Intramolecular excimer formation in naphthalene-containig polyesters. Bichromophoric model compounds derived from phathalic, siccinic or malonic acid and 2-hydroxynaphthalene or 2-hydroxy-methylnaphthalene.

Steady state fluorescence measurements in dilute solutions are performed for bis(2-naphthyl) phthalate, bis(2-naphthylmethyl) phthalate, bis(2-naphthyl) succinate, bis(2-naphthylmethyl) succinate, bis(2-naphthyl) malonate and bis(2-naphthylmethyl) malonate, as models for polyesters containing naphthalene in their rigid units and flexible spacers that impose differences in the types of interactions between successive naphthalene units. The amount of intramolecular excimer in dilute solution depends on the type of flexible spacer, and also whether the compound is derived from 2-naphthol or 2-hydroxymethylnaphthalene. No excimer is detected from the compounds derived from 2-naphthol, but all compounds derived from 2-hydroxymethylnaphthalene showed excimer formation. These results are rationalized with a theoretical analysis of the conformations of the flexible spacers.This research was supported by DGICYT PB91-0166 (FM) and by National Science Foundation grant DMR 9220369 (WLM)

Orbital Optimization in the Active Space Decomposition Model

We report the derivation and implementation of orbital optimization algorithms for the active space decomposition (ASD) model, which are extensions of complete active space self-consistent field (CASSCF) and its occupation-restricted variants in the conventional multiconfiguration electronic-structure theory. Orbital rotations between active subspaces are included in the optimization, which allows us to unambiguously partition the active space into subspaces, enabling application of ASD to electron and exciton dynamics in covalently linked chromophores. One- and two-particle reduced density matrices, which are required for evaluation of orbital gradient and approximate Hessian elements, are computed from the intermediate tensors in the ASD energy evaluation. Numerical results on 4-(2-naphthylmethyl)-benzaldehyde and [3$_6$]cyclophane and model Hamiltonian analyses of triplet energy transfer processes in the Closs systems are presented. Furthermore model Hamiltonians for hole and electron transfer processes in anti-[2.2](1,4)pentacenophane are studied using an occupation-restricted variant

Drug Candidate Discovery: Targeting Bacterial Topoisomerase I Enzymes for Novel Antibiotic Leads

Multi-drug resistance in bacterial pathogens has become a global health crisis. Each year, millions of people worldwide are infected with bacterial strains that are resistant to currently available antibiotics. Diseases such as tuberculosis, pneumonia, and gonorrhea have become increasingly more difficult to treat. It is essential that novel drugs and cellular targets be identified in order to treat this resistance. Bacterial topoisomerase IA is a novel drug target that is essential for cellular growth. As it has never been targeted by existing antibiotics, it is an attractive target. Topoisomerase IA is responsible for relieving torsional strain on DNA by relaxing supercoiled DNA following processes such as replication and transcription. The aim of this study is to find novel compounds that can be developed as leads for antibiotics targeting bacterial type IA topoisomerase. Various approaches were used in order to screen thousands of compounds against bacterial type IA topoisomerases, including mixture-based screening and virtual screening. In the mixture-based screen, scaffold mixtures were tested against the M. tuberculosis topoisomerase I enzyme and subsequently optimized for maximum potency and selectivity. The optimized compounds were effective at inhibiting the enzyme at low micromolar concentrations, as well as killing the tuberculosis bacteria. In a virtual screen, libraries with hundreds of thousands of compounds were screened against the E. coli and M. tuberculosis topoisomerase I crystal structures in order to find new classes of drugs. The top hits were effective at inhibiting the enzymes, as well as preventing the growth of M. smegmatis cells in the presence of efflux pump inhibitors. Organometallic complexes containing Cu(II) or Co(III) were tested as well against various topoisomerases in order to determine their selectivity. We discovered a poison for human type II topoisomerase that has utility as an anticancer agent, as it killed even very resistant cell lines of breast and colon cancer. The Co(III) complexes were found to inhibit the bacterial topoisomerase I very selectively over other topoisomerases. The various methods of drug discovery utilized here have been successful at identifying new classes of compounds that may be further developed into antibiotic drugs that specifically target bacterial type IA topoisomerases

