title: DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg²⁺ and Ca²⁺ ions.
abstract: 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+)(H2O)6, ΔH = -72.21 kcal mol(-1); for Rho B-Ca(2+)(H2O)6, ΔH = -72.53 kcal mol(-1); for Rho A-Mg(2+)(H2O)6, ΔH = -72.99 kcal mol(-1) and for Rho B-Mg(2+)(H2O)6, ΔH = -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.
authors.affiliation: Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Unidad Universitaria, Km 4.5 Carretera Pachuca-Tulancingo, 42184, Pachuca, Hidalgo, Mexico.
authors.forename: Christiaan
authors.initials: C
authors.lastname: Jardínez
authors.forename: Ines
authors.initials: I
authors.lastname: Nicolás-Vázquez
authors.forename: Julian
authors.initials: J
authors.lastname: Cruz-Borbolla
authors.forename: Cesar A
authors.initials: CA
authors.lastname: González-Ramírez
authors.forename: Miguel
authors.initials: M
authors.lastname: Cepeda
authors.forename: Jose
authors.initials: J
authors.lastname: Correa-Basurto
authors.forename: Thangarasu
authors.initials: T
authors.lastname: Pandiyan
authors.forename: Rene
authors.initials: R
authors.lastname: Miranda
mesh_terms: D002118:Calcium / Q000737:chemistry; D002413:Cations, Divalent / Q000737:chemistry*; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D011789:Quantum Theory; D013237:Stereoisomerism; D013307:Streptomycin / Q000031:analogs & derivatives* / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D002413:Cations, Divalent; C000588683:rhodostreptomycin A; D008274:Magnesium; D002118:Calcium; D013307:Streptomycin
references.citation: Protein Sci. 2005 Jun;14(6):1429-37
references.pmid: 15883187
references.citation: Phys Rev B Condens Matter. 1988 Jan 15;37(2):785-789
references.pmid: 9944570
references.citation: Int J Antimicrob Agents. 2010 Jun;35(6):566-72
references.pmid: 20227248
references.citation: J Phys Chem A. 2008 Sep 18;112(37):8542-50
references.pmid: 18729438
references.citation: Biochem Biophys Res Commun. 2003 Oct 3;309(4):879-84
references.pmid: 13679055
references.citation: Phys Rev A Gen Phys. 1988 Sep 15;38(6):3098-3100
references.pmid: 9900728
references.citation: Biochem J. 2012 Mar 1;442(2):443-51
references.pmid: 22115123
references.citation: Curr Opin Microbiol. 1998 Jun;1(3):319-29
references.pmid: 10066498
references.citation: Biochemistry. 2006 Nov 28;45(47):14064-74
references.pmid: 17115701
references.citation: Chem Biol. 1998 Jan;5(1):49-57
references.pmid: 9479479
references.citation: Curr Opin Plant Biol. 1999 Oct;2(5):398-403
references.pmid: 10508758
references.citation: Chem Rev. 2005 Aug;105(8):2999-3093
references.pmid: 16092826
references.citation: J Pediatr. 1976 Sep;89(3):479-82
references.pmid: 956979
references.citation: J Am Chem Soc. 2008 Jan 30;130(4):1126-7
references.pmid: 18179219
references.citation: Insect Biochem Mol Biol. 1999 Jun;29(6):481-514
references.pmid: 10406089
references.citation: J Comput Aided Mol Des. 2011 May;25(5):477-89
references.pmid: 21597992
references.citation: Phys Chem Chem Phys. 2012 Jan 14;14(2):823-34
references.pmid: 22120200
references.citation: J Surg Res. 1990 Jul;49(1):23-9
references.pmid: 2359290
references.citation: Drug Discov Today. 2003 Mar 15;8(6):239-40
references.pmid: 12623231
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: J Chem Theory Comput. 2010 Mar 12;6(4):1048-1063
references.pmid: 20419068
references.citation: Cancer. 2010 Feb 1;116(3):544-73
references.pmid: 19998273
references.citation: Eur J Pharm Biopharm. 2004 Sep;58(2):185-96
references.pmid: 15296948
references.citation: Drug Discov Today. 2002 Nov 15;7(22):1109-10
references.pmid: 12546845
references.citation: J Chem Phys. 2012 Sep 28;137(12):124502
references.pmid: 23020338
references.citation: J Phys Chem B. 2011 Jun 30;115(25):8304-16
references.pmid: 21650197
references.citation: J Phys Chem B. 2008 Aug 21;112(33):10158-64
references.pmid: 18651765
references.citation: Prev Vet Med. 2000 Dec 8;47(4):255-62
references.pmid: 11087956
references.citation: Adv Drug Deliv Rev. 2006 Oct 31;58(9-10):1009-29
references.pmid: 17005293
references.citation: Bioorg Med Chem Lett. 2006 Aug 1;16(15):3966-70
references.pmid: 16730172
references.citation: Biochim Biophys Acta. 1984 Sep 28;801(2):232-43
references.pmid: 6383483