Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2″)-Ia

Abstract

The APH(2″)-Ia aminoglycoside resistance enzyme forms the C-terminal domain of the bifunctional AAC(6')-Ie/APH(2″)-Ia enzyme and confers high-level resistance to natural 4,6-disubstituted aminoglycosides. In addition, reports have suggested that the enzyme can phosphorylate 4,5-disubstituted compounds and aminoglycosides with substitutions at the N1 position. Previously determined structures of the enzyme with bound aminoglycosides have not indicated how these noncanonical substrates may bind and be modified by the enzyme. We carried out crystallographic studies to directly observe the interactions of these compounds with the aminoglycoside binding site and to probe the means by which these noncanonical substrates interact with the enzyme. We find that APH(2″)-Ia maintains a preferred mode of binding aminoglycosides by using the conserved neamine rings when possible, with flexibility that allows it to accommodate additional rings. However, if this binding mode is made impossible because of additional substitutions to the standard 4,5- or 4,6-disubstituted aminoglycoside architecture, as in lividomycin A or the N1-substituted aminoglycosides, it is still possible for these aminoglycosides to bind to the antibiotic binding site by using alternate binding modes, which explains the low rates of noncanonical phosphorylation activities seen in enzyme assays. Furthermore, structural studies of a clinically observed arbekacin-resistant mutant of APH(2″)-Ia revealed an altered aminoglycoside binding site that can stabilize an alternative binding mode for N1-substituted aminoglycosides. This mutation may alter and expand the aminoglycoside resistance spectrum of the wild-type enzyme in response to newly developed aminoglycosides.

Spectral, XRD, morphological, DFT, and molecular modeling investigations of newly prepared isatin Schiff base complexes

“…Docked compounds had higher docking affinity to the binding region of aminoglycoside phosphotransferase 1 which is comparable to that of the native ligand, Amikacin, as shown in Figure 10a, b. Amikacin was hydrogen bonded to active residues: GLU411, GLU451, ASP374, and ASP396 (binding score −8 Kcal mol −1 ) 47 in addition to ionic interactions with GLU451, ASP374, and ASP396. Ligand docked to the binding residues through three hydrogen bonds between the isatin‐NH and carboxylic OH and GLU451 in addition to an extra hydrogen bond between isatin carbonyl moiety and ASN 373 with docking score (−8.4 Kcal mol −1 ).…”

Structural basis for plazomicin antibiotic action and resistance

“…Other AMEs may be able to accommodate one or both of the synthetic extensions of plazomicin, but this is invariably accompanied by a dramatic reduction in enzyme efficiency. For example, APH(2′′)-Ia has been shown to accept aminoglycosides containing the HABA tail, but this coincides with a compromised ability to phosphorylate these antibiotics 30 .…”

Molecular Docking Studies and Microbial Activities of Mono-, Di- and Tri-Substituted Simple Coumarins

“…The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank was used to provide three-dimensional crystal structures of these target proteins [28]. For use in docking calculations, structures with PDB IDs of XCS [29] for DNA gyrase, 6CGD [30] for Aminoglycoside Phosphotransferase (2'')-Ia, 5TZ1 [31] for sterol 14-alpha demethylase and 4P20 [32] for bacterial ribosomal decoding site were chosen as crystal structure models corresponding to these target proteins. The structure defects in the PDB protein models determined for the docking calculations were corrected with the "Structure Preparation" module of the MOE software according to the default parameters.…”