Displaying publications 121 - 140 of 200 in total

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  1. Samie N, Haerian B, Muniandy S, Green D, Ashouri M
    Appl Biochem Biotechnol, 2015 Apr;175(7):3397-417.
    PMID: 25820296 DOI: 10.1007/s12010-015-1513-6
    Our newly discovered metalloprotease, designated as ALP NS12 was selected using gelatin agar plates with incubation at 100 °C. Subcloning of the fragments in to pUC118 to make E. coli HB101 (pPEMP01NS) with following two-step chromatography using diethylaminoethyl sepharose (DEAE-sepharose) and Sephadex G-100 columns to purify 97-kDa expressed enzyme was performed. Although activity of immobilized ALP NS12 on glass surface was established at temperatures between 70 and 120 °C and pH ranges 4.0-13.0, the optimum temperature and pH were achieved at 100 °C and 11.0, respectively. Enhancement of enzyme activity was obtained in the presence of 5 mM MnCl2 (91 %), CaCl2 (357 %), FeCl2 (175 %), MgCl2 (94 %), ZnCl2 (412 %), NiCl (86 %), NaCl (239 %), and Na-sulfate (81 %) while inhibition was observed with EDTA (5 mM), PMSF (3 mM), urea (8 M), and SDS (1 %) at 65, 37, 33, and 42 %, respectively. Consequently, the enzyme was well analyzed using crystallography and protein modeling. ALP NS12 can be applied in industrial processes at extreme temperatures and under highly basic conditions, chelators, and detergents.
    Matched MeSH terms: Crystallography, X-Ray
  2. Usman A, Razak IA, Fun HK, Chantrapromma S, Zhao BG, Xu JH
    Acta Crystallogr C, 2002 Feb;58(Pt 2):o57-8.
    PMID: 11828107
    In the title compound, C(26)H(22)O(4), the pyranone ring adopts a twisted boat conformation, while the cyclohexane ring is close to an envelope conformation. The dihedral angle between the mean planes of the coumarin and naphthalene systems is 78.8(1) degree. The attached phenyl ring is in an equatorial position with respect to the cyclohexane ring.
    Matched MeSH terms: Crystallography, X-Ray
  3. Ataollahi F, Pramanik S, Moradi A, Dalilottojari A, Pingguan-Murphy B, Wan Abas WA, et al.
    J Biomed Mater Res A, 2015 Jul;103(7):2203-13.
    PMID: 24733741 DOI: 10.1002/jbm.a.35186
    Extracellular environments can regulate cell behavior because cells can actively sense their mechanical environments. This study evaluated the adhesion, proliferation and morphology of endothelial cells on polydimethylsiloxane (PDMS)/alumina (Al2 O3 ) composites and pure PDMS. The substrates were prepared from pure PDMS and its composites with 2.5, 5, 7.5, and 10 wt % Al2 O3 at a curing temperature of 50°C for 4 h. The substrates were then characterized by mechanical, structural, and morphological analyses. The cell adhesion, proliferation, and morphology of cultured bovine aortic endothelial (BAEC) cells on substrate materials were evaluated by using resazurin assay and 1,1'-dioctadecyl-1,3,3,3',3'-tetramethylindocarbocyanine perchlorate-acetylated LDL (Dil-Ac-LDL) cell staining, respectively. The composites (PDMS/2.5, 5, 7.5, and 10 wt % Al2 O3 ) exhibited higher stiffness than the pure PDMS substrate. The results also revealed that stiffer substrates promoted endothelial cell adhesion and proliferation and also induced spread morphology in the endothelial cells compared with lesser stiff substrates. Statistical analysis showed that the effect of time on cell proliferation depended on stiffness. Therefore, this study concludes that the addition of different Al2 O3 percentages to PDMS elevated substrate stiffness which in turn increased endothelial cell adhesion and proliferation significantly and induced spindle shape morphology in endothelial cells.
