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Themed collection Chemical biology in OBC

54 items
Perspective

From pirates and killers: does metabolite diversity drive bacterial competition?

This article discusses interspecies competition by sets of closely related metabolites with significantly different biological activities.

Graphical abstract: From pirates and killers: does metabolite diversity drive bacterial competition?
Review Article

Biosynthesis of the teleocidin-type terpenoid indole alkaloids

Teleocidin B is a terpenoid indole alkaloid with unique structures including indolactam and cyclic terpenoid, and is a strong protein kinase C activator. In this review, we describe the isolation and biosynthetic studies of teleocidins.

Graphical abstract: Biosynthesis of the teleocidin-type terpenoid indole alkaloids
From the themed collection: Chemical biology in OBC
Review Article

The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions

Nucleic acids, phospholipids and other organic phosphates play central roles in biological pathways.

Graphical abstract: The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions
From the themed collection: Chemical biology in OBC
Review Article

C8-Guanine modifications: effect on Z-DNA formation and its role in cancer

Participation of Z DNA in normal and disease related biological processes.

Graphical abstract: C8-Guanine modifications: effect on Z-DNA formation and its role in cancer
From the themed collection: Chemical biology in OBC
Review Article

Recent progress of C-glycosylation methods in the total synthesis of natural products and pharmaceuticals

C-Glycosylation has found widespread use in the synthesis of biomedically important natural products and pharmaceuticals.

Graphical abstract: Recent progress of C-glycosylation methods in the total synthesis of natural products and pharmaceuticals
From the themed collection: Chemical biology in OBC
Review Article

Target specificity of mammalian DNA methylation and demethylation machinery

We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.

Graphical abstract: Target specificity of mammalian DNA methylation and demethylation machinery
From the themed collection: Chemical biology in OBC
Review Article

The renascence of continuous-flow peptide synthesis – an abridged account of solid and solution-based approaches

Within a decade of Merrifield's seminal description of solid-phase peptide synthesis, the synergies between solid-phase approaches and flow synthesis were noted by a number of groups.

Graphical abstract: The renascence of continuous-flow peptide synthesis – an abridged account of solid and solution-based approaches
From the themed collection: Chemical biology in OBC
Open Access Review Article

Negishi cross-couplings in the synthesis of amino acids

The application of the Negishi cross-coupling reaction in the synthesis of amino acids is reviewed.

Graphical abstract: Negishi cross-couplings in the synthesis of amino acids
From the themed collection: Chemical biology in OBC
Review Article

25 years and still going strong: 2′-O-(pyren-1-yl)methylribonucleotides – versatile building blocks for applications in molecular biology, diagnostics and materials science

This review highlights the synthesis, biophysical properties, and wide range of applications of oligonucleotides modified with 2′-O-(pyren-1-yl)methyl-RNA monomers reported over the past 25 years.

Graphical abstract: 25 years and still going strong: 2′-O-(pyren-1-yl)methylribonucleotides – versatile building blocks for applications in molecular biology, diagnostics and materials science
From the themed collection: Chemical biology in OBC
Communication

Streamlined chemoenzymatic total synthesis of prioritized ganglioside cancer antigens

Highly efficient streamlined total synthesis of complex prioritized gangliosides was achieved chemoenzymatically by sequential one-pot multienzyme (OPME) reactions with facile C18 cartridge purification schemes followed by high-yield acylation.

Graphical abstract: Streamlined chemoenzymatic total synthesis of prioritized ganglioside cancer antigens
From the themed collection: Chemical biology in OBC
Communication

Palladium mediated deallylation in fully aqueous conditions for native chemical ligation at aspartic and glutamic acid sites

An efficient native chemical ligation approach at Asp and Glu sites is reported applying a hydrazide precursor, as a peptide thioester, and allyl protection at the side chain of Asp and Glu.

