scholarly journals Structure elucidation of β-cyclodextrin–xylazine complex by a combination of quantitative 1H–1H ROESY and molecular dynamics studies

2013 ◽  
Vol 9 ◽  
pp. 1917-1924 ◽  
Author(s):  
Syed Mashhood Ali ◽  
Kehkeshan Fatma ◽  
Snehal Dhokale
Keyword(s):  
Molecular Dynamics ◽  
Spin Diffusion ◽  
Structural Information ◽  
Mixing Time ◽  
H Nmr ◽  
Combined Use ◽  
Narrow Side ◽  
Roesy Spectrum ◽  
Cyclodextrin Cavity ◽  
Quantitative Roesy

The complexation of xylazine with β-cyclodextrin was studied in aqueous medium. 1H NMR titrations confirmed the formation of a 1:1 inclusion complex. A ROESY spectrum was recorded with long mixing time which contained TOCSY artifacts. It only confirmed the presence of xylazine aromatic ring in the β-cyclodextrin cavity. No information regarding the mode of penetration, from the wide or narrow side, could be obtained. We calculated the peak intensity ratio from the inter-proton distances for the most stable conformations obtained by molecular dynamics studies in vacuum. The results show that highly accurate structural information can be deduced efficiently by the combined use of quantitative ROESY and molecular dynamics analysis. On the other hand, a ROESY spectrum with no spin diffusion can only compliment an averaged ensemble conformation obtained by molecular dynamics which is generally considered ambiguous.

The Use of X-ray Absorption Spectra for Validation of Classical Force-Field Models

2016 ◽  
Vol 230 (4) ◽  
Author(s):  
Alexei Kuzmin ◽  
Andris Anspoks ◽  
Aleksandr Kalinko ◽  
Janis Timoshenko
Keyword(s):  
Molecular Dynamics ◽  
Fine Structure ◽  
Force Field ◽  
Structural Information ◽  
Md Simulations ◽  
Potential Models ◽  
X Ray ◽  
Combined Use ◽  
Complementary Techniques ◽  
X Ray Absorption

AbstractExtended X-ray absorption fine structure (EXAFS) spectroscopy and molecular dynamics (MD) simulations are two complementary techniques widely used to study the atomic structure of materials. Their combined use, known as the MD-EXAFS approach, allows one to access the structural information, encoded in EXAFS, far beyond the nearest coordination shells and to validate the accuracy of the interaction potential models. In this study we demonstrate the use of the MD-EXAFS method for a validation of several force-field models on an example of the cubic-perovskite SrTiO

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

scholarly journals Explanation of the Formation of Complexes between Representatives of Oxazolidinones and HDAS-β-CD Using Molecular Modeling as a Complementary Technique to cEKC and NMR

2021 ◽  
Vol 22 (13) ◽  
pp. 7139
Author(s):  
Wojciech Bocian ◽  
Elżbieta Bednarek ◽  
Katarzyna Michalska
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Chiral Separation ◽  
Structural Information ◽  
Binding Constants ◽  
Nmr Studies ◽  
Thermodynamics Of Complexation ◽  
Poisson Boltzmann ◽  
Explicit Water

Molecular modeling (MM) results for tedizolid and radezolid with heptakis-(2,3-diacetyl-6-sulfo)-β-cyclodextrin (HDAS-β-CD) are presented and compared with the results previously obtained for linezolid and sutezolid. The mechanism of interaction of chiral oxazolidinone ligands belonging to a new class of antibacterial agents, such as linezolid, tedizolid, radezolid, and sutezolid, with HDAS-β-CD based on capillary electrokinetic chromatography (cEKC), nuclear magnetic resonance (NMR) spectroscopy, and MM methods was described. Principles of chiral separation of oxazolidinone analogues using charged single isomer derivatives of cyclodextrin by the cEKC method were presented, including the selection of the optimal chiral selector and separation conditions, complex stoichiometry, and binding constants, which provided a comprehensive basis for MM studies. In turn, NMR provided, where possible, direct information on the geometry of the inclusion complexes and also provided the necessary structural information to validate the MM calculations. Consequently, MM contributed to the understanding of the structure of diastereomeric complexes, the thermodynamics of complexation, and the visualization of their structures. The most probable mean geometries of the studied supramolecular complexes and their dynamics (geometry changes over time) were determined by molecular dynamics methods. Oxazolidinone ligands have been shown to complex mainly the inner part of cyclodextrin, while the external binding is less privileged, which is consistent with the conclusions of the NMR studies. Enthalpy values of binding of complexes were calculated using long-term molecular dynamics in explicit water as well as using molecular mechanics, the Poisson–Boltzmann or generalized Born, and surface area continuum solvation (MM/PBSA and MM/GBSA) methods. Computational methods predicted the effect of changes in pH and composition of the solution on the strength and complexation process, and it adapted the conditions selected as optimal during the cEKC study. By changing the dielectric constant in the MM/PBSA and MM/GBSA calculations, the effect of changing the solution to methanol/acetonitrile was investigated. A fairly successful attempt was made to predict the chiral separation of the oxazolidinones using the modified cyclodextrin by computational methods.