    Matched MeSH terms: Crystallography, X-Ray
  4. Tiekink ER, Zukerman-Schpector J
    Chem Commun (Camb), 2011 Jun 21;47(23):6623-5.
    PMID: 21455512 DOI: 10.1039/c1cc11173f
    Crystal structures of transition and main group element 1,1-dithiolates are shown to be partially sustained by C-H···π(chelate) interactions. For the planar binary bisdithiocarbamates, C-H···π(MS(2)C) interactions lead to aggregation patterns ranging from a 0-D four molecule aggregate to a 3-D architecture but with the majority of structures featuring 1-D or 2-D supramolecular assemblies.
    Matched MeSH terms: Crystallography, X-Ray
  5. Challabi AJH, Chieng BW, Ibrahim NA, Ariffin H, Zainuddin N
    Polymers (Basel), 2019 Mar 13;11(3).
    PMID: 30960466 DOI: 10.3390/polym11030482
    The effectiveness of superheated steam (SHS) as an alternative, eco-friendly treatment method to modify the surface of pineapple leaf fiber (PALF) for biocomposite applications was investigated. The aim of this treatment was to improve the interfacial adhesion between the fiber and the polymer. The treatment was carried out in an SHS oven for different temperatures (190⁻230 °C) and times (30⁻120 min). Biocomposites fabricated from SHS-treated PALFs and polylactic acid (PLA) at a weight ratio of 30:70 were prepared via melt-blending techniques. The mechanical properties, dimensional stability, scanning electron microscopy (SEM), and X-ray diffraction (XRD) for the biocomposites were evaluated. Results showed that treatment at temperature of 220 °C for 60 min gave the optimum tensile properties compared to other treatment temperatures. The tensile, flexural, and impact properties as well as the dimensional stability of the biocomposites were enhanced by the presence of SHS-treated PALF. The SEM analysis showed improvement in the interfacial adhesion between PLA and SHS-treated PALF. XRD analysis showed an increase in the crystallinity with the addition of SHS-PALF. The results suggest that SHS can be used as an environmentally friendly treatment method for the modification of PALF in biocomposite production.
    Matched MeSH terms: Crystallography, X-Ray
  6. Yi YX, Gaurav A, Akowuah GA
    Curr Drug Discov Technol, 2020;17(2):248-260.
    PMID: 30332967 DOI: 10.2174/1570163815666181017091655
    INTRODUCTION: The primary aim of this study is to understand the binding of curcumin and its analogues to different PDE4 subtypes and identify the role of PDE4 subtype inhibition in the anti-inflammatory property of curcumin. Docking analysis has been used to acquire the above mentioned structural information and this has been further used for designing of curcumin derivatives with better anti-inflammatory activity.

    MATERIALS AND METHODS: Curcumin and its analogues were subjected to docking using PDE4A, PDE4B, PDE4C and PDE4D as the targets. A data set comprising 18 analogues of curcumin, was used as ligands for docking of PDE4 subtypes. Curcumin was used as the standard for comparison. Docking was performed using AutoDock Vina 1.1.2 software integrated in LigandScout 4.1. During this process water molecules were removed from proteins, charges were added and receptor structures were minimised by applying suitable force fields. The docking scores were compared, and the selectivity of compounds for PDE4B over PDE4D was calculated as well.

    RESULTS: All curcumin analogues used in the study showed good binding affinity with all PDE4 subtypes, with evident selectivity towards PDE4B subtype. Analogue A11 provides the highest binding affinity among all ligands.

    CONCLUSION: Curcumin and analogues have moderate to strong affinity towards all PDE4 subtypes and have evident selectivity towards PDE4B. The Oxygen atom of the methoxy group plays a key role in PDE4B binding and any alterations could interfere with the binding. Tetrahydropyran side chain and heterocyclic rings are also suggested to be helpful in PDE4B binding.

