Fig 1.
Computational chemogenomic analyses.
(A) Workflow diagram showing the computational steps and the number of drugs screened in each step. (B) Venn Diagram. Clusters generated by comparative analysis between therapeutic targets deriving from DrugBank (510 clusters comprising 1,402 orthologs) and Therapeutic Target (TTD) (192 clusters comprising 676 orthologs) databases and proteins deriving from Acinetobacter baumannii. (C) Therapeutic recommendation of 31 predicted drugs based on computational analysis.
Table 1.
Drugs predicted to act in Acinetobacter baumannii proteins and selected to be tested against strain ATCC 19606.
Table 2.
Tavaborole’s minimum inhibitory concentration (MIC, g/ml) against ATCC 19606 strain and 14 MDR Acinetobacter baumannii clinical isolates.
Fig 2.
Biofilm formation and tavaborole effect on mature biofilm of five Acinetobacter baumannii strains in polystyrene plates.
(A) Quantification of biofilm biomass formed after 48h incubation without the presence of the investigated drug determined through OD reading at 595 nm. Each symbol represents the mean of triplicates. (B) Percentage of OD reduction for biofilm biomass treated with 16 μg/ml tavaborole for 24h. (C) Metabolic activity reduction rate recorded for biofilm treated with 16 μg/ml tavaborole for 24h. The bars represent the mean and standard deviation of different experiments. Three independent experiments were performed.
Fig 3.
Leucyl-tRNA synthetase structural analysis and molecular docking.
(A) Predicted hot spots (yellow) in the AlphaFold structure. (B) Predicted hot spots (yellow) in the SWISS-MODEL structure. LeuRS’s CP1 and active site domains were highlighted in cyan and gray, respectively. (C) and (D) show the evolutionary conservation level of amino acids around the hot spots in the CP1 domain and in the active site, respectively. (E) Likely tavaborole-inhibition mechanism in LeuRS’s CP1 domain. The boron atom found in tavaborole triggers the attack on the 2’OH of the AMP ribose. Benzoxaborole, at the LeuRS CP1 domain, forms a covalent adduct with AMP by using its boron atom to bind with adenosine 2’ and 3’ oxygen atoms. The boron atom carries a negative charge within the tRNA-AN2690 adduct and achieves stabilization by interacting with a protonated water molecule. (F) and (G) represent tavaborole’s predicted binding modes in LeuRS’ CP1 domain and active site, respectively. Residues interacting with the ligand are shown in gray sticks, whereas the π-π stacking and hydrogen bonds are highlighted in green- and purple-dashed lines, respectively.
Table 3.
Best docking scores among the different LeuRS domains.