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.

Supramolecular self-assemblies of inverted cucurbit[7]uril with biogenic amines

2019 ◽  
Vol 43 (1) ◽  
pp. 407-412
Author(s):  
Pei-Hui Shan ◽  
Zhi-Rui Zhang ◽  
Dong Bai ◽  
Bing Bian ◽  
Zhu Tao ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Binding Affinity ◽  
Biogenic Amine ◽  
Binding Sites ◽  
Experimental Results ◽  
Binding Interactions ◽  
Strong Binding

The binding interactions between six biogenic amine guests and the iQ[7] host were investigated. The experimental results have revealed that iQ[7] shows strong binding affinity towards five of the studied biogenic amines, but not histamine, and that the binding sites are different depending on the structure of the biogenic amine.

Computational Design of Thiourea-based Cyclophane Sensors for Small Anions

2012 ◽  
Vol 65 (3) ◽  
pp. 303 ◽  
Author(s):  
Huifang Xie ◽  
Ming Wah Wong
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Density Functional ◽  
Computational Design ◽  
Binding Pocket ◽  
Solvent Medium ◽  
Guest Binding ◽  
Molecular Dynamics Calculations ◽  
Anion Complexes ◽  
Dynamics Simulations

The host–guest binding properties of a tri-thiourea cyclophane receptor (1) with several common anions have been investigated using density functional theory (DFT) and molecular dynamics calculations. Receptor 1 is predicted to be an effective receptor for binding small halogen and Y-shaped (NO3– and AcO–) anions in the gas phase, cyclohexane and chloroform. The calculated order of anion binding affinity for the receptor 1 in chloroform is F– > Cl– > AcO– > NO3– >Br– > H2PO4– > HSO4–. The binding free energies are strongly influenced by a dielectric solvent medium. The structures of the receptor–anion complexes are characterized by multiple (typically 6) hydrogen bonds in all cases. The overall binding affinity of various anions is determined by the basicity of anion, size and shape of the binding site, and solvent medium. Explicit chloroform solvent molecular dynamics simulations of selected receptor–anion complexes reveal that the anions are strongly bound within the binding pocket via hydrogen-bonding interactions to all the receptor protons throughout the simulation. A sulfur analogue of receptor 1 (2), with a larger central cavity, is shown to be a more effective sensor than 1 for small anions. Two different approaches to develop the thiourea-based cyclophane receptor into a chromogenic sensor were examined.

scholarly journals Correlation between Conformational Equilibria of Free Host and Guest Binding Affinity in Non-preorganized Receptors

2013 ◽  
Vol 78 (16) ◽  
pp. 7785-7795 ◽  
Author(s):  
Romen Carrillo ◽  
Ezequiel Q. Morales ◽  
Víctor S. Martín ◽  
Tomás Martín
Keyword(s):  
Binding Affinity ◽  
Guest Binding ◽  
Conformational Equilibria

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 Light-gated binding in double-motorized porphyrin cages

2021 ◽  
Author(s):  
Roeland Nolte ◽  
Pieter Gilissen ◽  
Nicolas Vanthuyne ◽  
Ben Feringa ◽  
Johannes Elemans
Keyword(s):  
Binding Affinity ◽  
1H Nmr ◽  
Molecular Motors ◽  
The Other ◽  
Chiral Chromatography ◽  
Guest Molecules ◽  
The Third ◽  
Guest Binding ◽  
Host Compound ◽  
Catalytic Applications

Molecular motors change conformation under the influence of light and when attached to host molecules they may find applications as sensors and switchable catalysts. Here we present a porphyrin macrocyclic host functionalized with two motor appendages for future catalytic applications. The compound is formed as a mixture of six stereoisomers (three sets of enantiomers), which have been separated by (chiral) chromatography. 1H NMR and chiral spectroscopy revealed that in one set of diastereomers the two motors interact with the cavity of the host (bound-bound), whereas in a second set one interacts and the other one does not (bound-loose). In the third set both motors do not interact with the host compound (loose-loose). The motorized hosts bind guest molecules in the order: (loose-loose) > (bound-loose) > (bound-bound). They can be switched with light to pseudo-identical diastereomers, leading to orthogonal behavior in the light-gated binding of guest molecules. Whereas the photo-isomerization of the diastereomer set loose-loose significantly lowers the binding affinity for viologen guests, the opposite is true for the diastereomer set bound-bound, i.e. the binding affinity increases. For the diastereomer set bound-loose no influence on guest binding is observed as the effect of photoisomerization on the motors is cancelled out.

scholarly journals Overview of the SAMPL6 host–guest binding affinity prediction challenge

2018 ◽  
Vol 32 (10) ◽  
pp. 937-963 ◽  
Author(s):  
Andrea Rizzi ◽  
Steven Murkli ◽  
John N. McNeill ◽  
Wei Yao ◽  
Matthew Sullivan ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Binding Affinity Prediction ◽  
Affinity Prediction ◽  
Guest Binding

scholarly journals Insight Derived from Molecular Docking and Molecular Dynamics Simulations into the Binding Interactions Between HIV-1 Protease Inhibitors and SARS-CoV-2 3CLpro

2020 ◽  
Author(s):  
peng sang ◽  
Shuhui Tian ◽  
Zhaohui Meng ◽  
Liquan Yang
Keyword(s):  
Molecular Docking ◽  
Protease Inhibitors ◽  
Binding Affinity ◽  
Proteinase Inhibitors ◽  
Binding Free Energy ◽  
Md Simulations ◽  
Respiratory Illness ◽  
Free Energy Calculations ◽  
Binding Interactions ◽  
Hiv 1

<p>A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) was identified from respiratory illness patients in Wuhan, Hubei Province, China, which has recently emerged as a serious threat to the world public health. Hower, no approved drugs have been found to effectively inhibit the virus. Since it has been reported that the HIV-1 protease inhibitors can be used as anti-SARS drugs by tegarting SARS-CoV 3CLpro, we choose six approved anti-HIV-1 drugs to investigate their binding interactions between 3CLpro, and to evaluate their potential to become clinical drugs for the new coronavirus pneumonia (COVID19) caused by SARS-CoV-2 infection. The molecular docking results indicate that, the 3CLpro of SARS-CoV-2 has a higher binding affinity for all the studied inhibitors than its SARS homologue. Two docking complexes (indinavir and darunavir) with high docking scores were futher subjected to MM-PBSA binding free energy calculations to detail the molecular interactions between these two proteinase inhibitors and the 3CLpro. Our results show that darunavir has the best binding affinity with SARS-CoV-2 and SARS-CoV 3CLpro among all inhibitors, indicating it has the potential to become an anti-COVID-19 clinical drug. The likely reason behind the increased binding affinity of HIV-1 protease inhibitors toward SARS-CoV2 3CLpro than that of SARS-CoV were investigated by MD simulations. Our study provides insight into the possible role of structural flexibility during interactions between 3CLpro and inhibitors, and sheds light on the structure-based design of anti-COVID-19 drugs targeting the SARS-CoV-2 3CLpro. </p><div><br></div>

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