New Dendrimers Containing a Single Cobaltocenium Unit Covalently Attached to the Apical Position of Newkome Dendrons:  Electrochemistry and Guest Binding Interactions with Cucurbit[7]uril†

Langmuir ◽  
2006 ◽  
Vol 22 (25) ◽  
pp. 10540-10544 ◽  
Author(s):  
David Sobransingh ◽  
Angel E. Kaifer
Keyword(s):  
Apical Position ◽  
Binding Interactions ◽  
Guest Binding

Tuning the Catalytic Activity of Cyclodextrin-Modified Palladium Nanoparticles through Host−Guest Binding Interactions

Langmuir ◽  
2001 ◽  
Vol 17 (22) ◽  
pp. 6762-6764 ◽  
Author(s):  
Jian Liu ◽  
Julio Alvarez ◽  
Winston Ong ◽  
Esteban Román ◽  
Angel E. Kaifer
Keyword(s):  
Catalytic Activity ◽  
Palladium Nanoparticles ◽  
Binding Interactions ◽  
Guest Binding

A Nexus between Theory and Experiment: Non-Empirical Quantum Mechanical Computational Methodology Applied to Cucurbit[n ]uril⋅Guest Binding Interactions

2016 ◽  
Vol 22 (48) ◽  
pp. 17226-17238 ◽  
Author(s):  
Jiří Hostaš ◽  
David Sigwalt ◽  
Marina Šekutor ◽  
Haresh Ajani ◽  
Matúš Dubecký ◽  
...  
Keyword(s):  
Quantum Mechanical ◽  
Binding Interactions ◽  
Guest Binding ◽  
Computational Methodology ◽  
Theory And Experiment

scholarly journals Enhancing binding affinity and selectivity through preorganization and cooperative enhancement of the receptor

2016 ◽  
Vol 52 (23) ◽  
pp. 4345-4348 ◽  
Author(s):  
Roshan W. Gunasekara ◽  
Yan Zhao
Keyword(s):  
Binding Affinity ◽  
Binding Interactions ◽  
Guest Binding

When direct host–guest binding interactions are weakened by unfavorable solvent competition, guest-triggered intrareceptor interactions could be used to augment the binding.

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

2020 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Computational Modelling ◽  
Free Energy Calculations ◽  
Energy Estimates ◽  
Binding Affinities ◽  
Spherical Coordinates ◽  
Collective Variables ◽  
Guest Binding ◽  
Starting Point ◽  
Sampl Challenge

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

Cambiarenes: Single-Step Synthesis and Anion Binding of a Clip- Shaped Macrocycle with a Redox-Active Core

2019 ◽  
Author(s):  
Riley J. Petersen ◽  
Brett J. Rozeboom ◽  
Shalisa Oburn ◽  
Nolan Blythe ◽  
Tanner Rathje ◽  
...  
Keyword(s):  
Electron Density ◽  
Single Step ◽  
Anion Binding ◽  
Host Molecule ◽  
Selective Binding ◽  
The Core ◽  
Redox Active ◽  
Active Core ◽  
Guest Binding

<div>We report the synthesis of a novel macrocyclic host molecule that forms in a single step from commercially available starting materials. The core of the macrocycle backbone possesses two quinone rings and, thus, is redox-active. Host-guest binding involving the clip-shaped cavity indicates selective binding of pyridine <i>N</i>-oxides based of the electron density of and steric bulk of the anionic oxygen.</div>

scholarly journals Front Cover: Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages (Eur. J. Org. Chem. 4/2021)

2021 ◽  
Vol 2021 (4) ◽  
pp. 512-512
Author(s):  
Jeroen P. J. Bruekers ◽  
Matthijs A. Hellinghuizen ◽  
Nicolas Vanthuyne ◽  
Paul Tinnemans ◽  
Pieter J. Gilissen ◽  
...  
Keyword(s):  
Front Cover ◽  
Double Decker ◽  
Guest Binding

scholarly journals Binding Interactions of Peptide Aptamers

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 6055
Author(s):  
Roger R. C. New ◽  
Tam T. T. Bui ◽  
Michal Bogus
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Cyclic Peptides ◽  
Binding Interactions ◽  
Peptide Aptamers ◽  
Linear Peptide ◽  
Signalling Molecules ◽  
Antibody Binding Site ◽  
Linear Chains ◽  
Protein Receptors

Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.

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