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Miri L.,Institute Pasteur du Maroc | Miri L.,CNRS Biomolecular Engineering Laboratory | Bouvier G.,French National Center for Scientific Research | Kettani A.,CNRS Biomolecular Engineering Laboratory | And 4 more authors.
Proteins: Structure, Function and Bioinformatics | Year: 2014

The HIV-1 integrase is an attractive target for the therapeutics development against AIDS, as no host homologue of this protein has been identified. The integrase strand transfer inhibitors (INSTIs), including raltegravir, specifically target the second catalytic step of the integration process by binding to the DDE motif of the catalytic site and coordinating Mg2+ ions. Recent X-ray crystallographic structures of the integrase/DNA complex from prototype foamy virus allowed to investigate the role of the different partners (integrase, DNA, Mg2+ ions, raltegravir) in the complex stability using molecular dynamics (MD) simulations. The presence of Mg2+ ions is found to be essential for the stability, whereas the simultaneous presence of raltegravir and Mg2+ ions has a destabilizing influence. A homology model of HIV-1 integrase was built on the basis of the X-ray crystallographic information, and protein marker residues for the ligand binding were detected by clustering the docking poses of known HIV-1 integrase inhibitors on the model. Interestingly, we had already identified some of these residues to be involved in HIV-1 resistance mutations and in the stabilization of the catalytic site during the MD simulations. Classification of protein conformations along MD simulations, as well as of ligand docking poses, was performed by using an original learning method, based on self-organizing maps. This allows us to perform a more in-depth investigation of the free-energy basins populated by the complex in MD simulations on the one hand, and a straightforward classification of ligands according to their binding residues on the other hand. Proteins 2014; 82:466-478. © 2013 Wiley Periodicals, Inc.


Arnold-Apostolides N.,Higher Institute for Agricultural Engineering for Mediterranean Countries | Cazier F.,Center Communications Of Mesures | Najm S.,Lebanese University | Labaki M.,Lebanese University | And 2 more authors.
Acta Horticulturae | Year: 2013

Satureja thymbra L. is a well known aromatic plant; endemic of the Mediterranean region and characterized by an oregano-like smell. It is frequently used as a spice and herbal tea in the Lebanese traditional medicine. Air dried aerial parts from S. thymbra were collected in Lebanon at random during April 2009. For 3 h the plant material was submitted to steam distillation using a clevenger-type apparatus to produce the essential oil with a yield of 0.84% (w/w). Oil was dried using anhydrous magnesium sulfate and stored at 4C. S. thymbra oil was analyzed by GC/MS. Nineteen compounds representing 98.8% of the oil sample were identified. The major components of Satureja thymbra L. oil were ?-terpinene (34.06%), carvacrol (23.07%) and thymol (18.82%). Also abundant were ?-cymene (7.58%), caryophyllene (3.96%), a-terpinene (3.53%) and myrcene (1.70%). The results of our study were compared to reports on the same or different species from other origins.


Apostolides N.A.,British Petroleum | El Beyrouthy M.,British Petroleum | Dhifi W.,Manouba University | Najm S.,Lebanese University | And 4 more authors.
Journal of Essential Oil-Bearing Plants | Year: 2013

Essential oil (EO) from fresh aerial parts of Rosmarinus officinalis L. growing wild in Lebanon, was analyzed by GC-MS. Altogether, twenty-seven compounds, accounting for 93.83 % of the whole oil, were identified. 1,8-cineole (32.83 %), β-caryophyllene (12.94 %), borneol (11.65 %), camphor (10.33 %), bornyl acetate (4.19 %), α-pinene (4.10 %), and α-terpineol (3.87 %) were the main components of the oil. © 2013 Copyright Har Krishan Bhalla & Sons.


El Beyrouthy M.,Holy Spirit University of Kaslik | Cazier F.,Center Communications Of Mesures | Arnold N.A.,Holy Spirit University of Kaslik | Aboukais A.,Laboratoire Of Catalyse Et Environnement
Journal of Essential Oil-Bearing Plants | Year: 2015

Abstract: Seasonal variation in chemical composition of essential oils obtained from fresh aerial parts of S. cuneifolia was determined by GC and GC-MS. The fresh plant materials were collected before and after flowering, and during beginning and maturation fruit stage from two different locations. Thirty five components were identified; carvacrol (20.4-52.1 %), p-cymene (9.1-30.2 %) and γ-terpinene (5.9-23.9 %) were the main components. In general, the qualitative composition of the components appeared to be relatively stable but carvacrol, p-Cymene and γ-terpinene showed variability. We also note that phenolics and monoterpene hydrocarbons were the major components. All the essential oils were found to be rich in carvacrol reaching the highest rate (52.1 %) during full blooming stage, while the highest percentage of thymol ranging (18.7 %) was reached only in the sample of essential oil from S. cuneifolia collected in the region of Ehden. © 2015 Har Krishan Bhalla & Sons.


Hafi M.A.,Holy Spirit University of Kaslik | Cazier F.,Center Communications Of Mesures | Aboukais A.,Laboratoire Of Catalyse Et Environnement | Jocelyne B.,Holy Spirit University of Kaslik | Beyrouthy M.E.,Holy Spirit University of Kaslik
Journal of Essential Oil-Bearing Plants | Year: 2015

The chemical composition of the water-distilled and free solvent (milestone) oils from several samples of cones (berries), leaves and twigs of Lebanese Juniperus excelsa M. Bieb. collected during two consecutive years were analyzed by GC and GC-MS. Thirty constituents were identified and accounted for 89.4-99.5 % of the total oil. The main component in the leaves, cones and twigs of the oil was α-pinene which accounted for 6.9 to 68.9; 78.3 to 89.8 and 75 to 95.2 % respectively in leaves, twigs and berries; we note here that big differences in α-pinene content in leaves were observed according to the year and distillation method: 6.9-27.7 (Leaves Milestone 2010), 30.6-49.5 (Leaves Clevenger 2010) and 52.8-68.8 (Leaves Clevenger 2011). The major component was followed by δ-3-carene whose respective amounts were of 3.3 to 22.1 in the leaves; 1.1 to 2.6 in the twigs and 0.9 to 2.4 in the berries and α-cedrol (8.7 to 57.0 in the leaves; 1.2 to 8.1 in the twigs and traces to 4.8 in the berries). The highest amounts of α-pinene were in the cones (95.3 %) whereas those of δ-3-carene and α-cedrol were in leaves (respectively 22.2 and 57 %). Their amounts in the different plant organs varied significantly. This study has demonstrated that the essential oils of Juniperus excelsa MB. leaves, cones and twigs exhibit changes in yields and compositions more likely due to the growth or ripening and climatic factors. © 2015 Har Krishan Bhalla & Sons.

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