Identification of an Inhibitor of the Aminoglycoside 6'- N-Acetyltransferase type Ib [AAC(6')-Ib] by Glide Molecular Docking

Abstract

The aminoglycoside 6'-N-acetyltransferase type Ib, AAC(6')-Ib, confers resistance to clinically relevant aminoglycosides and is the most widely distributed enzyme among AAC(6')-I-producing Gram-negative pathogens. An alternative to counter the action of this enzyme is the development of inhibitors. Glide is a computational strategy for rapidly docking ligands to protein sites and estimating their binding affinities. We docked a collection of 280,000 compounds from 7 sub-libraries of the Chembridge library as ligands to the aminoglycoside binding site of AAC(6')-Ib. We identified a compound, 1-[3-(2-aminoethyl)benzyl]-3-(piperidin-1-ylmethyl)pyrrolidin-3-ol (compound 1), that inhibited the acetylation of aminoglycosides in vitro with IC₅₀ values of 39.7 and 34.9 µM when the aminoglycoside substrates assayed were kanamycin A or amikacin, respectively. The growth of an amikacin-resistant Acinetobacter baumannii clinical strain was inhibited in the presence of a combination of amikacin and compound 1.

Fig. 1

Chemical structure of 1-[3-(2-aminoethyl)benzyl]-3-(piperidin-1-ylmethyl)pyrrolidin-3-ol (compound 1)

Fig. 2

Inhibition of AAC(6’)-Ib. A and B. The percentage of acetylating activity of kanamycin A (A) and amikacin (B) was calculated for reaction mixtures containing different concentrations of compound 1. C and D. Lineweaver-Burk plots obtained carrying out reactions containing variable concentrations of kanamycin A (C) or acetyl CoA (D). Insets are non linear fitting with the Michaelis-Menten function modified for mixed inhibition (C) or uncompetitive inhibition (D).

Fig. 3

Effect of compound 1 on resistance to amikacin. A. baumannii A155 cells were cultured in 100 µl Mueller-Hinton broth in microtiter plates at 37°C with the additions indicated in the figure, and the OD600 was periodically determined.