The affinity of the excised binding domain of FK-506 for the immunophilin FKBP12

Opportunities and Challenges of Small Molecule Induced Targeted Protein Degradation

Proteolysis targeting chimeras (PROTAC) represents a new type of small molecule induced protein degradation technology that has emerged in recent years. PROTAC uses bifunctional small molecules to induce ubiquitination of target proteins and utilizes intracellular proteasomes for chemical knockdown. It complements the gene editing and RNA interference for protein knockdown. Compared with small molecule inhibitors, PROTAC has shown great advantages in overcoming tumor resistance, affecting the non-enzymatic function of target proteins, degrading undruggable targets, and providing new rapid and reversible chemical knockout tools. At the same time, its challenges and problems also need to be resolved as a fast-developing newchemical biology technology.

Evaluation of synthetic FK506 analogues as ligands for the FK506-binding proteins 51 and 52

The FK506-binding proteins (FKBP) 51 and 52 are cochaperones that modulate the signal transduction of steroid hormone receptors. Both proteins have been implicated in prostate cancer. Furthermore, single nucleotide polymorphisms in the gene encoding FKBP51 have been associated with a variety of psychiatric disorders. Rapamycin and FK506 are two macrocyclic natural products that bind to these proteins indiscriminately but with nanomolar affinity. We here report the cocrystal structure of FKBP51 with a simplified α-ketoamide analogue derived from FK506 and the first structure-activity relationship analysis for FKBP51 and FKBP52 based on this compound. In particular, the tert-pentyl group of this ligand was systematically replaced by a cyclohexyl ring system, which more closely resembles the pyranose ring in the high-affinity ligands rapamycin and FK506. The interaction with FKBPs was found to be surprisingly tolerant to the stereochemistry of the attached cyclohexyl substituents. The molecular basis for this tolerance was elucidated by X-ray cocrystallography.

Design and synthesis of a rapamycin-based high affinity binding FKBP12 ligand

BACKGROUND

The immunosuppressants rapamycin, ascomycin, FK506, and cyclosporin act by binding to a class of cytosolic proteins, the immunophilins. In the case of FK506, ascomycin and cyclosporin, the target of the immunophilin-immunosuppressant complex is calcineurin; in the case of rapamycin, the target is FRAP (TOR/RAFT1). Rapamycin, ascomycin and FK506 have a common domain responsible for binding to FKBP12, their cellular receptor, and different effector domains that determine the target of the complex. Both domains are necessary for signal transduction and biological activity.

RESULTS

A hybrid molecule containing the rapamycin-FK506-ascomycin binding domain and a peptide tether has been designed, synthesized and biologically evaluated. The designed compound binds to FKBP12 with high affinity but has no biological activity, as expected from its lack of an effector domain.

CONCLUSIONS

The designed rapamycin-based FKBP12 ligand exhibits powerful binding properties but, unlike rapamycin, shows no activity in IL-6 dependent B-cell proliferation and, in contrast to FK506, shows no activity in the IL-2 reporter assay. The modular nature of this designed molecule should make it possible to generate a series of compounds with effector domains for targeting either calcineurin or FRAP (TOR/RAFT1) or both, as potential biological tools and immunosuppressive agents.