    Matched MeSH terms: Crystallography, X-Ray
  7. Al-Najjar BO, Wahab HA, Tengku Muhammad TS, Shu-Chien AC, Ahmad Noruddin NA, Taha MO
    Eur J Med Chem, 2011 Jun;46(6):2513-29.
    PMID: 21482446 DOI: 10.1016/j.ejmech.2011.03.040
    Peroxisome Proliferator-Activated Receptor γ (PPARγ) activators have drawn great recent attention in the clinical management of type 2 diabetes mellitus, prompting several attempts to discover and optimize new PPARγ activators. With this in mind, we explored the pharmacophoric space of PPARγ using seven diverse sets of activators. Subsequently, genetic algorithm and multiple linear regression analysis were employed to select an optimal combination of pharmacophoric models and 2D physicochemical descriptors capable of accessing self-consistent and predictive quantitative structure-activity relationship (QSAR) (r2(71)=0.80, F=270.3, r2LOO=0.73, r2PRESS against 17 external test inhibitors=0.67). Three orthogonal pharmacophores emerged in the QSAR equation and were validated by receiver operating characteristic (ROC) curves analysis. The models were then used to screen the national cancer institute (NCI) list of compounds. The highest-ranking hits were tested in vitro. The most potent hits illustrated EC50 values of 15 and 224 nM.
    Matched MeSH terms: Crystallography, X-Ray
  8. Takhi M, Sreenivas K, Reddy CK, Munikumar M, Praveena K, Sudheer P, et al.
    Eur J Med Chem, 2014 Sep 12;84:382-94.
    PMID: 25036796 DOI: 10.1016/j.ejmech.2014.07.036
    A novel and potent series of ene-amides featuring azetidines has been developed as FabI inhibitors active against drug resistant Gram-positive pathogens particularly staphylococcal organisms. Most of the compounds from the series possessed excellent biochemical inhibition of Staphylococcus aureus FabI enzyme and whole cell activity against clinically relevant MRSA, MSSA and MRSE organisms which are responsible for significant morbidity and mortality in community as well as hospital settings. The binding mode of one of the leads, AEA16, in Escherichia coli FabI enzyme was determined unambiguously using X-ray crystallography. The lead compounds displayed good metabolic stability in mice liver microsomes and pharmacokinetic profile in mice. The in vivo efficacy of lead AEA16 has been demonstrated in a lethal murine systemic infection model.
    Matched MeSH terms: Crystallography, X-Ray
  9. Naqeebullah, Farina Y, Chan KM, Mun LK, Rajab NF, Ooi TC
    Molecules, 2013 Jul 22;18(7):8696-711.
    PMID: 23881054 DOI: 10.3390/molecules18078696
    Three diorganotin(IV) complexes of the general formula R2Sn[RcC(O)N(RN)O] (Rc = aryl, RN = Alkyl) have been synthesized by refluxing in toluene the corresponding diorganotin(IV) oxides with the free ligand N-methyl p-fluorobenzohydroxamic acid, using a Dean and Stark water separator. The ligand was derived from the reaction of the corresponding p-fluorobenzoyl chloride and N-methylhydroxylamine hydrochloride in the presence of sodium hydrogen carbonate. The isolated free ligand and its respective diorganotin compounds have been characterized by elemental analysis, IR and 1H-, 13C-, 119Sn-NMR spectroscopies. The crystal structures of the diorganotin complexes have been confirmed by single crystal X-ray diffraction methods. The investigations carried out on the diorganotin(IV) complexes of N-methyl p-fluorobenzohydroxamic acid confirmed a 1:2 stoichiometry. The complex formation took place through the O,O-coordination via the carbonyl oxygen and subsequent deprotonated hydroxyl group to the tin atom. The crystal structures of three diorganotin complexes were determined and were found to adopt six coordination geometries at the tin centre with coordination to two ligand moieties.
    Matched MeSH terms: Crystallography, X-Ray
  10. van der Sar SA, Blunt JW, Cole AL, Din LB, Munro MH
    J Nat Prod, 2005 Dec;68(12):1799-801.
