Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.

We describe ADChemCast, a method for using results from virtual screening to create a richer representation of a target binding site, which may be used to improve ranking of compounds and characterize the determinants of ligand-receptor specificity. ADChemCast clusters docked conformations of ligands based on shared pairwise receptor-ligand interactions within chemically similar structural fragments, building a set of attributes characteristic of binders and nonbinders. Machine learning is then used to build rules from the most informational attributes for use in reranking of compounds. In this report, we use ADChemCast to improve the ranking of compounds in 11 diverse proteins from the Database of Useful Decoys-Enhanced (DUD-E) and demonstrate the utility of the method for characterizing relevant binding attributes in HIV reverse transcriptase.

chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery.

BACKGROUND: Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of command line programs with a wide range of functionalities for cheminformatics. The chemalot_knime package allows command line programs that read and write SD files from stdin and to stdout to be wrapped into KNIME nodes. The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster. RESULTS: Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure-activity or property analysis and other type of investigations, (2) The creation of a quantitative structure-property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database. CONCLUSIONS: The chemalot and chemalot_knime packages provide lightweight and powerful tools for many tasks in cheminformatics. They are easily integrated with other open source and commercial command line tools and can be combined to build new and even more powerful tools. The chemalot_knime package facilitates the generation and maintenance of user-defined command line workflows, taking advantage of the graphical design capabilities in KNIME. Graphical abstract Example KNIME workflow with chemalot nodes and the corresponding command line pipe.

Early developmental changes in [3H]nicotine binding in the human brainstem.

Little is known about the developmental profile of nicotinic cholinergic receptors in the developing human brain, despite the potential importance of such information in understanding the pathogenesis of neurological abnormalities or increased risk for the sudden infant death syndrome in offspring exposed to nicotine in utero. In this study, we determined the distribution of [3H]nicotine binding in the developing human brainstem by quantitative tissue autoradiography. In midgestational fetuses, [3H]nicotine binding sites were heavily concentrated in tegmental nuclei related to cardiopulmonary integration, arousal, attention, rapid eye movement sleep, and somatic motor control. Over the last half of gestation, [3H]nicotine binding decreased 60-70% in the tegmental nuclei, with a significant difference in binding between midgestation and early infancy. In contrast, there was essentially no change in [3H]nicotine binding in the major cerebellar-relay nuclei (principal inferior olive and griseum pontis) between the same time-points. Tritium quenching by increasing lipid (myelin) content in tissue sections did not account for the decreases in [3H]nicotine binding in tegmental nuclei. Based upon the high levels of [3H]nicotine binding at midgestation, combined with experimental data demonstrating trophic properties for acetylcholine, we postulate that nAChRs a role in the development of the brainstem tegmentum during this period, and that once this role is fulfilled, nicotinic cholinergic binding decreases and remains low thereafter. Alternatively, nicotinic cholinergic receptors may be critical for other developmentally related functions and/or neurotransmission in the brainstem tegmentum at midgestation. The high levels of [3H]nicotine binding in the brainstem tegmentum at midgestation and its rapidly changing profile over late gestation further suggest that mid-to-late gestation is a developmental period during which this region is likely to be most vulnerable to the harmful effects of nicotine in maternal cigarette smoke. The baseline information provided in this study is potentially relevant towards understanding attention deficits and risk for the sudden infant death syndrome in offspring exposed to cigarette smoke in utero.

1994 Molecular Graphics Art Show and Video Show.

The 1994 Molecular Graphics Art Show and Video Show were presented at the 13th annual international meeting of the Molecular Graphics and Modelling Society. The art show--shown in the Mary & Leigh Block Gallery on the campus of Northwestern University, Evanston, Illinois--included original artworks by eighteen artists and the video show included nine original animated works. All were chosen for their ability to present the complexity, diversity, and beauty of the molecular world in visual form. Works from a wide range of disciplines were represented, including work by scientists actively involved in structural research, by commercial illustrators presenting these results to students and physicians, and by fine artists exploring the meanings and implications of these molecules in our lives. Included in this issue of the Journal of Molecular Graphics are comments by the juror of the show, T.J. O'Donnell, a catalogue of the art show, and a catalogue of the video show.

Mechanism of inhibition of DNA gyrase by quinolone antibacterials: a cooperative drug--DNA binding model.

We have proposed a cooperative quinolone-DNA binding model for the inhibition of DNA gyrase. The essential feature of the model is that bound gyrase induces a specific quinolone binding site in the relaxed DNA substrate in the presence of ATP. The binding affinity and specificity are derived from two unique and equally important functional features: the specific conformation of the proposed single-stranded DNA pocket induced by the enzyme and the unique self-association phenomenon (from which the cooperativity is derived) of the drug molecules to fit the binding pocket with a high degree of flexibility. Supporting evidence for and implications of this model are provided.