Relationship between the solubility and properties of solid solutions in binary carbide systems with excess free binding energy

1967 ◽  
Vol 6 (3) ◽  
pp. 232-237
Author(s):  
V. F. Funke
Keyword(s):  
Binding Energy ◽  
Solid Solutions ◽  
Free Binding Energy ◽  
Binary Carbide

scholarly journals ANTI-PARKINSON POTENTIAL OF PERSEA AMERICANA SEED EXTRACTS THROUGH IN-SILICO DOCKING STUDY

2020 ◽  
pp. 152-155
Author(s):  
RACHAEL EVANGELINE ◽  
NIHAL AHMED
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Water Extract ◽  
Docking Study ◽  
Persea Americana ◽  
Ligand Docking ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Free Binding Energy

Objective: The aim of this study is to investigate the potential of Persea americana extracts for their Anti-Parkinson application through an in-silico docking study. Methods: PubChem and protein data bank databases were used to retrieve 3D structures. AutoDock4 was used to perform protein-ligand docking analysis. PyMOL was used to visualize the docking results. Results: Among the 30 ligand, the highest affinity was demonstrated by Hesperidin with a free binding energy of −6.8 kcal/mol and formation of five hydrogen bonds. The second highest significance was demonstrated by Biphenyl 4-(4-diethylaminobenzylidenamino) with a free binding energy of −5.9 kcal/mol with the formation of 2 hydrogen bonds. Among the three sets of phytochemicals from different solvent extracts, water extract demonstrated the highest potential as Anti-Parkinson active. Conclusion: P. americana extracts were analyzed for their Anti-Parkinson potential, and among the three extracts, the aqueous extract was predicted to have significant Anti-Parkinson potential, based on in silico docking analysis, due to the presence of active phytochemicals such as Hesperidin and others.

scholarly journals Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl Peptidase-IV Inhibitor

2017 ◽  
Vol 2017 ◽  
pp. 1-16 ◽  
Author(s):  
Lina Rozano ◽  
Muhammad Redha Abdullah Zawawi ◽  
Muhamad Aizuddin Ahmad ◽  
Indu Bala Jaganath
Keyword(s):  
Binding Energy ◽  
Bioactive Compounds ◽  
Dipeptidyl Peptidase ◽  
Dipeptidyl Peptidase Iv ◽  
Diabetic Patients ◽  
Caffeoylquinic Acid ◽  
Dicaffeoylquinic Acid ◽  
Free Binding Energy ◽  
Gynura Bicolor

The inhibition of dipeptidyl peptidase-IV (DPPIV) is a popular route for the treatment of type-2 diabetes. Commercially available gliptin-based drugs such as sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin were specifically developed as DPPIV inhibitors for diabetic patients. The use of Gynura bicolor in treating diabetes had been reported in various in vitro experiments. However, an understanding of the inhibitory actions of G. bicolor bioactive compounds on DPPIV is still lacking and this may provide crucial information for the development of more potent and natural sources of DPPIV inhibitors. Evaluation of G. bicolor bioactive compounds for potent DPPIV inhibitors was computationally conducted using Lead IT and iGEMDOCK software, and the best free-binding energy scores for G. bicolor bioactive compounds were evaluated in comparison with the commercial DPPIV inhibitors, sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin. Drug-likeness and absorption, distribution, metabolism, and excretion (ADME) analysis were also performed. Based on molecular docking analysis, four of the identified bioactive compounds in G. bicolor, 3-caffeoylquinic acid, 5-O-caffeoylquinic acid, 3,4-dicaffeoylquinic acid, and trans-5-p-coumaroylquinic acid, resulted in lower free-binding energy scores when compared with two of the commercially available gliptin inhibitors. The results revealed that bioactive compounds in G. bicolor are potential natural inhibitors of DPPIV.

scholarly journals The Computational Calculation and Molecular Docking of Aeroplysinin-1 As Antibacterial

2021 ◽  
Vol 9 (2) ◽  
pp. 124-128
Author(s):  
Mirella Fonda Maahury ◽  
Veliyana Londong Allo
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Energy ◽  
Gas Phase ◽  
Geometry Optimization ◽  
Dna Gyrase ◽  
Marine Sponges ◽  
E Coli ◽  
Free Binding Energy ◽  
Computational Calculation

Aeroplysinin-1 is naturally found from marine sponges as an anti-bacterial compound. Computational calculation and molecular docking were performed for aeroplysinin. Aeroplysinin as an inhibitor has optimized in the gas phase using DFT with 6-31G(d) functional. The structure from geometry optimization of aeroplysinin-1is, not in one plane. The interaction of aeroplysinin-1 with two different DNA gyrase from E. Coli and S. Aureus. In this research,aeroplysinin-1 can inhibit the protein with the free binding energy of about -5.7 kcal/mol and -6.35 kcal/mol, respectively, for E. Coli and S. Aureus. The dominant molecular interaction is the hydrogen bond.

