Acinetobacter baumannii FolD ligand complexes – potent inhibitors of folate metabolism and a re‐evaluation of the structure of LY374571

Abstract

The bifunctional N5,N10‐methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram‐negative pathogen Acinetobacter baumanni and determined high‐resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed. Database The coordinates have been deposited in the Protein Data Bank under accession numbers: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4B4U, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4B4V and http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4B4W. Structured digital abstract AbFolD and AbFolD bind by x-ray crystallography ( View interaction)

Characterization of 2,4-Diamino-6-oxo-1,6-dihydropyrimidin-5-yl Ureido Based Inhibitors of Trypanosoma brucei FolD and Testing for Antiparasitic Activity

“…The amino acids that form the cofactor-binding site and interact with the cofactor are highly conserved. 9 We previously noted in different crystal structures of bacterial FolD that the conformation of a loop adjacent to the active site, the β8-α10 loop, was variable. The loop occludes the active site in the structure of the Pseudomonas aeruginosa FolD ( Pa FolD).…”

“…This structural assignment is in agreement with data reported by Eadsforth et al dealing with the crystallographic analysis of an Acinetobacter baumanii FolD ligand complex. 9 …”

“…We initiated an inhibitor discovery program targeting the T. brucei enzyme ( Tb FolD) and selected as a lead compound LY374571 (compound 1 ) developed by Eli Lilly and Company because it inhibits bacterial and human FolD. 9 However, following the protocol reported for the synthesis of 1 , we obtained a new compound whose structure has been unambiguously determined as 2 ( Figure 2 ). We judge it likely that the original report refers to compound 2 not 1 .…”

One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

“…8C, overexpression of FolA from a multicopy-number plasmid led to only partial growth rescue). Therefore, we propose that inclusion of inhibitors that target FolD (42,43) along with TMP treatment could make for effective antibacterials.…”

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

“…The PDB is ah ugely valuabler esource for biochemical and medicinal chemistry research but unfortunately,s eriouse rrors in ligand-protein complexes are not uncommon. [8] For our own part, we previously identifiedt he incorrect structure of the potent antifolate anda nticancer agent assigned as LY374571, [19] and showedt hat structures of the fatty acid binding site of the human peroxisome proliferator-activated receptors-b/d are not occupiedb yl ipid-lowering synthetic agents but ratherb ye ndogenousl igands derived from the bacterial expression system. [20] In respect of the glutaminase domain of CTP synthetase from T. brucei,t hen our inspection identified deficiencies in the crystallographic model.T hese have been corrected andf uture effortst oo btain novel lead compounds might progress with an accurate template of the binding site occupied by an inhibitor and an anion now available.…”