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  • Chemistry
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  • 1
    Language: English
    In: Journal of Molecular Graphics and Modelling, September 2017, Vol.76, pp.152-160
    Description: Ion channels play a crucial role in the cardiovascular system. Our understanding of cardiac ion channel function has improved since their first discoveries. The flow of potassium, sodium and calcium ions across cardiomyocytes is vital for regular cardiac rhythm. Blockage of these channels, delays cardiac repolarization or tend to shorten repolarization and may induce arrhythmia. Detection of drug risk by channel blockade is considered essential for drug regulators. Advanced computational models can be used as an early screen for torsadogenic potential in drug candidates. New drug candidates that are determined to not cause blockage are more likely to pass successfully through preclinical trials and not be withdrawn later from the marketplace by manufacturer. Several different approved drugs, however, can cause a distinctive polymorphic ventricular arrhythmia known as torsade de pointes (TdP), which may lead to sudden death. The objective of the present study is to review the mechanisms and computational models used to assess the risk that a drug may TdP. There is strong evidence from multiple studies that blockage of the L-type calcium current reduces risk of TdP. Blockage of sodium channels slows cardiac action potential conduction, however, not all sodium channel blocking antiarrhythmic drugs produce a significant effect, while late sodium channel block reduces TdP. Interestingly, there are some drugs that block the hERG potassium channel and therefore cause QT prolongation, but they are not associated with TdP. Recent studies confirmed the necessity of studying multiple distinctionic ion channels which are responsible for cardiac related diseases or TdP, to obtain an improved clinical TdP risk prediction of compound interactions and also for designing drugs.
    Keywords: Artificial Neural Network ; Cardiac Arrhythmia ; Cardiotoxicity ; Cipa ; Herg ; Ion Channels ; Long Qt Syndrome ; Proarrhythmia ; Torsade de Pointes ; Tdp ; Chemistry
    ISSN: 1093-3263
    E-ISSN: 1873-4243
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  • 2
    Language: English
    In: Xenobiotica, 03 July 2017, Vol.47(7), pp.614-631
    Description: 1. Biliary excretion of compounds is dependant on several transporter proteins for the active uptake of compounds from the blood into the hepatocytes. Organic anion-transporting polypeptides (OATPs) are some of the most abundant transporter proteins in the sinusoidal membrane and have been...
    Keywords: Qsar ; Oatp ; Anion Transporters ; Hepatic Uptake ; Excretion Into Bile ; Pharmacy, Therapeutics, & Pharmacology ; Chemistry
    ISSN: 0049-8254
    E-ISSN: 1366-5928
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  • 3
    Language: English
    In: Medical Engineering and Physics, December 2017, Vol.50, pp.22-28
    Description: Elbow articular cartilage withstands high compressive and shear forces while protecting the bone from excessive loading. Better understanding of elbow cartilage contact mechanics can provide insight into cartilage degeneration. In this study a tactile pressure sensor was used to measure the contact pressure distribution within the ulno-humeral joint of two cadaver specimens at 20° flexion angle across three different axial loads of 80 N, 110 N, and 140 N. Corresponding 3D finite element (FE) models were constructed from magnetic resonance imaging (MRI) and contact analysis was performed for each specimen with boundary and loading conditions identical to the experiment. Direct comparison between FE results and experimental measurements was conducted for the validation of the FE models and a sensitivity analysis was employed for assessing the effect of cartilage parameters on the model's outputs. The results showed a good agreement between the FE models and the experiments in terms of contact characteristics. The sensitivity analysis demonstrated that outcomes of the model, particularly peak contact pressure is more sensitive to the Poisson's ratio rather than to Young's modulus under static conditions. This result suggests that selection of Poisson's ratio is very critical for accurate prediction of contact mechanics within the ulno-humeral joint.
