scholarly journals Generalized predictive model of estimation of inhibition of muscarinic receptors M1-M5

2020 ◽  
Vol 3 (3) ◽  
pp. e00129
Author(s):  
A.V. Mikurova ◽  
V.S. Skvortsov ◽  
V.V. Grigoryev
Keyword(s):  
Predictive Model ◽  
Muscarinic Receptors ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Regression Equations ◽  
Energy Characteristics ◽  
Value Prediction ◽  
M3 Receptor ◽  
The Mean

A general predictive model for assessing the inhibition constant (K<sub>i</sub>) value of human acetylcholine muscarinic receptors M1-M5 by potential ligands has been constructed. We used information on the three-dimensional structure of human M1, M2, M4, and M5 receptors, as well as a model of the M3 receptor constructed according to homology based on the structure of the rat M3 receptor. A set of complexes of known inhibitors with the target receptor constructed by means of molecular docking, was selected using an additional option: the coincidence of the spatial position of 4 pharmacophore points of a tested inhibitor and tiotropium, for which the position in the crystal structure was known. For five types of M receptors 199 complexes with known K<sub>i</sub> values were selected. Based on the data obtained during molecular dynamics simulation of these complexes by means of the MM-PBSA/MM-GBSA methods, their energy characteristics were calculated. They were used as independent variables in linear regression equations for pK<sub>i</sub> value prediction. The R<sup>2</sup> prediction for the generalized equation was 0.7, and the mean prediction error was 0.55 logarithmic units with a range for pK<sub>i</sub>=4.7.

scholarly journals Computational Evaluation of Selectivity of Inhibition of Muscarinic Receptors M1-M4

2018 ◽  
Vol 1 (3) ◽  
pp. e00072 ◽  
Author(s):  
A.V. Mikurova ◽  
V.S. Skvortsov ◽  
O.A. Raevsky
Keyword(s):  
Molecular Dynamics ◽  
Muscarinic Receptors ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Regression Equations ◽  
Energy Characteristics ◽  
Independent Variables ◽  
Computational Evaluation ◽  
Average Accuracy ◽  
M3 Receptor

A set of models for preliminary estimation of the inhibition constant values of potential ligands for the 4 acetylcholine muscarinic receptors M1-M4 was developed. The study uses an information about three-dimensional structure of human M1, M2 and M4 receptors, as well as the M3 receptor model, constructed by homology based on the structure of the rat M3 receptor. The Ki values for 42 compounds were obtained from the sources. Modeling of “protein-ligand” complexes was performed using molecular docking and molecular dynamics procedures. The component energy characteristics of the complexes were calculated from data obtained from simulation of molecular dynamics by the MM-PBSA/MM-GBSA methods. These characteristics were used as independent variables to construct the linear regression equations for pKi value predicting. The equations obtained for each receptors allow us to predict pKi with an average accuracy of 0.65 logarithmic units.

scholarly journals Brain capillary structures of schizophrenia cases and controls show a correlation with their neuron structures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rino Saiga ◽  
Masayuki Uesugi ◽  
Akihisa Takeuchi ◽  
Kentaro Uesugi ◽  
Yoshio Suzuki ◽  
...  
Keyword(s):  
Blood Vessels ◽  
Structural Parameters ◽  
Three Dimensional ◽  
Superior Temporal Gyrus ◽  
Anterior Cingulate ◽  
Dimensional Structure ◽  
Constant Diameter ◽  
The Mean ◽  
Cartesian Coordinate ◽  
Micrometer Scale

AbstractBrain blood vessels constitute a micrometer-scale vascular network responsible for supply of oxygen and nutrition. In this study, we analyzed cerebral tissues of the anterior cingulate cortex and superior temporal gyrus of schizophrenia cases and age/gender-matched controls by using synchrotron radiation microtomography or micro-CT in order to examine the three-dimensional structure of cerebral vessels. Over 1 m of cerebral blood vessels was traced to build Cartesian-coordinate models, which were then used for calculating structural parameters including the diameter and curvature of the vessels. The distribution of vessel outer diameters showed a peak at 7–9 μm, corresponding to the diameter of the capillaries. Mean curvatures of the capillary vessels showed a significant correlation to the mean curvatures of neurites, while the mean capillary diameter was almost constant, independent of the cases. Our previous studies indicated that the neurites of schizophrenia cases are thin and tortuous compared to controls. The curved capillaries with a constant diameter should occupy a nearly constant volume, while neurons suffering from neurite thinning should have reduced volumes, resulting in a volumetric imbalance between the neurons and the vessels. We suggest that the observed structural correlation between neurons and blood vessels is related to neurovascular abnormalities in schizophrenia.

