Development of Small Molecule Chimeras That Recruit AhR E3 Ligase to Target Proteins

Abstract

Targeted protein degradation using chimeric small molecules such as proteolysis-targeting chimeras (PROTACs) and specific and nongenetic inhibitors of apoptosis protein [IAP]-dependent protein erasers (SNIPERs) is an emerging modality in drug discovery. Here, we expand the repertoire of E3 ligases capable of ubiquitylating target proteins using this system. By incorporating β-naphthoflavone (β-NF) as a ligand, we developed a novel class of chimeric molecules that recruit the arylhydrocarbon receptor (AhR) E3 ligase complex. β-NF-ATRA, a chimeric degrader directed against cellular retinoic acid binding proteins (CRABPs), induced the AhR-dependent degradation of CRABP-1 and CRABP-2 via the ubiquitin-proteasome pathway. A similar compound ITE-ATRA, in which an alternative AhR ligand was used, also degraded CRABP proteins. Finally, we developed a chimeric compound β-NF-JQ1 that is directed against bromodomain-containing (BRD) proteins using β-NF as an AhR ligand. β-NF-JQ1 induced the interaction of AhR and BRD proteins and displayed effective anticancer activity that correlated with protein knockdown activity. These results demonstrate a novel class of chimeric degrader molecules based on the ability to bring a target protein and an AhR E3 ligase into close proximity.

Targeted Protein Degradation by Chimeric Compounds using Hydrophobic E3 Ligands and Adamantane Moiety

“…Interestingly, the 1-induced significant reduction of CRABP-2, but not of CRABP-1, was also observed in SH-SY5Y cells, which do not express AhR ( Figure S1 and S2). Similar results were also obtained by the treatment of the ITE-ATRA [16], in which an alternative AhR ligand was used ( Figure S3). The ligand-bound AhR forms a CUL4B-based E3 ligase complex [17].…”

“…We previously developed the chimeric compound β-NF-JQ1 that is directed against bromodomain-containing (BRD) proteins using β-NF or (+)-JQ1 as an AhR or BRD ligand, respectively. β-NF-JQ1 induced the AhR-dependent degradation of BRD proteins in MCF-7 cells expressing AhR [16]. However, the β-NF-JQ1-induced reduction of BRD3, but not of BRD2 or BRD4, was also observed in SH-SY5Y cells, which do not express AhR ( Figure S7), suggesting that BRD3 is also degraded by the AhR-independent mechanism.…”

“…Ad-JQ1(16) induces the degradation of BRD3 but not of BRD2 or BRD4. Protein knockdown activities of Ad-JQ1 in MCF-7 cells.…”

“…Recently, we developed a new class of small molecule chimeras that recruit the aryl hydrocarbon receptor (AhR) E3 ligase and induce the AhR-dependent degradation of target proteins [16]. β-NF-ATRA, 1 (Figure 1), a chimeric compound directed against cellular retinoic acid-binding proteins (CRABPs), induced the AhR-dependent degradation of CRABP-1 and CRABP-2 in MCF-7 and IMR-32 cells expressing AhR [16]. Interestingly, the 1-induced significant reduction of CRABP-2, but not of CRABP-1, was also observed in SH-SY5Y cells, which do not express AhR ( Figure S1 and S2).…”

PROTACs: great opportunities for academia and industry

“…65 Degraders recruiting IAP were named specific and nongenetic IAP-dependent protein erasers (SNIPERs). [66][67][68][69][70][71][72][73][74][75][76] Later, von Hippel-Lindau ligands used for PROTAC design were identified by the Ciulli laboratory. [77][78][79] Concurrently, it was found that the E3 cereblon (CRBN) was the molecular target of the immunomodulatory drugs (IMiDs), such as thalidomide, pomalidomide, and lenalidomide.…”