scholarly journals SEARCH FOR GLIOMA DIRECT BINDING SITE OF ALKALOID USING PROTEIN-LIGAND ANT SYSTEM®

2018 ◽  
Vol 11 (15) ◽  
pp. 65 ◽  
Author(s):  
Yusnita Rifai
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Internal Control ◽  
Data Bank ◽  
Protein Data Bank Code ◽  
Ant System ◽  
Hydrogen Bond Interaction ◽  
Good Score ◽  
Score Result ◽  
Native Ligand

Objective: This research aims to know the best affinity and the best chemical conformation of anticancer compounds from alkaloid groups that have closed direction to Glioma-associated oncogene using protein-ligand ant system (PLANTS®). The interaction energy and hydrogen bond are included as evaluated targets.Methods: In this research, 27 ligands with root mean square deviation score at 1.614 Å and cyclopamine as native ligand are used. Meanwhile, staurosporinone acts as gliomas directed-binding-site-internal-control. Each ligand is docked in GLI with Protein Data Bank code 2GLI using two methods, GLI contains water and without water.Results: PLANTS® score for native ligand in the first and the second method is −73.9002 and −73.2700, respectively. Pancracristine, homoharringtonine, and sanguinarine showed PLANTS® score closed to the cyclopamine score result, but their hydrogen bond interaction differed from native ligan interaction. Evodiamine ligand has a good score and hydrogen bond to the same amino acid of protein GLI, which are GLU 175 and THR 173. This result indicated that evodiamine has the same identical mechanism as staurosporinone.Conclusion: The evodiamine is determined to have the same working mechanism as a GLI inhibitor.

scholarly journals Study on the interaction between catechin and cholesterol by the density functional theory

2020 ◽  
Vol 18 (1) ◽  
pp. 357-368
Author(s):  
Kaiwen Zheng ◽  
Kai Guo ◽  
Jing Xu ◽  
Wei Liu ◽  
Junlang Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Density Functional ◽  
Antioxidant Properties ◽  
Micelle Formation ◽  
Aromatic Rings ◽  
Hydrogen Bond Interaction ◽  
Functional Theory ◽  
The Density Functional Theory

AbstractCatechin – a natural polyphenol substance – has excellent antioxidant properties for the treatment of diseases, especially for cholesterol lowering. Catechin can reduce cholesterol content in micelles by forming insoluble precipitation with cholesterol, thereby reducing the absorption of cholesterol in the intestine. In this study, to better understand the molecular mechanism of catechin and cholesterol, we studied the interaction between typical catechins and cholesterol by the density functional theory. Results show that the adsorption energies between the four catechins and cholesterol are obviously stronger than that of cholesterol themselves, indicating that catechin has an advantage in reducing cholesterol micelle formation. Moreover, it is found that the molecular interactions of the complexes are mainly due to charge transfer of the aromatic rings of the catechins as well as the hydrogen bond interactions. Unlike the intuitive understanding of a complex formed by hydrogen bond interaction, which is positively correlated with the number of hydrogen bonds, the most stable complexes (epicatechin–cholesterol or epigallocatechin–cholesterol) have only one but stronger hydrogen bond, due to charge transfer of the aromatic rings of catechins.

Iron-Blocking the High-Affinity Mn-Binding Site in Photosystem II Facilitates Identification of the Type of Hydrogen Bond Participating in Proton-Coupled Electron Transport via YZ•†

Biochemistry ◽  
2005 ◽  
Vol 44 (28) ◽  
pp. 9746-9757 ◽  
Author(s):  
Boris K. Semin ◽  
Elena R. Lovyagina ◽  
Kirill N. Timofeev ◽  
Ilya I. Ivanov ◽  
Andrei B. Rubin ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Electron Transport ◽  
Photosystem Ii ◽  
Binding Site ◽  
High Affinity

scholarly journals Atomic-level insights into the activation of nitrogen via hydrogen-bond interaction toward nitrogen photofixation

Chem ◽  
2021 ◽  
Author(s):  
Yue Xin ◽  
Sanmei Wang ◽  
Haibo Yuan ◽  
Tingting Hou ◽  
Wenkun Zhu ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Atomic Level ◽  
Hydrogen Bond Interaction ◽  
Bond Interaction

Fine-tuning of microsolvation and hydrogen bond interaction regulates substrate channelling in the course of flavonoid biosynthesis

2016 ◽  
Vol 18 (15) ◽  
pp. 10337-10345 ◽  
Author(s):  
Julien Diharce ◽  
Jérôme Golebiowski ◽  
Sébastien Fiorucci ◽  
Serge Antonczak
Keyword(s):  
Hydrogen Bond ◽  
Natural Compounds ◽  
Flavonoid Biosynthesis ◽  
Fine Tuning ◽  
Efficient Production ◽  
Substrate Channeling ◽  
Metabolite Formation ◽  
Hydrogen Bond Interaction ◽  
Bond Interaction ◽  
Substrate Channelling

In the course of metabolite formation, some multienzymatic edifices, the so-called metabolon, are formed and lead through substrate channeling to a more efficient production of the natural compounds.

scholarly journals Antifungal Activity of Phenyl Derivative of Pyranocoumarin fromPsoralea corylifoliaL. Seeds by Inhibition of Acetylation Activity of Trichothecene 3-O-Acetyltransferase (Tri101)

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Sangeetha Srinivasan ◽  
D. V. L. Sarada
Keyword(s):  
Hydrogen Bond ◽  
Antifungal Activity ◽  
Defense Mechanism ◽  
Petroleum Ether Extract ◽  
Ligand Docking ◽  
Molecular Formula ◽  
Trichothecene Mycotoxin ◽  
Hydrogen Bond Interaction ◽  
Phenyl Derivative ◽  
Bond Interaction

Antifungal activity of petroleum ether extract ofPsoralea corylifoliaL. seed, tested againstFusariumsp. namely,Fusarium oxysporum, Fusarium moniliforme,andFusarium graminearum, was evaluated by agar well diffusion assay. The chromatographic fractionation of the extract yielded a new phenyl derivative of pyranocoumarin (PDP). The structure of the PDP was confirmed using spectroscopic characterization (GC-MS, IR, and NMR), and a molecular mass ofm/z414 [M-2H]+with molecular formula C27H28O4was obtained. The PDP had a potent antifungal activity with a minimum inhibitory concentration of 1 mg/mL againstFusariumsp. Molecular docking using Grid-Based Ligand Docking with Energetics (GLIDE, Schrodinger) was carried out with the Tri101, trichothecene 3-O-acetyltransferase, as target protein to propose a mechanism for the antifungal activity. The ligand PDP showed bifurcated hydrogen bond interaction with active site residues at TYR 413 and a single hydrogen bond interaction at ARG 402 with a docking score −7.19 and glide energy of −45.78 kcal/mol. This indicated a strong binding of the ligand with the trichothecene 3-O-acetyltransferase, preventing as a result the acetylation of the trichothecene mycotoxin and destruction of the “self-defense mechanism” of theFusariumsp.

scholarly journals Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Yong Wang ◽  
Bin-Quan Luan ◽  
Zhiyu Yang ◽  
Xinyue Zhang ◽  
Brandon Ritzo ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Single Molecule ◽  
Metal Ion ◽  
Detection Method ◽  
Direct Detection ◽  
Alpha Hemolysin ◽  
Duplex Stability ◽  
Dynamics Simulations ◽  
Direct Detection Method

Abstract Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag+ with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag+, duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag+ induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag+. Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag+ binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.

Sign in / Sign up

Export Citation Format

Share Document