Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays

Abstract

The rapid spread on multi-drug resistant strains of Staphylococcus aureus requires not just novel treatment options, but the development of faster methods for the identification of new hits for drug development. The exponentially increasing speed of computational methods makes a more extensive use in the early stages of drug discovery attractive if sufficient accuracy can be achieved. Computational target identification using systems-level methods suggested the histidine biosynthesis pathway as an attractive target against S. aureus. Potential inhibitors for the pathway were identified through docking, followed by ensemble rescoring that is sufficiently accurate to justify immediate testing of the identified compounds by whole cell assays, avoiding the need for time-consuming and often difficult intermediary enzyme assays. This novel strategy is demonstrated for three key enzymes of the S. aureus histidine biosynthesis pathway, which is predicted to be essential for bacterial biomass productions. Virtual screening of a library of ~10 6 compounds identified 49 potential inhibitors of three enzymes of this pathway. 18 representative compounds were directly tested on three S. aureus-and two E. coli strains in standard disc inhibition assays. 13 compounds are inhibitors of some or all of the S. aureus strains, while 14 compounds weakly inhibit growth in one or both E. coli strains. The high hit rate obtained from a fast virtual screen demonstrates the applicability of this novel strategy to the histidine biosynthesis pathway.

Charting a Path to Success in Virtual Screening

“…For ensemble dockings, multiple receptor conformations can be selected from experimental structures [ 141 ] or generated through computational methods such as molecular dynamics simulations [ 142 ], or normal mode analysis [ 143 ]. Ensemble docking has been reported to improve the overall success rate in virtual screenings [ 9 , 141 , 144 , 145 , 146 ], although requirements of computation time and power can increase considerably, scaling linearly with the number of target structures considered. Massive virtual screening campaigns, involving large conformational ensembles of flexible proteins, have been made possible with the support from IBM and the computer time donated by volunteers participating to the World Community Grid initiative [ 147 ].…”

Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities

“…S5b ), thereby suggesting a specific, albeit weak inhibitory property of MES. Previously suggested carboxylate derivatives as inhibitors against Staphylococcus aureus HspAT 27 targeted only the phosphate binding residues of PLP and Hsp. We report the first inhibitor which specifically interacts with the hydroxyl group of Tyr127, a residue which is involved in amino-group recognition of Hsp.…”

Homology Modeling and Virtual Screening to Discover Potent Inhibitors Targeting the Imidazole Glycerophosphate Dehydratase Protein in Staphylococcus xylosus

“…However, the 3D structure of IGPD protein of S. xylosus has not been solved yet. Generally, it has been implemented that a protein sequence with 30% identity to a known structure is considered to be a threshold limit for the accuracy of homology modeling (Xiang, 2006 ; Henriksen et al, 2010 ). Recently, the 3D crystal structures of IGPD protein from S. aureus (Henriksen et al, 2010 ), Arabidopsis thaliana ( A. thaliana ) (Bisson et al, 2015 ), Cryptococcus neoformans ( C. neoformans ) (Chaudhuri et al, 2001 ) have been solved and are available in the protein databank, which provide us an opportunity to construct the 3D structure of IGPD of S. xylosus .…”