scholarly journals Theoretical studies on the binding affinities of β-cyclodextrin to small molecules and monosaccharides

2006 ◽  
Vol 4 (2) ◽  
pp. 223-233 ◽  
Author(s):  
Sicong Chen ◽  
Qiwen Teng ◽  
Shi Wu
Keyword(s):  
Binding Energy ◽  
Small Molecules ◽  
Am1 Method ◽  
Hydroxyl Groups ◽  
Binding Affinities ◽  
Binding Ability ◽  
Solvent Molecules ◽  
Equilibrium Geometries ◽  
Negative Binding Energy ◽  
Optimized Geometries

AbstractEquilibrium geometries and electronic structures of complexes between β-cyclodextrin (β-CD) and some small molecules as well as monosaccharides were investigated by Austin Model 1 (AM1) to obtain binding energy of the complexes. It was indicated that β-CD could bind the structurally similar solvent molecules and monosaccharides because of the negative binding energy of the complexes, and especially could show the chiral binding ability to monosaccharides with more hydroxyl groups, due to its chiral characteristics. The complexes were stabilized by the hydrogen bonding between β-CD and guests. Based on the AM1 optimized geometries, the IR spectra were calculated by AM1 method. Vibration frequencies of O-H bonds in the guests were red-shifted owing to the weakening of the O-H bonds with the formation of the complexes.

scholarly journals Hydrogen-bonded assembly and binding affinity of the multi-point acceptor and isophthalic acid

2006 ◽  
Vol 4 (4) ◽  
pp. 732-742 ◽  
Author(s):  
Lingjia Xu ◽  
Liangliang Zhu ◽  
Shi Wu ◽  
Xiaopeng Chen ◽  
Qiwen Teng
Keyword(s):  
Hydrogen Bonding ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Small Molecules ◽  
Electronic Spectra ◽  
Isophthalic Acid ◽  
Steric Effects ◽  
Am1 Method ◽  
Ir Frequencies ◽  
Negative Binding Energy

AbstractSupermolecular complexes formed by oligophenyleneethynylene derivatives and isophthalic acid were studied using AM1 method to obtain binding energy. Electronic spectra and IR spectra of the complexes were calculated by INDO/CIS and AM1 methods based on AM1 geometries. Results indicated that the dimer could be formed by the monomers via hydrogen bonding because of the negative binding energy. Binding energy of the complexes was affected by electronegativity and steric effects of the substituents. The first UV absorptions and IR frequencies of N-H bonds of the complexes were both red-shifted compared with those of the monomers. The complexes could bind small molecules via hydrogen bonds, resulting in the change in UV absorptions and an increase in IR frequencies of N-H bonds.

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

scholarly journals Supramolecular architectures of 4-hydroxytetraphenylporphyrin with aza-donors

2014 ◽  
Vol 70 (a1) ◽  
pp. C554-C554 ◽  
Author(s):  
Purnendu Nandy ◽  
V. Pedireddi
Keyword(s):  
Three Dimensional ◽  
Molecular Complexes ◽  
Hydroxyl Groups ◽  
X Ray Diffraction ◽  
X Ray ◽  
Supramolecular Architectures ◽  
Detailed Structural Analysis ◽  
Different Types ◽  
Solvent Molecules ◽  
Molecular Adducts

Molecular adducts of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (1) with aza-donors like 4,4'-bipyridine (a), 1,2-bis(4-pyridyl)ethane (b), trans-1,2-bis(4-pyridyl)ethylene (c), 4,4'-trimethylene-dipyridine (d), phenazine (e), 1,10-phenanthroline (f), 1,7-phenanthroline (g) and 4,7-phenanthroline (h) have been prepared. All the molecular complexes are crystallized along with the solvent of crystallization, except in the complex with the aza-donor b. Detailed structural analysis of the obtained complexes has been carried out by single crystal X-ray diffraction. The three dimensional structures of the molecular adducts are facilitated by directional hydrogen bonding features of hydroxyl groups with aza donors as well as solvent molecules, leading to the formation of different types of supramolecular architectures like sheets, tapes, host-guest assembly etc. For example, in the complex of 1 and aza donor a, which crystallizes as a hydrate, the porphyrin molecules interact with water and 4,4'-bipyridine through O-H...O and O-H...N hydrogen bonds, which leads to the formation of molecular sheets in two dimensional arrangement. An important noteworthy observation is that the molecular complexes are crystalline even after removal of the solvents by heating, as characterized by thermogravimetric analysis (TGA) and powder X-ray diffraction (PXRD). Further, all the complexes are found to be fluorescence sensitive, perhaps due to the porphyrin molecules.

