An Improved Model of the Trypanosoma brucei CTP Synthetase Glutaminase Domain–Acivicin Complex

Abstract

The natural product acivicin inhibits the glutaminase activity of cytidine triphosphate (CTP) synthetase and is a potent lead compound for drug discovery in the area of neglected tropical diseases, specifically trypanosomaisis. A 2.1‐Å‐resolution crystal structure of the acivicin adduct with the glutaminase domain from Trypanosoma brucei CTP synthetase has been deposited in the RCSB Protein Data Bank (PDB) and provides a template for structure‐based approaches to design new inhibitors. However, our assessment of that data identified deficiencies in the model. We now report an improved and corrected inhibitor structure with changes to the chirality at one position, the orientation and covalent structure of the isoxazoline moiety, and the location of a chloride ion in an oxyanion binding site that is exploited during catalysis. The model is now in agreement with established chemical principles and allows an accurate description of molecular recognition of the ligand and the mode of binding in a potentially valuable drug target.

Structural basis for isoform-specific inhibition of human CTPS1

“…Existing inhibitors of CTPS are primarily metabolite analogs, which can produce a variety of undesirable off-target effects. Acivin, a naturally occurring glutamine analog that nonspecifically inhibits most glutaminases, inhibits CTPS through irreversible covalent modification of the glutaminase domain active site ( 39 – 41 ). However, acivicin failed as a cancer treatment in phase-II clinical trials, owing to significant neurological toxicity ( 4 , 5 ).…”

Covalent inhibitors of GAPDH: From unspecific warheads to selective compounds

“…The mechanism of action was elucidated in chrystallographic studies using Acivicin co-crystallyzed with the glutaminase domain of T. brucei CTP synthetase. 212 Acivicin undergoes nucleophilic attack from the catalytic Cys residue leading to the formation of a tetrahedral oxyanion, with a sp 3 -hybridized C3, followed by the release of chloride and restoration of the sp 2 C3. Interestingly, the corresponding synthetic brominated analogue was shown to be more active than Acivicin, when tested against T. brucei CTP synthetase 213 due to the better leaving group properties of bromine.…”

Glutamine Analogues Impair Cell Proliferation, the Intracellular Cycle and Metacyclogenesis in Trypanosoma cruzi

“…ACV is an inhibitor of not only Gln-dependent enzymes but also enzymes with aldehyde dehydrogenase activity [45]. When studied in trypanosomatids, this Gln analogue was found to act as an inhibitor of CTPs in T. brucei, and was thus proposed as a compound useful for guiding the synthesis of new anti-T. brucei drugs [46]. Additionally, for T. brucei, ACV was described as an inhibitor of GMP synthase, another enzyme that utilizes Gln as an amide donor [47].…”