Fig 1.
Schr¨odinger’s CovDock workflow for covalent docking, adapted from Schr¨odinger’s documentation (release 2020–1).
Fig 2.
Clustered heatmaps of relative docking scores for each docked compound against TEM β-lactamase structures harboring mutations in active site residue alanine 237.
Black indicates that the docking algorithm could not find poses that bind in realistic conformations to the target due to overwhelmingly unfavorable interactions that lead to nonphysical energies, such as steric clashes introduced by the aromatic substitutions. Docking scores are normalized with respect to the wild type docking score of each compound.
Fig 3.
Clustered heatmaps of relative docking scores for each drug class against TEM β-lactamase structures harboring mutations in active site residue alanine 237.
Black indicates that no favorable poses were found, suggesting that the ligand was unable to bind. Docking scores are normalized with respect to the wild-type docking score.
Fig 4.
Comparison between changes in fitness upon treatment with either ampicillin (left) or cefixime (right) for E. coli carrying mutations in TEM’s codon 237 and the relative docking scores of each compound bound to each mutant structure.
Results are tabulated in S4 Table.
Fig 5.
Visual inspection of the intermolecular interactions with key active site residue 237 for ampicillin covalently bound to (a) TEM-1 and (b) TEM-Ala237Arg, and of cefixime covalently bound to (c) TEM-1 and (d) TEM-Ala237Arg.
Yellow dotted lines indicate hydrogen interactions, orange dotted lines indicate poor contacts/clashes, purple dotted lines indicate salt bridges, and green dotted lines indicate cation-pi interactions.
Fig 6.
Binding pose metadynamics results for complexes with ampicillin (left) and cefixime (right).
In addition to the ligand RMSD, for each set of simulations, we also report a measurement of the stability of the network of hydrogen bonds in the pre-simulation pose, called the PersScore, and the ligand RMSD for the final frame of the simulation in regards to the initial pose, called the PoseScore. All data shown are averaged over ten replicates. The shading denotes the standard deviation of the RMSD values for each system.
Fig 7.
Interaction analysis between the ligand and the active site residues of complexes with TEM-1 (left) and TEM-Ala237Arg (right).
Data are averaged from ten replicates of MD simulations. Ampicillin possesses a smaller number of pi interactions than cefixime because cefixime is more aromatic. In addition, pi interactions must fall into a very small range of angles to be considered present, and thus are more likely to be absent when the ligand binding mode is unstable. The shading denotes the standard deviation of the number of interactions for each system.
Fig 8.
Analysis of the number of interactions between ampicillin or cefixime and Arg237 of TEM-Ala237Arg complexes.
Data are averaged from ten replicates of MD simulations. The shading denotes the standard deviation of the number of interactions for each system.
Fig 9.
Aligned two-dimensional structural representations of the cephalosporins cefixime and ceftibuten, and of the monobactam carumonam.
The negatively charged R-groups that are stabilized by the Arg237 mutation are highlighted in fuchsia.
Fig 10.
Visual inspection of the intermolecular interactions with key active site residue 237 for ceftibuten covalently bound to (a) TEM-1 and (b) TEM-Ala237Arg, and for carumonam covalently-bound to (c) TEM-1 and (d) TEM-Ala237Arg.
Yellow dotted lines indicate hydrogen interactions, orange dotted lines indicate poor contacts/clashes, purple dotted lines indicate salt bridges, and green dotted lines indicate cation-pi interactions.
Fig 11.
Visual inspection of the intermolecular interactions with Lys237 for ligands covalently bound to TEM-Ala237Lys.
(a) Ampicillin, (b) Cefixime, (c) Ceftibuten, and (d) Carumonam. Yellow dotted lines indicate hydrogen interactions, orange dotted lines indicate poor contacts/clashes, purple dotted lines indicate salt bridges, and green dotted lines indicate cation-pi interactions.
Table 1.
Relative docking scores (RDS) and relative fitness values (when applicable) for TEM-Ala237Arg/Lys in complex with ampicillin (A), cefixime (C), ceftibuten (Cet), and carumonam (Car).