Molecular docking and structural analysis of cofactor-protein interaction between NAD+ and 11β-hydroxysteroid dehydrogenase type 2

Yamaguchi, Hideaki; Akitaya, Tatsuo; Tang, Yu; Kidachi, Yumi; Kamiie, Katsuyoshi; Noshita, Toshiro; Umetsu, Hironori; Ryoyama, Kazuo

doi:10.1007/s00894-011-1140-2

Cited by 8 publications

(4 citation statements)

References 45 publications

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“…The structural superimposition of S. aureus IDH with both human IDH isoforms (PDB ID: 1T09, 1TOL) showed considerable variations in both domain and non domain regions and these differences were also observed in the sequence and active site structures (Figure 4) [12, 13]. The docking of isocitrate to both human and S. aureus IDH structures revealed higher affinity for human IDH compared to S. aureus [7, 8] correlating with enzyme kinetics [21, 23] Table 2 (Figure 5). This pathogen colonizes mostly in the nasopharyngeal tract as biofilms by adjusting its metabolic flux [1, 3, 22] and regulates TCA cycle to produce virulence factors thus spreads its infection.…”

Section: Discussionmentioning

confidence: 99%

Structural and Functional analysis of Staphylococcus aureus NADP-dependent IDH and its comparison with Bacterial and Human NADP-dependent IDH

et al. 2014

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Staphylococcus aureus a natural inhabitant of nasopharyngeal tract mainly survives as biofilms and possess complete Krebs cycle which plays major role in its pathogenesis. This TCA cycle is regulated by Isocitrate dehydrogenase (IDH) we have earlier cloned, sequenced (HM067707), expressed and characterized this enzyme from S. aureus ATCC12600. We have observed only one type of IDH in all the strains of S. aureus which dictates the flow of carbon thereby controlling the virulence and biofilm formation, this phenomenon is variable among bacteria. Therefore in the present study comparative structural and functional analysis of IDH was undertaken. As the crystal structure of S. aureus IDH was not available therefore using the deduced amino sequence of complete gene the 3D structure of IDH was built in Modeller 9v8. The PROCHECK and ProSAweb analysis showed the built structure was close to the crystal structure of Bacillus subtilis. This structure when superimposed with other bacterial IDH structures exhibited extensive structural variations as evidenced from the RMSD values correlating with extensive sequential variations. Only 24% sequence identity was observed with both human NADP dependent IDHs (PDB: 1T09 and 1T0L) and the structural comparative studies indicated extensive structural variations with an RMSD values of 14.284Å and 10.073Å respectively. Docking of isocitrate to both human IDHs and S. aureus IDH structures showed docking scores of -11.6169 and -10.973 respectively clearly indicating higher binding affinity of isocitrate to human IDH.

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Section: Discussionmentioning

confidence: 99%

Structural and Functional analysis of Staphylococcus aureus NADP-dependent IDH and its comparison with Bacterial and Human NADP-dependent IDH

et al. 2014

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“…Characterizing Molecules Suitable for a JAMDA Docking Study. Depending on the focus of the study, molecular docking is applied for different ligand types, including cofactors, 139 peptides, 140 nucleic acids, 141 and oligosaccharides. 142 However, molecular docking is most frequently used to screen small molecule libraries to find novel leads or to predict the binding mode of experimental screening hits for SAR analyses and hit advancement.…”

Section: Comparison Of Jamda To Other Docking Methodsmentioning

confidence: 99%

Redocking the PDB

Flachsenberg,

Ehrt,

Gutermuth

et al. 2023

J. Chem. Inf. Model.

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Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to predict the 3D structure of a small molecule in the binding site of a receptor (often a protein). Despite being a common technique, it often necessitates multiple tools and involves manual steps. Here, we present the JAMDA preprocessing and docking workflow that is easy to use and allows fully automated docking. We evaluate the JAMDA docking workflow on binding sites extracted from the complete PDB and derive key factors determining JAMDA's docking performance. With that, we try to remove most of the bias due to manual intervention and provide a realistic estimate of the redocking performance of our JAMDA preprocessing and docking workflow for any PDB structure. On this large PDBScan22 data set, our JAMDA workflow finds a pose with an RMSD of at most 2 Å to the crystal ligand on the top rank for 30.1% of the structures. When applying objective structure quality filters to the PDBScan22 data set, the success rate increases to 61.8%. Given the prepared structures from the JAMDA preprocessing pipeline, both JAMDA and the widely used AutoDock Vina perform comparably on this filtered data set (the PDBScan22-HQ data set).

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“…To prepare the ligand, ChemBioDraw Ultra was used to draw, write, and save the dimensional structure of rhein as a PDB format [ 271 ]. Docking experiments were carried out using the docking algorithms employed in MOE [ 272 ]. Site Finder module of MOE was used to dig for the active site within the macromolecule.…”

Section: Docking Experiments Investigating Plausible Natural Effector...mentioning

confidence: 99%

“…Site Finder module of MOE was used to dig for the active site within the macromolecule. Hydrophobic pockets were considered as the active sites [ 272 ]. The Triangle Matcher method was used to evaluate the docking of ligand molecules within the active sites the receptors [ 273 ].…”

Section: Docking Experiments Investigating Plausible Natural Effector...mentioning

confidence: 99%

Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches

Shanak

Bassalat

Barghash

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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The growing smooth talk in the field of natural compounds is due to the ancient and current interest in herbal medicine and their potentially positive effects on health. Dozens of antidiabetic natural compounds were reported and tested in vivo, in silico, and in vitro. The role of these natural compounds, their actions on the insulin signaling pathway, and the stimulation of the glucose transporter-4 (GLUT4) insulin-responsive translocation to the plasma membrane (PM) are all crucial in the treatment of diabetes and insulin resistance. In this review, we collected and summarized a group of available in vivo and in vitro studies which targeted isolated phytochemicals with possible antidiabetic activity. Moreover, the in silico docking of natural compounds with some of the insulin signaling cascade key proteins is also summarized based on the current literature. In this review, hundreds of recent studies on pure natural compounds that alleviate type II diabetes mellitus (type II DM) were revised. We focused on natural compounds that could potentially regulate blood glucose and stimulate GLUT4 translocation through the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. On attempt to point out potential new natural antidiabetic compounds, this review also focuses on natural ingredients that were shown to interact with proteins in the insulin signaling pathway in silico, regardless of their in vitro/in vivo antidiabetic activity. We invite interested researchers to test these compounds as potential novel type II DM drugs and explore their therapeutic mechanisms.

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Molecular docking and structural analysis of cofactor-protein interaction between NAD+ and 11β-hydroxysteroid dehydrogenase type 2

Cited by 8 publications

References 45 publications

Structural and Functional analysis of Staphylococcus aureus NADP-dependent IDH and its comparison with Bacterial and Human NADP-dependent IDH

Structural and Functional analysis of Staphylococcus aureus NADP-dependent IDH and its comparison with Bacterial and Human NADP-dependent IDH

Redocking the PDB

Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches

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