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Search Results: 1 - 10 of 14085 matches for " Molecular Modeling "
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Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophilus  [PDF]
Angshuman Bagchi, Tapash Chandra Ghosh
Journal of Biophysical Chemistry (JBPC) , 2011, DOI: 10.4236/jbpc.2011.24047
Abstract: Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse set of microorganisms. The sulfur oxidizing gene cluster (sox) of thermo-neutrophilic bacterium Hydrogenobacter thermophilus consists of soxYZAXB. The bacterium shows optimal thiosulfate oxidation activity at 60°C. There are practically no reports regarding the structural biology of the sulfur oxidation proc- ess in this organism. In the present context, we employed homology modeling to construct the three dimensional structures of SoxY and SoxZ from Hydrogenobacter thermophilus. With the help of docking simulations we have identified the amino acid residues of these proteins in- volved in the interactions. The thermodynamics of the protein-protein interactions have also been analyzed. The probable biochemical mechanism of the binding of thiosulfate has been elucidated. Our study provides a rational framework to understand the molecular mechanism of the sulfur oxidation biochemistry.
Molecular Modeling, Docking and ADMET of Dimethylthiohydantoin Derivatives for Prostate Cancer Treatment  [PDF]
Khaled Lotfy
Journal of Biophysical Chemistry (JBPC) , 2015, DOI: 10.4236/jbpc.2015.64010
Abstract: In silico technique was applied to screen potential of 16 compounds of 5,5-dimethylthiohydantoin derivatives as androgen antagonist. The 3D structure of the protein was obtained from PDB database. Docking analysis of the compounds was performed using hex docking. Molecular modeling analysis exhibits relatively low LUMO-HOMO energy gap of the studied molecules, indicating that it would be kinetically stable. None of the compounds violated Lipinski’s parameters, making them potentially promising agents for biological activities. The title compounds exhibited the lowest docking energy of protein-ligand complex. Finally, the results indicate that these compounds are potentially as an androgen antagonist, and expected to be effective in prostate cancer treatment.
Investigation of Chiral Molecular Micelles by NMR Spectroscopy and Molecular Dynamics Simulation  [PDF]
Kevin F. Morris, Eugene J. Billiot, Fereshteh H. Billiot, Kenny B. Lipkowitz, William M. Southerland, Yayin Fang
Open Journal of Physical Chemistry (OJPC) , 2012, DOI: 10.4236/ojpc.2012.24032
Abstract: NMR spectroscopy and Molecular Dynamics (MD) simulation analyses of the chiral molecular micelles poly-(Sodium Undecyl-(L,L)-Leucine-Valine) (poly-SULV) and poly-(Sodium Undecyl-(L,L)-Valine-Leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide headgroups. To provide experimental support for the structures from MD simulations, NOESY spectra were used to identify protons in close spatial proximity. Results from the NOESY analyses were then compared to radial distribution functions from MD simulations. In addition, the hydrodynamic radii of both molecular micelles were calculated from NMR-derived diffusion coefficients. Corresponding radii from the MD simulations were found to be in agreement with these experimental results. NMR diffusion experiments were also used to measure association constants for polar and non-polar binaphthyl analytes binding to both molecular micelles. Poly (SUVL) was found to bind the non-polar analyte enantiomers more strongly, while the more polar analyte enantiomers interacted more strongly with poly(SULV). MD simulations in turn showed that poly(SULV) had a more open structure that gave greater access for water molecules to the dipeptide headgroup region.
A Molecular Dynamics Simulation Study of Two Dipeptide Based Molecular Micelles: Effect of Amino Acid Order  [PDF]
Kevin F. Morris, Eugene J. Billiot, Fereshteh H. Billiot, Kenny B. Lipkowitz, William M. Southerland, Yayin Fang
Open Journal of Physical Chemistry (OJPC) , 2013, DOI: 10.4236/ojpc.2013.31004

Molecular dynamics (MD) simulations were used to compare the structures of the chiral molecular micelles (MM) poly-(sodium undecyl-(L,L)-leucine-valine) (poly(SULV)) and poly-(sodium undecyl-(L,L)-valine-leucine) (poly (SUVL)). Both MM contained polymerized surfactant monomers terminated by chiral dipeptide headgroups. The study was undertaken to investigate why poly(SULV) is generally a better chiral selector compared to poly(SUVL) in electrokinetic chromatography separations. When comparing poly(SULV) to poly(SUVL), poly(SULV) had the more conformational flexible dipeptide headgroup and hydrogen bond analyses revealed that the poly(SULV) headgroup conformation allowed a larger number of intramolecular hydrogen bonds to form between monomer chains. In addition, a larger number of water molecules surrounded the chiral centers of the poly(SULV) molecular micelle. Poly(SULV) was also found to have a larger solvent accessible surface area (SASA) than poly(SUVL) and fluctuations in the poly(SULV) SASA during the MD simulation allowed dynamic monomer chain motions expected to be important in chiral recognition to be identified. Finally, approximately 50% of the Na+ counterions were found in the first three solvation shells surrounding both MM, with the remainder located in the bulk. Overall the MD simulations point to both greater headgroup flexibility and solvent and analyte access to the chiral centers of the dipeptide headgroup as factors contributing to the enhanced chiral selectivity observed with poly(SULV).