Direct Phenotypic Screening in Mice: Identification of Individual, Novel Antinociceptive Compounds from a Library of 734 821 Pyrrolidine Bis-piperazines

The hypothesis in the current study is that the simultaneous direct in vivo testing of thousands to millions of systematically arranged mixture-based libraries will facilitate the identification of enhanced individual compounds. Individual compounds identified from such libraries may have increased specificity and decreased side effects early in the discovery phase. Testing began by screening ten diverse scaffolds as single mixtures (ranging from 17 340 to 4 879 681 compounds) for analgesia directly in the mouse tail withdrawal model. The “all X” mixture representing the library TPI-1954 was found to produce significant antinociception and lacked respiratory depression and hyperlocomotor effects using the Comprehensive Laboratory Animal Monitoring System (CLAMS). The TPI-1954 library is a pyrrolidine bis-piperazine and totals 738 192 compounds. This library has 26 functionalities at the first three positions of diversity made up of 28 392 compounds each (26 × 26 × 42) and 42 functionalities at the fourth made up of 19 915 compounds each (26 × 26 × 26). The 120 resulting mixtures representing each of the variable four positions were screened directly in vivo in the mouse 55 °C warm-water tail-withdrawal assay (ip administration). The 120 samples were then ranked in terms of their antinociceptive activity. The synthesis of 54 individual compounds was then carried out. Nine of the individual compounds produced dose-dependent antinociception equivalent to morphine. In practical terms what this means is that one would not expect multiexponential increases in activity as we move from the all-X mixture, to the positional scanning libraries, to the individual compounds. Actually because of the systematic formatting one would typically anticipate steady increases in activity as the complexity of the mixtures is reduced. This is in fact what we see in the current study. One of the final individual compounds identified, TPI 2213-17, lacked significant respiratory depression, locomotor impairment, or sedation. Our results represent an example of this unique approach for screening large mixture-based libraries directly in vivo to rapidly identify individual compounds

Rescue of Glycosylphosphatidylinositol-Anchored Protein Biosynthesis Using Synthetic Glycosylphosphatidylinositol Oligosaccharides

The attachment of proteins to the cell membrane using a glycosylphosphatidylinositol (GPI) anchor is a ubiquitous process in eukaryotic cells. Deficiencies in the biosynthesis of GPIs and the concomitant production of GPI-anchored proteins lead to a series of rare and complicated disorders associated with inherited GPI deficiencies (IGDs) in humans. Currently, there is no treatment for patients suffering from IGDs. Here, we report the design, synthesis, and use of GPI fragments to rescue the biosynthesis of GPI-anchored proteins (GPI-APs) caused by mutation in genes involved in the assembly of GPI-glycolipids in cells. We demonstrated that the synthetic fragments GlcNAc-PI (1), Man-GlcN-PI (5), and GlcN-PI with two (3) and three lipid chains (4) rescue the deletion of the GPI biosynthesis in cells devoid of the PIGA, PIGL, and PIGW genes in vitro. The compounds allowed for concentration-dependent recovery of GPI biosynthesis and were highly active on the cytoplasmic face of the endoplasmic reticulum membrane. These synthetic molecules are leads for the development of treatments for IGDs and tools to study GPI-AP biosynthesis

Analyzing the Binding of Co(II)-specific Inhibitors to the Methionyl Aminopeptidases from \u3cem\u3eEscherichia coli\u3c/em\u3e and \u3cem\u3ePyrococcus furiosus\u3c/em\u3e

