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Small molecules have critical roles at all levels of biological complexity and yet remain orphans of the central dogma. Chemical biologists, working with small molecules, expand our understanding of these central elements of life.

Personalized, or genomic, medicine entails tailoring pharmacological therapies according to individual genetic variation at genomic loci encoding proteins in drug-response pathways. It has been previously shown that steady-state mRNA expression can be used to predict the drug response (i.e., sensitivity or resistance) of non-genotyped mammalian cancer cell lines to chemotherapeutic agents. In a real-world setting, clinicians would have access to both steady-state expression levels of patient tissue(s) and a patient's genotypic profile, and yet the predictive power of transcripts versus markers is not well understood. We have previously shown that a collection of genotyped and expression-profiled yeast strains can provide a model for personalized medicine. Here we compare the predictive power of 6,229 steady-state mRNA transcript levels and 2,894 genotyped markers using a pattern recognition algorithm. We were able to predict with over 70% accuracy the drug sensitivity of 104 individual genotyped yeast strains derived from a cross between a laboratory strain and a wild isolate. We observe that, independently of drug mechanism of action, both transcripts and markers can accurately predict drug response. Marker-based prediction is usually more accurate than transcript-based prediction, likely reflecting the genetic determination of gene expression in this cross.

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.

The kinase ATR appears to be closely associated with enzymes that remodel histones. ATR is an enzyme involved in the repair of DNA damage.

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.

Everyone has had the experience of stoking a fire; putting the logs close together causes flames to appear from previously dying embers. In a similar way, mere proximity might mediate qualitative biological responses. We discuss natural molecules that appear to have arisen to bring two proteins together and illustrate how this simple mechanism can be used to control a wide variety of biological processes.

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.

A comparative study of the oxidation of trans-2-phenylcyclohexanol and cholesterol by Dess-Martin periodinane (DMP) using three different procedures with corresponding anhydrous conditions reveals that the oxidation is slower under anhydrous conditions. Addition of wet CH2Cl2 to the alcohol-DMP complexes increases the rate of oxidation. The increase in the rate of oxidation due to the presence of water accounts for the higher oxidation rates obtained using impure samples of DMP.

The modification of the function of steroid receptors by rapamycin or FK506 is investigated using a model system of yeast, in which the human progesterone receptor from B (hPR-B) is converted with reporter gene. The possible occurrence of a modification is indicated by the binding property exhibited by rapamycin and FK506 with p59. The investigation reveals that the FK506 enhanced the progesterones' ability to activate the process of transcription. The involvement of calmidazolium also shows that the FK506 in association with calmidazolium increases the level of hPR-B phosphorylation.

Two dimensional NMR techniques were used to establish the solution structure of a peptide toxin isolated from funnel web spider venom, omega-Aga-IVB. The protein consists of four disulfide bonds. Random coil conformations are evident for the C-terminal 10 residues of this protein. Various positively charged amino acid side chains are regionalized on one side of the molecule.

Rabbit uterine and chick oviduct cytosols are used to separate FKBP59 as a big compound with hsp90, hsp70 and RP when it is bound with the immunosuppressant. The immune system is not the only domain of the connection between immunophilin, heat shock proteins and steroid receptors. The process of evolution reveals the conservation of the reaction between immunophilins and heat shock proteins, which shows a yeast FKBP59 homologue complexed with hsp70 and hsp90. The FKBP59 and heat shock protein complex reveal the presence of actin and a new protein, p63.

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 the C22-C42 segment of rapamycin represents the second stage towards the total synthesis of this antiproliferative agent. The modular construction process involves the coupling of a vinyllithium with a Weinreb amide and an etheric boron trifluoride-mediated epoxide opening and coupling with an alpha-lithio sulfone. The three main coupling units are obtained from the benzyl and t-butyldimethylsilyl ethers of 2-methyl-3-methoxy-3-propanone and from 4-methoxy-2-triisopropylsiloxycyclohexan-6-ol.

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.

Immunophilins from calf thymus, brain and spleen were purified and their 215 amino acid sequence was determined. FKBP25, FK506 and a rapamycin-binding protein were tested and results showed that the N-terminal area is hydrophilic and mainly alpha-helix in conformation. The C-terminal site is homologous with other FKBPs but is unique because of amino acid insertions and nuclear targetting sequence. Rotamase activity was seen with FKBP25 which is inhibited by rapamycin and FK506 but not cyclosporine A.

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.

1,1,7-Trimethoxy-2, 8-dimethyl-5-(t-butyldimethylsilyl)oxy-12-(oxodiphenyl)- phosphino-8, 10-dodecadiene represents the C10-C21 segment of rapamycin. Its synthesis involves an 11-step stereoselective process. A crucial step in the process is the opening of the intermediate hemithiolactol's ring, achieved through rapid warming and quenching with the aid of titanium tetrachloride. The phosphine oxide, obtained in 5% overall yield from the starting material (R)-methyl 3-hydroxy-2-methylpropionate, is converted to a model triene to test its readiness for subsequent assembly with the other rapamycin segments.

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.