scholarly journals Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach

2009 ◽  
Vol 131 (14) ◽  
pp. 144102 ◽  
Author(s):  
Li-Tien Cheng ◽  
Zhongming Wang ◽  
Piotr Setny ◽  
Joachim Dzubiella ◽  
Bo Li ◽  
...  
Keyword(s):  
Level Set ◽  
Hydrophobic Interactions ◽  
Implicit Solvent ◽  
Receptor Ligand

scholarly journals Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation

2013 ◽  
Vol 9 (3) ◽  
pp. 1778-1787 ◽  
Author(s):  
Zuojun Guo ◽  
Bo Li ◽  
Joachim Dzubiella ◽  
Li-Tien Cheng ◽  
J. Andrew McCammon ◽  
...  
Keyword(s):  
Free Energy ◽  
Level Set ◽  
Coulomb Field ◽  
Field Approximation ◽  
Implicit Solvent ◽  
Hydration Free Energy ◽  
Implicit Solvent Model ◽  
Solvent Model

scholarly journals Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

2016 ◽  
Vol 145 (5) ◽  
pp. 054114 ◽  
Author(s):  
Shenggao Zhou ◽  
Hui Sun ◽  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
Bo Li ◽  
...  
Keyword(s):  
Level Set ◽  
Implicit Solvent

scholarly journals Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

2012 ◽  
Vol 8 (2) ◽  
pp. 386-397 ◽  
Author(s):  
Zhongming Wang ◽  
Jianwei Che ◽  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
Bo Li ◽  
...  
Keyword(s):  
Level Set ◽  
Coulomb Field ◽  
Field Approximation ◽  
Implicit Solvent

scholarly journals Energy and Reactivity Profile and Proton Affinity Analysis of Rimegepant with Special Reference to its Potential Activity against SARS-Cov-2 Virus Proteins using Molecular Dynamics

2021 ◽  
Author(s):  
T Pooventhiran ◽  
Ephraim Felix Marondedze ◽  
Penny Poomani Govender ◽  
Utsab Bhattacharyya ◽  
D Jagadeeswara Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrophobic Interactions ◽  
Chemical Properties ◽  
Basis Set ◽  
Basis Sets ◽  
Implicit Solvent ◽  
B3lyp Functional ◽  
Potential Activity ◽  
Dynamics Simulations ◽  
Physical And Chemical

Abstract Rimegepant is a new medicine developed for the management of chronic headache due to migraine. This manuscript is an attempt to study the various structural, physical and chemical properties of the molecules. The molecule was optimised using B3LYP functional with 6-311G+(2d,p) basis set. Excited state properties of the compound were studied using CAM-B3LYP functional with same basis sets using IEFPCM model in methanol for the implicit solvent atmosphere. The various electronic descriptors helped to identify the reactivity behaviour and stability. The compound is found to possess good nonlinear optical properties in gas phase. The various intramolecular electronic delocalisations and non-covalent interactions were analysed and explained. As the compound contain several heterocyclic nitrogen atoms, they have potential proton abstraction features, which was analysed energetically. The most important result from this study is from the molecular docking analysis which indicates that rimegepant binds irreversibly with three established SARS-CoV-2 proteins with ID 6LU7, 6M03 and 6W63 with docking scores − 9.2988, -8.3629 and − 9.5421 kcal/mol respectively. Further assessment of docked complexes with molecular dynamics simulations revealed that hydrophobic interactions, water bridges and π – π interactions play a signification role in stabilising the ligand within the binding region of respective proteins. MMGBSA free energies further demonstrated that rimegepant is more stable when complexed with 6LU7 among the selected PDB models. As the pharmacology and pharmacokinetics of this molecule are already established, rimegepant can be considered as an ideal candidate with potential for use in the treatment of COVID patients after clinical studies.

scholarly journals Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach

2015 ◽  
Vol 11 (2) ◽  
pp. 753-765 ◽  
Author(s):  
Zuojun Guo ◽  
Bo Li ◽  
Li-Tien Cheng ◽  
Shenggao Zhou ◽  
J. Andrew McCammon ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Level Set ◽  
Binding Sites ◽  
Implicit Solvent ◽  
Ligand Binding Sites

Vergleich von Blutfluß und Benzodiazepin-Rezeptorverteilung bei fokaler Epilepsie: Vorläufige Ergebnisse einer SPECT-Studie

1989 ◽  
Vol 28 (05) ◽  
pp. 181-186
Author(s):  
A. Ludolph ◽  
O. Schober ◽  
G. Lottes ◽  
I. Böttger ◽  
H.-F. Beer ◽  
...  
Keyword(s):  
Human Brain ◽  
Receptor Binding ◽  
Brain Area ◽  
Brain Perfusion ◽  
Partial Epilepsy ◽  
Cerebral Lesion ◽  
Receptor Ligand ◽  
Receptor Mapping ◽  
Hmpao Spect ◽  
99Mtc Hmpao

99mTc-HMPAO-SPECT and SPECT with the 123I-labelled benzodiazepine (Bz) receptor ligand Ro 16-0154 were performed in 10 patients suffering from partial epilepsy, without cerebral lesion in MRT or CT. 2 h p.i. of Ro 16-0154 the distribution of activity correlated with the known distribution of Bz- receptors in the human brain. Perfusion and receptor-binding were found decreased in 7 patients of each study in the suspicious brain-area. 123l-labelled Ro 16-0154 is suitable for Bz-receptor mapping by SPECT. The decrease of Bz-receptor binding in epileptic foci, as described in PET-studies, was also detected by SPECT in 7 of 10 patients.

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