    Keywords: Ulno-Humeral Joint ; Elbow Joint ; Articular Cartilage ; Contact Mechanics ; Finite Element Analysis ; Parametric Study ; Medicine ; Engineering ; Chemistry
    ISSN: 1350-4533
    E-ISSN: 1873-4030
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  • 4
    Language: English
    In: Journal of Molecular Graphics and Modelling, September 2018, Vol.84, pp.74-81
    Description: The accuracy of protein synthesis is provided by the editing functions of aminoacyl-tRNA synthetases (aaRSs), a mechanism that eliminates misactivated amino acids or mischarged tRNAs. Despite research efforts, some molecular bases of these mechanisms are still unclear. The post-transfer editing pathway of leucyl-tRNA synthetase (LeuRS) carried out in a special insertion domain (the Connective Polypeptide 1 or CP1), as editing domain. Recently, it was shown by studies and was supported by mutagenesis, and the kinetics approaches that the CP1 domain of LeuRS has discriminatory power for different substrates. The goal of this work is to investigate the structural basis for amino acid recognition of LeuRS post-transfer editing processes with molecular dynamics (MD) simulation method. To pursue this aim, the molecular modeling studies on LeuRS (LeuRSTT) with two post-transfer substrates (norvalyl-tRNA and isoleucyl-tRNA ) was performed. Our results revealed that post-transfer substrate norvalyl-tRNA is more favorable. Moreover, the MD simulations show that branched side chain of Ile-A76 cannot allow water molecules to get close, which leads to a significant decrease in the rate of hydrolysis. Finally, the study showed that site mutation Asp347Ala has elucidated a number of fine structural differences in the binding mode of two post-transfer substrates to the active centre of LeuRS editing domain and two conserved threonines, namely Thr247 and Thr248, are responsible for the amino acid selection through the interaction with substrates.
    Keywords: Chemistry
    ISSN: 1093-3263
    E-ISSN: 1873-4243
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  • 5
    Language: English
    In: Cytotechnology, 2018, Vol.70(2), pp.603-614
    Description: The callus and hairy root cultures of Prosopis farcta were established to develop effective strategies to enhance its valuable and medicinally important flavonoid compounds. For callus induction, the hypocotyl, cotyledon and shoot explants were subjected to different plant hormones, naphthalene acetic acid (NAA), benzylaminopurine (BAP), kinetin and dichlorophenoxyacetic acid (2,4-D). Greater callus induction was obtained from hypocotyl explants on MS medium containing 3.0 mg L −1 NAA + 2.0 mg L −1 BAP. With the addition of 0.5 mg L −1 asparagine to this medium, the maximum callus growth was achieved. Hairy root culture of P. farcta was performed using transformation of different explants with strains of Agrobacterium rhizogenes LBA9404 , A4 , AR15834 . The AR15834 strain was more effective for hairy root induction where it caused hairy root formation on 59% of the infected cotyledon explants. We compared profiles of flavonoids isolated from seedling roots, hairy roots, and callus cultures of P. farcta . The colorimetric analysis showed that the content of total flavonoids of hairy roots was 1.54 and 2.52 times higher than in seedling roots and callus, respectively. The presence of flavonoids was verified by LC/MS in positive ion mode. The results showed that flavonoid composition was different in the roots and callus. Naringenin was the major constituent in callus, whereas resveratrol, quercetin and myricetin were the most abundant compounds found in hairy roots. The main objective of this research was to establish hairy roots in P. farcta to synthesize flavonoids at levels comparable to in vitro-grown roots. The present study also opens up a way to further improve the production of pharmaceutically valuable flavonoids and to produce desired metabolites using the hairy root culture system.
