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The development, scope and mechanism of general, efficient and atropdiastereoselective reactions leading to compounds having biaryl containing medium rings are reported. The process described outlines a pathway that will contribute to a systematic and comprehensive approach to exploring biology (chemical genetics).

1,3-dioxanes were synthesized to arrayed stock solutions of single compounds suitable for multiple phenotypic and protein binding assays.

Non-peptide binding elements for the leucine-proline binding pocket of the Src SH3 domain were unveiled using split-pool synthesis. The non-peptide elements were found to have peptide-like interactions, contrary to previous findings that non-peptide SH3 ligands have different interactions from peptide ligands. A comparison of a series of ligands that contains variants of the parent non-peptide binding structure was conducted to determine the binding characteristics of the protein pocket.

Ligands with greater affinity and enhanced selectivity for the SH3 domain of the tyrosine kinase Src were discovered by using the solution structure of the SH3 domain to design biased libraries. Spatially separated molecules were prepared using split-pool synthesis and designed to complement the topography of the specificity pocket. The procedure also yielded non-natural ligands that bind selectively to the SH3 domain of the tyrosine kinase Hck.

New chemical inducers of dimerization (CIDs) were synthesized using one-step dimerization of the immunosuppressant FK506 by olefin metathesis. These small-molecule protein dimerizers can activate signal transduction pathways and gene expression at low concentrations in mammalian cells as well as transgenic animals. Widespread usage of CIDs will be made possible by the ease of synthesis of these compounds.

Substrate-controlled diastereoselective reactions with (R)-pulegone have been used to synthesize the naturally-occurring diterpene (+)-epoxydictymene. Dicobalt hexacarbonyl complexes of alkynes were used in Lewis acid-promoted Nicholas and Pauson-Khand intramolecular reaction to form three octane ring systems: alpha-funebrene, pardalianchol and alpha-8-hydroxypresilphiperfolene.

A retrosynthetic route to the natural antipode and several variants of discodermolide, a marine natural product isolated from the sponge Discodermia dissoluta, is described. The procedure partitioned the polypropionate backbone into three sequences. The first, the C1-C7 lactone, requires the nucleophilic addition of a synthon to an aldehyde. The second is the C9-C15 fragment while the third is the C16-C24 ketone.

Trapoxin B, a cyclotetrapeptide isolated from the fungus Helicoma ambiens, was totally synthesized including (3H)-trapoxin B and an affinity reagent called K-trap. The synthesis involved the replacement of one of trapoxin's phenylalanine residues by a protected lysine residue. Synthetic reagents were utilized to purify trapoxin's biological target to homogenicity. The peptide sequence derived from the purified has enabled the cloning of the human gene encoding the elusive histone deacetylase.

Examination of the factors ruling the cycloaromatization of dynemicin A and related molecules reveals that the thermal reactivity of compounds containing an exo-epoxide is controlled by the stereochemistry at C10a. Structures with an alpha-substituent are unreactive, while those with a beta-substituent are cyclized at 80 degrees Celsius. This variation is attributed to a steric interaction caused by a conformational change in the alpha-substituted compounds. A newly synthesized C10a alpha-substituted endo-epoxide is cycloaromatized under mild acidic conditions through epoxide opening.

The synthesis of bis-phosphatidylethanolamine(trifluoromethyl)phenyldiazirine (DIPETPD) provides a photochemical probe for the labeling of hard-to-access hydrophobic membrane cores. The bipolar phospholipid has a covalently bonded side chain that can cross the membrane and a central TPD labeling moiety, designed to provide sharper labeling resolution by its ability to reach the photoreactive function in the center of the bilayer. DIPETPD is successfully incorporated into various liposomes and is shown not to hinder the latters' fusion with the influenza virus.

The synthesis of hikizimycin, a nucleoside disaccharide isolated from Streptomyces A-5 and Streptomyces longissimus, is reported. A two-directional approach is applied to the building of the undecose segment of hikizimycin. The required stereocenters are created via olefination/osmylation. Glycosidation of hindered glycosyl acceptors via sulfoxide activation solves the major problem associated with the synthetic process. Moreover, the electronic and conformational structures of hikizimycin are the basis of a series of deprotection reactions.

A new type of profiling experiment is described where the response of genetically similar but not identical cells to pairwise combinations of biologically active small molecules yields a network of chemical genetic interactions. The ability of combinations of small molecules to interact antagonistically or synergistically provides a chemical tool to resolve differences between biological networks.

A branching diversity-oriented synthesis (DOS) pathway that yields 29 400 discrete compounds comprising 10 distinct polycyclic skeletons is described. The six-step, stereoselective synthesis, which affords product having a central skeleton with between two and four rings and up to six stereocenters, is achieved using an inexpensive and accessible, 'one bead-one stock solution' technology platform.

A study is conducted to understand the higher network connectivity exhibited by the natural products target proteins with a high number of protein-protein functional interactions compared to the disease genes. The insights gained for the disruption of essential biological pathways leading in competitor death could be used to determine the additional sources of small molecules required for identifying drugs targeting the root causes of human disease in the future.

The X-ray crystallographic and H NMR spectroscopic analysis of vinylogous polypeptides show that these peptide backbones can adopt antiparallel, parallel and helical sheet secondary structures. These vinylogous contain repeating units of amino acid residues having (E)-ethenyl unit in between the carbonyl and C-alpha functionalities. Moreover, these polypeptides can serve as peptide templates for the synthesis of a new series of polypeptide-like substances exhibiting alternative backbones.

