Conformational changes in Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase induced by designed inhibitors

The glycolytic enzymes of trypanosomes are attractive drug targets, since t he blood-stream form of Trypanosoma brucei lacks a functional citric acid c ycle and is dependent solely on glycolysis for its energy requirements. Gly ceraldehyde-3-phosphate dehydrogenases (GAPDH) from the pathogenic trypanos omatids T. brucei, Trypanosoma cruzi and Leishmania mexicana are quite simi lar to each other, and yet have sufficient structural differences compared to the human enzyme to enable the structure-based design of compounds that selectively inhibit all three trypanosomatid enzymes but not the human homo logue. Adenosine analogs with substitutions on N-6 of the adenine ring and on the 2 ' position of the ribose moiety were designed, synthesized and tested for inhibition. Two crystal structures of L. mexicana glyceraldehyde-3-phospha te dehydrogenase in complex with high-affinity inhibitors that also block p arasite growth were solved at a resolution of 2.6 Angstrom and 3.0 Angstrom . The complexes crystallized in the same crystal form, with one and a half tetramers in the crystallographic asymmetric unit. There is clear electron density for the inhibitor in all six copies of the binding site in each of the two structures. The L. mexicana GAPDH subunit exhibits substantial stru ctural plasticity upon binding the inhibitor. Movements of the protein back bone, in response to inhibitor binding, enlarge a cavity at the binding sit e to accommodate the inhibitor in a classic example of induced fit. The ext ensive hydrophobic interactions between the protein and the two substituent s on the adenine scaffold of the inhibitor provide a plausible explanation for the high affinity of these inhibitors for trypanosomatid GAPDHs. (C) 20 01 Academic Press.