An evaluation of novel Cyanoacrylamides for use as covalent Kinase inhibitors in fragment-based drug discovery

Abstract

Kinase enzymes play an important role in many biological processes and their malfunction in the body can lead to diseases, such as cancer and muscular dystrophy. Covalent kinase inhibitors are a relatively new and exciting field of research in drug discovery due to advantages in selectivity, provided toxicity from off-targeting effects can be controlled. Our industrial partner (KeyOrganics) required a small but diverse fragment library of such molecules for fragment-based drug discovery (FBDD) applications. In this report, we present a versatile route to a wide variety of cyanoacrylamides for this purpose that is largely underrepresented in the literature; cyanoacrylamides have been shown to be reversible inhibitors and were of particular interest as a result.
To achieve this, cyano-acrylic acids were synthesised as precursors to the amide coupling step, and the ability to vary both the acids and the amines of this reaction sequence created a flexible method. 17 Fragments were made from 3 precursor acids using this approach, and the process was adapted and optimised over time using different coupling reagents and methods.
Due to the application of these fragments, testing was conducted by reacting the molecules with glutathione (in place of the reactive thiol residue present in kinase enzymes) to get relative comparisons of their binding affinities. This was monitored via 1H NMR, where the variation in size of the relevant integral on the inhibitor could be linked to reaction with glutathione. Most of the fragments tested binded to the thiol residue but in different extents, and the behaviour of the integral sizes over time was indicative of reversible inhibitors.
The binding affinities were compared by fitting the data to first order kinetics to yield a rate constant for the interaction. While the quality of fit was not good enough to give any quantitative data, it did allow for relative comparisons of inhibitors, and a trend could be seen in their performance based on estimated steric/inductive effects. However, the solvent used for this test likely interfered with the equilibrium (as seen in one case) by providing an oxidative environment, causing the glutathione to dimerise.

Date of Award	21 Jun 2019
Original language	English
Awarding Institution	University of Nottingham
Supervisor	Christopher Hayes (Supervisor)