ABSTRACT
A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.
ABSTRACT
Modeling and simulations of compartmentalization effects in tandem with nitroxide exit and entry have been performed for the nitroxide-mediated radical polymerization (NMP) of styrene in an aqueous dispersed system employing 2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO) at 125 °C. It is demonstrated that, even for a relatively water-insoluble nitroxide like TEMPO, exit and entry can strongly influence the polymerization kinetics in submicrometer-size droplets/particles. In such systems, the polymerization is expected to proceed at a markedly higher rate than the corresponding bulk system at the expense of control/livingness. Depending on the deactivator water solubility, these findings will apply qualitatively to all controlled/living radical polymerization systems governed by the persistent radical effect [e.g., NMP and atom transfer radical polymerization (ATRP)].
ABSTRACT
Pz peptidases A and B, from a thermophile Geobacillus collagenovorans MO-1, recognize collagen-specific tripeptide units (Gly-Pro-Xaa). They share similarities in function but extremely low identities in primary sequence with mammalian thimet oligopeptidase (TOP) and neurolysin. Three phosphine peptide inhibitors that selectively inhibit TOP and neurolysin on two bacterial Pz peptidases were investigated. They showed potent inhibition of both Pz peptidases in a range from 10 to 100 nM.
