Molecular Insights of an Avian Species with Low Oxygen Affinity, the Crystal Structure of Duck T-State Methemoglobin.

Hemoglobin (Hb) is the key metalloprotein within red blood cells involved in oxygen transportation from lungs to body cells. The heme-iron atom inherent within Hb effectuates the mechanism of oxygen transportation and carbon dioxide removal. Structural investigations on avian Hb are limited when compared with the enormous work has been carried out on mammalian Hb. Here, the crystal structure of T-state methemoglobin (T-metHb) from domestic duck (Anas platyrhynchos), a low oxygen affinity avian species, determined to 2.1Å resolution is presented. Duck T-metHb crystallized in the orthorhombic space group C2221 with unit cell parameters a = 59.89, b = 109.42 and c = 92.07Å. The final refined model with R-factor: 19.5% and Rfree: 25.2% was obtained. The structural analysis reveals that duck T-metHb adopts a unique quaternary structure that is distinct from any of the avian liganded Hb structures. Moreover, it closely resembles the deoxy Hb of bar-headed goose, a high oxygen-affinity species. Besides the amino acid αPro119 located in the α1ß1 interface, a unique quaternary structure with a constrained heme environment is attributed for the intrinsic low oxygen-affinity of duck Hb. This study reports the first protein crystal structure of low oxygen-affinity avian T-metHb from Anas platyrhynchos.

Synthesis, spectroscopic, dielectric, molecular docking and DFT studies of (3E)-3-(4-methylbenzylidene)-3,4-dihydro-2H-chromen-2-one: an anticancer agent.

BACKGROUND: Coumarin (2H-chromen-2-one) and its derivatives have a wide range of biological and pharmaceutical activities. They possess antitumor, anti-HIV, anticoagulant, antimicrobial, antioxidant, and anti-inflammatory activities. Synthesis and isolation of coumarins from different species have attracted the attention of medicinal chemists. Herein, we report the synthesis, molecular structure, dielectric, anticancer activity and docking studies with the potential target protein tankyrase. RESULTS: Molecular structure of (3E)-3-(4-methylbenzylidene)-3,4-dihydro-2H-chromen-2-one (MBDC) is derived from quantum chemical calculations and compared with the experimental results. Intramolecular interactions, stabilization energies, and charge delocalization are calculated by NBO analysis. NLO property and dielectric quantities have also been determined. It indicates the formation of a hydrogen bonding between -OH group of alcohol and C=O of coumarin. The relaxation time increases with the increase of bond length confirming the degree of cooperation and depends upon the shape and size of the molecules. The molecule under study has shown good anticancer activity against MCF-7 and HT-29 cell lines. Molecular docking studies indicate that the MBDC binds with protein. CONCLUSIONS: In this study, the compound (3E)-3-(4-methylbenzylidene)-3,4-dihydro-2H-chromen-2-one was synthesized and characterized by spectroscopic studies. The computed and experimental results of NMR study are tabulated. The dielectric relaxation studies show the existence of molecular interactions between MBDC and alcohol. Theoretical results of MBDC molecules provide the way to predict various binding sites through molecular modeling and these results also support that the chromen substitution is more active in the entire molecule. Molecular docking study shows that MBDC binds well in the active site of tankyrase and interact with the amino acid residues. These results are compared with the anti cancer drug molecule warfarin derivative. The results suggest that both molecules have comparable interactions and better docking scores. The results of the antiproliferative activity of MBDC and Warfarin derivative against MCF-7 breast cancer and HT-29 colon cancer cell lines at different concentrations exhibited significant cytotoxicity. The estimated half maximal inhibitory concentration (IC 50) value for MBDC and Warfarin derivative was 15.6 and 31.2 µg/ml, respectively. This enhanced cytotoxicity of MBDC in MCF-7 breast cancer and HT-29 colon cancer cell lines may be due to their efficient targeted binding and eventual uptake by the cells. Hence the compound MBDC may be considered as a drug molecule for cancer.Graphical abstractThe binding mode of the ligand MBDC at active site of protein and the graphical representation of cell inhibition for MCF-7 and HT-29 cell lines.

Crystal structure of piperazine-1,4-diium bis-(4-amino-benzene-sulfonate).

The asymmetric unit of the title salt, C4H12N2 (2+)·2C6H6NO3S(-), consists of half a piperazindiium dication, located about an inversion centre, and a 4-amino-benzene-sulfonate anion. The piperazine ring adopts a chair conformation. In the crystal, the cations and anions are linked via N-H⋯O and C-H⋯O hydrogen bonds, forming a three-dimensional framework. Within the framework there are C-H⋯π inter-actions and the N-H⋯O hydrogen bonds result in the formation of R 4 (4)(22) and R 3 (4)(13) ring motifs.

Structure of liganded T-state haemoglobin from cat (Felis silvestris catus), a low oxygen-affinity species, in two different crystal forms.

