Analysis of large screening data sets via adaptively grown phylogenetic-like trees.

As the use of high-throughput screening systems becomes more routine in the drug discovery process, there is an increasing need for fast and reliable analysis of the massive amounts of the resulting data. At the forefront of the methods used is data reduction, often assisted by cluster analysis. Activity thresholds reduce the data set under investigation to manageable sizes while clustering enables the detection of natural groups in that reduced subset, thereby revealing families of compounds that exhibit increased activity toward a specific biological target. The above process, designed to handle primarily data sets of sizes much smaller than the ones currently produced by high-throughput screening systems, has become one of the main bottlenecks of the modern drug discovery process. In addition to being fragmented and heavily dependent on human experts, it also ignores all screening information related to compounds with activity less than the threshold chosen and thus, in the best case, can only hope to discover a subset of the knowledge available in the screening data sets. To address the deficiencies of the current screening data analysis process the authors have developed a new method that analyzes thoroughly large screening data sets. In this report we describe in detail this new approach and present its main differences with the methods currently in use. Further, we analyze a well-known, publicly available data set using the proposed method. Our experimental results show that the proposed method can improve significantly both the ease of extraction and amount of knowledge discovered from screening data sets.

Synthesis and biological activity of peptidyl aldehyde urokinase inhibitors.

Solid- and solution-phase synthesis of peptidomimetic inhibitors of urokinase-type plasminogen activator based on the sequence dSerAlaArg-al are described. The biological activities of these unique inhibitors are reported herein. Carbonate prodrugs were prepared and tested as potential drug delivery systems.

Guanylpiperidine peptidomimetics: potent and selective bis-cation inhibitors of factor Xa.

A novel series of rigid P3-guanylpiperidine peptide mimics 3-14 was designed as potential factor Xa and prothrombinase inhibitors. Incorporation into a P2-gly-P1-argininal motif led to highly potent and selective inhibitors. The synthesis and biological activities of these derivatives are reported herein.

Novel benzo-fused lactam scaffolds as factor Xa inhibitors.

Rigid benzolactam P3-P2 dipeptide mimics were designed and prepared as potential inhibitors of blood coagulation factor Xa. Methoxy substitution of the tetrahydrobenzazepinone scaffold led to potent and selective inhibitors. The synthesis and biological activities of these derivatives are reported herein.

Investigation of the S3 site of thrombin: design, synthesis and biological activity of 4-substituted 3-amino-2-pyridones incorporating P1-argininals.

A novel scaffold for P4-P2 dipeptide mimics containing a rigid pyridone spacer was designed based on a virtual library strategy. Several selected nonpeptidic 4-aralkyl or 4-alkylpyridones incorporating a P1-argininal sequence were prepared. The modeling studies, synthesis and biological activities of these unique pyridone derivatives are reported herein.

Design of an effective mechanism-based inactivator for a zinc protease.

(R)-2-Benzyl-5-cyano-4-oxopentanoic acid (compound 4) was studied as a mechanism-based inactivator (suicide substrate) for the zinc protease carboxypeptidase A (CPA; peptidyl-L-amino-acid hydrolase, EC 3.4.17.1). This compound was designed rationally based on the knowledge of the active site topology and the reported stereospecific proton exchange on ketonic substrate analogue (R)-3-(p-methoxybenzoyl)-2-benzylpropanoic acid [Sugimoto, T. & Kaiser, E. T. (1978) J. Am. Chem. Soc. 100, 7750-7751] by CPA. It is suggested that enzymic deprotonation on the C-5 methylene moiety may result in the transient formation of a ketenimine as the key intermediate that partitions between turnover and enzyme inactivation. The enzyme inactivation exhibited pseudo-first-order kinetics, was irreversible, and could be fully prevented in the presence of the reversible inhibitor benzyl-succinate. The inactivation rate constant, kintact, was evaluated to be 0.083 +/- 0.003 min-1 and kcat was measured at 1.78 +/- 0.06 min-1. In turn, a partition ratio of 28 +/- 3 was calculated. The reversible inhibitor constant (Ki) was measured at 1.8 +/- 0.5 microM, indicative of a high affinity for compound 4 shown by CPA; however, Km for the turnover process was determined at 4.93 +/- 0.43 mM. Kinetic analysis and labeling by the radioactive form of the inactivator suggested that the stoichiometry for protein modification by compound 4 approaches a 1:1 ratio.

Chemical association in symbiosis sterol donors in planthoppers.

The role of intracellular symbionts contributing to their host has been investigated in the planthoppers,Nilaparvata lugens Stal andLaodelphax striatellus Fallen. We have found that the isolated yeastlike symbionts, identified as a member of the genusCandida, from the host's egg produce ergosterol when cultured. A comparative study of sterols in the cultured symbionts, the host insects, aposymbiotic host insects, and dietary plants demonstrated that ergosterol produced in the symbiotes is provided to the host insects and possibly transformed in the host insects into cholesterol via 24-methylenecholesterol. The conversion of injected 24-methylenecholesterol-d3 into cholesterol has been shown in the brown planthopper (N. lugens).

Antimutagenic unusual amino acids from plants.

Five unusual amino acids were identified as antimutagens against spontaneous mutation of Salmonella typhimurium TA100: L-azetidine-2-carboxylic acid (1) from Liliaceae plants, alpha-(methylenecyclopropyl)glycine (2) from Litchi chinensis seeds, and 2-amino-4-methylhex-5-ynoic acid (3), hypoglycin A (4), and (2S,4R)-2-amino-4-hydroxyhept-6-ynoic acid (5) from Euphoria longana seeds. The absolute stereochemistry of 5 was determined by its chiral synthesis from L-allylglycine, proving that 5 is the C-4 epimer of the amino acid previously isolated from dried longan seeds.