Ambara R. Pradipta

In Vivo Gold Complex Catalysis within Live Mice

Metal complex catalysis within biological systems is largely limited to cell and bacterial systems. In this work, a glycoalbumin-AuIII complex was designed and developed that enables organ-specific, localized propargyl ester amidation with nearby proteins within live mice. The targeted reactivity can be imaged through the use of Cy7.5- and TAMRA-linked propargyl ester based fluorescent probes. This targeting system could enable the exploitation of other metal catalysis strategies for biomedical and clinical applications.

Peptidoglycan as Nod1 ligand; fragment structures in the environment, chemical synthesis, and their innate immunostimulation.

Covering: up to 2011. This review focuses on the recent revealing of the immunostimulatory bacterial cell wall peptidoglycan (PGN) fragments as Nod1 ligands, especially a newly developed chemical synthesis of the partial structures, fragment structures in the environment and bacterial supernatant, and the immunostimulatory activities of the Nod1 ligands.

Development of bis-unsaturated ester aldehydes as amino-glue probes: sequential double azaelectrocyclization as a promising strategy for bioconjugation

The unsaturated ester aldehyde, (E)-3-alkoxycarbonyl-5-phenyl-2,4-dienal, was efficiently dimerized by applying the strain-promoted double-click reaction with sym-dibenzo-1,5-cyclooctadiene-3,7-diyne. The resulting dimerized probe was sequentially reacted first with one peptide molecule and then with a protein or the amino groups on the surface of a live cell through double azaelectrocyclization to achieve highly efficient bioconjugation.

Characterization of Natural Human Nucleotide-binding Oligomerization Domain Protein 1 (Nod1) Ligands from Bacterial Culture Supernatant for Elucidation of Immune Modulators in the Environment

Nucleotide-binding oligomerization domain protein 1 (Nod1) is an intracellular protein involved in recognition of the bacterial component peptidoglycan. This recognition event induces a host defense response to eliminate invading pathogens. The genetic variation of Nod1 has been linked to several inflammatory diseases and allergies, which are strongly affected by environmental factors. We have found that many of the bacteria that contain DAP-type peptidoglycan release Nod1 ligands into the environment. However, the structures of natural Nod1 ligands in the environment are not well understood. Herein, we report the isolation and structural elucidation of natural human Nod1 (hNod1) ligands from the Escherichia coli K-12 culture supernatant. The supernatant was fractionated with reversed-phase high performance liquid chromatography (RP-HPLC), resulting in the isolation of several hNod1 stimulatory fractions. Structural characterization studies demonstrated that the molecular structure of the most active fraction was the native hNod1 ligand GlcNAc-(β1–4)-(anhydro)MurNAc-l-Ala-γ-d-Glu-meso-DAP. We also found other peptidoglycan fragments using the 7-(diethylamino)coumarin-3-carbonyl labeling method to enhance sensitivity in mass spectroscopy studies. These results suggested that DAP-containing bacteria release certain hNod1 ligands to the environment, and these ligands would accumulate in the environment and regulate the immune system through Nod1.

Exclusive formation of imino[4 + 4]cycloaddition products with biologically relevant amines: plausible candidates for acrolein biomarkers and biofunctional modulators

We synthetically demonstrate that eight-membered heterocycles, namely, 2,6,9-triazabicyclo[3.3.1]nonanes and 1,5-diazacyclooctanes, are the exclusive products of the reaction of acrolein with biologically relevant amines via an imino[4 + 4]cycloaddition. These compounds are produced in much higher amounts and efficiencies than the acrolein biomarker in current use, 3-formyl-3,4-dehydropiperidine (FDP). Our results not only indicate that eight-membered heterocycles may potentially be used as new biomarkers, but also strongly suggest the involvement of these heterocycles in various important biological phenomena, e.g., an acrolein-mediated mechanism underlying oxidative stress.

