scholarly journals DESIGNING OF NANOCOMPOSITE MODEL STRUCTURE USING GLYCITEIN AND GENISTEIN WITH TWELVE DIFFERENT METAL ATOMS USING IN SILICO METHOD

2021 ◽  
Vol 8 (11) ◽  
pp. 14-22
Author(s):  
Doyel Chatterjee ◽  
Sukanya Basu Mallick ◽  
Debraj Hazra ◽  
Rajat Pal
Keyword(s):  
Binding Site ◽  
Energy Levels ◽  
Metal Atoms ◽  
Gold Silver ◽  
Iron Nickel ◽  
Silver Palladium ◽  
Least Energy ◽  
Saturated Structure ◽  
Selection Of ◽  
Palladium Platinum

Nanocomposite formulation is still in its evolving state. However due to its significant therapeutic applications it has grabbed the attention of many researchers. Isoflavonewhich is widely found in soy products have tremendous medicinal propertieswhen it interacts with nanoparticles can become a boon. Hence in this study, we are reporting the interaction properties/patterns of two ubiquitous flavones namelyGlycitein and Genistein forming a nanocomposite model with 12 different metals such as Gold, Silver, Palladium, Platinum, Ruthenium, Rhodium, Cadmium, Iron, Nickel, Zinc, Copper and Antimony based ontheir potency to form nanoparticles. To mimic the Nanocomposite, model the formulation was conducted in Avogadro Software for windows. Glycitein and Genistein create a possibility of selecting the most suitable -OH position that would serve as the binding site. On selection of the appropriate binding site the interaction amid two molecules of glycitein and genistein placed sidewise held together by above-mentioned metals also surrounded by the same metal on another vacant -OH position forming a close saturated structure subjected for interaction. Based on predominantly energy levels the least energy obtained model was Cadmium and the peak procured by Antimony making it least stable and unfavorable for the perceived result.

Preconcentration of gold, silver, palladium, platinum, and ruthenium with organophosphorus extractants

2009 ◽  
Vol 82 (2) ◽  
pp. 183-189 ◽  
Author(s):  
V. I. Men’shikov ◽  
I. Yu. Voronova ◽  
O. A. Proidakova ◽  
S. F. Malysheva ◽  
N. I. Ivanova ◽  
...  
Keyword(s):  
Gold Silver ◽  
Silver Palladium ◽  
Organophosphorus Extractants ◽  
Palladium Platinum

scholarly journals Au-Ag-Pd-Pt mineralization in sedimentary rocks associated with Triassic carbonaceous silicites of Sikhote-Alin

LITOSFERA ◽  
2018 ◽  
pp. 892-913
Author(s):  
Valentin T. Kazachenko ◽  
Elena V. Perevoznikova
Keyword(s):  
Organic Matter ◽  
Intermetallic Compounds ◽  
Sedimentary Rocks ◽  
Precious Metals ◽  
Contact Metamorphism ◽  
Sikhote Alin ◽  
Gold Silver ◽  
Silver Palladium ◽  
Platinum Mineralization ◽  
Palladium Platinum

Subject.The paper is devoted to the study of the gold-silver-palladium-platinum mineralization of the streaky systems in the sedimentary rocks associated within the Triassic carbonaceous silicites of the Taukhinsky and Samarkinsky terranes of the Sikhote-Alin.Materials and methods.In the process of investigations we studied the metamorphosed carbonaceous siliceous-clay rocks and systems of the mineralized fractures in the Triassic siliceous-clay and siliceous (including jaspers) rocks of Shirokopadninskaya, Vysokogorskaya and Gornaya areas, as well as in the sandstones (unclarified age) of Gornaya area. The samples for the analytical study were taken with the lump way. To estimate the content of precious metals in the rocks, cut by the systems of the mineralized fractures, we used the fire assay and atomic-absorption methods. The analyses of minerals (in polished sections) have been done using the JXA-5A and JXA8100 microanalysers.Results.The gold-silver-palladium-platinum mineralization in the siliceous and clay-siliceous rocks, as well as in the sandstones is restricted to the systems of the mineralized fractures and by many features are analogous to the precious-metal mineralization of the black-shale formations. It is represented by native forms, disordered solid solutions, and intermetallic compounds of different metals. The specificity of the Au-Ag-Pd-Pt mineralization is a wide distribution of copper gold, Ni-, Cu-, and Pbbearing gold, and Zn-bearing platinum. Native elements and intermetallic compounds, including those of precious metals, are not rarely associated with the organic matter testifying to the active participation of carbon and, probably, hydrogen that provided the high- and ultra-reduction character of the processes of mineral formation.Conclusions.The presence of the mineral forms of different maximum reduced metals is caused by the influence of the organic matter of the Triassic carbonaceous silicites. This consisted in the removal of the most volatile components, and first of all the poorly bound water and hydrocarbons from the carbonaceous rocks through the contact metamorphism related with the injection of the granitoid intrusions of Cretaceous plutonic and volcanoplutonic belts.

scholarly journals Nanocomposite Formulation of Ferulic Acid with Different Metals Using Computational Method

