A ribozyme for the aldol reaction

Directed in vitro evolution can create RNA catalysts for a variety of organic reactions, supporting the "RNA world" hypothesis, which proposes that metabolic transformations in early life were catalyzed by RNA molecules rather than proteins. Among the most fundamental carbon-carbon bond-forming reactions in nature is the aldol reaction, mainly catalyzed by aldolases that utilize either an enamine mechanism (class I) or a Zn(2+) cofactor (class II). We report on isolation of a Zn(2+)-dependent ribozyme that catalyzes an aldol reaction at its own modified 5' end with a 4300-fold rate enhancement over the uncatalyzed background reaction. The ribozyme can also act as an intermolecular catalyst that transfers a biotinylated benzaldehyde derivative to the aldol donor substrate, coupled to an external hexameric RNA oligonucleotide, supporting the existence of RNA-originated biosynthetic pathways for metabolic sugar precursors and other biomolecules.     

Fast and selective synthesis of novel cyclic sulfamide HIV-1 protease inhibitors under controlled microwave heating

A novel and highly selective silver-promoted monobenzylation method was developed to promote synthesis of nonsymmetrical sulfamide-based HIV-1 inhibitors. Microwave-accelerated palladium-catalyzed N-amide arylation- and aminocarbonylation reactions were employed for rapid and reliable compound generation. With this class of inhibitory agents, six active inhibitors were identified, the most potent inhibitor possessing a K_i-value of 20 nM.     

Practical synthesis of a peptidomimetic thrombin inhibitor

Compound 1 is a low molecular weight thrombin inhibitor developed for treatment of deep vein thrombosis and cardiovascular diseases. We herein report our efforts to develop a robust, efficient and reproducible process suitable for large-scale synthesis of compound 1.     

Discovery of kibdelomycin, a potent new class of bacterial type II topoisomerase inhibitor by chemical-genetic profiling in Staphylococcus aureus

Bacterial resistance to known therapeutics has led to an urgent need for new chemical classes of antibacterial agents. To address this we have applied?a Staphylococcus aureus fitness test strategy to natural products screening. Here we report the discovery of kibdelomycin, a novel class of antibiotics produced by a new member of the genus Kibdelosporangium. Kibdelomycin exhibits broad-spectrum, gram-positive antibacterial activity and is a potent inhibitor of DNA synthesis. We demonstrate through chemical genetic fitness test profiling and biochemical enzyme assays that kibdelomycin is a structurally new class of bacterial type II topoisomerase inhibitor preferentially inhibiting the ATPase activity of DNA gyrase and topoisomerase IV. Kibdelomycin is thus the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades.     

Oenothein B in Eucalyptus Leaf Extract Suppresses Fructose Absorption in Caco-2 Cells

Inhibition of fructose absorption may suppress adiposity and adiposity-related diseases caused by fructose ingestion. Eucalyptus leaf extract (ELE) inhibits intestinal fructose absorption (but not glucose absorption); however, its active compound has not yet been identified. Therefore, we evaluated the inhibitory activity of ELE obtained from Eucalyptus globulus using an intestinal fructose permeation assay with the human intestinal epithelial cell line Caco-2. The luminal sides of a cell monolayer model cultured on membrane filters were exposed to fructose with or without the ELE. Cellular fructose permeation was evaluated by measuring the fructose concentration in the medium on the basolateral side. ELE inhibited 65% of fructose absorption at a final concentration of 1 mg/mL. Oenothein B isolated from the ELE strongly inhibited fructose absorption; the inhibition rate was 63% at a final concentration of 5 μg/mL. Oenothein B did not affect glucose absorption. In contrast, the other major constituents (i.e., gallic acid and ellagic acid) showed little fructose-inhibitory activity. To our knowledge, this is the first report that oenothein B in ELE strongly inhibits fructose absorption in vitro. ELE containing oenothein B can prevent and ameliorate obesity and other diseases caused by dietary fructose consumption.     

Principles of formation of catalytic systems for oxidation of aliphatic thiols based on <Emphasis Type="Italic">d</Emphasis>-element complexes

Mechanism of catalytic selective oxidation of aliphatic thiols RSH into disulfides R₂S₂ has been suggested basing on quantum-chemical DFT simulation (M06/Def2-TZVP) of coordination compounds of d-elements and using the principle of complementarity. The active center of the catalytic system is a binuclear fragment {M(m-OH)₂M′}ⁿ⁺ formed due to hydrolysis of the starting mononuclear d-element compound. The catalysts based on Pd(II) and Pt(II) binuclear active centers are spatially similar throughout the process. The chief interrelated functions of the binuclear catalysts are spatial approaching of two thiolate anions RS^– in the inner sphere of the bridged coordination compound required for the disulfide (–S–S–) cross-linking and providing for two-electron redox transfer during the transformation of these anions into disulfide (СH₃)₂S₂.     

