Design and Evaluation of PROTACs Targeting Acyl Protein Thioesterase 1

PROTAC linker design remains mostly an empirical task. We employed the PRosettaC computational software in the design of sulfonyl‐fluoride‐based PROTACs targeting acyl protein thioesterase 1 (APT1). The software efficiently generated ternary complex models from empirically‐designed PROTACs and suggested alkyl linkers to be the preferred type of linker to target APT1. Western blotting analysis revealed efficient degradation of APT1 and activity‐based protein profiling showed remarkable selectivity of an alkyl linker‐based PROTAC amongst serine hydrolases. Collectively, our data suggests that combining PRosettaC and chemoproteomics can effectively assist in triaging PROTACs for synthesis and providing early data on their potency and selectivity. PROTAC linker design remains mostly an empirical task. The PRosettaC software successfully generated ternary complex models for empirically designed sulfonyl‐fluoride‐based PROTACs targeting Acyl Protein Thioesterase 1 (APT1). Western blotting analysis and activity‐based protein profiling (ABPP) revealed efficient degradation of APT1 with selected alkyl linker‐based PROTACs showing remarkable selectivity for APT1 within serine hydrolases.