SYNTHESIS OF 3,7,9- AND 2,6,9-TRIAZABICYCLO(3.3.1)NONANE DERIVATIVES

Due to their interesting chemical and biological properties, nitrogen containing-heterocycles represent indispensable moiety in organic chemistry. From the various types of nitrogen containing-heterocycles, azabicyclic compounds in particular are of considerable importance in many aspects and have attracted attention from wide range of fields, including in the study of natural products, coordination properties, or in the development of biologically and pharmacologically active compounds. This review focuses on the hitherto reported methods for the synthesis of the triazabicyclo(3.3.1)nonane derivatives, the bicyclic compound having two nitrogen atoms at the eight-membered ring and one nitrogen atom at the bridge position, which are less explored in the literature probably due to difficulties in their synthetic accessibility.

Synthesis of characteristic Mycobacterium peptidoglycan (PGN) fragments utilizing with chemoenzymatic preparation of meso-diaminopimelic acid (DAP), and their modulation of innate immune responses.

Peptidoglycan (PGN) is a major component of bacterial cell wall and is recognized as a potent immunostimulant. The PGN in the cell envelope of Mycobacterium Tuberculosis has been shown to possess several unique characteristics including the presence of N-glycolyl groups (in addition to N-acetyl groups) in the muramic acid residues, and amidation of the free carboxylic acid of d-Glu or of meso-DAP in the peptide chains. Using a newly developed, highly stereoselective, chemoenzymatic approach for the synthesis of meso-DAP in peptide stems, we successfully synthesized for the first time, a series of Mycobacterium PGN fragments that include both mono- and disaccharides of MurNGlyc or 1,6-anhydro-MurNGlyc, as well as peptide-amidated variants. The ability of these PGN fragments to stimulate the immune system through activation of human Nod1 and Nod2 was examined. The PGN fragments were found to modulate immune stimulation, specifically, amidation at the d-Glu and meso-DAP in the peptide stem strongly reduced hNod1 activation. This effect was dependent on modification position. Additionally, N-glycolyl (instead of acetyl) of muramic acid was associated with slightly reduced human Nod1 and Nod2 stimulatory capabilities.

Cinchonine induces apoptosis of HeLa and A549 cells through targeting TRAF6

BackgroundCancer cells are known to over-express TRAF6 that is critical for both AKT and TAK1 activations. The Really Interesting New Gene (RING) domain of TRAF6 is believed to be responsible for the E3 ligase activity, ZINC fingers of TRAF6 provide critical support for the activity of the RING domain which is critical for both AKT and TAK1 activations.MethodsWe employed computational docking program to identify small molecules that could effectively and competitively bind with the RING domain of TRAF6, which is believed to be responsible for its E3 ligase activity. MTT assay and flow cytometry were employed to analyze apoptosis of cancer cells. Signaling pathways were detected using immunoprecipitation and western blotting, and immunofluorescence was pursued to assess the nature of binding of cinchonine to TRAF6. We also performed animal experiments to test effect of cinchonine in vivo.ResultsCinchonine, a naturally occurring Cinchona alkaloid identified from the docking study, could bind to TRAF6 in HeLa and A549 cells and induce apoptosis of these cancer cells. We found that AKT ubiquitination and phosphorylation as well as phosphorylation of TAK1 were decreased. These activities would lead to subsequent suppression anti-apoptotic protein Bcl-2, while elevating pro-apoptotic protein Bax. Immunofluorescence staining unambiguously demonstrated the binding of cinchonine specifically at the RING domain of TRAF6 in cells, thereby validating the computational modeling. Animal experiments showed that cinchonine could suppress tumor growth in mice without showing significant acute toxicity.ConclusionThese investigations suggest that through competitive binding with the RING domain of TRAF6, cinchonine could induce apoptosis via inhibiting AKT and TAK1 signaling pathways.

Expanding the Applicability of the Metal Labeling of Biomolecules by the RIKEN Click Reaction: A Case Study with Gallium-68 Positron Emission Tomography

Radiolabeled biomolecules with short half‐life times are of increasing importance for positron emission tomography (PET) imaging studies. Herein, we demonstrate an improved and generalized method for synthesizing a [radiometal]‐unsaturated aldehyde as a lysine‐labeling probe that can be easily conjugated into various biomolecules through the RIKEN click reaction. As a case study, 68Ga‐PET imaging of U87MG xenografted mice is demonstrated by using the 68Ga‐DOTA‐RGDyK peptide, which is selective to αVβ3 integrins.