Professor of Structural Biochemistry
Malcolm Walkinshaw obtained his PhD in physical chemistry at Edinburgh University. After post-doc positions in Purdue and Gottingen he joined the Swiss company Sandoz (now Novartis) where he built and led the ‘Drug Discovery Group’ which made important contributions to understanding the mode of action of immunosuppressive drugs like cyclosporin. He was appointed to the Chair of Structural Biochemistry at the University of Edinburgh in 1995 and in 2007, with funding from the Wellcome Trust and BBSRC, he founded the Centre for Translational and Chemical Biology which continues to provide world class facilities for protein production. He has a broad interest in molecular aspects of drug-protein interactions. One major research theme has been around the enzymes of the glycolytic pathway as potential anti-infective drug targets. This work has led to the development of potent nanomolar inhibitors that kill trypanosomal parasites quickly and can cure mice infected with Tryprypanosoma brucei, the parasite that causes sleeping sickness.
Molecular recognition and ligand discovery in biological systems
The three-dimensional structure of proteins provides a useful starting point for the design of small molecule ligands that can be used to modulate signalling and metabolic pathways in the cell. We use a variety of biophysical and computational techniques to measure and visualise ligand-protein binding Recent research on the cyclophilin family of proteins shows that they play a central role in an ever expanding number of diseases. There are over 17 different human cyclophilin isoforms that are implicated in a range of conditions including sepsis, viral infection, ischemia and protein-folding pathologies like Parkinson and Alzheimer. A collaboration with Julien Michel has resulted in the design of a promising series of patented compounds (De Simone et al., 2019) that show excellent specificity for inhibiting the mitochondrial form of cyclophilin that regulates the Permeable Transition Pore.
For many metabolic pathways small molecule allosteric effector molecules along with post-translational modifications provide the principal mechanisms for modulating signal or flux. We have studied the allosteric regulatory mechanisms of key enzymes of the glycolytic pathway of trypanosome parasites and used ‘structure-based’ approaches to develop small molecule allosteric inhibitor molecules. This has resulted in the development of a family of patented molecules that selectively inhibit phosphofructokinase of Trypanosoma brucei (tbPFK), the causative agent of sleeping sickness. These compounds block glycolysis and kill parasites within minutes and provide an effective in vivo cure for sleeping sickness in a mouse model. Related kinetoplastid parasite species including Leishmania spp. and Trypanosoma cruzi, (the causative agent of Chagas’ disease) share a similar distinct cellular structure with organelles called glycosomes that contain most of the enzymes in the glycolytic pathway. The three parasites also share similar life cycles involving transmission by insect vectors to mammalian host. However, the last common ancestor of these three parasites is estimated to be about 600 MYA and they have evolved to adapt to different biological niches: in the mammalian host T. brucei is extracellular and lives in blood, T. cruzi is mainly intracellular in the cytosol and Leishmania inhabit the phagolysosmes in macrophages. Regulation of the glycolytic pathway has evolved separately to allow each organism to cope with their very different nutritional environments. Comparing the activities and structures of the key regulatory enzymes in the glycolytic pathway we have shown that in Leishmania, AMP acts as a sensitive allosteric switch to activate glycolysis and at the same time inhibits the reverse gluconeogenesis pathway (Figure 1) thus carefully regulating glucose in a nutrient poor environment(Yuan et al., 2017) (Fernandes et al., 2019). In contrast T. brucei has no need to make use of the gluconeogenic pathway in its already glucose rich environment and T. brucei PFK is constitutively active keeping the forward glycolytic activity permanently ‘on’. We are mapping out the different regulatory allosteric mechanisms of the glycolytic enzymes in these three medically important parasites (in particular PFK, fructosebisphosphatase and pyruvate kinase) and using the structural and biochemical information to design families of inhibitors as a potential new drug class.
De Simone, A., Georgiou, C., Ioannidis, H., Gupta, A.A., Juarez-Jimenez, J., Doughty-Shenton, D., Blackburn, E.A., Wear, M.A., Richards, J.P., Barlow, P.N., et al. (2019). A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors. Chemical science 10, 542-547.
Fernandes, P.M., Kinkead, J., McNae, I.W., Vasquez-Valdivieso, M., Wear, M.A., Michels, P.A.M., and Walkinshaw, M.D. (2019). Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis. The FEBS journal.
Yuan, M., Vasquez-Valdivieso, M.G., McNae, I.W., Michels, P.A.M., Fothergill-Gilmore, L.A., and 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, 3075-3089.
Leishmania occupies a glucose deprived environment within macrophages and uses AMP as an energy sensor to switch metabolic activity between gluconeogenesis and glycolysis.