DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg and Ca ions

The interactions of L-aminoglucosidic stereoisomers such as rhodostreptomycins A (Rho A) and B (Rho B) with cations (Mg, Ca, and H) were studied by a quantum mechanical method that utilized DFT with B3LYP/6-311G**. Docking studies were also carried out in order to explore the surface recognition properties of L-aminoglucoside with respect to Mg and Ca ions under solvated and nonsolvated conditions. Although both of the stereoisomers possess similar physicochemical/antibiotic properties against Helicobacter pylori, the thermochemical values for these complexes showed that its high affinity for Mg cations caused the hydration of Rho B. According to the results of the calculations, for Rho A-Ca(HO), ΔH = -72.21 kcal mol; for Rho B-Ca(H O), ΔH = -72.53 kcal mol; for Rho A-Mg(HO), ΔH = -72.99 kcal mol and for Rho B-Mg(HO), ΔH = -95.00 kcal mol, confirming that Rho B binds most strongly with hydrated Mg, considering the energy associated with this binding process. This result suggests that Rho B forms a more stable complex than its isomer does with magnesium ion. Docking results show that both of these rhodostreptomycin molecules bind to solvated Ca or Mg through hydrogen bonding. Finally, Rho B is more stable than Rho A when protonation occurs. © 2013 Springer-Verlag Berlin Heidelberg.