Publications (18)24.56 Total impact
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Article: 1,4-Bis(3-chloro-pyrazin-2-yl-oxy)benzene.
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ABSTRACT: In the title compound, C14H8Cl2N4O2, the pyrazine rings are orthogonal to the benzene ring, making dihedral angles of 88.42 (8) and 89.22 (8)°. The Cl atoms attached to the pyrazine rings deviate by -0.0597 (5) and 0.0009 (5) Å from the ring plane. The crystal structure features C-H⋯N hydrogen bonds.Acta Crystallographica Section E Structure Reports Online 04/2013; 69(Pt 4):o611. · 0.35 Impact Factor -
Article: Use of europium ions for SAD phasing of lysozyme at the Cu Kα wavelength.
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ABSTRACT: Europium is shown to be a good anomalous scatterer in SAD phasing for solving the structure of biological macromolecules. The large value of the anomalous contribution of europium, f'' = 11.17 e(-), at the Cu Kα wavelength is an advantage in de novo phasing and automated model building. Tetragonal crystals of hen egg-white lysozyme (HEWL) incorporating europium(III) chloride (50 mM) were obtained which diffracted to a resolution of 2.3 Å at a wavelength of 1.54 Å (Cu Kα). The master data set (360° frames) was split and analyzed for anomalous signal-to-noise ratio, multiplicity, completeness, SAD phasing and automated building. The structure solution and model building of the split data sets were carried out using phenix.autosol and phenix.autobuild. The contributions of the Eu ions to SAD phasing using in-house data collection are discussed. This study revealed successful lysozyme phasing by SAD using laboratory-source data involving Eu ions, which are mainly coordinated by the side chains of Asn46, Asp52 and Asp101 together with some water molecules.Acta Crystallographica Section F Structural Biology and Crystallization Communications 01/2013; 69(Pt 1):20-4. · 0.51 Impact Factor -
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Dataset: bt6861
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Dataset: bt6825
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Article: (E)-1-(5-Iodo-thio-phen-2-yl)-3-(3,4,5-trimeth-oxy-phen-yl)prop-2-en-1-one.
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ABSTRACT: In the title compound, C(16)H(15)IO(4)S, the dihedral angle between the thio-phene and benzene rings is 11.50 (2)°. The methoxy O atoms deviate by 0.0060 (2), -0.1319 (2) and 0.0426 (2) Å from the phenyl ring plane. The crystal packing features C-H⋯O hydrogen bonds, which link the molecules into C(11) chains propagating in [100xxx].Acta Crystallographica Section E Structure Reports Online 10/2012; 68(Pt 10):o2921. · 0.35 Impact Factor -
Article: (E)-1-(5-Iodothiophen-2-yl)-3-(3,4,5- trimethoxyphenyl)prop-2-en-1-one
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ABSTRACT: In the title compound, C 16 H 15 IO 4 S, the dihedral angle between the thiophene and benzene rings is 11.50 (2) . The methoxy O atoms deviate by 0.0060 (2), À0.1319 (2) and 0.0426 (2) Å from the phenyl ring plane. The crystal packing features C—HÁ Á ÁO hydrogen bonds, which link the molecules into C(11) chains propagating in [100xxx].: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP 3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009). The authors thank the TBI X-ray facility, CAS in Crystal-lography and Biophysics, University of Madras, India, for the data collection and TS thanks the DST for an Inspire fellowship.09/2012; -
Article: Molecular docking and ex vivo pharmacological evaluation of constituents of the leaves of Cleistanthus collinus (Roxb.) (Euphorbiaceae).
