Drug discovery and molecular recognition in biological systems
Organisms from bacteria to mammals have a remarkably well conserved glycolytic (and gluconeogenic) pathways that use the same ten enzymatic steps to convert glucose to pyruvate. Though the active sites have been conserved throughout 2 billion years of evolution, there is an interesting divergence in allosteric regulatory mechanisms. We have studied the enzymatic mechanisms of allosteric enzymes from mammals, trypanosomatid parasites and pathogenic bacteria including Mycobacterium tuberculosis.
By trapping the enzymes in different conformational states it is possible to show how small molecule effector molecules including amino acids, AMP and ADP can enhance or inhibit enzyme activities. For example, the enzyme FBPase from the Leishmania parasite can be regulated by a simple feedback mechanism with increasing concentration of AMP (1) that traps the tetramer in an inactive twisted form (Figure A). Pyruvate kinase from Mycobacterium tuberculosis can act like a logical ‘OR-gate’ (3) in which two metabolites (AMP and glucose-6-P) bind to different allosteric pockets and synergistically activate the tetramer (Figure B). More sophisticated still is the regulation of the M2 isoform of human pyruvate kinase (M2PYK) where we have shown that selected amino acids (Ala, Phe, Trp) and reactive oxidation species (ROS) are potent inhibitors while other metabolites and amino acids (His and Ser) are activators. M2PYK interprets these multiple input signals that display the nutritional and stress state of the cell providing an appropriate output response to rebalance cellular metabolism (Figure C). This competition at a single allosteric site between activators and inhibitors provides a novel regulatory mechanism by which M2PYK activity is finely tuned by the relative (but not absolute) concentrations of activator and inhibitor amino acids which we call ‘allostatic regulation’.
Apart from the basic biochemical, structural and evolutionary insights gained from these studies, the allosteric binding pockets all provide excellent targets for species-specific inhibitors. We have already identified Tb phosphofructokinase inhibitors that cure mouse models of African Trypanosomiasis. High throughput screens of bacterial targets have allowed us to identify a series of hit compounds currently being modified in collaboration with the European Lead Factory. The link between cancer and glycolysis and more recently as a regulator of immune response make glycolytic enzymes interesting and relatively unexplored therapeutic targets. We are currently screening human PFK isoforms for new families of allosteric inhibitors as anticancer therapeutics.
Yuan, M., Vasquez-Valdivieso, M.G, McNae, I.W., Michels, P.A.M., Fothergill-Gilmore, L.A., Walkinshaw, M.D. (2017). Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition. Journal of molecular biology. 429:3075-89.
Georgiou, C., McNae, I., Wear, M., Ioannidis, H., Michel, J., Walkinshaw, M. (2017). Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders. Journal of molecular biology. 429:2556-70.
Zhong, W., Cui, L., Goh, B.C., Cai, Q., Ho, P., Chionh, Y.H., et al. (2017). Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis. Nature communications. 8:1986