2020 ◽  
Vol 3 (1) ◽  
pp. 40-45
Author(s):  
Debraj Hazra ◽  
Rajat Pal
Keyword(s):  
Energy Level ◽  
Ferulic Acid ◽  
Metal Atom ◽  
Energy Levels ◽  
Computational Method ◽  
Gold Silver ◽  
Nickel Platinum ◽  
Model Structures ◽  
Angle Calculation ◽  
Selection Of

Formulation of Nanoparticle – drug composite is becoming a growing field of research in today’s scientific community. In comparison to the research on the experimental methods for these formulations and their application in various fields, the study of the interaction between drug and nanoparticle is less. In this study, we are reporting about the selection of metals for the formulation of nanocomposite with ferulic acid which is a well-known bioflavonoid having different medicinal activities. Ferulic acid contains only one –OH group which may reduce the conflict of selecting the metal atom binding site. For our study, we considered twelve metals which have been reported for having the potentiality to synthesis nanoparticles. These metals are gold, silver, copper, iron, zinc, nickel, platinum, palladium, rhodium, ruthenium, cadmium, and antimony. To mimic the actual nanocomposite structure, one metal atom has interacted with two molecules of ferulic acid. All nanocomposite model structures were designed using Avogadro software for windows. It was subjected to energy minimization and O-metal-O bond angle calculation. From the energy levels, it was observed that cadmium exhibited the lowest energy level and antimony showed the highest energy level suggesting their nanocomposite model structures as the most stable and unstable formulation respectively. 

Rapid Elaboration of Fragments into Leads Applied to Bromodomain-3 Extra Terminal Domain

2020 ◽  
Author(s):  
Luke Adams ◽  
Lorna E. Wilkinson-White ◽  
Menachem J. Gunzburg ◽  
Stephen J. Headey ◽  
Martin J. Scanlon ◽  
...  
Keyword(s):  
Binding Site ◽  
Systematic Approach ◽  
Structural Information ◽  
Peptide Binding ◽  
Chemical Diversity ◽  
Chemical Probes ◽  
Protein Targets ◽  
Structure Activity ◽  
Peptide Binding Site ◽  
Selection Of

The development of low-affinity fragment hits into higher affinity leads is a major hurdle in fragment-based drug design. Here we demonstrate an approach for the Rapid Elaboration of Fragments into Leads (REFiL) applying an integrated workflow that provides a systematic approach to generate higher-affinity binders without the need for structural information. The workflow involves the selection of commercial analogues of fragment hits to generate preliminary structure-activity relationships. This is followed by parallel microscale chemistry using chemoinformatically designed reagent libraries to rapidly explore chemical diversity. Upon completion of a fragment screen against Bromodomain-3 extra terminal (BRD3-ET) domain we applied the REFiL workflow, which allowed us to develop a series of tetrahydrocarbazole ligands that bind to the peptide binding site of BRD3-ET. With REFiL we were able to rapidly improve binding affinity >30-fold. The REFiL workflow can be applied readily to a broad range of protein targets without the need of a structure, allowing the efficient evolution of low-affinity fragments into higher affinity leads and chemical probes.<br>

Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of Leishmania mexicana

2020 ◽  
Vol 16 (6) ◽  
pp. 784-795
Author(s):  
Krisnna M.A. Alves ◽  
Fábio José Bonfim Cardoso ◽  
Kathia M. Honorio ◽  
Fábio A. de Molfetta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Point Of View ◽  
New Drugs ◽  
Leishmania Mexicana ◽  
Receptor Complexes ◽  
Starting Point ◽  
Dynamics Simulations ◽  
Selection Of

Background:: Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. Objective:: The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). Methods: A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. Results:: Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. Conclusion:: he use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.

scholarly journals DNA Binding Site Selection of Dimeric and Tetrameric Stat5 Proteins Reveals a Large Repertoire of Divergent Tetrameric Stat5a Binding Sites

2000 ◽  
Vol 20 (1) ◽  
pp. 389-401 ◽  
Author(s):  
Elisabetta Soldaini ◽  
Susan John ◽  
Stefano Moro ◽  
Julie Bollenbacher ◽  
Ulrike Schindler ◽  
...  
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Site Selection ◽  
Binding Sites ◽  
Tetramer Binding ◽  
Dna Binding Site ◽  
Potential Binding ◽  
Wide Range ◽  
Large Repertoire ◽  
Selection Of

ABSTRACT We have defined the optimal binding sites for Stat5a and Stat5b homodimers and found that they share similar core TTC(T/C)N(G/A)GAA interferon gamma-activated sequence (GAS) motifs. Stat5a tetramers can bind to tandemly linked GAS motifs, but the binding site selection revealed that tetrameric binding also can be seen with a wide range of nonconsensus motifs, which in many cases did not allow Stat5a binding as a dimer. This indicates a greater degree of flexibility in the DNA sequences that allow binding of Stat5a tetramers than dimers. Indeed, in an oligonucleotide that could bind both dimers and tetramers, it was possible to design mutants that affected dimer binding without affecting tetramer binding. A spacing of 6 bp between the GAS sites was most frequently selected, demonstrating that this distance is favorable for Stat5a tetramer binding. These data provide insights into tetramer formation by Stat5a and indicate that the repertoire of potential binding sites for this transcription factor is broader than expected.

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