Exploring Binding Mechanisms between Curcumin and Silkworm 30Kc19 Protein Using Spectroscopic Analyses and Computational Simulations

2018 ◽  
Vol 23 (5) ◽  
pp. 605-616 ◽  
Author(s):  
Md. Abdur Razzak ◽  
Ji Eun Lee ◽  
Hee Ho Park ◽  
Tai Hyun Park ◽  
Shin Sik Choi
Keyword(s):  
Computational Simulations ◽  
Spectroscopic Analyses ◽  
30Kc19 Protein ◽  
Binding Mechanisms

Investigating the interaction between three perfluorinated carboxylic acids and the G protein-coupled estrogen receptor: spectroscopic analyses and computational simulations

2020 ◽  
Vol 12 (31) ◽  
pp. 3944-3953 ◽  
Author(s):  
Li Yong ◽  
Manting Huang ◽  
Yuchen Wei ◽  
Jie Xu ◽  
Zhongsheng Yi
Keyword(s):  
Estrogen Receptor ◽  
G Protein ◽  
Carboxylic Acids ◽  
Perfluorooctanoic Acid ◽  
Computational Simulations ◽  
Spectroscopic Analyses ◽  
Perfluorinated Carboxylic Acids ◽  
G Protein Coupled

Here, perfluorobutyric acid (PFBA), perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA) were selected as typical representatives of perfluorinated carboxylic acids (PFCAs) to study the effects of PFCAs on the G protein-coupled estrogen receptor (GPER).

QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1

2019 ◽  
Vol 25 (10) ◽  
pp. 1059-1074 ◽  
Author(s):  
Raju Dash ◽  
Md. Arifuzzaman ◽  
Sarmistha Mitra ◽  
Md. Abdul Hannan ◽  
Nurul Absar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Kinase ◽  
Binding Site ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Selective Inhibitors ◽  
Conserved Residues ◽  
Protein Kinase D1 ◽  
Binding Mechanisms

Background: Although protein kinase D1 (PKD1) has been proved to be an efficient target for anticancer drug development, lack of structural details and substrate binding mechanisms are the main obstacles for the development of selective inhibitors with therapeutic benefits. Objective: The present study described the in silico dynamics behaviors of PKD1 in binding with selective and non-selective inhibitors and revealed the critical binding site residues for the selective kinase inhibition. Methods: Here, the three dimensional model of PKD1 was initially constructed by homology modeling along with binding site characterization to explore the non-conserved residues. Subsequently, two known inhibitors were docked to the catalytic site and the detailed ligand binding mechanisms and post binding dyanmics were investigated by molecular dynamics simulation and binding free energy calculations. Results: According to the binding site analysis, PKD1 serves several non-conserved residues in the G-loop, hinge and catalytic subunits. Among them, the residues including Leu662, His663, and Asp665 from hinge region made polar interactions with selective PKD1 inhibitor in docking simulation, which were further validated by the molecular dynamics simulation. Both inhibitors strongly influenced the structural dynamics of PKD1 and their computed binding free energies were in accordance with experimental bioactivity data. Conclusion: The identified non-conserved residues likely to play critical role on molecular reorganization and inhibitor selectivity. Taken together, this study explained the molecular basis of PKD1 specific inhibition, which may help to design new selective inhibitors for better therapies to overcome cancer and PKD1 dysregulated disorders.

Computational Simulations as Preformulation Perspective for the Delivery of NSAIDs Using .β-Cyclodextrin

2013 ◽  
Vol 10 (9) ◽  
pp. 853-858
Author(s):  
Amrish Kumar ◽  
Dinesh Mishra ◽  
Manoj Gautam ◽  
Suresh Thareja
Keyword(s):  
Computational Simulations

scholarly journals Exploratory Monitoring of the Quality and Authenticity of Commercial Honey in Ecuador

Foods ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 105 ◽  
Author(s):  
Lorena Salvador ◽  
Michelle Guijarro ◽  
Daniela Rubio ◽  
Bolívar Aucatoma ◽  
Tanya Guillén ◽  
...  
Keyword(s):  
Honey Bees ◽  
Reducing Sugars ◽  
Conductivity Measurement ◽  
Principal Component ◽  
Economic Importance ◽  
Critical Problem ◽  
Spectroscopic Analyses ◽  
Chemical Threats ◽  
Raman And Ir Spectroscopy