Methionine aminopeptidases (MetAPs) represent a unique class of protease that is capable of the hydrolytic removal of an N-terminal methionine residue from nascent polypeptide chains. MetAPs are physiologically important enzymes; hence, there is considerable interest in developing inhibitors that can be used as antiangiogenic and antimicrobial agents. A detailed kinetic and spectroscopic study has been performed to probe the binding of a triazole-based inhibitor and a bestatin-based inhibitor to both Mn(II)- and Co(II)-loaded type-I (Escherichia coli) and type-II (Pyrococcus furiosus) MetAPs. Both inhibitors were found to be moderate competitive inhibitors. The triazole-type inhibitor was found to interact with both active-site metal ions, while the bestatin-type inhibitor was capable of switching its mode of binding depending on the metal in the active site and the type of MetAP enzyme

Rescue of glycosylphosphatidylinositol-anchored protein biosynthesis using synthetic glycosylphosphatidylinositol oligosaccharides

The attachment of proteins to the cell membrane using a glycosylphosphatidylinositol (GPI) anchor is a ubiquitous process in eukaryotic cells. Deficiencies in the biosynthesis of GPIs and the concomitant production of GPI-anchored proteins lead to a series of rare and complicated disorders associated with inherited GPI deficiencies (IGDs) in humans. Currently, there is no treatment for patients suffering from IGDs. Here, we report the design, synthesis and use of GPI fragments to rescue the biosynthesis of GPI-anchored proteins caused by mutation in genes involved in the assembly of GPI-glycolipids in cells. We demonstrated that the synthetic fragments GlcNAc-PI (1), Man-GlcN-PI (5), and GlcN-PI with two (3) and three lipid chains (4) rescue the deletion of the GPI biosynthesis in cells devoid of the PIGA, PIGL, and PIGW genes in vitro. The compounds allowed for concentration-dependent recovery of GPI biosynthesis and were highly active on the cytoplasmic face of the ER membrane. These synthetic molecules are leads for the development of treatments for IGDs and tools to study GPI-APs biosynthesis

Synthesis of Two Tetrasaccharide Pentenyl Glycosides Related to the Pectic Rhamnogalacturonan I Polysaccharide

The synthesis of two protected tetrasaccharide pentenyl glycosides with diarabinan and digalactan branching related to the pectic polysaccharide rhamnogalacturonan I is reported. The strategy relies on the coupling of N-phenyl trifluoroacetimidate disaccharide donors to a common rhamnosyl acceptor. The resulting trisaccharide thioglycosides were finally coupled to an n-pentenyl galactoside acceptor to access the two protected branched tetrasaccharides

Synthesis of isoindolinones by Pd-catalyzed coupling between N-methoxybenzamide and styrene derivatives

An atom-economical protocol for a tandem process involving Fujiwara-Moritani-aza-Wacker reactions has been developed for the Pd-catalyzed coupling between N-methoxy benzamide with styrene derivatives. The generality of the methodology was demonstrated by the synthesis of a library of twenty-five 3-benzylidene isoindolinones in moderate to good yields. A further twenty-two 3-benzyl derivatives were obtained by telescoping the process with a catalytic hydrogenation reaction

Synthesis of Oligosaccharide Antigens as Glycoconjugate Vaccine Candidates against Bacterial Pathogens

Capsular polysaccharides (CPSs) from the bacterial cell surface are important virulence factors and play an essential role for bacterial survival. CPSs are also important antigens capable of inducing a specific immune response rending these structurally unique glycans attractive targets for antibacterial vaccines development. The first part of the dissertation describes the construction of a collection of 15 novel synthetic oligosaccharides resembling the capsular polysaccharides of Streptococcus suis serotype 9. Differently protected monosaccharide building blocks were synthesized and employed into glycosylations to assemble the oligosaccharides. The second part of the dissertation focused on a multi-drug resistant bacterium Acinetobacter baumannii. The synthesis of repeating unit of CPS from A. baumannii AB5075 as well as two analogues is described. The synthetic oligosaccharides bearing an amine linker are ready for glycan microarray study, identification of the minimal epitope and conjugation