Yong-Uk Kwon

High-throughput evaluation of relative cell permeability between peptoids and peptides

Peptides are limited in their use as drugs due to low cell permeability and vulnerability to proteases. In contrast, peptoids are immune to enzymatic degradation and some peptoids have been shown to be relatively cell permeable. In order to facilitate future design of peptoid libraries for screening experiments, it would be useful to have a high-throughput method to estimate the cell permeability of peptoids containing different residues. In this paper, we report the strengths and limitations of a high-throughput cell-based permeability assay that registers the relative ability of steroid-conjugated peptides and peptoids to enter a cell. A comparative investigation of the physicochemical properties and side chain composition of peptoids and peptides is described to explain the observed higher cell permeability of peptoids over peptides. These data suggest that the conversion of the monomeric residues in peptides to an N-alkylglycine moiety in peptoids reduced the hydrogen-bonding potential of the molecules and is the main contributor to the observed permeability improvement.

Ring-Closing Metathesis Approaches for the Solid-Phase Synthesis of Cyclic Peptoids

Cyclic peptoids were efficiently synthesized on a solid phase in high yields utilizing ring-closing metathesis (RCM). This method should be a valuable tool for easy access to cyclic peptoid libraries and various cyclic compounds.

Chemo-enzymatic synthesis of 11-hydroxyundecanoic acid and 1,11-undecanedioic acid from ricinoleic acid

A practical chemoenzymatic synthetic method for 11-hydroxyundecanoic acid and 1,11-undecanedioic acid from ricinoleic acid (12-hydroxyoleic acid) was investigated. Biotransformation of ricinoleic acid into the ester (3) via 12-ketooleic acid (2) was driven by recombinant Escherichia coli cells expressing an alcohol dehydrogenase from Micrococcus luteus and the Baeyer–Villiger monooxygenase from Pseudomonas putida KT2440. The carbon–carbon double bond of the ester (3) was chemically reduced, and the ester bond was hydrolyzed to afford n-heptanoic acid (5) and 11-hydroxyundecanoic acid (7), which were converted into other related derivatives. For example, 11-hydroxyundecanoic acid was transformed into 1,11-undecanedioic acid (8) under fairly mild reaction conditions. Whole-cell biotransformation at high cell density (i.e., 20 g dry cells per L) allowed the final ester product concentration and volumetric productivity to reach 53 mM and 6.6 mM h−1, respectively. The overall molar yield of 1,11-undecanedioic acid from ricinoleic acid was 55% based on the biotransformation and chemical transformation conversion yields of 84% and 65%, respectively.

Recognition of myo-inositol 1,4,5-trisphosphate using a fluorescent imidazolium receptor

The first example of an imidazolium-based fluorescent receptor for D-myo-inositol 1,4,5-trisphosphate (IP(3)) is reported in this study. The fluorescent receptor 1 bearing four imidazolium and pyrene groups displayed a large fluorescent quenching effect with myo-IP(3) compared to fluorescent changes with various IP series, pyrophosphate, and ATP.

Microbial synthesis of plant oxylipins from γ-linolenic acid through designed biotransformation pathways.

Secondary metabolites of plants are often difficult to synthesize in high yields because of the large complexity of the biosynthetic pathways and challenges encountered in the functional expression of the required biosynthetic enzymes in microbial cells. In this study, the biosynthesis of plant oxylipins--a family of oxygenated unsaturated carboxylic acids--was explored to enable a high-yield production through a designed microbial synthetic system harboring a set of microbial enzymes (i.e., fatty acid double-bond hydratases, alcohol dehydrogenases, Baeyer-Villiger monooxygenases, and esterases) to produce a variety of unsaturated carboxylic acids from γ-linolenic acid. The whole cell system of the recombinant Escherichia coli efficiently produced (6Z,9Z)-12-hydroxydodeca-6,9-dienoic acid (7), (Z)-9-hydroxynon-6-enoic acid (15), (Z)-dec-4-enedioic acid (17), and (6Z,9Z)-13-hydroxyoctadeca-6,9-dienoic acid (2). This study demonstrated that various secondary metabolites of plants can be produced by implementing artificial biosynthetic pathways into whole-cell biocatalysis.

Cross metathesis assisted solid-phase synthesis of glycopeptoids.