scholarly journals SPECTRAL FEATURES AND HYDROGEN BOND STRUCTURE OF AQUEOUS SOLUTIONS OF ETHANOL

2021 ◽  
pp. 30-33
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Aqueous Solutions ◽  
Gaseous Medium ◽  
Water Molecules ◽  
Structural Reorganization ◽  
Intermolecular Hydrogen Bonds ◽  
Method Of Molecular Dynamics ◽  
Combined Use ◽  
Structure Of Aqueous Solutions

The aim of this work is develop an approach that makes it possible to study the spectral properties and structure of intermolecular hydrogen bonds in aqueous solutions of ethanol formed in systems whose existence in a gaseous medium or an isolated state is practically impossible. This approach bases on the combined use of infrared spectroscopy and molecular dynamics (MD) methods. An analysis give the structural reorganization of water molecules depending on the concentration of ethanol alcohol. It has been shown that the method of molecular dynamics with classical force fields makes it possible to explicitly take into account the molecules of the solvent and solute, and, thus, to investigate hydrogen bonds in the system and to interpret with the experimental data obtained by vibrational spectroscopy.

scholarly journals Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

2009 ◽  
Vol 62 (9) ◽  
pp. 1054 ◽  
Author(s):  
Defang Ouyang ◽  
Hong Zhang ◽  
Dirk-Peter Herten ◽  
Harendra S. Parekh ◽  
Sean C. Smith
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Structural Information ◽  
Structural Parameters ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Viral Gene ◽  
Conformational Structure ◽  
Crystal Forms ◽  
Gene Delivery Vectors

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A′-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist – over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A′-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

Heteroassociation of meso-sulfonatophenylporphyrins with β- and γ-cyclodextrin

2001 ◽  
Vol 05 (05) ◽  
pp. 465-473 ◽  
Author(s):  
ZOUBIR EL-HACHEMI ◽  
JOAN-ANTON FARRERA ◽  
HECTOR GARCÍA-ORTEGA ◽  
OSCAR RAMÍREZ-GUTÍERREZ ◽  
JOSEP M. RIBÓ
Keyword(s):  
Inclusion Complexes ◽  
Bulk Water ◽  
Hydrophobic Region ◽  
Water Solutions ◽  
H Nmr ◽  
Cyclodextrin Inclusion Complexes ◽  
Cyclodextrin Inclusion ◽  
Cyclodextrin Cavity ◽  
Nuclear Overhauser ◽  
Derivatives Of

The effect of the addition of β- and γ-cyclodextrin (β-CD, γ-CD) to water solutions ( D 2 O ) of the 4'-sulfonato derivatives of meso-tetraphenylporphyrin (TPPS4, TPPS3, TPPS2o and TPPS2a) was studied by 1 H NMR at several temperatures. In all cases the disaggregation of the porphyrin homoassociates was detected, although in most cases it was only partial. Nuclear Overhauser signals (ROESY) show that cyclodextrin inclusion complexes were formed with TPPS4, TPPS3, and TPPS2o, but not with TPPS2a. These complexes include the sulfonatophenyl groups as guest, but not the hydrophobic phenyl substituents. The geometry of the complexes corresponds to that in which the sulfonatophenyl substituent is introduced through the secondary face of β-CD and through the primary face of γ-CD. In the inclusion complexes the polar sulfonato group is inside the cyclodextrin cavity but near to the hydrophilic interface with the bulk water. This explains the absence of complexation in the case of cationic porphyrins such as 5,10,15,20-tetrakis(N-methylpyridin-4-yl)porphyrin (TMPyP), and the decrease in the solubility when the β-CD complex of 5,15-bis(4-sulfonatophenyl)porphyrin (DPPS2o) forms. Complexes of the cyclodextrins with porphyrin homoassociates were also detected. This indicates that the heteroassociation avoids the formation of staggered stacks of porphyrin homoassociates, but has less effect on the association through the hydrophobic region of the phenyl substituents. This last type of aggregation, which is not significantly affected by the addition of α-CD, explains why the hydrophobic phenyl substituents are not complexed by the cyclodextrins.

Recognition of bio-relevant dicarboxylate anions by an azacalix[2]arene[2]triazine derivative decorated with urea moieties

2015 ◽  
Vol 13 (10) ◽  
pp. 3070-3085 ◽  
Author(s):  
Miguel M. Santos ◽  
Igor Marques ◽  
Sílvia Carvalho ◽  
Cristina Moiteiro ◽  
Vítor Félix
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Affinity ◽  
H Nmr ◽  
Triazine Derivative ◽  
Wide Range ◽  
Dynamics Simulations ◽  
Nmr Titrations

The binding affinity of a dichlorocalix[2]arene[2]triazine based bis-urea azamacrocycle was investigated towards a wide range of bio-relevant dicarboxylate anions by a combination of 1H NMR titrations in CDCl3 and molecular dynamics simulations.

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