DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg2+ and Ca2+ ions
The interactions of L -aminoglucosidic stereoisomers such as rhodostreptomycins A (Rho A) and B (Rho B) with cations (Mg 2+ , Ca 2+ , 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 rec...
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Published in | Journal of molecular modeling Vol. 19; no. 11; pp. 4823 - 4836 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Berlin/Heidelberg
Springer Berlin Heidelberg
01.11.2013
|
Subjects | |
Online Access | Get full text |
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Summary: | The interactions of
L
-aminoglucosidic stereoisomers such as rhodostreptomycins A (Rho A) and B (Rho B) with cations (Mg
2+
, Ca
2+
, 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
2+
and Ca
2+
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
2+
cations caused the hydration of Rho B. According to the results of the calculations, for Rho A–Ca
2+
(H
2
O)
6
, Δ
H
= −72.21 kcal mol
−1
; for Rho B–Ca
2+
(H
2
O)
6
, Δ
H
= −72.53 kcal mol
−1
; for Rho A–Mg
2+
(H
2
O)
6
, Δ
H
= −72.99 kcal mol
−1
and for Rho B–Mg
2+
(H
2
O)
6
, Δ
H
= −95.00 kcal mol
−1
, confirming that Rho B binds most strongly with hydrated Mg
2+
, 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
2+
or Mg
2+
through hydrogen bonding. Finally, Rho B is more stable than Rho A when protonation occurs.
Figure
Rho B–H showed higher stability since it is considered a proton pump inhibitor, and is therefore a stronger inhibitor of Helicobacter pylori |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1610-2940 0948-5023 |
DOI: | 10.1007/s00894-013-1952-3 |