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ABSTRACT: To investigate the involvement of alpha adrenergic receptors in hypotension induced by cleistanthin A and cleistanthin B. Cleistanthins A and B were isolated from the leaves of Cleistanthus collinus using a column chromatographic method and purified. Structures were confirmed by spectroscopic analysis. The compounds were prepared for molecular docking studies using Ligprep 2.3 module and Induced Fit Docking was carried out against α-1 adrenergic receptors using Glide. The ex vivo experiments were carried out on male Wistar rats. Under anaesthesia, the femoral vein and carotid artery were cannulated for drug administration and for monitoring the blood pressure, respectively. The effect of epinephrine, norepinephrine, acetylcholine, histamine and dopamine were recorded before and after the administration of cleistanthin A or cleistanthin B. The molecular docking studies showed favorable molecular interactions, glide score, energy and emodel. Cleistanthins A and B per se reduced the mean blood pressure and the effect was dose dependent. Both the compounds reduced the effect of epinephrine, norepinephrine and α-1 receptor activity of dopamine. Cleistanthin B significantly increased the duration of action of acetylcholine on mean blood pressure. The molecular docking and ex vivo studies conclude that cleistanthin A and cleistanthin B have significant α-1 adrenergic receptor antagonist effect on the peripheral vascular system.Indian Journal of Pharmacology 03/2012; 44(2):197-203. · 0.27 Impact Factor -
Article: Designing of Protein Kinase C β-II Inhibitors against Diabetic complications: Structure Based Drug Design, Induced Fit docking and analysis of active site conformational changes.
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ABSTRACT: Protein Kinase C β-II (PKC β-II) is an important enzyme in the development of diabetic complications like cardiomyopathy, retinopathy, neuropathy, nephropathy and angiopathy. PKC β-II is activated in vascular tissues during diabetic vascular abnormalities. Thus, PKC β-II is considered as a potent drug target and the crystal structure of the kinase domain of PKC β-II (PDB id: 2I0E) was used to design inhibitors using Structure-Based Drug Design (SBDD) approach. Sixty inhibitors structurally similar to Staurosporine were retrieved from PubChem Compound database and High Throughput Virtual screening (HTVs) was carried out with PKC β-II. Based on the HTVs results and the nature of active site residues of PKC β-II, Staurosporine inhibitors were designed using SBDD. Induced Fit Docking (IFD) studies were carried out between kinase domain of PKC β-II and the designed inhibitors. These IFD complexes showed favorable docking score, glide energy, glide emodel and hydrogen bond and hydrophobic interactions with the active site of PKC β-II. Binding free energy was calculated for IFD complexes using Prime MM-GBSA method. The conformational changes induced by the inhibitor at the active site of PKC β-II were observed for the back bone Cα atoms and side-chain chi angles. PASS prediction tool was used to analyze the biological activities for the designed inhibitors. The various physicochemical properties were calculated for the compounds. One of the designed inhibitors successively satisfied all the in silico parameters among the others and seems to be a potent inhibitor against PKC β-II.Bioinformation 01/2012; 8(12):568-73. -
Article: In-house SAD phasing with surface-bound cerium ions.
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ABSTRACT: The anomalous signal of cerium(III) ions present in a derivative of hen egg-white lysozyme (HEWL) crystals obtained by the addition of 0.025 M cerium chloride to the crystallization medium was used for phasing. X-ray intensity data were collected to 2 Å resolution using an in-house Cu Kα radiation data-collection facility. Phasing of a single-wavelength data set purely based on its f'' led to a clearly interpretable electron-density map. Automated substructure solution by AutoSol in PHENIX resulted in four highest peaks corresponding to cerium(III) ions with data limited to 3 Å resolution, and about 90% of the residues were built automatically by AutoBuild in PHENIX. Cerium(III) ions bound on the surface of the enzyme are found to interact mainly with the main-chain and side-chain carbonyl groups of Asn, Glu, Tyr and Asp and with water molecules. Ce(3+) ions were used as potential anomalous scatterers for the in-house single-wavelength anomalous scattering technique, and this is proposed as a tool for macromolecular phasing and for the study of the interactions of trivalent metal ions with proteins and other macromolecules.Acta Crystallographica Section F Structural Biology and Crystallization Communications 12/2011; 67(Pt 12):1662-5. · 0.51 Impact Factor -
Article: Active compound from the leaves of Vitex negundo L. shows anti-inflammatory activity with evidence of inhibition for secretory Phospholipase A2 through molecular docking