Graphical abstract: Palladium mediated deallylation in fully aqueous conditions for native chemical ligation at aspartic and glutamic acid sites
From the themed collection: Chemical biology in OBC
Communication

In vivo and in vitro identification of Z-BOX C – a new bilirubin oxidation end product

A new bilirubin degradation end product was isolated and characterized.

Graphical abstract: In vivo and in vitro identification of Z-BOX C – a new bilirubin oxidation end product
Communication

Secondary amine salt catalyzed controlled activation of 2-deoxy sugar lactols towards alpha-selective dehydrative glycosylation

An organocatalytic alpha-selective dehydrative glycosylation method for the synthesis of 2-deoxyglycosides.

Graphical abstract: Secondary amine salt catalyzed controlled activation of 2-deoxy sugar lactols towards alpha-selective dehydrative glycosylation
From the themed collection: Chemical biology in OBC
Communication

Synthesis of CID-cleavable protein crosslinking agents containing quaternary amines for structural mass spectrometry

Two novel cyclic quaternary amine crosslinking probes are synthesized for structural mass spectrometry of protein complexes in solution and for analysis of protein interactions in organellar and whole cell extracts.

Graphical abstract: Synthesis of CID-cleavable protein crosslinking agents containing quaternary amines for structural mass spectrometry
From the themed collection: Chemical biology in OBC
Communication

Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA

In this paper, we report the development of a new G-4 alkylating molecule and the evaluation of the properties of the alkylated G-4 DNA.

Graphical abstract: Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA
From the themed collection: Chemical biology in OBC
Communication

A double-click approach to the protecting group free synthesis of glycoconjugates

The use of a bi-functional linker, containing an alkyne and an alkene, allows the protecting group free conjugation of reducing sugars to thiols via a double click process.

Graphical abstract: A double-click approach to the protecting group free synthesis of glycoconjugates
From the themed collection: Chemical biology in OBC
Communication

Can strand displacement take place in DNA triplexes?

Toehold-mediated strand displacement can take place in the context of DNA triplexes, slowly.

Graphical abstract: Can strand displacement take place in DNA triplexes?
From the themed collection: Chemical biology in OBC
Communication

An intramolecular tryptophan-condensation approach for peptide stapling

Stapled peptides are gaining tremendous interest as next-generation therapeutic agents to target protein–protein interactions. Herein, we report an intramolecular peptide stapling method which links two tryptophan residues at C2 position of the indole moieties via acid-mediated condensation with an aldehyde.

Graphical abstract: An intramolecular tryptophan-condensation approach for peptide stapling
From the themed collection: Chemical biology in OBC
Communication

Contiguous hydrophobic and charged surface patches in short helix-constrained peptides drive cell permeability

Different ways to get peptides into cells.

Graphical abstract: Contiguous hydrophobic and charged surface patches in short helix-constrained peptides drive cell permeability
From the themed collection: Chemical biology in OBC
Communication

Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries

DNA encoded ligands are self-assembled into bivalent complexes and chemically ligated to link their identities.

Graphical abstract: Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries
From the themed collection: Chemical biology in OBC
Open Access Communication

Automated glycan assembly of galactosylated xyloglucan oligosaccharides and their recognition by plant cell wall glycan-directed antibodies

Automated glycan assembly enabled the synthesis of galactosylated xyloglucan oligosaccharides from the plant cell wall. The synthetic glycans were differentially recognized by a number of xyloglucan-directed antibodies.

Graphical abstract: Automated glycan assembly of galactosylated xyloglucan oligosaccharides and their recognition by plant cell wall glycan-directed antibodies
From the themed collection: Chemical biology in OBC
Paper

Stabilization of an intermolecular i-motif by lipid modification of cytosine-oligodeoxynucleotides

High stability of intermolecular i-motif structures in lipid-modified C-oligodeoxynucleotides.

Graphical abstract: Stabilization of an intermolecular i-motif by lipid modification of cytosine-oligodeoxynucleotides
From the themed collection: Chemical biology in OBC
Paper

Unraveling the 4n − 1 rule for DNA i-motif stability: base pairs vs. loop lengths

The 4n − 1 repeat pattern for poly-2′-deoxycytidine i-motifs results from ideal loop lengths and core base pairs.

