Comparative analysis of biophysical methods for monitoring protein proximity induction in the development of small molecule degraders.

BACKGROUND: Targeted protein degradation relies on inducing proximity between an E3 ubiquitin ligase and a target protein, and subsequent proteasomal degradation of the latter. Biophysical methods allow the measurement of the ternary complex formation by recombinant target and E3 ligase proteins in the presence of molecular glues and bifunctional degraders. The development of new chemotypes of degraders mediating ternary complex formation of unknown dimensions and geometries requires the use of different biophysical approaches. METHODS: The TR-FRET and AlphaLISA platforms have been applied to study molecular glues and bifunctional degraders. The performance of the label-based proximity assays was compared with the BLI method, which is a label-free, sensor-based approach. RESULTS: We present and compare two commonly used assays to monitor proximity induction, AlphaLISA and TR-FRET. The LinkScape system consisting of the CaptorBait peptide and the CaptorPrey protein is a novel method of protein labeling compatible with TR-FRET assay. CONCLUSIONS: The TR-FRET and AlphaLISA proximity assays enable detection of ternary complexes formed between an E3 Ligase, a target protein and a small molecule degrader. Experiments with different chemotypes of GSPT1 degraders showed that ALphaLISA was more susceptible to chemotype-dependent interference than TR-FRET assay. GENERAL SIGNIFICANCE: The discovery and optimization of small-molecule inducers of ternary complexes is greatly accelerated by using biophysical assays. The LinkScape-based TR-FRET assay is an alternative to antibody-based proximity assays due to the CaptorPrey's subnanomolar affinity to the CaptorBait-tagged protein target, and the 10-fold lower molecular weight of the CaptorPrey protein compared to the antibody.

A route to a cyclobutane-linked double-looped system via a helical macrocycle.

Macrocycles built of carbazole and pyridine fragments with alkene/alkane linkers constitute a helical structure as documented structurally and spectroscopically. The 'solid-state' prearrangement observed for two C[double bond, length as m-dash]C bonds leads to unprecedented transformation to a cyclobutane in a head-to-tail (rtct) geometry with two macrocyclic loops in a perpendicular orientation.

Recent advances in the synthesis of indolizines and their π-expanded analogues.

Indolizine (pyrrolo[1,2-a]pyridine) is one of the five isomers of indole and it serves as a precursor for widespread indolizidine alkaloids. The straightforward synthesis of indolizines based on classical methodologies such as Scholtz or Chichibabin reactions has overshadowed numerous new strategies that have been revealed especially within the last ten years. The desire to achieve substitution patterns which were hard to build sparked the discovery of completely new pathways, e.g. transition metal-catalyzed reactions and approaches based on oxidative coupling. In this review, selected strategies toward indolizines published since 2005 are briefly summarized, commented upon, compared, and illustrated. The literature discussed here involves reactions based on either pyridine or pyrrole scaffolds, as well as selected methodologies leading to π-expanded indolizines.

Reversible O-O bond cleavage and formation between Mn(IV)-peroxo and Mn(V)-oxo corroles.

Mn(IV)-peroxo and Mn(V)-oxo corroles were synthesized and characterized with various spectroscopic techniques. The intermediates were directly used in O-O bond cleavage and formation reactions. Upon addition of proton to the Mn(IV)-peroxo corrole, the formation of the Mn(V)-oxo corrole was observed. Interestingly, addition of base to the Mn(V)-oxo corrole afforded the formation of the Mn(IV)-peroxo corrole. Thus, we were able to report the first example of reversible O-O bond cleavage and formation reactions using in situ generated Mn(IV)-peroxo and Mn(V)-oxo corroles.

Unprecedented 1,3-dipolar cycloaddition: from 1,4,5,8-naphthalene bisimides to a new heterocyclic skeleton.

1,4,5,8-Naphthalene bisimides react as dipolarophiles with in situ formed azomethine ylides. Double 1,3-dipolar cycloaddition is followed by unique ring rearrangement and leads to the formation of two six-membered rings. The formation of hexacyclic products is rationalized based on DFT calculations.