Biopolym. Cell. 2026; 42(Special Issue):118.
Other Translational Studies
Discovery of quinoline-type CRBN ligands and their application in the PROTAC development
1, 2Stadnichenko V. O., 1Beshtynarska A. O., 1Borysko P. O., 1Shyshlyk O. S., 2Tolstanova G. M.
  1. Enamine Ltd.
    78, Winston Churchill Str., Kyiv, Ukraine, 02094
  2. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01601

Abstract

Background/Aim. The application of CRBN ligands in degrader design represents one of the most prominent approaches during the development and optimization of PROTACs [1]. This work aims to investigate the efficiency of synthesized CRBN:BRD4 PROTACs with quinoline-type binders as warheads targeting the CRBN E3 ligase. Methods. To evaluate ligand and bifunctional degrader binding to the CRBN protein, a TR-FRET assay was used. The ternary complex formation between the protein of interest (POI), PROTAC, and the E3 ligase was assessed using the developed TCF TR-FRET method [2]. Results. The quinoline-type compounds were selected during virtual screening and tested for their ability to bind CRBN in vitro. The 3 potent molecules demonstrated IC50 values of 1.2 μM, 2.4 μM, and 3.5 μM in the TR-FRET displacement assay. The set of 9 PROTAC degraders based on quinoline-type CRBN ligands was synthesized by Enamine’s Chemistry Department. As a POI, the BRD4 enzyme was selected, and its wellknown binder, JQ-1, serves as the warhead for the degrader design. The synthesized PROTACs have been tested in the binary TR-FRET assay, in which competitive binding to the CRBN/DDB1 complex was observed with the tested samples at 1.11 μM (n = 4) and the Thalidomide-labeled probe. As a result, 2 out of 9 tested degraders bound the CRBN/DDB1 complex, with inhibition values >25% at the indicated concentration. Next, the 2 selected PROTACs were tested in dose-response for the ability to form a ternary complex between CRBN/DDB1 and BRD4 (BD1 domain) using the biochemical TCF TR-FRET assay. The known degrader dBET1 was used as an assay control. The EC50 values for the 2 tested PROTACs were below 35 nM. Notably, PROTAC 1a demonstrated EC50 and ECmax values lower than those of the reference compound dBET1: 14 nM vs 31 nM and 285 vs 370 nM, respectively. Conclusions. According to ternary complex formation analysis, the synthesized PROTAC 1a outperforms the glutarimide-based tool compound dBET1, suggesting that the quinoline moiety in the CRBN warhead represents a novel and potent approach for the PROTAC development.
Keywords: PROTAC, CRBN, ternary complex formation, dBET1