Roth, Hans-Joerg, Stein, Richard and Fouche, Marianne (2023) Estimating intrinsic cooperativities and concentrations of ternary complexes in biochemical or cellular environments from binary dissociation constants, apparent cooperativities and total or free ligand concentrations. RSC Chemical Biology themed collection – Molecular Glues.

Abstract

There is an increasing interest to modulate difficult-to-tackle but disease-relevant target proteins by involving them with a chaperone protein into a compound-mediated ternary complex. In general, ternary complex-forming compounds can be classified by their direct affinity to chaperone and target protein and their degree of cooperativity which they exhibit upon ternary complex formation. As a trend, the smaller ternary complex-forming compounds are the stronger is the contribution of the intrinsic cooperativity to their thermodynamic stability relative to direct target (or chaperone) binding. This highlights the importance of the cooperativity as a desirable feature for the optimization of ternary complex-forming compounds – even more so as it provides higher and easier to achieve selectivity to target isoforms and allows the assessment of target occupancy via estimated concentrations of ternary complexes.
All of this emphasizes the need to quantify the natural constant of intrinsic cooperativity α which is defined as the gain (or loss) in affinity of a compound to its target in pre-bound vs. unbound state. In this publication, a workflow involving a mathematical model is presented that requires the input of the two relevant binary Kds and the two protein concentrations of target and chaperone for estimating the intrinsic cooperativity from experimentally observed apparent cooperativities. Intrinsic cooperativities are in the simplest version assessable through EC50 shifts in binary binding curve(s) of the ternary complex-forming compound with either target or chaperone relative to the same experiment but in the presence of also the counter protein.
This approach is then extended from closed systems (like biochemical assays) to the open system of a cellular assay by accounting for differences in total ligand vs. free ligand concentrations, which then allows calculating ternary complexes concentrations. Finally, this model is used to translate biochemical potency of ternary complex-forming compounds into expected cellular target occupancy, which could ultimately serve as way for validation or de-validation of hypothesized biological mechanisms of action.

Item Type:	Article
Keywords:	Ternary complexes, Chaperone, Intrinsic cooperativity, Apparent cooperativity
Date Deposited:	01 Sep 2023 00:45
Last Modified:	01 Sep 2023 00:45
URI:	https://oak.novartis.com/id/eprint/48654