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ABSTRACT: Novel compounds with significant medicinal properties have gained much interest in therapeutic approaches for treating various inflammatory disorders like arthritis, odema and snake bites and the post-envenom (impregnating with venom) consequences. Inflammation is caused by the increased concentration of secretory Phospholipases A2 (sPLA2s) at the site of envenom. A novel compound Tris(2,4-di-tert-butylphenyl) phosphate (TDTBPP) was isolated from the leaves of Vitex negundo and the crystal structure was reported recently. The acute anti-inflammatory activity of TDTBPP was assessed by Carrageenan-induced rat paw odema method. TDTBPP reduced the raw paw odema volume significantly at the tested doses of 50 mg/kg and 70 mg/kg body weight. Molecular docking studies were carried out with the X-ray crystal structures of Daboia russelli pulchella’s (Vipera russelli, Indian Russell’s viper) venom sPLA2 and Human non-pancreatic secretory PLA2 (Hnps PLA2) as targets to illustrate the antiinflammatory and antidote activities of TDTBPP. Docking results showed hydrogen bond (H-bond) interaction with Lys69 residue lying in the anti-coagulant loop of D. russelli’s venom PLA2, which is essential in the catalytic activity of the enzyme and hydrophobic interactions with the residues at the binding site (His48, Asp49). Docking of TDTBPP with Hnps PLA2 structure showed coordination with calcium ion directly as well as through the catalytically important water molecule (HOH1260) located at the binding site.Bioinformation 10/2011; -
Article: Active compound from the leaves of Vitex negundo L. shows anti-inflammatory activity with evidence of inhibition for secretory Phospholipase A(2) through molecular docking.
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ABSTRACT: Novel compounds with significant medicinal properties have gained much interest in therapeutic approaches for treating various inflammatory disorders like arthritis, odema and snake bites and the post-envenom (impregnating with venom) consequences. Inflammation is caused by the increased concentration of secretory Phospholipases A(2) (sPLA(2)s) at the site of envenom. A novel compound Tris(2,4-di-tert-butylphenyl) phosphate (TDTBPP) was isolated from the leaves of Vitex negundo and the crystal structure was reported recently. The acute anti-inflammatory activity of TDTBPP was assessed by Carrageenan-induced rat paw odema method. TDTBPP reduced the raw paw odema volume significantly at the tested doses of 50 mg/kg and 70 mg/kg body weight. Molecular docking studies were carried out with the X-ray crystal structures of Daboia russelli pulchella's (Vipera russelli, Indian Russell's viper) venom sPLA(2) and Human non-pancreatic secretory PLA(2) (Hnps PLA(2)) as targets to illustrate the antiinflammatory and antidote activities of TDTBPP. Docking results showed hydrogen bond (H-bond) interaction with Lys69 residue lying in the anti-coagulant loop of D. russelli's venom PLA(2), which is essential in the catalytic activity of the enzyme and hydrophobic interactions with the residues at the binding site (His48, Asp49). Docking of TDTBPP with Hnps PLA(2) structure showed coordination with calcium ion directly as well as through the catalytically important water molecule (HOH1260) located at the binding site.Bioinformation 01/2011; 7(4):199-206. -
Article: Selection of an improved HDAC8 inhibitor through structure-based drug design.
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ABSTRACT: Histone deacetylases (HDACs) are enzymes, which catalyze the removal of acetyl moiety from acetyl-lysine within the histone proteins and promote gene repression and silencing resulting in several types of cancer. HDACs are important therapeutic targets for the treatment of cancer and related diseases. Hydroxamic acid inhibitors show promising results in clinical trials against carcinogenesis. 120 hydroxamic acid derivatives were designed as inhibitors based on hydrophobic pocket and the Zn (II) catalytic site of HDAC8 active site using Structure Based Drug Design (SBDD) approach. High Throughput Virtual screening (HTVs) was used to filter the effective inhibitors. Induced Fit Docking (IFD) studies were carried out for the screening of eight inhibitors using Glide software. Hydrogen bond, hydrophobic interactions and octahedral coordination geometry with Zn (II) were observed in the IFD complexes. Prime MM-GBSA calculation was carried out for the binding free energy, to observe the stability of docked complexes. The Lipinski's rule of five was analyzed for ADME/Tox drug likeliness using Qikprop simulation. These inhibitors have good inhibitory properties as they have favorable docking score, energy, emodel, hydrogen bond and hydrophobic interactions, binding free energy and ADME/Tox. However, one compound (Cmp22) successively satisfied all the studies among the eight compounds screened and seems to be a promising potent inhibitor against HDAC8.Bioinformation 01/2011; 7(3):134-41. -
Article: Structural analysis of actinidin and a comparison of cadmium and sulfur anomalous signals from actinidin crystals measured using in-house copper- and chromium-anode X-ray sources.