scholarly journals (3R,5S,7R,8R,9S,10S,12S,13R,14S)-10,13-Dimethyl-17-[5-oxo-5-(prop-2-yn-1-yloxy)pentan-2-yl]hexadecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triyl triacetate

IUCrData ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
T. Kavitha ◽  
Devaraj Anandkumar ◽  
Perumal Rajakumar ◽  
Srinivasan Bargavi ◽  
Srinivasakannan Lakshmi
Keyword(s):  
Hydrogen Bonds ◽  
Cholic Acid ◽  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Terminal Alkyne ◽  
Compound C ◽  
Cyclopentane Ring ◽  
The Mean

In the title compound, C33H48O8, four terminal H atoms of cholic acid are replaced by three acetyl and one terminal alkyne group. All the acetyl residues are twisted with respect to the rings (A, B and C) to which they are attached. The cyclopentane ring D adopts an envelope conformation with the methyl-substituted C atom as the flap. Rings A, B and C have chair conformations. The dihedral angle between the mean planes of rings C and D is 4.70 (11)°. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming a three-dimensional structure.

scholarly journals Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca

2021 ◽  
Author(s):  
Patrick Brendan Timmons ◽  
Chandralal M Hewage
Keyword(s):  
Sodium Dodecyl ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Peptide Sequence ◽  
Helical Conformation ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Anticancer Activities ◽  
American Bullfrog ◽  
Α Helix

Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defense peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-d3 mixture. The structure is defined by an α-helix that spans between Ile6-Ala26, and a cyclic disulphide bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide's interactions with sodium dodecyl sulphate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its α-helical conformation between residues Ile6-Ala26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.

scholarly journals Crystal structure of ethyl 2′′,3-dioxo-7′,7a'-dihydro-1′H,3H,3′H-dispiro[benzo[b]thiophene-2,6′-pyrrolo[1,2-c]thiazole-5′,3′′-indoline]-7′-carboxylate

2015 ◽  
Vol 71 (3) ◽  
pp. o148-o149
Author(s):  
M. P. Savithri ◽  
M. Suresh ◽  
R. Raghunathan ◽  
R. Raja ◽  
A. SubbiahPandi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Ring System ◽  
Dimensional Structure ◽  
Thiazole Ring ◽  
Pyrrolidine Ring ◽  
Compound C ◽  
The Mean ◽  
Ring Motif

In the title compound, C23H20N2O4S2, the central pyrrolidine ring adopts an envelope conformation with the spiro C atom, shared with the benzothiophene ring system, as the flap. The thiazole ring has a twisted conformation on the S—C bond, where the C atom is that closest to methine C atom. The mean planes of the benzothiophene and indoline ring systems are inclined to the mean plane of the central pyrrolidine ring by 82.75 (8) and 80.03 (8)°, respectively, and to each other by 61.49 (6)°. In the crystal, molecules are linkedviapairs of N—H...O hydrogen bonds, forming inversion dimers with anR22(8) ring motif. The dimers are linkedviaC—H...O and C—H...N hydrogen bonds, forming a three-dimensional structure. The ethoxycarbonyl group is disordered over two orientations, with an occupancy ratio of 0.717 (12):0.283 (12).

scholarly journals Crystal structure of 10-ethyl-7-(9-ethyl-9H-carbazol-3-yl)-10H-phenothiazine-3-carbaldehyde

2017 ◽  
Vol 73 (5) ◽  
pp. 726-728 ◽  
Author(s):  
Vairavan Mahalakshmi ◽  
Siddan Gouthaman ◽  
Madurai Sugunalakshmi ◽  
Srinivasan Bargavi ◽  
Srinivasakannan Lakshmi
Keyword(s):  
Crystal Structure ◽  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Single Bond ◽  
Π Interactions ◽  
Compound C ◽  
Benzene Rings ◽  
The Mean

The title compound, C29H24N2OS, contains a phenothiazine moiety linked to a planar carbazole unit (r.m.s. deviation = 0.029 Å) by a C—C single bond. The phenothiazine moiety possesses a typical non-planar butterfly structure with a fold angle of 27.36 (9)° between the two benzene rings. The dihedral angle between the mean planes of the carbazole and phenothiazine units is 27.28 (5)°. In the crystal, molecules stack in pairs along thec-axis direction, linked by offset π–π interactions [intercentroid distance = 3.797 (1) Å]. There are C—H...π interactions present linking these dimers to form a three-dimensional structure.