Haemoglobin (Hb) is an iron-containing metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. Hb is in equilibrium between low-affinity tense (T) and high-affinity relaxed (R) states associated with its unliganded and liganded forms, respectively. Mammalian species can be classified into two groups on the basis of whether they express `high' or `low' oxygen-affinity Hbs. Although Hbs from the former group have been studied extensively, a more limited number of structural studies have been performed for low oxygen-affinity Hbs. Here, the crystal structure of low oxygen-affinity cat methaemoglobin (metHb) has been solved at 2.0 and 2.4 Šresolution in two different crystal forms. Even though both structures are fully liganded, they unusually adopt a T-state-like quaternary conformation but with several localized R-like tertiary-structural and quaternary-structural features. The study provides atomic-level insights into the ligand-binding properties of this Hb, including its low cooperativity, blunt response to allosteric effectors and low affinity for oxygen, as well as further contributing to the mechanism underlying Hb allostery.

Ethyl 3-(4-chloro-phen-yl)-2-phenyl-3-(4-phenyl-1,2,3-selena-diazol-5-yl)propano-ate.

In the title compound, C25H21ClN2O2Se, the selena-diazole ring is almost planar [maximum deviation = 0.004 (2) Å], and the adjacent benzene ring is twisted by 50.6 (1)° with respect to this ring.

1-Di-chloro-acetyl-t-3-isopropyl-r-2,c-6-di-phenyl-piperidin-4-one.

In the title compound, C22H23Cl2NO2, the piperidine ring adopts a twist-boat conformation. The phenyl rings substituted at the 2- and 6-positions of the piperidine ring subtend dihedral angles of 60.6 (2) and 84.2 (1)°, respectively, with the mean plane of the piperidine ring. In the crystal, mol-ecules are linked by C-H⋯O inter-actions into zigzag chains running along the c-axis direction.

Structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution.

Haemoglobin (Hb) is a tetrameric iron-containing protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. Pisces are the advanced aquatic vertebrates capable of surviving at wide depth ranges. The shortfin mako shark (SMS) is the pelagic, largest, fastest and most sophisticated species of the shark kingdom with well developed eyes. Mostly the pisces species are cold blooded in nature. Distinctly, the SMSs are warm-blooded animals with an advanced circulatory system. SMSs are capable of maintaining elevated muscle temperatures up to 33 K above the ambient water temperatures at a depth of 150-500 m. SMSs have a diverged air-breathing mechanism compared with other vertebrates. The haemoglobin molecule consists of four polypeptide chains, namely two α chains, each with 140 amino acids and two ß chains each having 136 amino acids. The SMS Hb was found to crystallize in monoclinic space group P21 using the hanging-drop vapour-diffusion method at room temperature. The crystal packing parameters for the SMS Hb structure contain one whole biological molecule in the asymmetric unit with a solvent content of 47%. The SMS Hb quaternary structural features interface-interface interactions and heme binding sites are discussed with different state Hbs and the results reveal that SMS Hb adopts an unliganded deoxy T state conformation.

3,5-Dimethyl-1-{2-[(5-methyl-1,3,4-thia-diazol-2-yl)sulfan-yl]acet-yl}-2,6-diphenylpiperidin-4-one.

In the title compound, C24H25N3O2S2, the piperidine ring adopts a distorted boat conformation. The phenyl rings subtend angles of 75.6 (1)° and 86.3 (1)° with the mean plane of the piperidine ring. In the crystal, mol-ecules are linked through a network C-H⋯N hydrogen bonds, forming zigzag chains along [100]. The thia-diazol ring methyl group is disordered over two positions with an occupancy ratio of 0.69 (4):0.31 (4).

2-Chloro-1-(2,4,4-trimethyl-2,3,4,5-tetra-hydro-1H-1,5-benzodiazepin-1-yl)ethanone.

In the title compound, C14H19ClN2O, the diazepine ring adopts a boat conformation. The Cl atom of the chloro-acetyl group is trans to the N atom of the diazepine ring. In the crystal, the mol-ecules form chains running along the diagonal of the ac plane through N-H⋯O hydrogen bonds.

4-(2-Hy-droxy-phen-yl)-3,5-di-thia-hepta-ne-dioic acid.

In the crystal of the title compound, C11H12O5S2, mol-ecules are linked by O-H⋯O hydrogen bonds and C-H⋯O inter-actions, forming a three-dimensional network.

1-(2,2-Di-chloro-acet-yl)-3-ethyl-2,6-di-phenyl-piperidin-4-one.

The asymmetric unit of the title compound, C21H21Cl2NO2, contains two independent mol-ecules that show similar geometrical features. The piperidine ring adopts a distorted boat conformation. The phenyl rings substituted at the 2- and 6-positions of the piperidine ring are oriented at angles of 65.4 (1) [64.7 (2)°] and 89.2 (1)° [86.3 (2)°] with respect to the least-squares plane of the piperidine ring. In the crystal, adjacent mol-ecules are linked by a network of C-H⋯O inter-actions, forming a C(6) chain along the c-axis direction.