    PMID: 16378381
    A new dichlorinated pulvinic acid derivative, methyl-3',5'-dichloro-4,4'-di-O-methylatromentate, was isolated from the fruiting body of a Scleroderma sp. The structure was determined using spectroscopic methods, and an X-ray analysis was carried out for confirmation of the structure. Compound was found to display moderate antimicrobial activity against Bacillus subtilis.
    Matched MeSH terms: Crystallography, X-Ray
  11. Kumar BS, Saraswathi R, Kumar KV, Jha SK, Venkates DP, Dhanaraj SA
    Drug Deliv, 2014 May;21(3):173-84.
    PMID: 24102185 DOI: 10.3109/10717544.2013.840690
    Novel LNCs (lipid nanocrystals) were developed with an aim to improve the solubility, stability and targeting efficiency of the model drug glibenclamide (GLB). PEG 20000, Tween 80 and soybean lecithin were used as polymer, surfactant and complexing agent, respectively. GLB nanocrystals (NCs) were prepared by precipitation process and complexed using hot and cold melt technique. The LNCs were evaluated by drug loading, saturation solubility (SL), optical clarity, in vitro dissolution, solid state characterization, in vivo and stability analysis. LNCs exhibited a threefold increase in SL and a higher dissolution rate than GLB. The percentage dissolution efficiency was found to decrease with increase in PEG 20000. The average particle size was in the range of 155-842 nm and zeta potential values tend to increase after complexation. X-ray powder diffractometry and differential scanning calorimetry results proved the crystallinity prevailed in the samples. Spherical shaped particles (<1000 nm) with a lipid coat on the surface were observed in scanning electron microscopy analysis. Fourier transform infrared results proved the absence of interaction between drug and polymer and stability study findings proved that LNCs were stable. In vivo study findings showed a decrease in drug concentration to pancreas in male Wistar rats. It can be concluded that LNCs are could offer enhanced solubility, dissolution rate and stability for poorly water soluble drugs. The targeting efficiency of LNCs was decreased and further membrane permeability studies ought to be carried out.
    Matched MeSH terms: Crystallography, X-Ray
  12. Zuhailawati Hussain, Yong, Tuck Leong
    MyJurnal
    In this paper, densification of in-situ copper-niobium carbide composite using cold pressing technique was addressed. Mixtures of Cu-20vol%NbC powder were prepared by two methods.
    In first method, a mixture of Cu-15.79wt%Nb-2.04wt%C powder was milled at 400 rpm for 35 hours in a planetary mill. In second method, Cu and commercial NbC powder was mixed at 100 rpm for 2 hours in a jar mill. Then, both powders were pressed at different pressure (i.e. 350 MPa, 450 MPa, 550 MPa and 650 MPa) and sintered at 900 o C for 1 hour. Sample of in-situ and ex-situ Cu-20vol%NbC composite were characterized for density, hardness, phase formation by x-ray diffraction analysis and microstructure by scanning electron microscope. Xray diffraction analysis showed that NbC phase was formed in the in-situ processed sample. Hardness of in-situ processed copper composite was higher than that of the ex-situ processed copper composite due to good interface between coper matrix and niobium carbide reinforcement particle as well as distribution of finer niobium carbide particles in copper matrix. Sintered density of in-situ composite is lower than density of ex-situ composite beacuse of work hardening of the Cu-Nb-C mixture powder during powder to ball collision. Density and hardness of the in-situ and ex-situ Cu-20vol%NbC composites increase with the increase in compaction pressure as porosity is eliminated at higher compaction pressure.
    Matched MeSH terms: Crystallography, X-Ray
  13. Abdul Rahman MB, Karjiban RA, Salleh AB, Jacobs D, Basri M, Thean Chor AL, et al.
    Protein Pept Lett, 2009;16(11):1360-70.