    Keywords: Prosopis farcta ; Hairy root ; Agrobacterium rhizogenes ; Callus culture ; Flavonoids ; HPLC ; LC/MS
    ISSN: 0920-9069
    E-ISSN: 1573-0778
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  • 6
    Language: English
    In: Plant Physiology and Biochemistry, October 2016, Vol.107, pp.374-384
    Description: Manipulation of cell culture media by elicitors is one of most important strategies to inducing secondary metabolism for the production of valuable metabolites. In this investigation, inducing effect of chitosan on physiological, biochemical, and molecular parameters were investigated in cell suspension cultures of Boiss. The results showed that chitosan concentration and time of elicitation are determinants of the effectiveness of the elicitor. Accumulation of aromatic amino acids (phenylalanine [Phe] and tyrosine [Tyr]), phenylpropanoid compounds (phenolic acids [PAs] and echinacoside [ECH]), hydrogen peroxide (H O ) production, phenylalanine ammonia-lyase (PAL) activity and gene expression, and antioxidant enzymes (superoxide dismutase [SOD], peroxidase [POX], catalase [CAT]) activities were altered by changing the exposure time of elicitation. Results showed that, upon elicitation with chitosan, oxidative events were induced, antioxidant responses of . cells were boosted through enhanced activity of an effective series of scavenging enzymes (SOD, CAT, and POX), and biosynthesis of non-enzymatic antioxidants (ECH and PAs [cinnamic, -coumaric and, caffeic acids]). The increase in amino acid content and PAL activity at early days of exposure to chitosan was related with rises in phenolic compounds. These results provide evidence that chitosan by up-regulation of gene differentially improves the production of phenylpropanoid compounds, which are of medical commercial value with good biotechnological prospects.
    Keywords: Aromatic Amino Acids ; Antioxidant Enzymes ; Chitosan ; Phenylalanine Ammonia-Lyase ; Phenylpropanoid Compounds ; Plant Cell Culture ; Scrophularia Striata Boiss ; Botany ; Chemistry
    ISSN: 0981-9428
    E-ISSN: 1873-2690
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  • 7
    Language: English
    In: Plant Physiology and Biochemistry, September 2018, Vol.130, pp.139-147
    Description: Plants respond to water stress through a variety of mechanisms, depending on metabolites preferences and their available resources. This work was performed to elucidate the cross-talk between signaling molecules (polyamines (PAs), hydrogen peroxide (H O ) and nitric oxide (NO)), phenolic compounds and osmolytes (phenylethanoid glycosides (PhGs), phenolic acids, flavonoids, soluble sugars and amino acids) under water stress in plants. The results revealed that PAs, NO levels were enhanced in the plants, earlier in response to polyethylene glycol-induced water stress. The antioxidative mechanisms with increased activity of catalase (CAT), guaiacol peroxidase (GPX) and superoxide dismutase (SOD) and also phenylalanine ammonia-lyase (PAL), tyrosine ammonia-lyase (TAL), as key enzymes in phenolic pathway were deployed in response to the stress. Mannose, glucose, xylose/rhamnose which are involved in PhGs biosynthesis as well as in serving osmotic adjustment were modulated. The elevated content of arginine and methionine as PAs precursors and tyrosine and phenylalanine as PhGs precursors was enhanced by water stress and was significantly associated with PAs and PhGs accumulations. Metabolic profiling revealed new information about relationship between stress signal molecules; PAs, NO and H O , osmolytes (sugers, PhGs) and phenolic compounds which involved in the improvement of water stress tolerance in .
    Keywords: Phenylethanoid Glycosides ; Polyamines ; Nitric Oxide ; Water Stress ; Scrophularia Striata ; Botany ; Chemistry
    ISSN: 0981-9428
    E-ISSN: 1873-2690
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  • 8
    Language: English
    In: Plant Physiology and Biochemistry, February 2016, Vol.99, pp.11-20
    Description: Lead (Pb) is a hazardous heavy metal present in the environment which elicits oxidative stress in plants. To characterize the physiological and biochemical basis of Pb tolerance, seedlings were exposed to Hoagland's solutions at six different Pb concentrations (0, 80, 160, 320, 400 and 480 μM) for different periods of time. As expected, application of Pb significantly increased hydrogen peroxide (H O ) content. In response, deployed the antioxidative defence mechanisms with significantly higher activities of superoxide dismutase (SOD), enzymes related to H O removal, and also the increases in proline as a solute marker of stress. Increases were observed in nitric oxide (NO) production which could also act in triggering defense functions to detoxify Pb. Enhanced phenylalanine ammonia-lyase (PAL) activity at early days of exposure to Pb was correlated with increases in phenolic compounds. Significant increases in phenolic acids and flavonoids; daidzein, vitexin, ferulic acid and salicylic acid were observed with Pb treatment. Furthermore, the stress effects were followed by changes in free amino acid content and composition. Aspartic acid and glycine content was increased but glutamic acid significantly decreased. It is likely that stress signal transduction by NO and H O mediated defence responses to Pb by coordination of antioxidative system and metabolic pathways of phenylpropanoid and amino acids.
