Molecular Binding Behavior of Pyridine-2,6-dicarboxamide-Bridged Bis(β-cyclodextrin) with Oligopeptides:  Switchable Molecular Binding Mode

2004 ◽  
Vol 15 (2) ◽  
pp. 300-306 ◽  
Author(s):  
Yu Liu ◽  
Guo-Song Chen ◽  
Yong Chen ◽  
Fei Ding ◽  
Tao Liu ◽  
...  
Keyword(s):  
Binding Mode ◽  
Molecular Binding ◽  
Binding Behavior

Molecular binding behavior of bipyridium derivatives by water-soluble carboxylato-biphen[3]arene

2015 ◽  
Vol 51 (30) ◽  
pp. 6621-6624 ◽  
Author(s):  
Junwei Ma ◽  
Hongmei Deng ◽  
Suxiang Ma ◽  
Jian Li ◽  
Xueshun Jia ◽  
...  
Keyword(s):  
Water Soluble ◽  
Molecular Binding ◽  
Binding Behavior

Complexation of paraquat derivatives and bis(N-mono-substituted bipyridine) cations by a negatively charged carboxylato-biphen[3]arene in water is described.

Molecular binding behavior of a bispyridinium-containing bis(β-cyclodextrin) and its corresponding [2]rotaxane towards bile salts

2014 ◽  
Vol 12 (16) ◽  
pp. 2559 ◽  
Author(s):  
Ying-Ming Zhang ◽  
Ze Wang ◽  
Yong Chen ◽  
Hong-Zhong Chen ◽  
Fei Ding ◽  
...  
Keyword(s):  
Bile Salts ◽  
Molecular Binding ◽  
Binding Behavior

scholarly journals Molecular binding mode of PF-232798, a clinical anti-HIV candidate, at chemokine receptor CCR5

2018 ◽  
Vol 40 (4) ◽  
pp. 563-568 ◽  
Author(s):  
Ya Zhu ◽  
Yan-long Zhao ◽  
Jian Li ◽  
Hong Liu ◽  
Qiang Zhao ◽  
...  
Keyword(s):  
Chemokine Receptor ◽  
Binding Mode ◽  
Molecular Binding ◽  
Chemokine Receptor Ccr5 ◽  
Anti Hiv ◽  
Receptor Ccr5

Spectrophotometric study of the selective binding behavior of aliphatic oligopeptides by bridged bis(β-cyclodextrin) linked by a 4,4′-diaminodiphenyl disulfide tether

2010 ◽  
Vol 88 (12) ◽  
pp. 1205-1212 ◽  
Author(s):  
Yang Yong-Cun ◽  
Chi Shao-Ming ◽  
Liu Ming-Hua ◽  
Huang Rong ◽  
Wang Yu-Fei ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Fluorescence Enhancement ◽  
Fluorescent Sensor ◽  
Binding Constants ◽  
2D Nmr ◽  
Binding Mode ◽  
Spectrophotometric Study ◽  
2D Nmr Spectroscopy ◽  
Binding Behavior ◽  
Guest Binding

The conformation and binding behavior of 4,4′-diaminodiphenyl disulfide bridged bis(β-cyclodextrin) (1) towards representative aliphatic oligopeptides, i.e., Leu-Gly, Gly-Leu, Glu-Glu, Met-Met, Gly-Gly, Gly-Gly-Gly, and Gly-Pro, were investigated by circular dichroism, fluorescence, and 1H and 2D NMR spectroscopy at 25 °C in phosphate buffer (pH 7.20). The results indicated that 1 acts as an efficient fluorescent sensor and displays remarkable fluorescence enhancement upon addition of optically inert oligopeptides. Owing to the cooperative host–linker–guest binding mode in which the linker and guest are coincluded in the two cyclodextrin cavities, the bis(β-cyclodextrin) 1 gives high binding constants of up to 103–104 (mol/L)–1 for oligopeptides. The bis(β-cyclodextrin) 1 can recognize not only the size and shape of oligopeptides but also the hydrophobicity, giving an exciting residue selectivity of up to 61.3 for the Gly-Leu/Glu-Glu pair. These phenomena are discussed from the viewpoints of multiple recognition and induce-fit interactions between host and guest.