SHOCKLEY-TYPE SURFACE STATES ON THE (111) AND (110) SURFACES OF Cu-BASED ALLOYS WITH NOBLE AND TRANSITION METAL IMPURITIES

1993 ◽  
Vol 07 (01) ◽  
pp. 25-31 ◽  
Author(s):  
A. Y. SERAGELDIN ◽  
R. PRASAD ◽  
A. BANSIL
Keyword(s):  
Binding Energy ◽  
Solid Solutions ◽  
Surface States ◽  
Binding Energies ◽  
Bulk Alloy ◽  
Metal Impurities ◽  
Disordered Alloys ◽  
Good Accord ◽  
Transition Metal Impurities ◽  
Theoretical Predictions

We have investigated Shockley-type surface states (SSS's) on ideal semi-infinite surfaces of randomly disordered alloys, Cu 70 Ni 30, Cu 80 Ni 20, Cu 90 Ni 10, Cu 85 Pd 15, Cu 95 Pd 5, and Cu 90 Au 10 using a Green's function approach. In particular, the binding energies and disorder induced smearings of the [Formula: see text]-centered SSS's on the (111) surfaces and the [Formula: see text]-centered SSS's on the (110) surfaces of these alloys are presented. Our theoretical predictions are in good accord with the available angle-resolved photoemission measurements, although the experimental results in this regard for well-characterized alloy surfaces appear to be limited to the (111) surfaces of CuPd and CuAu solid solutions. The binding energy of the SSS's is found to decrease roughly linearly with decreasing e/a ratio, but significant deviations from such a rigid-band behavior are noted for various impurities. The SSS's investigated in this article lie in the [Formula: see text] gap in the bulk alloy electronic spectrum, and their character (changes in binding energy on alloying, and disorder induced smearing) is correlated with that of the L2′ bulk level.

scholarly journals THE INTERACTION OF miR-4258, miR-3960, miR-211-3p AND miR-3155b WITH mRNAs GENES OF NON-POLYGLUTAMINE TRINUCLEOTIDE DISORDERS

2020 ◽  
Vol 1 (337) ◽  
pp. 25-32 ◽  
Author(s):  
Belkozhayev A.M. ◽  
Niyazova R.Ye.
Keyword(s):  
Binding Energy ◽  
Binding Sites ◽  
Trinucleotide Repeat ◽  
Neurological Diseases ◽  
Repeat Expansion ◽  
Binding Characteristics ◽  
Human Genes ◽  
Free Binding Energy ◽  
Nucleotide Repeats ◽  
Cug Repeats

Trinucleotide repeat expansion disorders constitute a group of dominantly inherited neurological diseases that are incurable and ultimately fatal. In the present work, miRNA binding sites were predicted by the MirTarget program. It was given characteristics of miRNAs binding sites in 5' and 3' UTR mRNAs genes of non-polyglutamine trinucleotide disorders with CGG, GCC, CUG repeats. Binding sites of 2567 miRNAs with mRNAs of 17494 human genes were determined. 206 genes with nucleotide repeats, mRNAs of which are bind with miRNA in the 5'UTR and 3'UTR, were observed. From thus, 2668 miRNAs binding sites are located in the 5'UTR, 3853 – in the 3'UTR with ΔG/ΔGm values equal to 85 % and more. It was found that 34 gene’s mRNA having trinucleotide (CGG\GCC\CUG) repeats were targets for miR-4258, miR-3960 miR-211-3p and miR-3155b. miR-4258 binds to mRNA of ADARB1, C11orf87 and CBFB genes with free binding energy - 93 kJ/mole and ΔG/ΔGm 91%, to mRNA of ARHGEF7, BCR, BRSK2 and C9orf91 genes with free binding energy - 91 kJ/mole and ΔG/ΔGm 89%. miR-3960 binds in GCC repeats to mRNA of ABCC1 and BLMH genes with free binding energy - 116 kJ/mole. miR-211-3p and miR-3155b interact with mRNA of ACACA and ANKRD13D genes in 5’-3’untranslated regions. Studying binding characteristics of miRNA and genes will help identify association of miRNAs with genes with trinucleotide repeats for recommending for the diagnosis of nucleotide repeat expansion disorders.

