Application of combinatorial chemistry to antimicrobial drug discovery.

The emergence of pathogens resistant to currently available treatments is seen as a public health crisis. Since few new classes of antimicrobial drugs have been developed in the last two decades, it is becoming increasingly probable that healthcare providers will be faced with infections for which no chemotherapeutic agent is available. A renewed emphasis is being placed on employing the most advanced drug discovery technologies in the development of new antimicrobials.

Agonists of the follicle stimulating hormone receptor from an encoded thiazolidinone library.

The design, synthesis, characterization, and screening of a large, encoded thiazolidinone library are described. Three sets of 35 building blocks were combined by encoded split-pool synthesis to give a library containing more than 42 000 members. Building block selection was based in part on a novel small molecule follicle stimulating hormone receptor agonist hit and in part for diversity.

An atom-economical approach to conformationally constrained tricyclic nitrogen heterocycles via sequential and tandem Ugi/intramolecular Diels-Alder reaction of pyrrole.

An efficient approach to rigid tricyclic nitrogen heterocycles via sequential and tandem Ugi/intramolecular Diels-Alder (IMDA) cycloaddition of pyrrole is described. The one-pot Ugi four-component condensation (4CC) reaction was used as the key transformation to prepare trienes with a carboxamide substituent on the tether. The use of acrylic acid (21) and N-propyl- and N-benzylmaleamic acids (24b and 24C) as the acid components provided trienes 22, 25b, and 25c, respectively, which upon heating at 120 degrees C for 12 h yielded the corresponding [4 + 2] cycloaddition products.

Safety-catch linker strategies for the production of radiopharmaceuticals labeled with positron-emitting isotopes.

A novel synthetic stratetegy for compounds labeled with the positron-emitting isotope carbon-11 is described. The use of precursors attached to a solid support via safety-catch linkers allows selective release of radiolabeled material, leaving unreacted precursor attached to the support. Two different linkers demonstrate the application to the preparation of radiolabeled N-alkyl tertiary amines and N-alkylsulfonamides.

Cell surface expression of single chain antibodies with applications to imaging of gene expression in vivo.

Imaging of gene expression in vivo has many potential uses for biomedical research and drug discovery, ranging from the study of gene regulation and cancer to the non-invasive assessment of gene therapies. To streamline the development of imaging marker gene technologies for nuclear medicine, we propose a new approach to the design of reporter/probe pairs wherein the reporter is a cell surface-expressed single chain antibody variable fragment that has been raised against a low molecular weight imaging probe with optimized pharmacokinetic properties. Proof of concept of the approach was achieved using a single chain antibody variable fragment that binds with high affinity to fluorescein and an imaging probe consisting of fluorescein isothiocyanate coupled to the chelator diethylene triamine penta-acetic acid labeled with the gamma-emitter (111)In.

Software for automating analysis of encoded combinatorial libraries.

This paper describes the applications which are used to automate the analysis of encoded combinatorial libraries. Commercial packages from MDL, Oracle and Agilent are linked with application software written in C/C++, in Microsoft Access and in ChemStation macro language. Encoding correspondence lists for each of up to three synthetic steps are conveniently associated with building block lists using the first application, CodeGen.

Gene expression changes associated with cytotoxicity identified using cDNA arrays.

In order to investigate gene expression changes associated with cytotoxicity, we used cDNA arrays to monitor the expression of over 5,000 genes in response to toxic stress in the HepG2 liver cell line. Cells were treated with cytotoxic doses of acetaminophen, caffeine or thioacetamide for nine time points ranging from 1 to 24 h. Samples of mRNA from each time point were used to prepare radiolabeled cDNA, which was hybridized to nylon-membrane-based cDNA arrays.

Discovery of substrate for type I signal peptidase SpsB from Staphylococcus aureus.

Based on the kinetic model of substrate phage proteolysis, we have formulated a strategy for best manipulating the conditions in screening phage display libraries for protease substrates (Sharkov, N. A., Davis, R.

