The structure of a valinomycin–hexaaquamagnesium trifluoromethanesulfonate compound

2016 ◽  
Vol 72 (8) ◽  
pp. 627-633
Author(s):  
Megumi Fujita ◽  
Amaan M. Kazerouni ◽  
John Bacsa
Keyword(s):  
Hydrogen Bonds ◽  
Metal Binding ◽  
Binding Mode ◽  
Cation Binding ◽  
Acetonitrile Solution ◽  
Binding Modes ◽  
Carbonyl Groups ◽  
Amide Hydrogen ◽  
Amide Carbonyl

Valinomycin is a naturally occurring cyclic dodecadepsipeptide with the formulacyclo-[D-HiVA→L-Val →L-LA→L-Val]3(D-HiVA is D-α-hydroxyisovaleic acid, Val is valine and LA is lactic acid), which binds a K+ion with high selectively. In the past, several cation-binding modes have been revealed by X-ray crystallography. In the K+, Rb+and Cs+complexes, the ester O atoms coordinate the cation with a trigonal antiprismatic geometry, while the six amide groups form intramolecular hydrogen bonds and the network that is formed has a bracelet-like conformation (Type 1 binding). Type 2 binding is seen with the Na+cation, in which the valinomycin molecule retains the bracelet conformation but the cations are coordinated by only three ester carbonyl groups and are not centrally located. In addition, a picrate counter-ion and a water molecule is found at the center of the valinomycin bracelet. Type 3 binding is observed with divalent Ba2+, in which two cations are incorporated, bridged by two anions, and coordinated by amide carbonyl groups, and there are no intramolecular amide hydrogen bonds. In this paper, we present a new Type 4 cation-binding mode, observed in valinomycin hexaaquamagnesium bis(trifluoromethanesulfonate) trihydrate, C54H90N6O18·[Mg(H2O)6](CF3SO3)2·3H2O, in which the valinomycin molecule incorporates a whole hexaaquamagnesium ion, [Mg(H2O)6]2+,viahydrogen bonding between the amide carbonyl groups and the hydrate water H atoms. In this complex, valinomycin retains the threefold symmetry observed in Type 1 binding, but the amide hydrogen-bond network is lost; the hexaaquamagnesium cation is hydrogen bonded by six amide carbonyl groups.1H NMR titration data is consistent with the 1:1 binding stoichiometry in acetonitrile solution. This new cation-binding mode of binding a whole hexaaquamagnesium ion by a cyclic polypeptide is likely to have important implications for the study of metal binding with biological models under physiological conditions.

scholarly journals 2-({[(Pyridin-1-ium-2-ylmethyl)carbamoyl]formamido}methyl)pyridin-1-ium bis(3,5-dicarboxybenzoate): crystal structure and Hirshfeld surface analysis

2016 ◽  
Vol 72 (2) ◽  
pp. 241-248 ◽  
Author(s):  
Mukesh M. Jotani ◽  
Sabrina Syed ◽  
Siti Nadiah Abdul Halim ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Torsion Angle ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Carbonyl Groups ◽  
Amide Hydrogen ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
First Approximation

The asymmetric unit of the title salt, C14H16N4O22+·2C9H5O6−, comprises half a dication, being located about a centre of inversion, and one anion, in a general position. The central C4N2O2group of atoms in the dication are almost planar (r.m.s. deviation = 0.009 Å), and the carbonyl groups lie in anantidisposition to enable the formation of intramolecular amide-N—H...O(carbonyl) hydrogen bonds. To a first approximation, the pyridinium and amide N atoms lie to the same side of the molecule [Npy—C—C—Namidetorsion angle = 34.8 (2)°], and theantipyridinium rings are approximately perpendicular to the central part of the molecule [dihedral angle = 68.21 (8)°]. In the anion, one carboxylate group is almost coplanar with the ring to which it is connected [Cben—Cben—Cq—O torsion angle = 2.0 (3)°], whereas the other carboxylate and carboxylic acid groups are twisted out of the plane [torsion angles = 16.4 (3) and 15.3 (3)°, respectively]. In the crystal, anions assemble into layers parallel to (10-4)viahydroxy-O—H...O(carbonyl) and charge-assisted hydroxy-O—H...O(carboxylate) hydrogen bonds. The dications are linked into supramolecular tapes by amide-N—H...O(amide) hydrogen bonds, and thread through the voids in the anionic layers, being connected by charge-assisted pyridinium-N—O(carboxylate) hydrogen bonds, so that a three-dimensional architecture ensues. An analysis of the Hirshfeld surface points to the importance of O—H...O hydrogen bonding in the crystal structure.

scholarly journals Structural Effects of Cation Binding to DPPC Monolayers

2020 ◽  
Author(s):  
Matti Javanainen ◽  
Wei Hua ◽  
Ondrej Tichacek ◽  
Pauline Delcroix ◽  
Lukasz Cwiklik ◽  
...  
Keyword(s):  
Radical Change ◽  
Binding Mode ◽  
Cation Binding ◽  
Head Group ◽  
Binding Modes ◽  
Sum Frequency ◽  
Area Per Lipid ◽  
Simulation And Experiment ◽  
Lipid Head Group ◽  
Dynamics Simulations