Graphical abstract: Unraveling the 4n − 1 rule for DNA i-motif stability: base pairs vs. loop lengths
From the themed collection: Chemical biology in OBC
Accepted Manuscript - Paper

Bifunctional mannoside-glucosinolate glycoconjugates as enzymatically triggered isothiocyanates and FimH ligands.

From the themed collection: Chemical biology in OBC
Open Access Paper

Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA

2′-Deoxyribonucleoside triphosphates containing 5-(hydroxymethyl)cytosine protected with photocleavable groups were prepared and studied as substrates for the enzymatic synthesis of DNA containing a photocaged epigenetic 5hmC base.

Graphical abstract: Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA
From the themed collection: Chemical biology in OBC
Paper

Activation of disulfide bond cleavage triggered by hydrophobization and lipophilization of functionalized dihydroasparagusic acid

Introduction of a hydrophilic group into dihydroasparagusic acid (DHAA) indicated higher reduction ability of disulfide in protein and lower air oxidation.

Graphical abstract: Activation of disulfide bond cleavage triggered by hydrophobization and lipophilization of functionalized dihydroasparagusic acid
From the themed collection: Chemical biology in OBC
Paper

Aziridine based electrophilic handle for aspartic acid ligation

A one-pot ligation strategy at aspartic acid junction has been described by incorporating aziridin-2,3-dicarboxylate to the N-side of a peptide fragment that ligates with a variety of small peptide thio acids to afford native peptides in good yields.

Graphical abstract: Aziridine based electrophilic handle for aspartic acid ligation
From the themed collection: Chemical biology in OBC
Open Access Paper

Synthetic antibody protein mimics of infliximab by molecular scaffolding on novel CycloTriVeratrilene (CTV) derivatives

Downsizing of antibodies: molecular construction of chemo-synthetic antibodies of infliximab by scaffolding of three CDR loops yields synthetic antibodies binding hTNFα.

Graphical abstract: Synthetic antibody protein mimics of infliximab by molecular scaffolding on novel CycloTriVeratrilene (CTV) derivatives
Paper

Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite

Asymmetrically-protected branching unit enables synthesis of comb-shaped DNAs for imaging and diagnostics applications.

Graphical abstract: Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite
From the themed collection: Chemical biology in OBC
Open Access Paper

Probing the competition between duplex and G-quadruplex/i-motif structures using a conformation-sensitive fluorescent nucleoside probe

A conformation-sensitive fluorescent nucleoside analog serves as an efficient probe to study the competition between duplex and G-quadruplex/i-motif structures.

Graphical abstract: Probing the competition between duplex and G-quadruplex/i-motif structures using a conformation-sensitive fluorescent nucleoside probe
From the themed collection: Chemical biology in OBC
Paper

“siRNA traffic lights”: arabino-configured 2′-anchors for fluorescent dyes are key for dual color readout in cell imaging

The arabino-configured nucleotide anchor improves the red-to-green fluorescence readout by energy transfer.

Graphical abstract: “siRNA traffic lights”: arabino-configured 2′-anchors for fluorescent dyes are key for dual color readout in cell imaging
From the themed collection: Chemical biology in OBC
Paper

Chemo-enzymatic synthesis of isotopically labeled nicotinamide riboside

A versatile chemo-enzymatic synthesis of isotopically labeled nicotinamide riboside (NR) was developed.

Graphical abstract: Chemo-enzymatic synthesis of isotopically labeled nicotinamide riboside
From the themed collection: Chemical biology in OBC
Paper

Interrogation of biosynthetic pathways of the cruciferous phytoalexins nasturlexins with isotopically labelled compounds

A biosynthetic map of the precursors of the phytoalexins nasturlexins and cyclonasturlexin is established.

