Design, Synthesis and Testing of New Classes of Phosphatase Inhibitor Using Novel Computational Methods

Abstract

The regulation of phosphorylation levels within cells, by the opposing actions of phosphatase and kinase enzymes, is a process of huge therapeutic potential and is well established by the dozens of FDA-approved small molecule kinase inhibitors. In contrast to this, and despite the fact that they have been implicated in numerous diseases, there is yet to be a single approved protein tyrosine phosphatase (PTP) inhibitor. The nature of the PTP active site, being shallow, highly conserved and “designed” for the binding of phosphate-containing substrates, means that early PTP inhibitors suffered from poor selectivity, poor cell permeability and limited oral bioavailability. As a result, phosphatases were widely dismissed as “undruggable” targets. This work explores the use of computational approaches to both build a model for the prediction of PTP inhibitor binding affinities and to design a small series of PTP inhibitors with a novel scaffold. Chapter 2 applied the computational “theoceptor” methodology to PTP1B, a widely studied human PTP implicated in diabetes, for the prediction of PTP1B inhibitor binding affinities. First, the methodology, which combines quantum mechanically computed ligand binding energy with ligand LogP, predicted the disputed protonation state of residues in the PTP active site and the PTP ligand. Following this, a full theoceptor model of PTP1B was constructed utilising a training set of 18 inhibitors, achieving an RSE of 0.59 and R2 of 0.65. This model has application in both future inhibitor design and screening. Chapter 3 applied the virtual screening tool VSPipe to MptpA, a PTP and virulence factor secreted by the Mycobacterium tuberculosis. Targeting MptpA may offer a new method of treatment for TB which overcomes the urgent issue of antibacterial resistance. Following the virtual screen and subsequent rounds of compound design, synthesis and testing for the improvement of potency and aqueous solubility, a small series of novel compounds was shown to bind to, and inhibit, MptpA. The most potent of the series inhibits MptpA in the low micromolar range (IC50 7.7 µM). Substantial efforts were also made to obtain a structure of the MptpA-inhibitor complex, through X-ray crystallisation and computational methods (docking and “theoceptor” methodology).

Date of Award	10 Dec 2025
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Andrew Leach (Main Supervisor), Sam Butterworth (Co Supervisor) & Lydia Tabernero (Co Supervisor)