Structural insight into the glucokinase-ligands interactions. Molecular docking study

Ермакова, Елена

doi:10.1016/j.compbiolchem.2016.08.001

Cited by 15 publications

(5 citation statements)

References 38 publications

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“…Pharmaceutical Sciences (Indexed in ISI and Scopus) https://ps.tbzmed.ac.ir/ hundred independent runs with the grid box 126×126×126 Å (grid spacing=0.375Å) was performed to evaluate the binding energy and other results of the inhibitors within the macromolecules. 38,39 Results and discussion…”

Section: Molecular Dockingmentioning

confidence: 99%

In vitro and In silico studies on the anticancer and antimicrobial activity of Cu(II), Ni(II) and Co(II) complexes with bis (pyrazolyl) borate derivative ligand

Ghorbanpour¹,

Soltani²,

Molavi³

et al. 2022

Pharm Sci

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A bidentate N-donor pyrazole-based ligand abbreviated as K[H2B(PzMe2)2] and corresponding complexes with Cu(II), Ni(II) and Co(II) were synthesized and characterized, where PzMe2=3,5-dimethylpyrazole. The synthesized ligand and complexes were evaluated for anticancer activities against (MDA-MB-231) human breast cell line. Their Antibacterial activity against gram-positive and gram-negative bacteria was investigated. Also, their molecular docking with YmaH (PDB ID: 3HSB), ecKAS III (PDB ID: 1HNJ) protein and DNA dodecamer (PDB ID: 1BNA) as the possible targets was performed. In silico molecular docking along with the experimental MTT assay and antibacterial studies, indicated the metal complexes are more bioactive than free uncoordinated ligand and can be excellent candidates for further evaluations in the biological area.

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Section: Molecular Dockingmentioning

confidence: 99%

In vitro and In silico studies on the anticancer and antimicrobial activity of Cu(II), Ni(II) and Co(II) complexes with bis (pyrazolyl) borate derivative ligand

Ghorbanpour¹,

Soltani²,

Molavi³

et al. 2022

Pharm Sci

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“…Diabetes is related to the inactivation of GK, while hypoglycemia is linked to an increase in GK operation. The possibility of controlling GK activity with small chemical compounds acting as allosteric activators has piqued scientists' interest in studying the process of new allosteric GK activators are being developed [16] . The first phase in the complicated mechanism that regulates GK function is the interaction of GK with ligands.…”

Section: Selection Of Protein Data Bank (Pdb) Id-1va5mentioning

confidence: 99%

Novel In Silico and In Vivo Insights of Flavonoids as Anti-Diabetic and Anti-Oxidant in Rodent Models

Mudunuri¹,

Gandamalla²,

Vanukuru³

2022

IJPS

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Mudunuri et al.: Flavonoids as Antidiabetic and AntioxidantInsulin sensitivity is a symptom of diabetes, which is caused by insulin resistance, decreasing insulin production and ultimately pancreatic cancer. The current study is focused on the anti-diabetic and antioxidant properties of Chrysanthemum indicum flower extract and to scientifically validate the claim by in silico docking studies of natural compounds present in the extract for their respective sites against selected proteins. Pharmacological evaluations were done using 200 and 400 mg/kg body weight of the extract. Upon treatment with methanolic extract of Chrysanthemum indicum at 200 mg/kg body weight, 400 mg/ kg body weight and glibenclamide 0.5 mg/kg body weight, significant reduction in blood glucose levels was observed. The extract was screened against reducing power assay and hydrogen peroxide scavenging assay for its anti-oxidant potential and the results were compared with the standard ascorbic acid. In both assays, the findings clearly demonstrated the extract's ability to scavenge free radicals. Docking studies were performed for natural compounds present in the extract such as epigallactocatechin, quercetin, kaempferol, apigenin, myrcetin, rutin, luteolin and standard drug glibenclamide against protein data bank ID: 1VA5, protein data bank ID: 1Z2C, protein data bank ID: 5WUA using Mcule software. The statistical verification of the model was evaluated with PROCHEK; a structure verification program relies on Ramachandran plot which determines the quality of the predicted structures. The results revealed that epigallactocatechin and rutin had shown highest glide scores which indicates a stronger receptor-ligand binding affinity among the various phytochemical constituents present in the extract and this might be the possible mechanism by which the extract showed antidiabetic and antioxidant activities. From the above, it is concluded that the extract possess anti-diabetic and anti-oxidant activity.

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“…where ∆G vdw , ∆G hbond and ∆G elec are the typical molecular mechanics energy terms for van der Waals, hydrogen bonding, and electrostatics interactions, respectively [26]. While ∆G tor characterizes the loss of torsional entropy upon binding and ∆G sol displays the desolvation upon the ligand binding and corresponding hydrophobic effect [27].…”

Section: Molecular Dockingmentioning

confidence: 99%

Insights into Binding Affinity of Flavonoid Compounds from Thai Herbs against 2009 H1N1 Hemagglutinin

2022

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Outbreak of influenza virus is one of serious concerns for public health. Hemagglutinin (HA), a spike-shaped glycoprotein on the viral surface, plays an important role during the early stage of influenza infection. In the present work, a set of flavonoids were screened against 2009 H1N1 HA by computational chemistry techniques. Among 35 flavonoids, the docking results showed that the epicatechin gallate (ECG) and puerarin exhibited a good binding affinity towards 2009 H1N1 HA. These 2 compounds were then studied by all-atom molecular dynamics (MD) simulations. The predicted binding free energy of the H1-puerarin complex (–25.86 ± 2.92 kcal/mol) was slightly greater than that of H1-ECG (–22.81 ± 2.19 kcal/mol), suggesting that the puerarin and ECG could provide similar binding affinity towards 2009 H1 HA target. However, the stronger electrostatic energy contribution of ~10 kcal/mol was found in the puerarin binding to 2009 H1N1 HA. This molecular information of ligand-protein interaction could be helpful in further drug design and development for influenza treatment. HIGHLIGHTS The 35 flavonoid bioactive compounds were screened against 2009 H1N1 HA by molecular docking The epicatechin gallate (ECG) and puerarin exhibited a good binding affinity and were then studied by all-atom molecular dynamics (MD) simulations The predicted binding free energy revealed that the puerarin and ECG could provide similar binding affinity towards 2009 H1 HA target GRAPHICAL ABSTRACT

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Structural insight into the glucokinase-ligands interactions. Molecular docking study

Cited by 15 publications

References 38 publications

In vitro and In silico studies on the anticancer and antimicrobial activity of Cu(II), Ni(II) and Co(II) complexes with bis (pyrazolyl) borate derivative ligand

In vitro and In silico studies on the anticancer and antimicrobial activity of Cu(II), Ni(II) and Co(II) complexes with bis (pyrazolyl) borate derivative ligand

Novel In Silico and In Vivo Insights of Flavonoids as Anti-Diabetic and Anti-Oxidant in Rodent Models

Insights into Binding Affinity of Flavonoid Compounds from Thai Herbs against 2009 H1N1 Hemagglutinin

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