rather than occupancy-based mechanism of action.

“PROTACs can achieve high cellular potency due to their catalytic rather than occupancy-based mechanism of action 11,14,22”

PROTACs do not need to bind potently to E3 ligases.

“PROTACS do not need to bind potently to E3 ligases”

A PROTAC recruiting VHL with a Kd of 320 nM affinity degrades RIPK2 with IC50 of 1 nM in cells.

“a PROTAC recruiting the E3 ligase VHL with a Kd of 320 nM affinity degrades its target RIPK2 with IC50 of 1 nM in cells) 14”