    Keywords: Lead ; Enzymatic Antioxidant ; Nitric Oxide ; Phenylalanine Ammonia-Lyase ; Phenolic Acids ; Amino Acids ; Botany ; Chemistry
    ISSN: 0981-9428
    E-ISSN: 1873-2690
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  • 9
    Language: English
    In: Plant Physiology and Biochemistry, September 2017, Vol.118, pp.98-106
    Description: is a very destructive plant pathogen. Selection of effective biological agents against this pathogen depends on more insight into molecular plant defence responses during the biocontrol agent-pathogen interaction. Auxin as a phytohormone is a key contributor in pathogenesis and plant defence and accumulation of auxin transport carriers are accompanied by increasing in flavonoid and miRNAs concentrations during plant interactions with bacteria. The aim of this research was molecular analysis of (ATCC21332) biocontrol effect against (IBRC-M10701) pathogen interacting with plants. Tobacco plants were either treated with both or one of the challenging bacteria and the expression of miRNAs inside the plants were analysed through qRT-PCR. The results indicated that the bacterial treatments affect expression level of nta-miRNAs. In tobacco plants treated only with the expression of nta-miR393 was more than that was recorded for nta-miR167 (3.8 folds, P 〈 0.05 in 3dpi). While the expression level of nta-miR167 was more than the expression of nta-miR393 in other treatments including tobacco plants treated only with (2.1 folds, P 〈 0.05) and the plants treated with both of the bacteria (3.9 folds, P 〈 0.05) in 3 dpi. Also, the composition and concentration of rutin, myrecetin, daidzein and vitexin flavanoid derivatives were detected using HPLC and analysed according the standard curves. All of the tested flavanoid compounds were highly detected in Tobacco plants which were only challenged with The amount of these compounds in the plants which were challenged with the alone, was similar to the amount recorded for the plants challenged with the both bacteria. This study suggests a relationship between the upregulation of nta-miR167, nta-miR393 and accumulation of flavanoid compounds. Overall, the expression of these miRNAs as well as flavonoid derivatives has the potential of being used as biomarkers for the interaction of and model system in .
    Keywords: Nta-Mirnas ; Flavanoids ; Agrobacterium Tumefaciens ; Bacillus Subtilis ; Botany ; Chemistry
    ISSN: 0981-9428
    E-ISSN: 1873-2690
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  • 10
    Language: English
    In: Plant Physiology and Biochemistry, February 2019, Vol.135, pp.359-371
    Description: Hydrogen sulfide (H S) has been recently found as an important signaling molecule especially in root system architecture of plants. The regulation of root formation through H S has been reported in previous works; while the profiling of metabolites in response to H S is not clearly discussed. To this end, different concentrations of sodium hydrosulfide (an H S donor) were applied to the culture of hairy roots. Subsequently, the amino acid profiles, soluble carbohydrates, and central intermediates of phenylpropanoid pathway with two branches of lignans and flavonoids were assessed by spectroscopy and high performance liquid chromatography techniques. An analysis of the signaling molecules (nitric oxide, hydrogen peroxide, and salicylic acid) was also conducted as they proposed to act in conjunction with H S. The H S activated antioxidant systems and caused a shift from flavonoid to lignan production (podophyllotoxin and 6-methoxypodophyllotoxin); although, some of the flavonoids increased in a dose-dependent manner. The H S decreased the contents of phenylalanine and tyrosine as substrates of the phenylpropanoid pathway, but increased proline and histidine as an osmolyte and antioxidant, respectively. These findings propose that H S modulates other signaling molecules, regulates free amino acids, and mediates biosynthesis of lignans and flavonoids in the phenylpropanoids biosynthesis pathway.
    Keywords: Hairy Root ; Hydrogen Sulfide ; Linum Album ; Phenylpropanoid ; Signaling ; Botany ; Chemistry
    ISSN: 0981-9428
    E-ISSN: 1873-2690
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