Drying in Pharmaceutical and Biotechnological Industries

The process used for drying pharmaceuticals has a high impact on the final product characteristics, both on the active ingredient (high chemical purity product) and the end drug product (complexgalenic formulation). For example, it is well-known that there is a direct relation between the absorption of the active ingredient and its characteristic crystalline or polymorphic form. In some cases, the latter is related to the procedure and conditions of drying. The consequences of the process used to dry a pharmaceutical product may be different depending on the development phase: pre-clinical studies or manufacture (production). The drying process may greatly influence the quality of the drug substances in several aspects: the polymorphic form of the active ingredient, the structural changes that may have an effect on the activity of the substance, the degradation products formed due to the drying conditions and the presence of residual solvents undesirable or above the permitted limits after drying. Consequently, it is important to know the influence of all the factors and to establish the product specifications, as well as the nature and limits of residual solvents, in agreement with current regulations.

Modeling cyclooxygenase inhibition. Implication of active site hydration on the selectivity of ketoprofen analogues

Molecular modeling studies performed on the two cyclooxygenase isozymes (COXs) suggest that active site hydration is crucial for understanding inhibitor selectivity. In this work, models have been constructed considering some implicit water molecules, placed in the position suggested by GRID, that participate in the dynamic hydrogen-bonding network at the polar active site entrance together with protein residues 355, 524, 120, and 513. The selectivity observed for ketoprofen (1) and the structural analogues 2 and 3 may be rationalized in terms of such implicit hydration.

Derivation of pharmacophore and CoMFA models for leukotriene D(4) receptor antagonists of the quinolinyl(bridged)aryl series

The present work focuses on the study of the three-dimensional (3D) structural requirements for the leukotriene D(4) (LTD(4)) antagonistic activity of compounds having the basic quinolinyl(bridged)aryl framework. An approach combining pharmacophore mapping, molecule alignment, and CoMFA models was used to derive a hypothesis for a series of LTD(4) antagonists having the basic diaryl-bridged framework. In this compound series, the produced pharmacophore hypotheses have shown to yield molecule alignments suitable to derive valuable CoMFA models. Model selection focused on (1) obtention of coherent modeling results, (2) consistency with the available SAR data, and (3) ability to predict the activity of an independent set of congeneric molecules. This approach resulted in a combined pharmacophore and CoMFA model that can generally represent the antagonistic activity within a log unit of the measured value for compounds of the series. The resulting pharmacophore (model C) consists of an acidic or negative ionizable function (AC), a hydrogen-bond acceptor (HBA), and three hydrophobic regions (HY) and produces chemically meaningful alignments with the most active compounds of the series mapping the pharmacophore in a extended energetically favorable conformation.

Structural basis of the dynamic mechanism of ligand binding to cyclooxygenase

Molecular modeling studies performed on the two cyclooxygenase (COX) isozymes suggest that the cavity at the mouth of the active site on the membrane domain that may act as an actual binding site of COX ligands. Actual docking of different inhibitors at this site provides a structural basis to explain the dynamics of COX inhibition.

Comparative molecular modeling study of the three-dimensional structures of prostaglandin endoperoxide H2 synthase 1 and 2 (COX-1 and COX-2)

To understand the structural features that dictate the selectivity of diverse nonsteroidal antiinflammatory drugs for the two isoforms of the human prostaglandin H2 synthase (PGHS), the three-dimensional (3D) structure of human COX-2 was assessed by means of sequence homology modeling. The ovine COX-1 structure, solved by X-ray diffraction methods and sharing a 61% sequence identity with human COX-2, was used as template. Both structures were energy minimized using the AMBER 4.0 force field with a dielectric constant of 4r. (S)-Flurbiprofen, a nonselective COX inhibitor, and SC-558, a COX-2-selective ligand, were docked at the cyclooxygenase binding site in both isozymes, evidencing the role of different residues in the ligand-protein interaction. The 3D structures of the constructed four ligand-enzyme complexes were refined by energy minimization. Molecular dynamics simulations were also carried out, to understand more deeply the structural origins of the selectivity. Distances calculated during the dynamics process between the different ligands and the interacting residues of the two PGHS isozymes provided evidence of the flexible nature of the cyclooxygenase active site, permitting the identification of different conserved and nonconserved residues as responsible for ligand selectivity.

Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors

The effects of data pretreatment, data scaling, and variable selection on three-dimensional quantitative structure-activity relationships derived by comparative molecular field analysis (CoMFA) using the GRID energy function were studied in detail for a set of inhibitors of the human synovial fluid phospholipase A2 (HSF-PLA2). The quality of the models was evaluated for predictive power and ability to map the receptor binding site by (a) comparison of predicted and experimental activities using cross-validation and external validation sets and (b) comparison of the regions selected in space in the CoMFA models with a crystal structure of a HSF-PLA2-inhibitor complex, with optimized comparative binding energy analysis (COMBINE) models (Ortiz et al., 1995) and with structure-activity relationships derived previously for different sets of compounds. It is found that (1) data scaling and dielectric modeling strongly influence CoMFA results. Unscaled data and a uniform dielectric constant of 4 are well suited to GRID-CoMFA studies for the present compound set. (2) The GOLPE and Q2-GRS variable selection methods select variables in roughly the same regions in Cartesian space, but they produce different models in chemometric space and differ in their sensitivity to data scaling and pretreatment and their tendency to overfitting. (3) CoMFA models are consistent with COMBINE models in that they identify approximately the same intermolecular interactions as relevant for activity. Our study provides support for the qualitative receptor-mapping properties of CoMFA models and for the validity of variable selection when applied with care and also provides guidelines for how to evaluate the quality of CoMFA models.