Biomedical subjects

M Jalaie

Publications and source records attributed to M Jalaie.

3 recordsLinked to original sources

PubMed2000

Enantiodiscrimination by a quinine-based chiral stationary phase: a computational study.

A detailed computational study of a derivatized quinine chiral stationary phase (CSP) interacting with enantiomeric 3, 5-dinitrobenzoyl derivatives of leucine was carried out to understand where and how chiral discrimination takes place. The most stable structure of the CSP derived from a conformer search gave a structure whose geometry agrees with an X-ray structure (rmsd 0.6 A). The computed retention order and enantiodiscriminating free energy differences also agree with chromatographic data. The location and characteristics of the analyte binding site were assessed. An evaluation of total energies and intermolecular energies responsible for complex formation and for chiral discrimination was performed. Molecular dynamics trajectories of those intermolecular forces as well as distributions of the stabilizing and destabilizing forces are presented. A partitioning of the CSP into molecular fragments and the role each fragment plays in complexation and chiral recognition is also described.

Binding Sites↗

PubMed2000

Comparative molecular field analysis of quinine derivatives used as chiral selectors in liquid chromatography: 3D QSAR for the purposes of molecular design of chiral stationary phases.

A comparative molecular field analysis (CoMFA) was carried out on a set of aligned quinine-based stationary phase molecules used in enantioselective chromatography. The best QSAR derived has a cross-validated (predictive) r(2)(cv) = 0.671 and a normal r(2) = 0.998. For CoMFAs using both steric and electrostatic fields as descriptors, the steric field descriptors explained more than 91% of the variance while the electrostatic descriptors explained less than 9% of the variance. It is concluded that the long-range electrostatic potential surrounding the positively charged CSPs are not enantiodiscriminating, while the van der Waals and local electrostatic surface features of these CSPs are highly discriminating. Quantum mechanical calculations back up this claim by showing a relatively symmetric electrostatic iso-contour surface. From the QSAR derived here, a region around the carbamate moiety was located where placement of steric bulk is predicted to enhance chiral discrimination. A set of possible synthetic target molecules is presented.

Chromatography, Liquid↗

PubMed2000

Homology model directed alignment selection for comparative molecular field analysis: application to photosystem II inhibitors.

The use of a computational docking protocol in conjunction with a protein homology model to derive molecular alignments for Comparative Molecular Field Analysis (CoMFA) was examined. In particular, the DOCK program and a model of the herbicidal target site, photosystem II (PSII), was used to derive alignments for two PSII inhibitor training sets, a set of benzo- and napthoquinones and a set of butenanilides. The protein design software in the QUANTA molecular modeling package was used to develop a homology model of spinach PSII based on the reported amino acid sequence and the X-ray crystal structure of the purple bacterium reaction center. The model is very similar to other reported PSII protein homology models. DOCK was then used to derive alignments for CoMFA modeling by docking the inhibitors in the PSII binding pocket. The molecular alignments produced from docking yielded highly predictive CoMFA models. As a comparison, the more traditional atom-atom alignments of the same two training sets failed to produce predictive CoMFA models. The general utilities of this application for homology model refinement and as an alternative scoring method are discussed.

Amino Acid Sequence↗