Oxidative halogenation of substituted pyrroles with Cu(II). Part IV. Bromination of 2-(2′-hydroxybenzoyl)pyrrole. A new synthesis of bioactive analogs of monodeoxypyoluteorin

The selective bromination with copper(II) bromide of the pyrrole ring in 2-(2′-hydroxybenzoyl)pyrrole II in the heterogeneous phase is described giving in almost quantitative yield the 4,5-dibromo derivative VI. The subsequent introduction of halogen into the phenol moiety was observed when the reaction was performed in the homogeneous phase with an excess of halogenating agent. The pentabromo derivative IX , a compound very active against Staphylococcus aureus (mic = 17 nmoles per dm^?3), was obtained by exhaustive bromination of the title compound. Poor yields of chloro derivatives of II were obtained by reaction of the parent compound with copper(II) chloride.     

Catalytic inhibition of topoisomerase II by a novel rationally designed ATP-competitive purine analogue

Background

Topoisomerase II poisons are in clinical use as anti-cancer therapy for decades and work by stabilizing the enzyme-induced DNA breaks. In contrast, catalytic inhibitors block the enzyme before DNA scission. Although several catalytic inhibitors of topoisomerase II have been described, preclinical concepts for exploiting their anti-proliferative activity based on molecular characteristics of the tumor cell have only recently started to emerge. Topoisomerase II is an ATPase and uses the energy derived from ATP hydrolysis to orchestrate the movement of the DNA double strands along the enzyme. Thus, interfering with ATPase function with low molecular weight inhibitors that target the nucleotide binding pocket should profoundly affect cells that are committed to undergo mitosis.

Results

Here we describe the discovery and characterization of a novel purine diamine analogue as a potent ATP-competitive catalytic inhibitor of topoisomerase II. Quinoline aminopurine compound 1 (QAP 1) inhibited topoisomerase II ATPase activity and decatenation reaction at sub-micromolar concentrations, targeted both topoisomerase II alpha and beta in cell free assays and, using a quantitative cell-based assay and a chromosome segregation assay, displayed catalytic enzyme inhibition in cells. In agreement with recent hypothesis, we show that BRCA1 mutant breast cancer cells have increased sensitivity to QAP 1.

Conclusion

The results obtained with QAP 1 demonstrate that potent and selective catalytic inhibition of human topoisomerase II function with an ATP-competitive inhibitor is feasible. Our data suggest that further drug discovery efforts on ATP-competitive catalytic inhibitors are warranted and that such drugs could potentially be developed as anti-cancer therapy for tumors that bear the appropriate combination of molecular alterations.     

Metalloform-selective inhibitors of escherichia coli methionine aminopeptidase and X-ray structure of a Mn(II)-form enzyme complexed with an inhibitor

Methionine aminopeptidase (MetAP) enzymes require a divalent metal ion such as Mn(II), Fe(II), Co(II), Ni(II), or Zn(II) for its removal of the N-terminal methionine from newly synthesized proteins, but it is not certain which of these ions is most important in vivo. Metalloform-selective MetAP inhibitors could be valuable for defining which metals are physiologically relevant for MetAP activation and could serve as leads for development of new therapeutic agents. We have screened a library of 43 736 small drug-like molecules against Escherichia coli MetAP and identified two groups of potent and highly metalloform-selective inhibitors of the Co(II)-form, and of the Mn(II)-form, of this enzyme. Compound 1 is 790-fold more selective for the Co(II)-form, while compound 4 is over 640-fold more potent toward the Mn(II)-form. The X-ray structure of a di-Mn(II) form of E. coli MetAP complexed with the Mn(II)-form-selective compound 4 was obtained, and it shows that the inhibitor interacts with both Mn(II) ions through the two oxygen atoms of its free carboxylate group. The preferential coordination of the hard (oxygen) donors to Mn(II) may contribute to its superb selectivity toward the Mn(II)-form.     

Design, synthesis, and evaluation of a mechanism-based inhibitor for gelatinase A

[structure: see text] Matrix metalloproteinases (MMPs), of which 26 are known, have been implicated in a number of pathological conditions, including tumor metastasis. We have previously described the first mechanism-based inhibitor for MMPs (J. Am. Chem. Soc. 2000, 122, 6799-6800), which in chemistry mediated by the active site zinc ion selectively and covalently inhibits MMP-2, -3, and -9. Computational analyses indicated that this selectivity in inhibition of MMPs could be improved by design of new variants of the inhibitor class. We report herein the syntheses of methyl 2-(4-{4-[(2-thiiranylpropyl)sulfonyl]phenoxy}phenyl)acetate (3) and 2-(4-{4-[(2-thiiranylpropyl)sulfonyl]phenoxy}phenyl)acetic acid (4), and show that compound 3 serves as a mechanism-based inhibitor exclusively for MMP-2. This molecule should prove useful in delineating the functions of MMP-2 in biological systems.     