scholarly journals Crystal structure of 13-(2-methoxyphenyl)-3,4-dihydro-2H-indazolo[1,2-b]phthalazine-1,6,11(13H)-trione

2015 ◽  
Vol 71 (8) ◽  
pp. o604-o605 ◽  
Author(s):  
Abdelmalek Bouraiou ◽  
Sofiane Bouacida ◽  
Hocine Merazig ◽  
Aissa Chibani ◽  
Zouhair Bouaziz
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Dimensional Structure ◽  
Π Interactions ◽  
Compound C ◽  
Cyclohexene Ring ◽  
Centroid Distance ◽  
The Mean

In the title compound, C22H18N2O4, the three fused rings of the pyrazolophthalazine moiety are coplanar (r.m.s. deviation = 0.027 Å). The cyclohexene ring fused to the pyrazolidine ring, so forming the indazolophthalazine unit, has a half-chair conformation. The benzene ring is almost normal to the mean plane of the pyrazolophthalazine moiety, with a dihedral angle of 87.21 (6)° between their planes. In the crystal, molecules are linked by pairs of C—H...O hydrogen bonds forming inversion dimers. The dimers are linkedviaC—H...π interactions, forming slabs parallel to (100). Between the slabs there are weak π–π interactions [shortest inter-centroid distance = 3.6664 (9) Å], leading to the formation of a three-dimensional structure.

scholarly journals Crystal structure of 1-[(2S*,4R*)-6-fluoro-2-methyl-1,2,3,4-tetrahydroquinolin-4-yl]pyrrolidin-2-one

2014 ◽  
Vol 70 (9) ◽  
pp. 153-156
Author(s):  
P. S. Pradeep ◽  
S. Naveen ◽  
M. N. Kumara ◽  
K. M. Mahadevan ◽  
N. K. Lokanath
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Bond Distance ◽  
Chair Conformation ◽  
Dimensional Structure ◽  
Pyrrolidine Ring ◽  
Charge Delocalization ◽  
Compound C ◽  
The Mean ◽  
Bond Character

In the title compound, C14H17FN2O, the 1,2,3,4-tetrahydropyridine ring of the quinoline moiety adopts a half-chair conformation, while the pyrrolidine ring has an envelope conformation with the central methylene C atom as the flap. The pyrrolidine ring lies in the equatorial plane and its mean plane is normal to the mean plane of the quinoline ring system, with a dihedral angle value of 88.37 (9)°. The bridging N—C bond distance [1.349 (3) Å] is substantially shorter than the sum of the covalent radii (dcov: C—N = 1.47 Å and C=N = 1.27 Å), which indicates partial double-bond character for this bond, resulting in a certain degree of charge delocalization. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds, forming sheets lying parallel to (10-1). These two-dimensional networks are linkedviaC—H...F hydrogen bonds and C—H...π interactions, forming a three-dimensional structure.

scholarly journals 4-(2-Nitrobenzyl)-3-phenyl-3,4-dihydro-2H-1,4-benzoxazin-2-ol

2014 ◽  
Vol 70 (8) ◽  
pp. o863-o864 ◽  
Author(s):  
Louisa Chouguiat ◽  
Raouf Boulcina ◽  
Sofiane Bouacida ◽  
Hocine Merazig ◽  
Abdelmadjid Debache
Keyword(s):  
Hydrogen Bonds ◽  
Phenyl Ring ◽  
Three Dimensional ◽  
Ring System ◽  
Dimensional Structure ◽  
Asymmetric Unit ◽  
Compound C ◽  
Dimensional Network ◽  
Oxazine Ring ◽  
The Mean

The title compound, C21H18N2O4, crystallizes with two independent molecules (AandB) in the asymmetric unit. In both molecules the oxazine ring has an envelope conformation with the hydroxyl-substituted C atom as the flap. The nitrobenzyl ring and the phenyl ring are almost normal to the mean plane of the benzooxazine ring system with dihdral angles of 85.72 (15) and 82.69 (15)°, respectively, in molecule A, and 85.79 (15) and 87.72 (15)°, respectively, in molecule B. The main difference in the conformation of the two molecules concerns the dihedral angle between the nitrobenzyl ring and the phenyl ring,viz.79.67 (18) in moleculeAand 71.13 (18)° in moleculeB. In the crystal, theAandBmolecules are linked by an O—H...O hydrogen bond. These units are then linkedviaC—H...O hydrogen bonds, forming sheets lying parallel to (010). Further C—H...O hydrogen bonds link the sheets to form a three-dimensional network. There are also O—H...π and C—H...π interactions present, reinforcing the three-dimensional structure.

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