Chaperone-like activity of α-cyclodextrin via hydrophobic nanocavity to protect native structure of ADH

Barzegar, Abolfazl; Moosavi-Movahedi, Ali Akbar; Mahnam, Karim; Ashtiani, Saman Hosseini

doi:10.1016/j.carres.2009.11.008

Cited by 14 publications

(13 citation statements)

References 31 publications

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“…Prediction from the molecular docking method reduces time while increasing accuracy and precision in chiral recognition since it allows a quick screening of a large database for a potential chiral selector or drugs that would otherwise require tedious work in the laboratory . Binding energy difference, chiral recognition mechanism resulting from CDs guest inclusion complex, geometry, and the interaction energy of the inclusion complex can be elucidated by computer simulation methods, in which case molecular docking enables the prediction of the strength of association or binding affinity between two molecules using scoring functions …”

Section: Resultsmentioning

confidence: 99%

Theoretical and Molecular Docking Study of Ketoconazole on Heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin as Chiral Selector

et al. 2015

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A molecular docking study, using molecular mechanics calculations with AutoDock and semi-empirical PM3 calculations, was used to predict the enantiodiscrimination of heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβCD) and ketoconazole (KTZ) enantiomers. A Density Functional Theory (DFT) single-point calculation at the level of B3LYP/6-311G (d,p) was performed for the PM3-optimized complexes to obtain more accurate binding energy and the electronic structures of the complexes. The difference in energies of the inclusion complexes between the KTZ enantiomers and TMβCD is probably a measure of chiral discrimination, which results in the separation of the enantiomers as observed in the experimental studies.

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Section: Resultsmentioning

confidence: 99%

Theoretical and Molecular Docking Study of Ketoconazole on Heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin as Chiral Selector

et al. 2015

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“…CDs are usually called chemical chaperones [15][16][17][18][19]. It is interesting to compare the chaperone-like activity of CDs and that of small heat shock proteins (sHsps).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, ␣-, ␤-and especially ␥-CD inhibit thermal aggregation of ␣-chymotrypsin [15]. The ability of ␣-CD to suppress thermal aggregation of horse liver alcohol dehydrogenase has been revealed [16,17]. The study of the influence of ␤-CD and various ␤-CD derivatives on protein aggregation at elevated temperature demonstrated that ␤-CD was able to inhibit aggregation of ␣-amylase [18], indole-␤-CD was found to be able to prevent aggregation of citrate synthase [19] and HP-␤-CD as well as methylated ␤-CD suppressed thermal aggregation of salmon polypeptide calcitonin [20].…”

Section: Introductionmentioning

confidence: 97%

Effect of 2-hydroxypropyl-β-cyclodextrin on thermal inactivation, denaturation and aggregation of glyceraldehyde-3-phosphate dehydrogenase from rabbit skeletal muscle

Maloletkina

Markossian

Asryants

et al. 2010

International Journal of Biological Macromolecules

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“…Molecular docking is an important tool in structural biology and computational drug design. It is commonly used to calculate the binding modes of ligands and drug candidates to their protein/nucleic acid targets to predict the affinity and activity of the small molecule drugs [28]. Consequently, there is a wide range of uses and applications for molecular docking, including drug discovery and affinity prediction [29].…”

Section: Molecular Dockingmentioning

confidence: 99%

Riboswitches as Potential Targets for Aminoglycosides Compared with rRNA Molecules: In Silico Study

Aghdam¹,

Hejazi²

2015

J Microb Biochem Technol

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Riboswitches are cis acting riboregulaters in non-coding region of the mRNAs. Their possible contribution in antibiotic targeting especially for FMN, TPP and lysine riboswitches in bacteria has been revealed since a decade ago. Regarding some studies on the possibility of the interaction between aminoglycosides and the artificial riboswitches, in this study we attempted to evaluate the binding potential of different types of aminoglycosides including gentamicin, amikacin, kanamycin, neomycin, tobramaycin, sisomicin and paromomycin with various classes of riboswitches using computational methods. Applying Auto Dock vina, it was shown that the binding energy of each kind of riboswitches with different types of aminoglycosides (riboswitches/aminoglycosides) is almost similar or sometimes more than the binding energy of the aminoglycoside with the corresponding binding cage of "16S rRNA A site" (16S rRNA A site/aminoglycosides) as aminoglycosides' target site. The affinity between riboswitches and aminoglycosides is almost the same or higher than the affinity of riboswitches/natural ligands. In this study ampicillin was used as the negative control antibiotic and 5S rRNA was employed as the negative control RNA. Results showed that the binding energies of riboswitches/ampicillin and 5S rRNA/aminoglycosides are usually lower than the energy of riboswitches/aminoglycosides. Accordingly, lysine, glycine and SAM-I riboswitches were recognized as the best RNA targets for all of the aminoglycosides because of their higher binding energy. In the next step, docking results were further validated by rDock program. Furthermore, it was shown that hydrogen binding makes a key role in the binding energy between aminoglycosides and riboswitches. Moreover, MD simulation studies on lysine riboswitch/paromomycin complex confirmed the stability of the docked structure in the solvent containing magnesium and chloride ions.

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Chaperone-like activity of α-cyclodextrin via hydrophobic nanocavity to protect native structure of ADH

Cited by 14 publications

References 31 publications

Theoretical and Molecular Docking Study of Ketoconazole on Heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin as Chiral Selector

Theoretical and Molecular Docking Study of Ketoconazole on Heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin as Chiral Selector

Effect of 2-hydroxypropyl-β-cyclodextrin on thermal inactivation, denaturation and aggregation of glyceraldehyde-3-phosphate dehydrogenase from rabbit skeletal muscle

Riboswitches as Potential Targets for Aminoglycosides Compared with rRNA Molecules: In Silico Study

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