Refined structure of the FKBP12–rapamycin–FRB ternary complex at 2.2 Å resolution

Abstract

The structure of the FKBP12-rapamycin-FRB ternary complex has now been refined at 2.2 A resolution. The cell-cycle arrest agent rapamycin binds FK506-binding protein (FKBP12) and the FKBP12-rapamycin binding (FRB) domain of FKBP12-rapamycin associated protein (FRAP) simultaneously, and the inhibition of FRAP is responsible for rapamycin's biological activity. The conformation of rapamycin in the ternary complex is very similar to that observed in the FKBP12-rapamycin binary complex, with an r.m.s. difference of only 0.30 A. However, a slight (9 degrees ) rotation repositions the FRB-binding face of rapamycin in the ternary complex. There are extensive rapamycin-protein interactions and relatively few interactions between the two protein partners FKBP12 and FRB, these interactions mainly involving residues in the 40s and 80s loops of FKBP12 and alpha1 and alpha4 of FRB. The high-resolution refinement has revealed the crucial role of several buried waters in the formation of the ternary complex.

Structure-Activity Analysis of Niclosamide Reveals Potential Role for Cytoplasmic pH in Control of Mammalian Target of Rapamycin Complex 1 (mTORC1) Signaling

“…mTORC1 is therefore regarded as an attractive target for cancer therapy, and there is currently a high level of interest in the development of pharmacological inhibitors of mTORC1. mTORC1 is inhibited allosterically by the natural product rapamycin (sirolimus), which interacts with the FKBP12-rapamycin-binding domain in mTOR in complex with FKBP12 (25,26). Rapamycin has been shown previously to abolish the binding of raptor to mTOR in phosphate-containing buffers (27,28).…”

Biochemical, Cellular, and In vivo Activity of Novel ATP-Competitive and Selective Inhibitors of the Mammalian Target of Rapamycin

“…The rapamycins (rapamycin and rapalogs) are allosteric inhibitors that, in complex with FKBP12, target the FRB domain adjacent to the catalytic site of mTOR (9,10). Intriguingly, both in vitro and in vivo studies showed that the FRB in mTORC2 is inaccessible to rapamycins as indicated by the lack of suppression of the mTORC2 substrate AKT (11,12).…”

Beyond Rapalog Therapy: Preclinical Pharmacology and Antitumor Activity of WYE-125132, an ATP-Competitive and Specific Inhibitor of mTORC1 and mTORC2

“…Clinically used rapamycins (rapamycin and rapalogs) partially inhibit mTOR through allosteric binding to the FKBP12-rapamycin binding domain adjacent to the catalytic site of mTORC1 (12,13). These compounds do not directly target mTORC2 and do not completely block all mTORC1 outputs.…”