Discovery of fully synthetic FKBP12-mTOR molecular glues

02 July 2024, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Molecular glues are a class of drug modalities with the potential to engage otherwise undruggable targets. However, the rational discovery of molecular glues for desired targets is a major challenge and most known molecular glues have been discovered by serendipity. Here we present the first fully synthetic FKBP12-mTOR molecular glues, which were discovered from a FKBP-focused, target-unbiased ligand library. Our biochemical screening of >1000 in-house FKBP ligands yielded one hit that induced dimerization of FKBP12 and the FRB domain of mTOR. The crystal structure of the ternary complex revealed that the hit targeted a similar surface on FRB domain compared to natural product rapamycin but with a radically different interaction pattern. Structure-guided optimization improved potency 500-fold and led to compounds, which initiate FKBP12-FRB complex formation in cells. Our results show that molecular glues targeting flat surfaces can be discovered by focused screening and support the use of FKBP12 as a versatile presenter protein for molecular glues.

Keywords

Molecular Glue
FKBP12
Rapamycin
ternary complex
proximity-based pharmacology

Supplementary materials

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Table of Contents 2 Compound synthesis 4 Competitive fluorescence polarisation assays for binding to FKBP target proteins 24 Fluorescence polarization assay for the determination of the binding affinity towards FKBP12 24 Crystal structure data 25 HTRF-assay optimization 26 In-house FKBP focused library 27 HTRF response of compound 6 27 Native MS measurements of compound 10k and rapamycin 28 WRX606 measured in our assays 29 NMR spectra 30 HPLC traces 50 References 59 References 59
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