Assay technologies for screening ion channel targets.

The sequence of the human genome will soon provide researchers with hundreds of new ion channel genes. To create a successful ion channel drug discovery program, it is necessary to quickly develop reliable and robust high-throughput screening (HTS) assays for those ion channels implicated in important diseases. Ion channels are dynamic proteins, and therefore require assays that 'sense' their various functional states.

Stereoselective Solid-Phase Synthesis of a Triaza Tricyclic Ring System: A New Chemotype for Lead Discovery.

Sequential pyrrolidine and hydantoin ring-forming reactions have been applied in the stereoselective solid-phase synthesis of a conformationally constrained, tricyclic triazacyclopenta[c]pentalene scaffold. These novel compounds share the structural complexity characteristic of certain alkaloid natural products and represent a source of chemical diversity that complements more traditional classes of heterocyclic compounds of interest as potential pharmaceutical agents. They are assembled in a 12-step reaction sequence from 4 variable building blocks by combining an intramolecular azomethine ylide cycloaddition reaction with a final cyclative cleavage from resin.

Solid-Phase Synthesis of beta-Sultams.

Solid-phase synthesis of beta-sultams amenable for construction of sulfonyl beta-lactam analogue combinatorial libraries is reported. Imine intermediates generated from polymer-immobilized amino acids and aldehydes are reacted with (chlorosulfonyl)acetates in the presence of pyridine to afford the solid-phase-tethered beta-sultam products. The latter can be released from support by acidic cleavage (TFA) or photocleavage, depending on the nature of the linker employed (acid-labile or photolabile linkers).

The reversed Kenner linker: a new safety-catch linker for the preparation of N-alkyl sulfonamides.

A new strategy for the solid-phase synthesis of sulfonamides is described. The Kenner safety-catch strategy has been modified such that the carboxylic acid component remains attached to the solid support while the sulfonamide portion is released into solution. An initial demonstration of the scope of this strategy is presented, along with an analysis of the cleavage characteristics and extension to more elaborate products via Suzuki reaction and thiazolidinone synthesis.

Capillary electrochromatography-laser-induced fluorescence method for separation and detection of dansylated dialkylamine tags in encoded combinatorial libraries.

LC-fluorescence and LC-MS methods have been previously reported for use in decoding bead-based combinatorial libraries. We present the use of capillary electrochromatography (CEC) for highly selective decoding in combination with laser-induced fluorescence (LIF) detection for high sensitivity. The results are compared to prior data obtained using HPLC with fluorescence detection.

A traceless perfluoroalkylsulfonyl (PFS) linker for the deoxygenation of phenols.

[reaction: see text]. The synthesis of a novel perfluoroalkylsulfonyl (PFS) fluoride is described for use as a traceless linker in solid-phase organic synthesis. Attachment to the resin and subsequent coupling of a phenol affords a stable arylsulfonate that behaves as a support-bound aryl triflate.

Evaluation of a single-pass intestinal-perfusion method in rat for the prediction of absorption in man.

Prediction of the fraction of dose absorbed from the intestine (Fa) in man is essential in the early drug discovery stage. In-vitro assays in Caco-2 and MDCK cells are routinely used for that purpose, and their predictive value has been reported. However, in-situ techniques might provide a more accurate estimation of Fa.

Traceless solid-phase synthesis of substituted benzimidazoles via a base-cleavable linker.

[figure: see text] A solid-phase route to substituted benzimidazoles has been developed using a modified base-labile linker strategy to release the final products in a traceless manner. This approach permits the synthesis of diverse compounds in moderate yields and high purity.

On-line sample preparation for high throughput reversed-phase LC/MS analysis of combinatorial chemistry libraries.