    PMID: 20001926
    The stability of biocatalysts is an important criterion for a sustainable industrial operation economically. T1 lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1 (T1 lipase) that was isolated from palm oil mill effluent (POME) in Malaysia. We report here the results of high temperatures molecular dynamics (MD) simulations of T1 lipase in explicit solvent. We found that the N-terminal moiety of this enzyme was accompanied by a large flexibility and dynamics during temperature-induced unfolding simulations which preceded and followed by clear structural changes in two specific regions; the small domain (consisting of helices alpha3 and alpha5, strands beta1 and beta2, and connecting loops) and the main catalytic domain or core domain (consisting of helices alpha6- alpha9 and connecting loops which located above the active site) of the enzyme. The results suggest that the small domain of model enzyme is a critical region to the thermostability of this organism.
    Matched MeSH terms: Crystallography, X-Ray
  14. Von ST, Seng HL, Lee HB, Ng SW, Kitamura Y, Chikira M, et al.
    J Biol Inorg Chem, 2012 Jan;17(1):57-69.
    PMID: 21833656 DOI: 10.1007/s00775-011-0829-0
    By inhibiting only two or three of 12 restriction enzymes, the series of [M(phen)(edda)] complexes [M(II) is Cu, Co, Zn; phen is 1,10-phenanthroline; edda is N,N'-ethylenediaminediacetate] exhibit DNA binding specificity. The Cu(II) and Zn(II) complexes could differentiate the palindromic sequences 5'-CATATG-3' and 5'-GTATAC-3', whereas the Co(II) analogue could not. This and other differences in their biological properties may arise from distinct differences in their octahedral structures. The complexes could inhibit topoisomerase I, stabilize or destabilize G-quadruplex, and lower the mitochondrial membrane potential of MCF7 breast cells. The pronounced stabilization of G-quadruplex by the Zn(II) complex may account for the additional ability of only the Zn(II) complex to induce cell cycle arrest in S phase. On the basis of the known action of anticancer compounds against the above-mentioned individual targets, we suggest the mode of action of the present complexes could involve multiple targets. Cytotoxicity studies with MCF10A and cisplatin-resistant MCF7 suggest that these complexes exhibit selectivity towards breast cancer cells over normal ones.
    Matched MeSH terms: Crystallography, X-Ray
  15. Sim DS, Chong KW, Nge CE, Low YY, Sim KS, Kam TS
    J Nat Prod, 2014 Nov 26;77(11):2504-12.
    PMID: 25333996 DOI: 10.1021/np500589u
    Seven new indole alkaloids (1-7) comprising four vobasine, two tacaman, and one corynanthe-tryptamine bisindole alkaloid were isolated from the stem-bark extract of a Malayan Tabernaemontana. Two of the new vobasine alkaloids (1, 3), as well as 16-epivobasine (15) and 16-epivobasenal (17), showed appreciable cytotoxicity toward KB cells (IC50 ca. 5 μg/mL). The structure of the known Tabernaemontana alkaloid tronoharine (8) was revised based on newly acquired NMR data, as well as X-ray diffraction analysis.
    Matched MeSH terms: Crystallography, X-Ray
  16. Santiago C, Fitchett C, Munro MH, Jalil J, Santhanam J
    PMID: 22454674 DOI: 10.1155/2012/689310
    An endophytic fungus isolated from the plant Cinnamomum mollissimum was investigated for the bioactivity of its metabolites. The fungus, similar to a Phoma sp., was cultured in potato dextrose broth for two weeks, followed by extraction with ethyl acetate. The crude extract obtained was fractionated by high-performance liquid chromatography. Both crude extract and fractions were assayed for cytotoxicity against P388 murine leukemic cells and inhibition of bacterial and fungal pathogens. The bioactive extract fraction was purified further and characterized by nuclear magnetic resonance, mass spectral and X-ray crystallography analysis. A polyketide compound, 5-hydroxyramulosin, was identified as the constituent of the bioactive fungal extract fraction. This compound inhibited the fungal pathogen Aspergillus niger (IC(50) 1.56 μg/mL) and was cytotoxic against murine leukemia cells (IC(50) 2.10 μg/mL). 5-Hydroxyramulosin was the major compound produced by the endophytic fungus. This research suggests that fungal endophytes are a good source of bioactive metabolites which have potential applications in medicine.
