Structural and inhibition study of phosphoserine phosphatase (SerB2) from Mycobacterium tuberculosis

PhD thesis defended by Marie HAUFROID (Prof. Johan WOUTERS) - 25/03/2022



Prof. Johan WOUTERS, UNamur, Department of chemistry, Laboratory of structural biological chemistry (CBS) 

  • Prof. Steve LANNERS (département de chimie, UNamur), président
  • Prof. Johan WOUTERS (département de chimie, UNamur), secrétaire
  • Prof. Xavier DE BOLLE (département de biologie, UNamur)
  • Prof. Paulette CHARLIER (cristallographie des macromolécules biologies, ULiège)
  • Dr Marie LEDECQ (UCB Pharma)

The World Health Organisation still counts tuberculosis as one of the leading causes of death in the world and the leading cause of death caused by a treatable pathogen. Many efforts are being made by research laboratories to try to discover new therapeutic targets and drugs to finally put an end to this epidemic affecting the most disadvantaged areas of our globe. In this context, the serine pathway and in particular the phosphoserine phosphatase MtSerB2 have been identified as a promising therapeutic target. MtSerB2 has acquired the ability to dephosphorylate proteins necessary for the survival of macrophages, an immune cell required to fight infection. 

In order to understand and inhibit MtSerB2, mechanistic research was carried out on this enzyme and its human homologue by protein crystallography, docking and molecular dynamics. Key residues enabling the catalytic reaction of MtSerB2 and those involved in the dephosphorylation of essential macrophage proteins will be highlighted. This mechanistic information is of significant help in the search for and development of inhibitors of the enzyme.

Subsequently, two classical drug design approaches were used to find hits for MtSerB2 inhibition. The first approach is a classical screening approach of a chemical library of compounds on the targeted enzyme via the malachite green enzymatic assay. It led to the discovery of 4 good MtSerB2 inhibitors that also had an effect on Mycobacterium tuberculosis. The second approach is a fragment-based approach, as fragments have more easily modulated pharmacokinetic properties. Techniques such as ligand-based NMR, DSF and high concentration enzyme assays were performed to measure the affinity of fragments from a virtual screen. Docking and co-crystal analyses of the enzyme with these fragments allowed the development of a pharmacophore model. Finally, some fragments with little affinity for the enzyme of interest could nevertheless be crystallised within an oligomerisation site of the enzyme. These results could pave the way for the development of disruptors of the oligomerisation state of MtSerB2.