scholarly journals Interactions between osmium atoms dissolved in iron observed by the 57Fe Mössbauer spectroscopy

Nukleonika ◽  
2015 ◽  
Vol 60 (1) ◽  
pp. 75-79 ◽  
Author(s):  
Robert Konieczny ◽  
Rafał Idczak ◽  
Jan Chojcan
Keyword(s):  
Binding Energy ◽  
Solid Solutions ◽  
Qualitative Agreement ◽  
Room Temperature ◽  
Mössbauer Spectra ◽  
Enthalpy Of Solution ◽  
Atomic Model ◽  
Mossbauer Spectra ◽  
Model Predictions ◽  
Iron Based

Abstract The room temperature 57Fe Mössbauer spectra for binary iron-based solid solutions Fe1−xOsx, with x in the range 0.01 ≤ x ≤ 0.05, were analyzed in terms of binding energy Eb between two Os atoms in the Fe-Os system. The extrapolated values of Eb for x = 0 were used for computation of enthalpy of solution of osmium in iron. The result was compared with that resulting from the cellular atomic model of alloys by Miedema. The comparison shows that our findings are in qualitative agreement with the Miedema's model predictions.

scholarly journals Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor model.

2012 ◽  
Vol 59 (4) ◽  
Author(s):  
Karol Kamel ◽  
Andrzej Kolinski
Keyword(s):  
Binding Energy ◽  
Dihydroxyvitamin D3 ◽  
Dihydroxyvitamin D ◽  
Anticancer Properties ◽  
1,25 Dihydroxyvitamin D ◽  
Distinct Mechanism ◽  
Relative Binding Affinity ◽  
Relative Binding ◽  
Free Binding Energy ◽  
Eb 1089

1,25-dihydroxyvitamin D(3) has quite significant anticancer properties, but its strong calcemic effect in principle excludes it as a potential anticancer drug. Currently, a lot of effort is being devoted to develop potent anticancer analogs of 1,25-dihydroxyvitamin D(3) that would not induce hypercalcemia during therapy. In this work, the free binding energy of the VDR receptor with 1,25-dihydroxyvitamin D(3) and its three potent analogs (EB 1089, KH 1060 and RO 25-9022) is calculated and compared with each other. With this approach, we could estimate the relative binding affinity of the most potent analog, RO 25-9022, and also revealed a quite distinct mechanism of its interaction with VDR.

scholarly journals In Silico Study on Interaction and Preliminary Toxicity Prediction of Eleutherine americana Components as an Antifungal and Antitoxoplasmosis Candidate

2020 ◽  
Vol 20 (4) ◽  
pp. 899
Author(s):  
Sophi Damayanti ◽  
Nadiyah Athifah Salim Martak ◽  
Benny Permana ◽  
Adi Suwandi ◽  
Rika Hartati ◽  
...  
Keyword(s):  
Binding Energy ◽  
In Silico ◽  
Aquatic Toxicity ◽  
Three Dimensional ◽  
Positive Control ◽  
Toxicity Prediction ◽  
Target Proteins ◽  
Discovery Studio ◽  
Free Binding Energy ◽  
Eleutherine Americana

Red bulbs of Eleutherine americana (Aubl.) Merr. ex K. Heyne has been known for its high content of naphthoquinones that have antifungal and antiparasitic activities. In this research, in silico interaction study was performed between 31 compounds reported to be found in E. americana with the selected target proteins for antifungal and antitoxoplasmosis activity using the molecular docking method. An ORPs (OSBP-related proteins), Osh4 (PDB ID: 1ZHX), and N-myristoyltransferase (Nmt, PDB ID: 1IYL) were used as the antifungal target proteins. Toxoplasma gondii purine nucleoside phosphorylase (TgPNP, PDB ID: 3MB8) and calcium-dependent protein kinase-1 (TgCDPK1, PDB ID: 4M84) were used as antitoxoplasmosis target proteins. Three-dimensional structures of the test compounds were made and optimized using GaussView 6.0 and Gaussian 09W. The target proteins were prepared using the Discovery Studio 2016 Program. Aquatic toxicity prediction as the preliminary assessment of the safety of the compounds was performed using ECOSAR v2.0. The results suggest that the compound having both the smallest free binding energy compared with positive control and other test compounds and low predicted toxicity is β-sitosterol with a free binding energy of ‒11.55 and ‒11.18 kcal/mol towards Osh4 and Nmt and ‒8.06 and ‒10.29 kcal/mol towards TgPNP and TgCDPK1, respectively.