Molecular Interactions of Fullerene-Based Derivatives and SARS-CoV-2

2020 ◽  
Author(s):  
Alaa El-DinA. Gawad ◽  
Ahmed M. Bayoumy ◽  
Medhat A. Ibrahim
Keyword(s):  
Molecular Docking ◽  
Hydrogen Bonds ◽  
Binding Sites ◽  
Electrostatic Interactions ◽  
Binding Mode ◽  
Spike Protein ◽  
Promising Candidate ◽  
Binding Behavior ◽  
Computer Aided ◽  
Differential Binding

Abstract There are no expedient proven to stop the outbreak of SARS-CoV-2 at this phase. This leads to diversity of endeavors to find out the effective drug or vaccine. One of these possibilities is to exploit the unique characteristics of fullerene-based derivatives. A computer-aided method (molecular docking) was applied to assess the differential binding behavior of these compounds and determining hydrophobic forces, electrostatic interactions, and hydrogen bonds played vital roles in the interactions with SARS-CoV-2 spike protein. The molecular docking calculation clarifies the binding mode and the binding sites may facilitate the development of new or improved therapeutic regimes effective against COVID-19. Fulleropyrrolidine-NH2 seems to be promising candidate for interacting with SARS-CoV-2 binding site.

scholarly journals Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Meng-Hsuan Lin ◽  
Chao-Cheng Cho ◽  
Yi-Chih Chiu ◽  
Chia-Yu Chien ◽  
Yi-Ping Huang ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Binding Mode ◽  
Biological Functions ◽  
Binding Properties ◽  
Binding Ability ◽  
Nad Metabolism ◽  
Ligand Selectivity ◽  
Physiological Temperature ◽  
Binding Behavior ◽  
Macro Domain

AbstractThe macro domain is an ADP-ribose (ADPR) binding module, which is considered to act as a sensor to recognize nicotinamide adenine dinucleotide (NAD) metabolites, including poly ADPR (PAR) and other small molecules. The recognition of macro domains with various ligands is important for a variety of biological functions involved in NAD metabolism, including DNA repair, chromatin remodeling, maintenance of genomic stability, and response to viral infection. Nevertheless, how the macro domain binds to moieties with such structural obstacles using a simple cleft remains a puzzle. We systematically investigated the Middle East respiratory syndrome-coronavirus (MERS-CoV) macro domain for its ligand selectivity and binding properties by structural and biophysical approaches. Of interest, NAD, which is considered not to interact with macro domains, was co-crystallized with the MERS-CoV macro domain. Further studies at physiological temperature revealed that NAD has similar binding ability with ADPR because of the accommodation of the thermal-tunable binding pocket. This study provides the biochemical and structural bases of the detailed ligand-binding mode of the MERS-CoV macro domain. In addition, our observation of enhanced binding affinity of the MERS-CoV macro domain to NAD at physiological temperature highlights the need for further study to reveal the biological functions.

Molecular binding behavior of water-soluble calix[4]arenes with asymmetric 4,4′-bipyridinium guests in aqueous solution: regioselective recognition or not?

2016 ◽  
Vol 14 (46) ◽  
pp. 10804-10811 ◽  
Author(s):  
Kui Wang ◽  
Jian-Hua Cui ◽  
Si-Yang Xing ◽  
Hong-Xi Dou
Keyword(s):  
Aqueous Solution ◽  
Water Soluble ◽  
Molecular Binding ◽  
Binding Behavior

A unique regioselective recognition of N-methyl-N′-(naphthalen-2-ylmethyl)-4,4′-bipyridinium bromide iodide using a p-sulfonatocalix[4]arene was found.

scholarly journals Improving Small-Molecule Force Field Parameters in Ligand Binding Studies

2021 ◽  
Vol 8 ◽  
Author(s):  
Stefano Raniolo ◽  
Vittorio Limongelli
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Small Molecules ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Binding Studies ◽  
Torsion Angles ◽  
Molecular Binding ◽  
Future Drug ◽  
Force Field Parameters

Small molecules are major players of many chemical processes in diverse fields, from material science to biology. They are made by a combination of carbon and heteroatoms typically organized in system-specific structures of different complexity. This peculiarity hampers the application of standard force field parameters and their in silico study by means of atomistic simulations. Here, we combine quantum-mechanics and atomistic free-energy calculations to achieve an improved parametrization of the ligand torsion angles with respect to the state-of-the-art force fields in the paradigmatic molecular binding system benzamidine/trypsin. Funnel-Metadynamics calculations with the new parameters greatly reproduced the high-resolution crystallographic ligand binding mode and allowed a more accurate description of the binding mechanism, when the ligand might assume specific conformations to cross energy barriers. Our study impacts on future drug design investigations considering that the vast majority of marketed drugs are small-molecules.

High affinity of p-sulfonatothiacalix[4]arene with phenanthroline-diium in aqueous solution

RSC Advances ◽  
2015 ◽  
Vol 5 (4) ◽  
pp. 2640-2646 ◽  
Author(s):  
Kui Wang ◽  
En-Cui Yang ◽  
Xiao-Jun Zhao ◽  
Yu Liu
Keyword(s):  
Aqueous Solution ◽  
Molecular Binding ◽  
Binding Behavior ◽  
High Affinity ◽  
Order Of Magnitude ◽  
Sulfonated Calixarenes

The molecular binding behavior of sulfonated calixarenes with phenanthroline-diium guests were systemically investigated. p-Sulfonatothiacalix[4]arene shows a high affinity with phenanthroline-diium guests in the order of magnitude of 105 M−1.

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