Ions at the two sides of the plasma membrane maintain the transmembrane potential, participate in signaling, and affect the properties of the membrane itself. The extracellular leaflet is particularly enriched in phosphatidylcholine lipids an under the influence of Na+, Ca2+, and Cl− ions. In this work, we combined molecular dynamics simulations performed using state-of-the-art models with vibrational sum frequency generation (VSFG) spectroscopy to study the effects of these key ions on the structure of dipalmitoylphosphatidylcholine. We used lipid monolayers as a proxy for membranes, as this approach enabled a direct comparison between simulation and experiment. We find that the effects of Na+ are minor. Ca2+, on the other hand, strongly affects the lipid head group conformations and induces a tighter packing of lipids, thus promoting the liquid condensed phase. It does so by binding to both the phosphate and carbonyl oxygens via direct and water-mediated binding modes, the ratios of which depend on the monolayer packing. Clustering analysis performed on simulation data revealed that changes in area per lipid or CaCl2 concentration both affect the head group conformations, yet their effects are anti-correlated. Cations at the monolayer surface also attract Cl−, which at large CaCl2 concentrations penetrates deep to the monolayer. This phenomenon coincides with a radical change in the VSFG spectra of the phosphate group, thus indicating the emergence of a new binding mode.

scholarly journals (2R,3R)-3-O-Benzoyl-N-benzyltartramide

2012 ◽  
Vol 68 (6) ◽  
pp. o1891-o1892
Author(s):  
Izabela D. Madura ◽  
Janusz Zachara ◽  
Urszula Bernaś ◽  
Halina Hajmowicz ◽  
Ludwik Synoradzki
Keyword(s):  
Hydrogen Bonds ◽  
Molecular Conformation ◽  
Layer Structure ◽  
Supramolecular Assembly ◽  
Double Layers ◽  
Carbonyl Groups ◽  
Compound C ◽  
Double Layer Structure ◽  
Oxobutanoic Acid ◽  
Amide Carbonyl

The title compound, C18H17NO6 [systematic name: (2R,3R)-4-benzylamino-2-benzoyloxy-3-hydroxy-4-oxobutanoic acid], is the first structurally characterized unsymmetrical monoamide–monoacyl tartaric acid derivative. The molecule shows a staggered conformation around the tartramide Csp3 —Csp3 bond with trans-oriented carboxyl and amide groups. The molecular conformation is stabilized by an intramolecular N—H...O hydrogen bond. In the crystal, molecules are linked by O—H...O hydrogen bonds between the carboxyl and amide carbonyl groups, forming translational chains along [001]. Further O—H...O and N—H...O hydrogen bonds as well as weaker C—H...O and C—H...π intermolecular interactions extend the supramolecular assembly into a double-layer structure parallel to (100). There are no directional interactions between the double layers.

scholarly journals Structural Effects of Cation Binding to DPPC Monolayers

2020 ◽  
Author(s):  
Matti Javanainen ◽  
Wei Hua ◽  
Ondrej Tichacek ◽  
Pauline Delcroix ◽  
Lukasz Cwiklik ◽  
...  
Keyword(s):  
Radical Change ◽  
Binding Mode ◽  
Cation Binding ◽  
Head Group ◽  
Binding Modes ◽  
Sum Frequency ◽  
Area Per Lipid ◽  
Simulation And Experiment ◽  
Lipid Head Group ◽  
Dynamics Simulations

Ions at the two sides of the plasma membrane maintain the transmembrane potential, participate in signaling, and affect the properties of the membrane itself. The extracellular leaflet is particularly enriched in phosphatidylcholine lipids an under the influence of Na+, Ca2+, and Cl− ions. In this work, we combined molecular dynamics simulations performed using state-of-the-art models with vibrational sum frequency generation (VSFG) spectroscopy to study the effects of these key ions on the structure of dipalmitoylphosphatidylcholine. We used lipid monolayers as a proxy for membranes, as this approach enabled a direct comparison between simulation and experiment. We find that the effects of Na+ are minor. Ca2+, on the other hand, strongly affects the lipid head group conformations and induces a tighter packing of lipids, thus promoting the liquid condensed phase. It does so by binding to both the phosphate and carbonyl oxygens via direct and water-mediated binding modes, the ratios of which depend on the monolayer packing. Clustering analysis performed on simulation data revealed that changes in area per lipid or CaCl2 concentration both affect the head group conformations, yet their effects are anti-correlated. Cations at the monolayer surface also attract Cl−, which at large CaCl2 concentrations penetrates deep to the monolayer. This phenomenon coincides with a radical change in the VSFG spectra of the phosphate group, thus indicating the emergence of a new binding mode.

scholarly journals Crystallization-induced amide bond formation creates a boron-centered spirocyclic system