A solid-phase synthesis of glycopeptoids was explored through olefin cross metathesis (CM). Peptoids and sugar derivatives with appropriate olefin moieties were coupled in the presence of an olefin metathesis catalyst to afford glycopeptoids in good yields. This systematic solid-phase CM study can provide facile access to the molecular sources of glycopeptidomimetics and postchemical modifications on various molecular scaffolds.

Facile Solid-Phase Parallel Synthesis of Linear and Cyclic Peptoids for Comparative Studies of Biological Activity

A series of linear and cyclic peptoids, which were expected to possess better pharmacokinetic properties and biological activities for blocking the interaction between apolipoprotein E and amyloid-β, were designed and synthesized as possible therapeutic agents. Peptoids were easily synthesized on solid-phase by the submonomer strategy and polar side chain-containing amines were effectively introduced under the modified reaction conditions. For the synthesis of cyclic peptoids, β-alanine protected with the 2-phenylisopropyl group, which could be selectively removed by 2% TFA, was used as a primary amine to afford a complete peptoid unit. The macrolactamization between the carboxylic acid of β-alanine moiety and terminal amine of peptoids was successfully performed in the presence of the PyAOP coupling agent on solid-phase in all the cases, providing various sizes of cyclic peptoids. In particular, some cyclic peptoids prepared in this study are the largest in size among cyclic peptoids reported to date. The synthetic strategy which was adopted in this study can also provide a robust platform for solid-phase construction of cyclic peptoid libraries. Currently, synthetic peptoids have been used to test interesting biological activities including the ApoE/Aβ interaction inhibition, nontoxicity, the blood-brain barrier permeability, etc.

Efficient Solid-Phase Synthesis of a Series of Cyclic and Linear Peptoid−Dexamethasone Conjugates for the Cell Permeability Studies

Cyclic peptides and their cyclic analogs have received a great deal of attention because of their numerous interesting biological activities and their challenging chemical synthesis. It has also been hypothesized that they might improve the cell permeability compared to linear molecules by providing internal hydrogen bonding and generally decreasing the conformational flexibility. In this study, a series of cyclic and linear peptoid-dexamethasone conjugates were rationally designed and efficiently synthesized on solid-phase for systematic cell permeability studies using reporter gene-based assays. These model compounds should be used to reveal how the cell permeability of cyclic molecules is affected by several physicochemical properties, especially, the reduced conformational flexibility and the ring size. In addition, the synthetic strategy that was adopted in this study can also provide a robust platform for postchemical modifications of various molecular scaffolds in solid-phase or solution-phase syntheses.

Synthetic glycosylphosphatidylinositol microarray reveals differential antibody levels and fine specificities in children with mild and severe malaria.

Glycosylphosphatidylinositol (GPI) glycolipids abound on the cell surface at the merozoite stage of Plasmodium falciparum life cycle are a central toxin in malaria. The contribution of GPI specific humoral immune responses to protection against malaria pathology is not clear, since studies on the correlation between anti-GPI antibody titers and disease severity have yielded contradictory results. Here, we present the application of a carbohydrate microarray based on synthetic PfGPI glycans to assess levels and fine specificities of anti-GPI antibody responses in healthy and malaria diseased individuals. Furthermore, the age dependent development of humoral immune responses against GPI in malaria-exposed children was investigated. Anti-GPI antibodies were only rarely found in children under the age of 18 months. Sera from subjects with severe malaria and healthy children contained antibodies that recognized predominantly synthetic Man(3)-GPI and Man(4)-GPIs. In contrast, antibodies in sera of children with mild malaria also showed substantial reactivity with truncated glycans comprising glucosamine-inositol moieties without mannose or with only one or two mannose residues.

Construction and Evaluation of an Automated Light Directed Protein-Detecting Microarray Synthesizer

We have designed, constructed, and evaluated an automated instrument that has produced high-density arrays with more than 30 000 peptide features within a 1.5 area of a glass slide surface. These arrays can be used for high throughput library screening for protein binding ligands, for potential drug candidate molecules, or for discovering biomarkers. The device consists of a novel fluidics system, a relay control electrical system, an optics system that implements Texas Instrumentspsila digital micromirror device (DMD), and a microwave source for accelerated synthesis of peptide arrays. The instrument implements two novel solid phase chemical synthesis strategies for producing peptide and peptoid arrays. Biotin-streptavidin and DNP anti-DNP (dinitrophenol) models of antibody small molecule interactions were used to demonstrate and evaluate the instruments capability to produce high-density protein detecting arrays. Several screening assay and detection schemes were explored with various levels of efficiency and assays with sensitivity of 10 nM were also possible.