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ABSTRACT: The structure of the 24 kDa cysteine protease saru-actinidin from the fruit of Actinidia arguta Planch. (sarunashi) was determined by the cadmium/sulfur-SAD method with X-ray diffraction data collected using in-house Cu Kα and Cr Kα radiation. The anomalous scatterers included nine sulfurs and several cadmium ions from the crystallization solution. The high quality of the diffraction data, the use of chromium-anode X-ray radiation and the substantial anomalous signal allowed structure determination and automated model building despite both a low solvent content (<40%) and low data multiplicity. The amino-acid sequence of saru-actinidin was deduced from the cDNA and was modified based on experimental electron-density maps at 1.5 Å resolution. The active site of saru-actinidin is occupied by a cadmium ion and the active-site cysteine is found to be in an unmodified, cysteine sulfenic acid or cysteine sulfinic acid form. The cadmium sites, coordination geometries and polygonal water structures on the protein surface have also been extensively analyzed. An analysis and comparison of the sulfur/cadmium anomalous signals at the Cu Kα and Cr Kα wavelengths was carried out. It is proposed that the inclusion of cadmium salts in crystallization solutions coupled with chromium-anode radiation can provide a convenient route for structure determination.Acta crystallographica. Section D, Biological crystallography 12/2010; 66(Pt 12):1323-33. · 12.67 Impact Factor -
Article: Synthesis and structural study of thiacyclophanes utilizing dibromides and methane dithiolate.
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ABSTRACT: The synthesis of a series of thiacyclophanes and optically active binaphthol-based chiral thiacyclophanes is reported with XRD structure. Two diastereomeric tetrathiacyclophanes are designed and synthesized. The two diastereomers are evidenced by crystal structure; the single-crystal X-ray studies reveal that one of the isomers possesses an inherent property of self-assembling into a vertical stack of tunnel-like structures.The Journal of Organic Chemistry 05/2005; 70(8):3267-70. · 4.45 Impact Factor -
Article: Stereoselective synthesis of optically active disilanes and selective functionalization by the cleavage of silicon-naphthyl bonds with bromine.
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ABSTRACT: Optically active disilanes with one chiral silicon center, (R)-1,2-dimethyl-1-(naphth-1-yl)-1,2,2-triphenyldisilane and (R)-1,2,2-trimethyl-2-(4-methoxynaphth-1-yl)-1-(naphth-1-yl)-1-phenyldisilane, were obtained by the reaction of (S)-methyl(naphth-1-yl)phenylchlorosilane (> 99% ee) with methyldiphenylsilyllithium or by the reaction of methyldiphenylchlorosilane with optically active (S)-methyl(naphth-1-yl)phenylsilyllithium and by the reaction of (S)-methyl(naphth-1-yl)phenylchlorosilane (> 99% ee) with dimethyl(4-methoxynaphth-1-yl)silyllithium. Under the optimized conditions, the reactions proceeded with almost complete inversion for the cholorosilanes and retention for the silyl anions. Optically active disilanes with two chiral centers, (1R,2R)-1,2-dimethyl-1,2-di(naphth-1-yl)-1,2-diphenyldisilane and (1S,2S)-1,2-di(4-methoxynaphth-1-yl)-1,2-dimethyl-1,2-diphenyldisilane, were obtained in high optical purity by the reactions of corresponding optically active halogenosilanes (Cl or F) with optically active silyllithiums. The silicon-silicon bond and the silicon-naphthyl bond of (R)-1,1,2-trimethyl-1,2-di(naphth-1-yl)-2-phenyldisilane and (1R,2R)-1,2-dimethyl-1,2-di(naphth-1-yl)-1,2-diphenyldisilane were cleaved without selectivity on bromination. The silicon-(4-methoxynaphth-1-yl) bond of (R)-1,2,2-trimethyl-2-(4-methoxynaphth-1-yl)-1-(naphth-1-yl)-1-phenyldisilane was regiospecifically cleaved, followed by the stereoselective cleavage of the remaining chiral silicon-naphthyl bond (94% inversion). Although the silicon-(4-methoxynaphth-1-yl) bonds of (1S,2S)-1,2-di(4-methoxynaphth-1-yl)-1,2-dimethyl-1,2-diphenyldisilane (> 99% ee) were regioselectively cleaved without silicon-silicon bond scission, remarkable racemization could not be avoided during the one-pot reaction.The Journal of Organic Chemistry 09/2004; 69(16):5383-9. · 4.45 Impact Factor -