2017 ◽  
Vol 23 (3) ◽  
pp. 167-169 ◽  
Author(s):  
Brighid B. Pappin ◽  
Stephan M. Levonis ◽  
Peter C. Healy ◽  
Milton J. Kiefel ◽  
Michela I. Simone ◽  
...  
Keyword(s):  
Amide Bond ◽  
Lewis Acidity ◽  
Carbonyl Groups ◽  
Amide Hydrogen ◽  
Tetrahedral Complex ◽  
Packing Structure ◽  
Amide Bond Formation ◽  
Amide Carbonyl ◽  
Crystallization Conditions ◽  
Aminophenylboronic Acid

AbstractThe 5-nitrosalicylate ester of 2-acetamidophenylboronic acid (C15H10BN2O6) is formed under crystallization conditions from the 5-nitrosalicylate ester of 2-aminophenylboronic acid. The boron at the center of this structure exists as a tetrahedral complex produced by a dative bond with the amide carbonyl. The perpendicular shape produces an unusual packing structure including a bifurcated hydrogen bond between the amide hydrogen and carbonyl groups on two neighboring molecules. We propose that this reaction occurs due to increased Lewis acidity of the nitrosalicylate ester of 2-aminophenylboronic acid.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

2017 ◽  
Author(s):  
Samuel Gill ◽  
Nathan M. Lim ◽  
Patrick Grinaway ◽  
Ariën S. Rustenburg ◽  
Josh Fass ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Recent Success ◽  
Multiple Binding ◽  
Proper Sampling

<div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div>

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

2018 ◽  
Author(s):  
Samuel Gill ◽  
Nathan M. Lim ◽  
Patrick Grinaway ◽  
Ariën S. Rustenburg ◽  
Josh Fass ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Recent Success ◽  
Multiple Binding ◽  
Proper Sampling

<div>Accurately predicting protein-ligand binding is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation timescales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes.</div><div><br></div><div>In this technique the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over two orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step towards applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding Modes of Ligands using Enhanced Sampling (BLUES) package which is freely available on GitHub.</div>

scholarly journals Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 686 ◽  
Author(s):  
Alexander Neumann ◽  
Viktor Engel ◽  
Andhika B. Mahardhika ◽  
Clara T. Schoeder ◽  
Vigneshwaran Namasivayam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
G Protein ◽  
Phenyl Ring ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Modes ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.

scholarly journals Discovery of New Inhibitors of Transforming Growth Factor-Beta Type 1 Receptor by Utilizing Docking and Structure-Activity Relationship Analysis

2019 ◽  
Vol 20 (17) ◽  
pp. 4090 ◽  
Author(s):  
Jiang ◽  
Deng
Keyword(s):  
Molecular Docking ◽  
Growth Factor ◽  
Transforming Growth Factor Beta ◽  
Transforming Growth Factor ◽  
Binding Modes ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Growth Factor Beta ◽  
New Compounds

The transforming growth factor-beta (TGF-β) plays an important role in pathological fibrosis and cancer transformation. Therefore, the inhibition of the TGF-β signaling pathway has therapeutic potential in the treatment of cancer. In this study, the binding modes between 47 molecules with a pyrrolotriazine-like backbone structure and transforming growth factor-beta type 1 receptor (TβR1) were simulated by molecular docking using Discovery Studio software, and their structure–activity relationships were analyzed. On the basis of the analysis of the binding modes of ligands in the active site and the structure–activity relationships, 29,254 new compounds were designed for virtual screening. According to the aforementioned analyses and Lipinski’s rule of five, five new compounds (CQMU1901–1905) with potential activity were screened through molecular docking. Among them, CQMU1905 is an attractive molecule composed of 5-fluorouracil (5-FU), 6-mercaptopurine (6-MP), and 5-azacytosine. Interestingly, 5-FU, 6-MP, and 5-azacytidine are often used as anti-metabolic agents in cancer treatment. Compared with existing compounds, CQMU1901–1905 can interact with target proteins more effectively and have good potential for modification, making them worthy of further study.

Crystal structure of pomalidomide Form I, C13H11N3O4

2021 ◽  
pp. 1-6
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Carbonyl Groups ◽  
Hydrogen Atoms ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
Amine Hydrogen

The crystal structure of pomalidomide Form I has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pomalidomide Form I crystallizes in the space group P-1 (#2) with a = 7.04742(9), b = 7.89103(27), c = 11.3106(6) Å, α = 73.2499(13), β = 80.9198(9), γ = 88.5969(6)°, V = 594.618(8) Å3, and Z = 2. The crystal structure is characterized by the parallel stacking of planes parallel to the bc-plane. Hydrogen bonds link the molecules into double layers also parallel to the bc-plane. Each of the amine hydrogen atoms acts as a donor to a carbonyl group in an N–H⋯O hydrogen bond, but only two of the four carbonyl groups act as acceptors in such hydrogen bonds. Other carbonyl groups participate in C–H⋯O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

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