Pharmacophore modeling and three-dimensional database searching for drug design using catalyst.

Perceiving a pharmacophore is the first essential step towards understanding the interaction between a receptor and a ligand. Once a pharmacophore is established, a beneficial use of it is 3D database searching to retrieve novel compounds that would match the pharmacophore, without necessarily duplicating the topological features of known active compounds (hence remain independent of existing patents). As the 3D searching technology has evolved over the years, it has been effectively used for lead optimization, combinatorial library focusing, as well as virtual high-throughput screening. Clearly established as one of the successful computational tools in rational drug design, we present in this review article a brief history of the evolution of this technology and detailed algorithms of Catalyst, the latest 3D searching software to be released. We also provide brief summary of published successes with this technology, including two recent patent applications.

Discovery of novel mesangial cell proliferation inhibitors using a three-dimensional database searching method.

A three-dimensional pharmacophore model of mesangial cell (MC) proliferation inhibitors was generated from a training set of 4-(diethoxyphosphoryl)methyl-N-(3-phenyl-[1,2,4]thiadiazol-5-yl)benzamide, 2, and its derivatives using the Catalyst/HIPHOP software program. On the basis of the in vitro MC proliferation inhibitory activity, a pharmacophore model was generated as seven features consisting of two hydrophobic regions, two hydrophobic aromatic regions, and three hydrogen bond acceptors. Using this model as a three-dimensional query to search the Maybridge database, structurally novel 41 compounds were identified. The evaluation of MC proliferation inhibitory activity using available samples from the 41 identified compounds exhibited over 50% inhibitory activity at the 100 nM range. Interestingly, the newly identified compounds by the 3D database searching method exhibited the reduced inhibition of normal proximal tubular epithelial cell proliferation compared to a training set of compounds.

Three-dimensional quantitative structure-activity relationships (3D-QSAR) of antidiabetic thiazolidinediones.

Thiazolidine-2,4-diones (TZDs) are novel insulin resistance releasing compounds that serve as orally active antidiabetic agents. Many TZDs have been synthesized and evaluated by in vivo screening for over 20 years. Recently, TZDs have been found to be selective agonists of peroxisome proliferator-activated receptor-y (PPAR-gamm), which is believed to work in the regulation of insulin resistance. This paper reports our efforts for the pharmacophore modeling study through 3D (three-dimensional) structure-activity relationship of TZDs to gain an insight into their molecular mechanism as well as the relation between antihyperglycemic and PPAR-gamma agonistic activities. The modeling study was carried out by conformational analysis along with the Apex-3D QSAR method to identify molecular features common to a series of 7 selected TZDs. Although the number of compounds included in the study was rather low, the variations in the activities were nicely elucidated with 3D-site specific physiochemical parameters significantly.

Synthesis and hypolipidemic activities of novel 2-[4-[diethoxyphosphoryl)methyl]phenyl]quinazolines and 4(3H)-quinazolinones.

The novel compound NO-1886, 4-[(diethoxyphosphoryl)methyl]-N-(4-bromo-2-cyanophenyl)-ben zamide, is a hypolipidemic agent, which appears to increase lipoprotein lipase activity in rats. Various analogs of NO-1886 were synthesized to study the structure-activity relationship of this hypolipidemic drug. A novel series of quinazolines and 4(3H)-quinazolinones were prepared by cyclization of NO-1886 derivatives. Derivatives bearing a 4-[(diethoxyphosphoryl)-methyl]phenyl] group at the 2-position were found to lower triglyceride and total cholesterol levels. In accord with the decrease in log P*, quinazolines and 4(3H)-quinazolinones showed good absorption and hypolipidemic activity. When the quinazolinone ring system is substituted at positions 6 and 7 with methoxy groups, increased hypolipidemic activity was observed. The highest hypolipidemic activity was observed when the 3-position was substituted by a methyl or benzyl group.

Purification and properties of RNA polymerases from mother cells and forespores of sporulating cells of Bacillus subtilis.

Bacillus subtilis sporulating cells at stage III were fractionated into mother cell and forespore fractions by means of a lysozyme-detergent method. Three forms of DNA-dependent RNA polymerase enzymes, termed M sigma, F sigma, and F delta, in addition to core enzyme (alpha 2, beta', and beta) have been purified from the cell fractions. Enzymes M sigma and F sigma are present in the mother cell and forespore, respectively, and contain sigma factor of 55,000 daltons in addition to the core subunits. On the other hand, enzyme F delta is present specifically in the forespore and contains delta 1 factor of 28,000 daltons instead of the sigma factor. The amount of RNA polymerase in the forespore is about twice that in the mother cell. The enzymes M sigma and F sigma also differed in their elution profiled from DEAE-cellulose columns and in their heat stabilities indicating that the two sigma-containing holoenzyme forms may be different in their structural properties. The enzyme F delta transcribed B. subtilis DNA about 1.6 times more actively than enzyme F sigma, and the enzymes M sigma and F sigma transcribed the DNA about 2.2 times more actively than did core enzyme.

Purification of polypeptide P6 with a molecular weight of 6,000 from the vegetative chromosomes of Bacillus subtilis.

Folded chromosomes were prepared as membrane-associated complexes from vegetative cells of Bacillus subtilis by stepwise sucrose gradient centrifugation. From nucleoids, a deoxyribonucleic acid-bound polypeptide with a molecular weight of 6,000 (P6) was purified by KCl-(NH4)2SO4 salting out, diethylaminoethyl cellulose column chromatography, and deoxyribonucleic acid cellulose column chromatography. The amino acid composition of polypeptide P6 was determined.

Fractionation and biochemical properties of the mother cell and forespore functions from sporulating cells of Bacillus subtilis.

A lysozyme-detergent method was developed for the fractionation of sporulating cells of B. subtilis 168 wild type into mother cell and forespore fractions. The method is very mild and is reproducible with optimum concentrations of Brij-58, deoxycholic acid and sucrose. The results were confirmed by application of the method to temperature sensitive mutants. Ts-1 and Ts-3. The amounts of proteins, and the activities of protease, alkaline phosphatase and glucose dehydrogenase were about 55, 56, 91, and 40%, respectively, in the mother cell fraction, and about 45, 44, 9, and 60%, respectively, in the forespore fraction, taking the totals for the combined fractions as 100%. Slab gel electrophoretic patterns indicated that many species of proteins with different molecular weights were present in the two fractions. Pulse-labeling with [3H]UTP was carried out in vivo at stage III, and 35.2 and 64.8% of the [3H]UMP incorporated into RNAs were distributed in the mother cell and forespore fractions, respectively. The results indicate that more RNA synthesis occurs in the forespores than in the mother cells of sporulating cells.

Cooperative effects of daunorubicin and actinomycin D on the sporulation of Bacillus subtilis.

Actinomycin D allowed 3.6% of spore formation and 4.9% of dipicolinic acid synthesis of control cultures when added at 0.4 microM at late stage (T6.5) during sporulation process of Bacillus subtilis although the drug inhibited sporulation almost completely when added at log phase and early stages. Daunorubin added at log phase, on the other hand, did not inhibit either growth and sporulation of the bacteria up to a concentration of 2.9 microM. The joint use of both antibiotics at late stages decreased the levels of spore formation and the synthesis of dipicolinic acid allowed by the use of actinomycin D alone to 0.9% and 2.1% respectively, and also inhibited the synthesis of spore coat protein in a cooperative manner.