scholarly journals IN SILICO MOLECULAR DOCKING OF XANTHONE DERIVATIVES AS CYCLOOXYGENASE-2 INHIBITOR AGENTS

2017 ◽  
Vol 9 (3) ◽  
pp. 98 ◽  
Author(s):  
Isnatin Miladiyah ◽  
Jumina Jumina ◽  
Sofia Mubarika Haryana ◽  
Mustofa Mustofa
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Site ◽  
In Silico ◽  
Cyclooxygenase 2 ◽  
Xanthone Derivatives ◽  
In Silico Studies ◽  
Free Binding Energy ◽  
Cox 2 ◽  
Cox 1

Objective: To demonstrate the potential ofdifferent xanthone derivatives as cyclooxygenase-2 (COX-2) inhibitor agents and their selectivity against cycloooxygenase-1 (COX-1) and COX-2 using molecular simulation.Methods: Nine novel xanthone derivatives (compounds A-I) were employed to dock against protein COX-2 (Protein Data Bank/PDB ID: 1CX2) and COX-1 (PDB ID: 3N8Z). Celecoxib, a selective COX-2 inhibitor, was chosen as a control compound. The free binding energy produced by the docking was scored using Protein-Ligand Ant System (PLANTS) and the hydrogen bonds (H-bonds) between ligands and enzymes were visualised using Pymol.Results: Molecular docking studies revealed that celecoxib docked to the active site of COX-2 enzyme, but not to COX-1; whereasxanthone derivatives docked to the active site of both COX-2 and COX-1. Free binding energy of xanthone derivatives ranged between-73,57 to-79,18 and between-73,06 to-79,25 against COX-2 and COX-1, respectively, and-78,13 against celecoxib. H-bonds in the molecule of xanthone derivatives and COX-2 protein were found in amino acid residues Arg120, Tyr355, Tyr385,and Ser353. There was an insignificant difference between the free binding energyof xanthone derivatives against COX-2 and against COX-1, suggesting that their inhibition was non-selective.Conclusion: In conclusion, in silico studies showed that xanthone derivatives could be effective as potential inhibitors against COX-2, although they are not selective.

scholarly journals Skrining Senyawa dari Tanaman Rhodomyrtus tomentosa (Aiton) Hassk terhadap SARS-CoV-2 ORF3a

2021 ◽  
Vol 6 (2) ◽  
pp. 162-166
Author(s):  
Samsul Hadi
Keyword(s):  
Binding Energy ◽  
Ion Channel ◽  
Screening Method ◽  
Channel Activity ◽  
Methyl Cinnamate ◽  
Computational Screening ◽  
Pulmonary Epithelial Cells ◽  
Free Binding Energy ◽  
The Stability ◽  
Rhodomyrtus Tomentosa

The ORF3a protein from SARS-CoV has functions in terms of ion channel activity, modulates the trafficking properties of SARS-CoV spike (S) protein, increases fibrinogen expression in pulmonary epithelial cells, and induces apoptosis. So that research is needed to overcome the ORF3a experiment. The method in this research uses the computational screening method with autodok4 software. The results of this study resulted in free binding energy between Hassk Rhodomyrtus tomentosa (Aiton) and ORF3a compounds, namely: α-tocopherol-quinone (-5.86); blumeatin (-4.98); methyl cinnamate (-4.44); myricetin (-4.49); naringenin (-4.93); quercetin (-4,9); rhodomyrtone (-6); rhodomyrtosone B (-7.11); rhodomyrtosone C (-6.77); tetrahydroxyflavanone (-4.91); α-tocopherol A (-6.72); verimol K (-4.89); watsonianone A (-7.55). Based on the data obtained, the ligand with the most potential due to the stability of the bond is watsonianone A.

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