Article: A novel discrete dinuclear copper(II)–gadolinium(III) complex derived from a Schiff base ligand [Cu(salbn)Gd(NO3)3·H2O] (salbn): N,N′-butylenebis(salicylideaminato)
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ABSTRACT: The synthesis, X-ray and e.p.r. spectral studies of a 3d–4f couple are described here. The crystal structure of [Cu(salbn)Gd(NO3)3H2O], (2), salbn = N,N-butylenebis(salicylideaminato), has been determined by X-ray crystallography. Compound (2) crystallizes in the monoclinic system, space group p21/n, with a = 9.025(1), b = 22.912(1), c = 12.790(1) , = 99.36(1), Z = 4. The deviations of the four coordinating atoms (O(1)O(2)N(1) and N(2) of salbn and the copper atom is displaced from the plane in spite of the lack of any apical ligand. The gadolinium(III) ion is nine-coordinated by the two oxygen atoms of the salbn moiety, three bidentate nitrate ions and one water molecule. The geometry of GdIII can be described as a square antiprism, in which compound CuII and GdIII are bridged by the two phenolic oxygens of salbn. The CuII–GdIII distance is 3.269(1) . The bridging core CuO2Gd is a butterfly shape. Significant distortion was observed for the complex having the larger diamino string. The title compound exhibits seven e.s.r. transitions with |D| = 0.0467 cm–1, which demonstrates the existence of zero field splitting. This outcome indicates that compound (2) consists of a perfectly isolated dinuclear Cu–Gd core and steric bulk alters the dihedral angle in the Cu–O–Gd bridge.Transition Metal Chemistry 01/2003; 28(6):644-649. · 1.02 Impact Factor -
Article: A novel discrete dinuclear copper(II)–gadolinium(III) complex derived from a Schiff base ligand [Cu(salbn)Gd(NO 3 ) 3 ·H 2 O] (salbn): N , N ′-butylenebis(salicylideaminato)
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ABSTRACT: The synthesis, X-ray and e.p.r. spectral studies of a 3d–4f couple are described here. The crystal structure of [Cu(salbn)Gd(NO 3 ) 3 ·H 2 O], (2) , salbn = N , N ′-butylenebis(salicylideaminato), has been determined by X-ray crystallography. Compound (2) crystallizes in the monoclinic system, space group p21/n, with a = 9.025(1), b = 22.912(1), c = 12.790(1) Å, β = 99.36(1), Z = 4. The deviations of the four coordinating atoms (O(1)O(2)N(1) and N(2) of salbn and the copper atom is displaced from the plane in spite of the lack of any apical ligand. The gadolinium(III) ion is nine-coordinated by the two oxygen atoms of the salbn moiety, three bidentate nitrate ions and one water molecule. The geometry of Gd III can be described as a square antiprism, in which compound Cu II and Gd III are bridged by the two phenolic oxygens of salbn. The Cu II –Gd III distance is 3.269(1) Å. The bridging core CuO2Gd is a butterfly shape. Significant distortion was observed for the complex having the larger diamino string. The title compound exhibits seven e.s.r. transitions with | D | = 0.0467 cm −1 , which demonstrates the existence of zero field splitting. This outcome indicates that compound (2) consists of a perfectly isolated dinuclear Cu–Gd core and steric bulk alters the dihedral angle in the Cu–O–Gd bridge. Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/43854/1/11243_2004_Article_5115383.pdf
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Institutions
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2005–2013
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University of Madras
- • Department of Crystallography and Biophysics
- • Department of Organic Chemistry
Chennai, State of Tamil Nadu, India
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2003
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Pondicherry University
Pondicherry, Union Territory of Puducherry, India
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