Docking Studies, Synthesis, and Evaluation of Antioxidant Activities of N-Alkylated, 1,2,4-Triazole, 1,3,4-Oxa-, and Thiadiazole Containing the Aminopyrazolopyridine Derivatives  [PDF]
Yasser K. Abdelmonem, Farag A. El-Essawy, Saeda A. Abou El-Enein, Mona M. El-Sheikh-Amer
International Journal of Organic Chemistry (IJOC) , 2013, DOI: 10.4236/ijoc.2013.33026
Abstract: Synthesis of some 1,3,4-thia-, oxa-diazol and 1,2,4 triazole incorporated the biologically active and the pyrazolopyri-dine derivative. Molecular modeling and docking of the active compounds into AKR1C3 complexed with its bound inhibitor indomethacin using Molsoft ICM 3.4-8C program were performed in order to predict the affinity and orientation of the synthesized compounds at the active site.
Molecular Modeling and Synthesis of Ethyl Benzyl Carbamates as Possible Ixodicide Activity  [PDF]
Vázquez-Valadez Víctor Hugo, Hernández-S. Manuel Alejandro, Velázquez-S. Ana María, Rosales-H. María, Leyva-R. Marco Antonio, Prado-O. María Guadalupe, Mu?oz-G. Marco Antonio, Alba-H. Fernando, Abrego Víctor, Cruz-A. Diego, ángeles Enrique
Computational Chemistry (CC) , 2019, DOI: 10.4236/cc.2019.71001
Carbamates are molecules that have different types of biological activities and provide a particular chemical control against ticks. The new structures of the proposed compounds were optimized and synthetized respectively, through a molecular model using the methods:PM3, HF and DFT applying the B3LYP functional, with the basis 6-31+G(d) and 6-311+G(d,p), BVP86 and PBEPBE with 6-31+G(d) and the vibrational frequencies computed. These calculated frequencies were compared with the experimental ones to determine the most accurate level of theory for the prediction of vibrational frequencies of the compounds. The best results were obtained through HF/631+G(d). Additionally, we report a modification to obtain this type of compounds, and based on the amino-dehalogenation of ethyl chloroformate, different benzyl ethyl carbamates were synthesized modifying the base molecule. The performances obtained were compared to others already reported. The methodology used allowed us to synthesize new carbamates using benzylamine derivatives through a modification on the basic catalysis of the addition-elimination reaction.
Boletín de la Sociedad Chilena de Química , 2000, DOI: 10.4067/S0366-16442000000100002
Abstract: in this paper we studied using molecular modeling techniques several quinoline analogs of nalidixic acid, compound with known antibacterial activity, synthesized and in vitro tested, in order to look for common structural patterns that could be related to their biological activity. we used nalidixic acid as reference compound, its structure was taken from cambridge structural database, and to locate the ester group we used the reported bioactive conformation of norfloxacin. we made a conformational analysis using molecular mechanics and molecular dynamics, and then we used the lower enegy conformations to run quantum mechanical calculations. as a first report the evaluated properties were related with the in vitro activity against escherichia coli for each compound, and a regression analysis was made, concluding that the energetic difference betwen the frontier orbitals, the dipolar moment and steric factors could be related to to the quinoline analogs in vitro antibacterial activity.
1,3-Butadiene hydrogenation on pd-supported systems: geometric effects
Souza, P.R.N.;Pereira, M.M.;Antunes, O.A.C.;Aranda, D.A.G.;Carneiro, J.W.M.;
Brazilian Journal of Chemical Engineering , 2002, DOI: 10.1590/S0104-66322002000200005
Abstract: a strong metal support interaction (smsi) effect was observed on pd/nb2o5 and pd/tio2 catalysts, and it produces small, exposed pd ensembles. a decrease in the trans/cis 2-butene ratio was observed after reduction at 773 k. selectivity changes were ascribed to the decoration model. theoretical models were developed based on semi-empirical molecular-orbital calculations for 1,3-butadiene and pdn clusters. experimental results are in agreement with our theoretical model, which proposes a greater stabilization of the cisoid intermediate on small pd ensembles.
1,3-Butadiene hydrogenation on pd-supported systems: geometric effects
Souza P.R.N.,Pereira M.M.,Antunes O.A.C.,Aranda D.A.G.
Brazilian Journal of Chemical Engineering , 2002,
Abstract: A strong metal support interaction (SMSI) effect was observed on Pd/Nb2O5 and Pd/TiO2 catalysts, and it produces small, exposed Pd ensembles. A decrease in the trans/cis 2-butene ratio was observed after reduction at 773 K. Selectivity changes were ascribed to the decoration model. Theoretical models were developed based on semi-empirical molecular-orbital calculations for 1,3-butadiene and Pd n clusters. Experimental results are in agreement with our theoretical model, which proposes a greater stabilization of the cisoid intermediate on small Pd ensembles.
Computer-Aided Drug Design: An Innovative Tool for Modeling  [PDF]
Pranita P. Kore, Madhavi M. Mutha, Rishikesh V. Antre, Rajesh J. Oswal, Sandip S. Kshirsagar
Open Journal of Medicinal Chemistry (OJMC) , 2012, DOI: 10.4236/ojmc.2012.24017
Abstract: Strategies for CADD vary depending on the extent of structural and other information available regarding the target (enzyme/receptor) and the ligands. Computer-aided drug design (CADD) is an exciting and diverse discipline where various aspects of applied and basic research merge and stimulate each other. In the early stage of a drug discovery process, researchers may be faced with little or no structure activity relationship (SAR) information. The process by which a new drug is brought to market stage is referred to by a number of names most commonly as the development chain or “pipeline” and consists of a number of distinct stages. To design a rational drug, we must firstly find out which proteins can be the drug targets in pathogenesis. In present review we reported a brief history of CADD, DNA as target, receptor theory, structure optimization, structure-based drug design, virtual high-throughput screening (vHTS), graph machines.
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