Honey is one of the oldest sweetening foods and has economic importance, making this product attractive to adulteration with cheap sugars. This can cause a critical problem in the honey industry and a possible health risk. The present work has the aim of evaluating the authenticity of honey commercialized in two different provinces of Ecuador (Pichincha and Loja) by performing physicochemical and spectroscopic analyses. For this study 25 samples were collected from different places and markets and characterized by water, sucrose, reducing sugars and electric conductivity measurement. Also, their Raman and Infrared (IR) spectra were recorded and analysed using a Principal Component Analysis (PCA) in order to verify the quality of the honeys. In addition, a screening of several pesticides was performed in order to verify possible chemical threats to human health and honey bees. It was found that 8 samples have a deviation from the Standard established parameters. Two of them have a high difference in the content of sucrose and reducing sugars, which are located deviated from all the other samples in the PCA of the applied vibrational spectroscopy (IR/Raman), shaping two clear clusters. The results show that Raman and IR spectroscopy is appropriate techniques for the quality control of honey and correlates well with the physicochemical analyses.

scholarly journals Targeted Isolation of Xenicane Diterpenoids from Taiwanese Soft Coral Asterospicularia laurae

Marine Drugs ◽  
2021 ◽  
Vol 19 (3) ◽  
pp. 123
Author(s):  
Yu-Chi Lin ◽  
Yi-Jen Chen ◽  
Shu-Rong Chen ◽  
Wan-Ju Lien ◽  
Hsueh-Wei Chang ◽  
...  
Keyword(s):  
Cytotoxic Effect ◽  
Soft Coral ◽  
Ethanol Extract ◽  
2D Nmr ◽  
Ionization Mass ◽  
Spectroscopic Analyses ◽  
Potential Source ◽  
First Case ◽  
The Family ◽  
Mcf 7

Application of LC-MS/MS-based molecular networking indicated the ethanol extract of octocoral Asterospicularia laurae is a potential source for the discovery of new xenicane derivatives. A natural product investigation of this soft coral resulted in the isolation of four new xenicane diterpenoids, asterolaurins O‒R (1‒4), together with six known compounds, xeniolide-A (5), isoxeniolide-A (6), xeniolide-B (7), 7,8-epoxyxeniolide-B (8), 7,8-oxido-isoxeniolide-A (9), and 9-hydroxyxeniolide-F (10). The structures of isolated compounds were characterized by employing spectroscopic analyses, including 2D-NMR (COSY, HMQC, HMBC, and NOESY) and high-resolution electrospray ionization mass spectrometry (HRESIMS). Asterolaurin O is the first case of brominated tricarbocyclic type floridicin in the family Xeniidae. Concerning bioactivity, the cytotoxic activity of those isolates was evaluated. As a result, compounds 1 and 2 demonstrated a selective cytotoxic effect against the MCF-7 cell line at IC50 of 14.7 and 25.1 μM, respectively.

scholarly journals Cylindromicin from Arctic-Derived Fungus Tolypocladium sp. SCSIO 40433

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1080
Author(s):  
Imran Khan ◽  
Jing Peng ◽  
Zhuangjie Fang ◽  
Wei Liu ◽  
Wenjun Zhang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Nuclear Overhauser Effect ◽  
Inhibition Activity ◽  
Tyrosinase Inhibition ◽  
Bioactive Natural Products ◽  
Chemical Structures ◽  
Overhauser Effect ◽  
Spectroscopic Analyses ◽  
Potential Resource ◽  
Nuclear Overhauser

The fungus strain SCSIO 40433 was isolated from an Arctic-derived glacier sediment sample and characterized as Tolypocladium cylindrosporum. A new compound, cylindromicin (1), and seven known secondary metabolites (2–8) were isolated from this strain. The chemical structures of these compounds were elucidated by comprehensive spectroscopic analyses. Cylindromicin (1) featured a 3,4-dihydro-2H-pyran skeleton. The absolute configuration of compound 1 was assigned via interpretation of key Nuclear Overhauser Effect Spectroscopy (NOESY) correlations and Electronic Circular Dichroism (ECD) calculation. Cylindromicin (1) exhibited significant tyrosinase inhibition activity. This study highlights Polar fungi as a potential resource for new bioactive natural products.

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