An on-line sample preparation method utilizing a time-programmed autosampler is described for high throughput liquid chromatography/mass spectrometry (LC/MS). This approach is particularly helpful for the LC/MS analysis of samples which require solvents incompatible with HPLC in the sample preparation process. The on-line sample preparation approach minimizes a bottleneck in throughput and improves sample recovery under some circumstances.

Comparison of chromatographic and spectroscopic methods used to rank compounds for aqueous solubility.

Rapid methods for ranking the solubility of compounds in aqueous media using commercial, 96-well ultraviolet-visible (UV-vis) and nephelometric plate readers are described. The methods were evaluated using commercially available compounds from a variety of structural classes as well as a series of structurally related compounds derived from combinatorial synthesis. Samples were predissolved in dimethyl sulfoxide (DMSO) and then added to the study solvent to attain a final concentration of DMSO in the aqueous solution of 5%.

Reaction kinetics of protease with substrate phage. Kinetic model developed using stromelysin.

Peptide libraries generated using phage display have been widely applied to proteolytic enzymes for substrate selection and optimization, but the reaction kinetics between the enzyme and substrate phage are not well understood. Using a quantitative ELISA assay to monitor the disappearance of substrate, we have been able to follow the course of reaction between stromelysin, a metalloprotease, and its substrate phage. We found that under the proteolytic conditions where the enzyme was present in nanomolar concentration or higher, in excess over the substrate, the proteolysis of substrate phage was a single exponential event and the observed rate linear with respect to enzyme concentration.

Expediting the method development and quality control of reversed-phase liquid chromatography electrospray ionization mass spectrometry for pharmaceutical analysis by using an LC/MS performance test mix.

Mass spectrometry combined with liquid chromatography (LC/MS) has become an important analytical methodology in both pharmaceutical and biomolecule analyses. LC/MS, especially with reversed-phase HPLC (RP-LC), is extensively used in the separation and structural identification of pharmaceutical samples. However, many parameters have to be considered when a new LC/MS method is developed for either separation and structural analysis of unknown mixtures or quantitative analysis of a set of known compounds in an assay.

A novel approach to high-throughput quality control of parallel synthesis libraries.

Combinatorial chemistry is a powerful tool to enhance drug discovery efforts in the pharmaceutical industry. One type of combinatorial chemistry, parallel synthesis, is now widely used to prepare numerous compounds of structural diversity. A novel high-throughput method for quality control of parallel synthesis libraries has been developed.

Peptide agonists of the thrombopoietin receptor.

We have screened a variety of L-amino acid peptide libraries against the extracellular domain of the human thrombopoietin (HuTPO) receptor, c-Mpl. A large number of peptide ligands were recovered and categorized into two families. Peptides from each family compete with the binding of HuTPO and with the binding of peptides from the other familiy.

Solid-phase synthesis of 1,2,3,4-tetrahydro-2-pyridones via aza-annulation of enamines.

An efficient solid-phase approach has been developed to prepare nitrogen heterocycles with a 1,2,3,4-tetrahydro-2-pyridone core via aza-annulation of enamines. Immobilized enamines were prepared from the reaction of primary amines with propynoic acid derivatives or ketones. Aza-annulation reactions were carried out by reacting resin-bound enamines with symmetrical alpha,beta-unsaturated acid anhydrides or alpha,beta-unsaturated acids in the presence of DPPA and TEA.

A potent dimeric peptide antagonist of interleukin-5 that binds two interleukin-5 receptor alpha chains.

Two series of peptides that specifically bind to the extracellular domain of the alpha chain of the human interleukin-5 receptor (IL-5Ralpha), but share no primary sequence homology to IL-5, were identified from libraries of random recombinant peptides. Affinity maturation procedures generated a 19-aa peptide that binds to the IL-5 receptor alpha/beta heterodimer complex with an affinity equal to that of IL-5 and is a potent and specific antagonist of IL-5 activity in a human eosinophil adhesion assay. The active form of the peptide is a disulfide-crosslinked dimer that forms spontaneously in solution.