Detection of Sn(II) ions via quenching of the fluorescence of carbon nanodots

We report that fluorescent carbon nanodots (C-dots) can act as an optical probe for quantifying Sn(II) ions in aqueous solution. C-dots are synthesized by carbonization and surface oxidation of preformed sago starch nanoparticles. Their fluorescence is significantly quenched by Sn(II) ions, and the effect can be used to determine Sn(II) ions. The highest fluorescence intensity is obtained at a concentration of 1.75 mM of C-dots in aqueous solution. The probe is highly selective and hardly interfered by other ions. The quenching mechanism appears to be predominantly of the static (rather than dynamic) type. Under optimum conditions, there is a linear relationship between fluorescence intensity and Sn(II) ions concentration up to 4 mM, and with a detection limit of 0.36 μM.

Biosynthetic origins of the natural product,thiolactomycin: a unique and selective inhibitor of type II dissociated fatty acid synthases

Thiolactomycin (TLM), a natural product produced by both Nocardia and Streptomyces spp., is a potent and highly selective inhibitor of the type II dissociated fatty acid synthases of plants and bacteria. The unique mode of action of TLM and its low toxicity make it an attractive compound for development of new antimicrobial agents. In this study, incorporation studies with 13C-labeled precursors demonstrate that TLM is derived from one acetate-derived starter unit and three methylmalonate-derived extender units. The unusual thiolactone represented by TLM represents a novel class of polyketide-derived antibiotics in which an unusual cyclization process, which terminates the biosynthetic pathway, involves incorporation of a sulfur atom from l-cysteine. Manipulation of this pathway through techniques such a combinatorial biosynthesis and mutasynthesis may provide a new route for economically viable production of useful TLM analogues.     

Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity

Casein kinases 1 (CK1) are key signaling molecules that have emerged recently as attractive therapeutic targets in particular for the treatment of hematological malignancies. Herein, we report the identification of a new class of potent and highly selective inhibitors of CK1α, δ and ϵ. Based on their optimal in vitro and in vivo profiles and their exclusive selectivity, MU1250, MU1500 and MU1742 were selected as quality chemical probes for those CK1 isoforms. At proper concentrations, MU1250 and MU1500 allow for specific targeting of CK1δ or dual inhibition of CK1δ/ϵ in cells. The compound MU1742 also efficiently inhibits CK1α and, to our knowledge, represents the first potent and highly selective inhibitor of this enzyme. In addition, we demonstrate that the central 1H-pyrrolo[2,3-b]pyridine-imidazole pharmacophore can be used as the basis of highly selective inhibitors of other therapeutically relevant protein kinases, e.g. p38α, as exemplified by the compound MU1299.     

Serendipitous discovery of light-induced (<Emphasis Type="Italic">In Situ</Emphasis>) formation of an Azo-bridged dimeric sulfonated naphthol as a potent PTP1B inhibitor

Background

Protein tyrosine phosphatases (PTPs) like dual specificity phosphatase 5 (DUSP5) and protein tyrosine phosphatase 1B (PTP1B) are drug targets for diseases that include cancer, diabetes, and vascular disorders such as hemangiomas. The PTPs are also known to be notoriously difficult targets for designing inihibitors that become viable drug leads. Therefore, the pipeline for approved drugs in this class is minimal. Furthermore, drug screening for targets like PTPs often produce false positive and false negative results.

Results

Studies presented herein provide important insights into: (a) how to detect such artifacts, (b) the importance of compound re-synthesis and verification, and (c) how in situ chemical reactivity of compounds, when diagnosed and characterized, can actually lead to serendipitous discovery of valuable new lead molecules. Initial docking of compounds from the National Cancer Institute (NCI), followed by experimental testing in enzyme inhibition assays, identified an inhibitor of DUSP5. Subsequent control experiments revealed that this compound demonstrated time-dependent inhibition, and also a time-dependent change in color of the inhibitor that correlated with potency of inhibition. In addition, the compound activity varied depending on vendor source. We hypothesized, and then confirmed by synthesis of the compound, that the actual inhibitor of DUSP5 was a dimeric form of the original inhibitor compound, formed upon exposure to light and oxygen. This compound has an IC₅₀ of 36 μM for DUSP5, and is a competitive inhibitor. Testing against PTP1B, for selectivity, demonstrated the dimeric compound was actually a more potent inhibitor of PTP1B, with an IC₅₀ of 2.1 μM. The compound, an azo-bridged dimer of sulfonated naphthol rings, resembles previously reported PTP inhibitors, but with 18-fold selectivity for PTP1B versus DUSP5.