Graphical abstract: Interrogation of biosynthetic pathways of the cruciferous phytoalexins nasturlexins with isotopically labelled compounds
From the themed collection: Chemical biology in OBC
Paper

How are 1,2,3-triazoles accommodated in helical secondary structures?

Peptaibols were used as templates to monitor the impact of 1,2,3-triazole (Tz) insertion in place of amide bonds in a helix structure.

Graphical abstract: How are 1,2,3-triazoles accommodated in helical secondary structures?
From the themed collection: Chemical biology in OBC
Paper

Relevance of the deletion of the Tatri4 gene in the secondary metabolome of Trichoderma arundinaceum

A study of the secondary metabolome of single culture of the mutant TaΔTri4, and of a co-culture with B. cinerea, was carried out. The results shed a light on the chemical cross-talk and ecological interactions between these fungi.

Graphical abstract: Relevance of the deletion of the Tatri4 gene in the secondary metabolome of Trichoderma arundinaceum
From the themed collection: Chemical biology in OBC
Paper

α-Methyl phenylglycines by asymmetric α-arylation of alanine and their effect on the conformational preference of helical Aib foldamers

Asymmetric arylation of an alanine derivative provides (R)-α-methyl phenylglycine, which induces a right handed screw sense in an Aib oligomer.

Graphical abstract: α-Methyl phenylglycines by asymmetric α-arylation of alanine and their effect on the conformational preference of helical Aib foldamers
From the themed collection: Chemical biology in OBC
Open Access Paper

The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis

TamA is the adenylating enzyme that selects and activates fatty acids for tambjamine biosynthesis.

Graphical abstract: The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis
From the themed collection: Chemical biology in OBC
Paper

Phenanthroline polyazamacrocycles as G-quadruplex DNA binders

Several phenanthroline polyazamacrocycles are proposed as ligands for c-MYC and telomeric G-quadruplex structures.

Graphical abstract: Phenanthroline polyazamacrocycles as G-quadruplex DNA binders
From the themed collection: Chemical biology in OBC
Paper

Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides

The synthesis of a new dimeric G-quadruplex-based DNA aptamer endowed with anti-HIV activity is reported.

Graphical abstract: Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides
From the themed collection: Chemical biology in OBC
Paper

Synthesis of thioureido peptidomimetics employing alkyl azides and dithiocarbamates

An efficient and one pot protocol for the synthesis of thioureidopeptidomimetics is described.

Graphical abstract: Synthesis of thioureido peptidomimetics employing alkyl azides and dithiocarbamates
From the themed collection: Chemical biology in OBC
Paper

DNA damage photo-induced by chloroharmine isomers: hydrolysis versus oxidation of nucleobases

Photo-excited chloroharmines selectively induce different types of DNA damage, depending on the relative position of the chlorine atom in the β-carboline ring.

Graphical abstract: DNA damage photo-induced by chloroharmine isomers: hydrolysis versus oxidation of nucleobases
From the themed collection: Chemical biology in OBC
Paper

Synthetic polyprenol-pyrophosphate linked oligosaccharides are efficient substrates for mycobacterial galactan biosynthetic enzymes

Synthetic glycosyl polyprenol phosphates are substrates for enzymes required for cell wall assembly in mycobacteria, including the organism that causes tuberculosis.

Graphical abstract: Synthetic polyprenol-pyrophosphate linked oligosaccharides are efficient substrates for mycobacterial galactan biosynthetic enzymes
Paper

Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes

Synthesis and biological evaluation of tRNA analogues containing a terminal ribose locked in the South conformation.

Graphical abstract: Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes
From the themed collection: Chemical biology in OBC
Paper

An organocatalyzed Stetter reaction as a bio-inspired tool for the synthesis of nucleic acid-based bioconjugates

An NHC-catalyzed Stetter reaction as a conjugation step to provide nucleic acid-based bioconjugates.