    Matched MeSH terms: Crystallography, X-Ray
  17. Shaibullah S, Mohd-Sharif N, Ho KL, Firdaus-Raih M, Nathan S, Mohamed R, et al.
    Acta Crystallogr F Struct Biol Commun, 2014 Dec 01;70(Pt 12):1697-700.
    PMID: 25484229 DOI: 10.1107/S2053230X14025278
    Melioidosis is an infectious disease caused by the pathogenic bacterium Burkholderia pseudomallei. Whole-genome sequencing revealed that the B. pseudomallei genome includes 5855 coding DNA sequences (CDSs), of which ∼25% encode hypothetical proteins. A pathogen-associated hypothetical protein, BPSL1038, was overexpressed in Escherichia coli, purified and crystallized using vapour-diffusion methods. A BPSL1038 protein crystal that grew using sodium formate as precipitant diffracted to 1.55 Å resolution. It belonged to space group C2221, with unit-cell parameters a = 85.36, b = 115.63, c = 46.73 Å. The calculated Matthews coefficient (VM) suggests that there are two molecules per asymmetric unit, with a solvent content of 48.8%.
    Matched MeSH terms: Crystallography, X-Ray
  18. Shariff FM, Rahman RN, Ali MS, Chor AL, Basri M, Salleh AB
    PMID: 20516608 DOI: 10.1107/S174430911001482X
    Purified thermostable recombinant L2 lipase from Bacillus sp. L2 was crystallized by the counter-diffusion method using 20% PEG 6000, 50 mM MES pH 6.5 and 50 mM NaCl as precipitant. X-ray diffraction data were collected to 2.7 A resolution using an in-house Bruker X8 PROTEUM single-crystal diffractometer system. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 A. The asymmetric unit contained one single molecule of protein, with a Matthews coefficient (V(M)) of 2.85 A(3) Da(-1) and a solvent content of 57%.
    Matched MeSH terms: Crystallography, X-Ray
  19. Khusaini MS, Rahman RN, Mohamad Ali MS, Leow TC, Basri M, Salleh AB
    PMID: 21393852 DOI: 10.1107/S1744309111002028
    An organic solvent-tolerant lipase from Bacillus sp. strain 42 was crystallized using the capillary-tube method. The purpose of studying this enzyme was in order to better understand its folding and to characterize its properties in organic solvents. By initially solving its structure in the native state, further studies on protein-solvent interactions could be performed. X-ray data were collected at 2.0 Å resolution using an in-house diffractometer. The estimated crystal dimensions were 0.09×0.19×0.08 mm. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a=117.41, b=80.85, c=99.44 Å, β=96.40°.
    Matched MeSH terms: Crystallography, X-Ray
  20. Mohd-Sharif N, Shaibullah S, Givajothi V, Tan CS, Ho KL, Teh AH, et al.
    Acta Crystallogr F Struct Biol Commun, 2017 02 01;73(Pt 2):109-115.
    PMID: 28177322 DOI: 10.1107/S2053230X17001212
    TylP is one of five regulatory proteins involved in the regulation of antibiotic (tylosin) production, morphological and physiological differentiation in Streptomyces fradiae. Its function is similar to those of various γ-butyrolactone receptor proteins. In this report, N-terminally His-tagged recombinant TylP protein (rTylP) was overproduced in Escherichia coli and purified to homogeneity. The rTylP protein was crystallized from a reservoir solution comprising 34%(v/v) ethylene glycol and 5%(v/v) glycerol. The protein crystals diffracted X-rays to 3.05 Å resolution and belonged to the trigonal space group P3121, with unit-cell parameters a = b = 126.62, c = 95.63 Å.
    Matched MeSH terms: Crystallography, X-Ray
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