Gold(I)-catalyzed cascade reactions of easily prepared propargyl propiolates are developed as a means to achieve effective intermolecular coupling reactions for the build/couple/pair strategy. The intramolecular pairing reactions have included one based on a novel aza-Wittig-6[pi]-electrocyclization sequence and others based on ring-closing metathesis reactions.

The peptide isosteres of the naturally occurring and potent histone deacetylase (HDAC) inhibitors FK228 and largazole are prepared and analyzed along with FK228, largazole, and SAHA for inhibition of the class I HDACs.

The design and synthesis of a reliable fluorescent probe for use in cell-based screening for myogenesis is described. The results provide insight into the cell-state selectivity of compound flourescence which are used as probes for high-throughput screening.

The role of stereochemical and skeletal variation on assay outcomes, albeit within a limited structure space is assessed using multidimensional screening along with the small-molecule synthesis. A new approach is provided as a framework to assess the role of a main-group element on assay outcomes.

The split-pool synthesis of more than 3000 spirooxindoles on high capacity macrobeads is reported. A high-throughput chemical genetic modifier screen performed using stock solutions of the resultant products to demonstrate the utility of the discovery process.

Systematic and quantitative measurements of the roles of stereochemistry and skeleton-dependent conformational restriction are made using multidimensional screening. The studies show a quantitative method for measuring stereochemical and skeletal diversity of small molecules and their cellular consequences.

A synthesis strategy is described that uses common reaction conditions to transform a collection of similar substrates into a collection of products having distinct molecular skeletons. The substrates have different appendages that pre-encode skeletal information, called sigma-elements.

A new catalyst system that extends the scope and selectivity of the [3+2] azomethine ylide cycloaddition is described. It is compatible with reagents used in a one-stock solution technology platform for diversity-oriented synthesis.

A two-step process, involving the assembly of monomers and the rigidification of the resulting oligomers is described that provides an alternative means to the assembly of widely varied molecular architectures. The discovery of a cascade annulation reaction of a linear eye-diyne has demonstrated the ability of the oligomerization/folding process to enable chemical discovery in addition to generating skeletally diverse small molecules.

A specific disruption of DNA-protein or protein-protein interaction is required to inhibit the function of a transcription factor. Diversity-oriented synthesis (DOS) could be a source of candidate antagonist of these interactions. To test this possibility, a small molecule microarray-based screen aimed at identifying the DOS derived small molecules that directly bind and modulate the transcriptional activity of Hap3p was devised.

The structural dissection of two 1,3-oxidanes is used with in-cell HDAC paralog selectivity to identify key elements for selective HDAC inhibitors. The SAHA substructure alone is insufficient for HDAC6 paralog selectivity in cells.

It has been possible to identify readily synthesized substrates that experience two forms of medium ring-forming reactions producing two classes of complex structures, one patterned after the biaryl natural products and the other a metal-inserted variant.

The ring-closing metathesis (RCM) reaction was used to study macrocylization reactions.

A role for copper in specific gene activation was revealed using chemical genetic and genomic approaches.

A study on the identification of specific small molecule ligands for any protein in a cell, tissue or organism developed a technique termed small molecule printing. Experimental testing demonstrated that this new approach enables thousands of binding assays to be performed in a parallel fashion using compounds released from a single synthesis bead. In principle then, it can be used to construct thousands of identical microarrays from a single split-pool library.

More than two million compounds having structures that are identical to natural products and consistent with miniaturized assays were synthesized via a six-step reaction sequence. The technique involved a number of coupling processes and split-pool methodologies to produce multiple products. Moreover, it required water-compatible photolabile supports when implementing large numbers of miniaturized cell culture assays targeted at isolating cell permeable ligands. The resulting compounds were structurally diverse, stereochemically defined and rigid.

The enantiomer Mn20 was synthesized to study the effect of inverting the stereochemistry on the binding of the Src SH3-NL2 Ac-Mn18-Mn1-PLPPLP-NH2 complex. Multidimensional nuclear magnetic resonance was utilized to determine the structure of the SH3-NL2R complex. The common peptidic PLPPLP fragments of the ligands adopted the same polyproline type II helix conformation. Results showed that monomers Mn18 and Mn20 can adopt conformations that present overall similar molecular surfaces contacting the SH3 domain.

Alpha-cyclopentylsarcosine11-cyclosporin A (CsA*), a rationally modified immunosuppressive drug cyclosporin A (CsA) that does not bind to cyclophilin (Cyp) and therefore does not inhibit calcineurin (Cn) in cells, was synthesized. Also, a modified Cyp with compensatory mutations in its CsA-binding pocket that promote high affinity complexation with CsA* was investigated. The resulting Cyp*CsA* complex indicated a composite surface that binds Cn with high affinity. Thus, Cn inhibition by CsA* was restored in cells expressing Cyp*.

FKBP25 is the third member of the family of binding proteins that has an immunosuppressive function. Its C-terminal domain has been suggested to contain a nuclear localization sequence that can be used as a binding site. X-ray diffraction of the C-terminal domain, which was performed by complexing it with rapamycin, revealed a predominant secondary structure consisting of a curved beta-sheet made from five antiparallel beta strands. Adjacent to the beta sheet is a short turn of alpha-helix which contributes a tryptophan to the binding pocket.

A new strategy for identifying ligands that contain non-peptide structural elements has been developed by targeting specific protein-ligand complexes. The approach involves linking potential ligands to a particular protein to determine ligand specificity. A schematic approach for the rational design of a library of ligands is presented.