Conclusion

We report the identification of a potent PTP1B inhibitor that was initially identified in a screen for DUSP5, implying common mechanism of inhibitory action for these scaffolds.

     

Mcm-41 Materials as Catalysts for the Synthesis of Alkyl Fructosides

ABSTRACT

Alkylation of saccharides combines the essential characteristics of two major renewable classes, viz. triglycerides and carbohydrates, while leading to biofriendly surfactants and emulsifiers. The development of alkylated derivatives of fructose has lagged because no efficient synthesis was available. We have found that mesoporous materials of the MCM-41 type are active and selective catalysts for the alkylation of fructose. Quantitative yields were obtained in the reaction of fructose with lower alcohols, up to C4. For long chain alcohols yields were moderate but the alkyl fructopyranosides could be easily purified. The other isomers could be isolated by chromatography.     

Kinetic inhibitor of hydrate crystallization

We present the results of a combined theoretical/experimental study into a new class of kinetic inhibitor of gas hydrate formation. The inhibitors are based on quaternary ammonium zwitterions, and were identified from a computational screen. Molecular dynamics simulations were used to characterize the effect of the inhibitor on the interface between a type II hydrate and natural gas. These simulations show that the inhibitor is bifunctional, with the hydrophobic end being compatible with the water structure present at the hydrate interface, while the negatively charged functional group promotes a long ranged water structure that is inconsistent with the hydrate phase; the sulfonate-induced structure was found to propagate strongly over several solvation shells. The compound was subsequently synthesized and used in an experimental study of both THF and ethane hydrate formation, and was shown to have an activity that was comparable with an existing commercial kinetic inhibitor: PVP.     

Dithizone-modified nanoporous fructose as a novel sorbent for solid-phase extraction of ultra-trace levels of heavy metals

We are introducing nanoporous fructose (np-F) modified with dithizone as a new solid-phase for extraction of heavy metals ions including cadmium(II), copper(II), nickel(II) and lead(II). Effects of pH value, flow rates, type, concentration and volume of the eluent, breakthrough volume, and of other ions were studied. Under optimized conditions, the extraction efficiency is >97 %, and the limits of detection are 0.025, 0.15, 0.5 and 1.2 ng mL^?1 for the ions of cadmium, copper, nickel, and lead, respectively, and the adsorption capacities for these ions are 101, 81, 74 and 178 mg g^?1. The modified np-F sorbent was characterized by thermogravimetric analysis, differential thermal analysis, transmission electron microscopy, Fourier transform infrared spectrometry, X-ray diffraction, and nitrogen adsorption surface area (BET) measurements.

Expedient Synthesis of C‐Aryl Carbohydrates by Consecutive Biocatalytic Benzoin and Aldol Reactions

The introduction of aromatic residues connected by a C?C bond into the non‐reducing end of carbohydrates is highly significant for the development of innovative structures with improved binding affinity and selectivity (e.g., C?aril‐sLex). In this work, an expedient asymmetric “de novo” synthetic route to new aryl carbohydrate derivatives based on two sequential stereoselectively biocatalytic carboligation reactions is presented. First, the benzoin reaction of aromatic aldehydes to dimethoxyacetaldehyde is conducted, catalyzed by benzaldehyde lyase from Pseudomonas fluorescens biovar I. Then, the α‐hydroxyketones formed are reduced by using NaBH₄ yielding the anti diol. After acetal hydrolysis, the aldol addition of dihydroxyacetone, hydroxyacetone, or glycolaldehyde catalyzed by the stereocomplementary D ‐fructose‐6‐phosphate aldolase and L ‐rhamnulose‐1‐phosphate aldolase is performed. Both aldolases accept unphosphorylated donor substrates, avoiding the need of handling the phosphate group that the dihydroxyacetone phosphate‐dependent aldolases require. In this way, 6‐C‐aryl‐L ‐sorbose, 6‐C‐aryl–L ‐fructose, 6‐C‐aryl–L ‐tagatose, and 5‐C‐aryl‐L ‐xylose derivatives are prepared by using this methodology.     

Synthesis of chiral 2-(4-phenoxyphenylsulfonylmethyl)thiiranes as selective gelatinase inhibitors

[reactions: see text] Compound 1, 2-(4-phenoxyphenylsulfonylmethyl)thiirane, is a selective inhibitor of gelatinases, which is showing high promise in studies of animal models for cancer metastasis and stroke. The (R)-1 and (S)-1 enantiomers of compound 1 were each synthesized in this study and were shown to be equally active in inhibition of gelatinases.