1-Dichloro-acetyl-t-3,t-5-dimethyl-r-2,c-6-diphenyl-piperidin-4-one.

In the title compound, C21H21Cl2NO2, the piperidine ring adopts a distorted boat conformation. The phenyl rings substituted at the 2- and 6-positions of the piperidine ring subtend angles of 87.9 (7) and 70.8 (9)°, respectively, with the best plane through the piperidine ring. In the crystal, mol-ecules are connected by C-H⋯O and C-H⋯Cl inter-actions into layers in the ab plane.

2-Amino-6-methyl-pyridinium 4-hy-droxy-benzoate.

In the title mol-ecular salt, C6H9N2 (+)·C7H5O3 (-), the dihedral angle between the benzene ring and the CO2 group in the anion is 6.1 (2)°. In the crystal, the cation and anion are linked by N-H⋯O and C-H⋯O hydrogen bonds, and the anions are connected by O-H⋯O hydrogen bonds, forming a three-dimensional network.

5-[1-(4-Methyl-phen-yl)-2-nitro-but-yl]-4-phenyl-1,2,3-selenadiazole.

In the title compound, C19H19N3O2Se, the selenadiazole ring is roughly planar [maximum deviation 0.033 (6) Å]. The attached phenyl ring is twisted away at an angle of 47.5 (1)°. The butyl group is in an extended conformation [C-C-C-C torsion angle = 174.7 (2)°]. In the crystal, C-H⋯O inter-actions form C(10) chains running aling the c-axis direction.

Purification, crystallization and preliminary crystallographic studies of haemoglobin from mongoose (Helogale parvula) in two different crystal forms induced by pH variation.

Haemoglobin (Hb) is a respiratory pigment; it is a tetrameric protein that ferries oxygen from the lungs to tissues and transports carbon dioxide on the return journey. The oxygen affinity of haemoglobin is regulated by the concentration of oxygen surrounding it and several efforts have revealed the shapes of Hb in different states and with different functions. However, study of the molecular basis of Hbs from low-oxygen-affinity species is critically needed in order to increase the understanding of the mechanism behind oxygen adaptation. The present study reports the preliminary crystallographic study of low-oxygen-affinity haemoglobin from mongoose, a burrowing mammal. Haemoglobin from mongoose was purified by anion-exchange chromatography, crystallized using the hanging-drop vapour-diffusion method and diffraction data sets were collected from monoclinic (2.3 Å resolution) and orthorhombic (2.9 Å resolution) crystal forms obtained by pH variation. The monoclinic and orthorhombic asymmetric units contained half and a whole biological molecule, respectively.

3-Isopropyl-1-{2-[(1-methyl-1H-tetra-zol-5-yl)sulfan-yl]acet-yl}-2,6-di-phenyl-piperidin-4-one hemihydrate.

In the title compound, C24H27N5O2S·0.5H2O, the piperidine ring adopts a distorted boat conformation. The phenyl rings subtend dihedral angles of 69.7 (1) and 88.7 (1)° with the best plane through the piperidine moiety. In the crystal, symmetry-related mol-ecules are linked through a network of C-H⋯O and C-H⋯N inter-actions, the former connecting them into zigzag chains along the c-axis direction and the latter forming an R (2) 2(4)motif. The dimer formation (C-H⋯N) and the repetition of symmetry-related molecules (C-H⋯O) along the b-axis direction stabilize the packing mode. The water mol-ecule is located on a twofold rotation axis.

r-2,c-6-Di-phenyl-piperidine.

In the title compound, C17H19N, the piperidine ring adopts a chair conformation. The phenyl rings substituted at the 2- and 6-positions of the piperidine ring subtend dihedral angles of 81.04 (7) and 81.10 (7)° with the best plane of the piperidine ring. The crystal packing features C-H⋯π inter-actions.

3-Ethyl-cis-2,6-di-phenyl-piperidine.

In the title compound, C19H23N, the piperidine ring adopts a chair conformation. The phenyl rings at the 2,6-positions of the piperidine ring occupy equatorial orientations. The crystal structure features C-H⋯π inter-actions.

Ethyl 3-(4-meth-oxy-phen-yl)-2-phenyl-3-(4-phenyl-1,2,3-selenadiazol-5-yl)propano-ate.

In the title compound, C(26)H(24)N(2)O(3)Se, the selenadiazole ring is planar [maximum deviation = 0.002 (2) Å]. The dihedral angle between the selenadiazole ring and the attached phenyl ring is 49.00 (13)°. The crystal structure is stabilized by inter-molecular C-H⋯N and C-H⋯π inter-actions.