Graphical abstract: An organocatalyzed Stetter reaction as a bio-inspired tool for the synthesis of nucleic acid-based bioconjugates
From the themed collection: Chemical biology in OBC
Open Access Paper

Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA

Protected 5-(hydroxymethyl)uracil nucleotides bearing photocleavable groups as building blocks for polymerase synthesis of photocaged DNA.

Graphical abstract: Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA
From the themed collection: Chemical biology in OBC
Paper

Teaching an old scaffold new recognition tricks: oligopyrrolamide antagonists of IAPP aggregation

An oligopyrrolamide was identified as a potent antagonist of the aggregation of IAPP, a process associated with type 2 diabetes.

Graphical abstract: Teaching an old scaffold new recognition tricks: oligopyrrolamide antagonists of IAPP aggregation
From the themed collection: Chemical biology in OBC
Paper

Synthesis and characterization of water-soluble macrocyclic peptides stabilizing protein α-turn

Macrocyclic peptides mimic tight “non-classical” α-turn type II-αLS found in proteins, as shown by spectroscopic and computational analysis of their equilibrating conformations.

Graphical abstract: Synthesis and characterization of water-soluble macrocyclic peptides stabilizing protein α-turn
From the themed collection: Chemical biology in OBC
Paper

Side chain-specific 11/9-helix propensity of α/β-peptides with alternating residue types

The 11/9-helix propensity of α/β-peptides is dependent on a specific side chain group of α- or β3-residue.

Graphical abstract: Side chain-specific 11/9-helix propensity of α/β-peptides with alternating residue types
From the themed collection: Chemical biology in OBC
Paper

Stereocontrolled glycoside synthesis by activation of glycosyl sulfone donors with scandium(III) triflate

Activation of armed glycosyl sulfone donors, using scandium(III) triflate under microwave irradiation, provides a selective preparation of α-mannosides.

Graphical abstract: Stereocontrolled glycoside synthesis by activation of glycosyl sulfone donors with scandium(iii) triflate
From the themed collection: Chemical biology in OBC
Open Access Paper

Synthesis and structural investigation of a series of mannose-containing oligosaccharides using mass spectrometry

Gas-phase collision-induced dissociation and acid hydrolysis of mannose-containing oligosaccharides were performed, which revealed the reactivity order of linkage isomers.

Graphical abstract: Synthesis and structural investigation of a series of mannose-containing oligosaccharides using mass spectrometry
From the themed collection: Chemical biology in OBC
Paper

Perylenediimide-based glycoclusters as high affinity ligands of bacterial lectins: synthesis, binding studies and anti-adhesive properties

Rapid access to perylenediimide-based glycoclusters allowed their evaluation as high affinity ligands of bacterial lectins and their potential as anti-adhesive antibacterials.

Graphical abstract: Perylenediimide-based glycoclusters as high affinity ligands of bacterial lectins: synthesis, binding studies and anti-adhesive properties
From the themed collection: Chemical biology in OBC
Paper

Design and self-assembly of PBLG-b-ELP hybrid diblock copolymers based on synthetic and elastin-like polypeptides

The synthesis and self-assembly of amphiphilic copolypeptides containing a recombinant elastin-like polypeptide block used as a macroinitiator for the ROP of γ-BLG NCA are presented.

Graphical abstract: Design and self-assembly of PBLG-b-ELP hybrid diblock copolymers based on synthetic and elastin-like polypeptides
From the themed collection: Chemical biology in OBC
Paper

Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications

Structural information provides important insight to how major groove-modified triazole-containing siRNAs selectively knockout their intended target.

Graphical abstract: Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications
From the themed collection: Chemical biology in OBC
Paper

β-Alanine and N-terminal cationic substituents affect polyamide–DNA binding

The binding preference of a systematic set of designed polyamides with β-inserts and cationic-substitutions with cognate DNA.

Graphical abstract: β-Alanine and N-terminal cationic substituents affect polyamide–DNA binding
From the themed collection: Chemical biology in OBC
54 items

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The latest articles published in Organic and Biomolecular Chemistry related to chemical biology research.

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