Our research program emphasizes the importance of small molecule interactions within biological systems. New synthetic methodology will drive the synthesis of natural products and fragment based small molecule collections. An ancillary, yet possibly more profound goal of this program is to arm our national screening infrastructure with skeletally intriguing small molecules. These collaborative efforts will facilitate the discovery of new targets and strategies for the advancement of biomedical research. Initially, these synthetic achievements will support the exploration of post-translational arginine modifications in cell signaling. The recent implication of these events in a number of disease states (multiple sclerosis, rheumatoid arthritis, glaucoma and tumorogenesis) encourages the preparation of biological tools and therapeutic leads. Projects poised to deliver antibiotic collections for the inhibition of prokaryotic protein synthesis will also be initiated. Molecules with purported rRNA binding interactions that are uncharacterized or non-overlapping with known sites of resistance will be targeted to advance our understanding of RNA's binding topology.

I. inhibitors of peptidylarginine deiminase

Compounds that are pre-disposed to inhibiting peptidylarginine deiminases (PADs), enzymes that have recently been implicated in chromatin modification, will be prepared. Identification of a selective PAD inhibitor will permit the systematic study of this enzyme's function and leads for novel therapeutics. In concert with the known small molecule inhibitors of histone deacetylaces (tubacin) and peptidylarginine methyl transferases, these compounds will enable the dissection of these epigenetic marks and their implications in gene regulation and tumorogenesis. The mechanism of these enzymes has recently been elucidated and shown to involve an active site Cys. The synthesis of novel arginine mimetics will be pursued to evaluate the irreversible inhibition of these enzymes.

 II. Natural product synthesis: unique phenotypes inspire small molecule collections The NA229598 scaffold offers an exciting starting point for the synthesis of small molecule collections that rigorously explore stereochemical diversity. The natural product itself displays an engaging phenotype, inhibiting the growth of human colon cancer DLD-1 cells in suspension cultures orders of magnitude more strongly than in substratum-attached monolayer cultures. Further it arrests the cell cycle progression in early G1, decreasing the activation of cdk2 and inhibiting the synthesis of cyclinD1 without altering mRNA levels! Synthetic endeavors will facilitate the dissection of this remarkably selective translational repression. The parent natural product poses a synthetic challenge as the stereochemistry of the skipped diamino-diol is unkown, encouraging the exploration of strategies capable of producing all stereochemical variants. It also possesses a rare carbamoylated guanidine, prompting the development of novel methods for the regioselective installation of this function. These synthetic achievements will be exploited in the synthesis of small-molecule collections based on this motif, to generate structural and skeletal variants for SAR and for small molecule screening collaborations. The regioselective functionalization of the imidazoline-imine will also enable the synthesis of Mannopeptimycin. This glycopeptide antibiotic has shown good activity against methicillin resistant Staphylococcus aureus and in vivo activities an order of magnitude greater that other glycopeptides such as vancomycin.

III. 2-aminoimidazoles

A decade ago several 2-amino-imidazole natural products were isolated from marine sponges, but their biological roles remained hidden. Since then, bioassay guided isolation has unearthed a wide variety of biological activities for these natural products. An efficient synthesis of the naamine core will permit a number of biomimetic transformations will access related metabolites. These short synthetic sequences are intended to generate small molecule collections to enter national screening platforms (i.e. the Molecular Libraries Screening Centers Network (MLSCN) sponsored by the NIH Roadmap) to illuminate a more global purpose for the conservation of this skeleton. Our synthetic sequence will be of additional utility and provide rapid access to diversified histidine analogues of the GE81112 natural product family. Three antibacterial factors, namely GE81112 A, B and B1, have very recently been isolated from a Streptomyces sp.. These compounds appear to be selective inhibitors of protein synthesis initiation in prokaryotes, as they bind to the 30s ribosomal subunit. Cross-resistance studies to a number of common antibiotics support a novel mechanism of action for this antibiotic.

IV. Synthesis of constrained amicetin analogues

The hexose-cytosine antibiotic amicetin has long been valued for its potent inhibition of protein synthesis. While the X-ray structure of the compound itself shows an elongated resting state, recent NMR studies of amicetin with synthetic RNA suggests the active conformer to be folded. Although highly strained, this structure may be stabilized by p -stacking interactions and an extensive hydrogen-bonding network between the saccharide and peptide constituents. We will validate and improve the specificity of this interaction by creating a subset of amicetin “turn” mimetics. Synthetic intermediates will be deployed to define the exact binding site of this antibiotic to domain V of the 23s rRNA sequence through small molecule-rRNA crosslinking experiments. This information will aid ongoing efforts to explore rRNA binding topology and generate novel scaffolds for antimicrobial therapeutics.