Influence of Human Serum Albumin Glycation on the Binding Affinities for Natural Flavonoids

2019 ◽  
Vol 17 (1) ◽  
pp. 806-812
Author(s):  
Liangliang Liu ◽  
Yi Liu ◽  
Aiping Xiao ◽  
Shiyong Mei ◽  
Yixi Xie
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Small Molecules ◽  
Human Body ◽  
Binding Sites ◽  
Plasma Proteins ◽  
Fluorescence Spectra ◽  
Binding Affinities ◽  
Dietary Flavonoids

AbstractIncreasing the degree of glycation in diabetes could affect the ability of plasma proteins in binding to small molecules and active compounds. In this study, the influence of glycation of Human serum albumin (HSA) on the binding affinities for six dietary flavonoids was investigated by fluorescence spectra. Glycated HSA was prepared through incubation with glucose and characterized by several methods to confirm the glycation. It was found that the level of glycation increased with the increasing incubation time. The glycation of HSA increased the binding affinities for flavonoids by 1.40 to 48.42 times, which indicates that modifications caused by the glycation may have different influences on the interactions of flavonoids with HSA at separate binding sites on this protein. These results are valuable for understanding the influence of diabetes on the metabolism of flavonoids and other bioactive small molecules in human body.

scholarly journals Probing the interaction of nanoparticles with small molecules in real time via quartz crystal microbalance monitoring

Nanoscale ◽  
2019 ◽  
Vol 11 (23) ◽  
pp. 11107-11113 ◽  
Author(s):  
Ye Yang ◽  
Guillaume Poss ◽  
Yini Weng ◽  
Runzhang Qi ◽  
Hanrui Zheng ◽  
...  
Keyword(s):  
Small Molecules ◽  
Real Time ◽  
Quartz Crystal Microbalance ◽  
Quartz Crystal ◽  
Binding Affinities ◽  
Target Analytes

We report on a novel screening route to obtain quantitative measures for nanoparticle binding affinities to target analytes.

Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis

1995 ◽  
Vol 38 (14) ◽  
pp. 2681-2691 ◽  
Author(s):  
Angel R. Ortiz ◽  
M. Teresa Pisabarro ◽  
Federico Gago ◽  
Rebecca C. Wade
Keyword(s):  
Binding Energy ◽  
Energy Analysis ◽  
Drug Binding ◽  
Binding Affinities ◽  
Comparative Binding ◽  
Binding Energy Analysis

scholarly journals Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules

2020 ◽  
Vol 14 ◽  
pp. 117793222096550
Author(s):  
Loubna Allam ◽  
Fatima Ghrifi ◽  
Hakmi Mohammed ◽  
Naima El Hafidi ◽  
Rachid El Jaoudi ◽  
...  
Keyword(s):  
Small Molecules ◽  
Binding Sites ◽  
Epigallocatechin Gallate ◽  
Host Cells ◽  
Spike Protein ◽  
Target Cells ◽  
Binding Affinities ◽  
Rapid Spread ◽  
Inhibitor Compounds ◽  
Potential Inhibitors

The global burden of infections and the rapid spread of viral diseases show the need for new approaches in the prevention and development of effective therapies. To this end, we aimed to explore novel inhibitor compounds that can stop replication or decrease the viral load of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there is currently no approved treatment. Besides using the angiotensin-converting enzyme (ACE2) receptor as a main gate, the CoV-2 can bind to the glucose-regulating protein 78 (GRP78) receptor to get into the cells to start an infection. Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. These inhibitors were discovered through an approach of in silico screening of available databases of bioactive peptides and polyphenolic compounds and the analysis of their docking modes. This process led to the selection of 9 compounds with optimal binding affinities to the target sites. The peptides (satpdb18674, satpdb18446, satpdb12488, satpdb14438, and satpdb28899) act on regions III and IV of the viral Spike protein and on its binding sites in GRP78. However, 4 polyphenols such as epigallocatechin gallate (EGCG), homoeriodictyol, isorhamnetin, and curcumin interact, in addition to the Spike protein and its binding sites in GRP78, with the ATPase domain of GRP78. Our work demonstrates that there are at least 2 approaches to block the spread of SARS-CoV-2 by preventing its fusion with the host cells via GRP78.

An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules

2020 ◽  
Vol 60 (10) ◽  
pp. 5188-5202
Author(s):  
Jean-Rémy Marchand ◽  
Tim Knehans ◽  
Amedeo Caflisch ◽  
Andreas Vitalis
Keyword(s):  
Small Molecules ◽  
Binding Affinities

scholarly journals Voltage-dependent blockade of muscle Na+ channels by guanidinium toxins.

1984 ◽  
Vol 84 (5) ◽  
pp. 687-704 ◽  
Author(s):  
E Moczydlowski ◽  
S Hall ◽  
S S Garber ◽  
G S Strichartz ◽  
C Miller
Keyword(s):  
Voltage Dependence ◽  
Single Channel ◽  
Membrane Vesicles ◽  
Hydroxyl Groups ◽  
Binding Affinities ◽  
Na Channels ◽  
Plasma Membrane Vesicles ◽  
Toxin Binding ◽  
Voltage Dependent ◽  
Toxin Receptor

Na+ channels from rat muscle plasma membrane vesicles were inserted into neutral planar phospholipid bilayers and were activated by batrachotoxin. Single channel blocking events induced by the addition of various guanidinium toxins were analyzed to derive the rates of channel-toxin association and dissociation. Blocking by tetrodotoxin, saxitoxin, and six natural saxitoxin derivatives containing sulfate or hydroxyl groups were studied. Although the binding affinities vary over 2,000-fold, all of the toxins exhibit identical voltage dependence of the blocking reactions, regardless of the toxin's net charge. The results suggest that the voltage dependence of toxin binding is due to a voltage-dependent conformational equilibrium of the toxin receptor, rather than to direct entry of the charged toxin molecule into the applied transmembrane electric field.

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