Cover Pictures

Free Access

Front Cover: N-Hydroxysuccinimide-Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates (ChemBioChem 1-2/2020)

  • Pages: 1
  • First Published: 30 December 2019
Description unavailable

NHS-phosphonamidate-superglue: Ethynylphosphonamidate building blocks carrying an NHS residue selectively connect antibody lysine residues with thiol-containing drugs or proteins. Outstanding selectivity for cysteine under physiological conditions can reduce the homo-crosslinking side products in the lysine-modification step that can occur with alternative linker systems such as SMCC. The highly stable phosphonamidate–cysteine adduct “locks” a toxic payload to an antibody, thereby giving rise to a new generation of stably linked antibody–drug conjugates. In addition, enantiomerically pure building blocks enable the synthesis of protein conjugates with defined configuration. Image designed and created by Barth van Rossum. More information can be found in the full paper by M.-A. Kasper, C. P. R. Hackenberger, et al. on page 113 in Issue 1, 2020 (DOI: 10.1002/cbic.201900587).

Free Access

Cover Feature: A Quencher-Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue (ChemBioChem 1-2/2020)

  • Pages: 2
  • First Published: 30 December 2019
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A quencher-free linear probe composed of serinol nucleic acid (SNA) with a fluorescent uracil analogue (PeU) can selectively light-up a target RNA. In the single-stranded state, a flexible SNA scaffold (yellow strand) facilitates the quenching of monomer emission by aggregation of PeU residues. Upon the formation of a duplex with the target RNA (white strand), the PeU is separated by base pairs, resulting in “light-up” detection with high sensitivity. This linear probe also discriminated a fully matched RNA strand from a single-base mismatch. More information can be found in the full paper by H. Asanuma and K. Murayama on page 120 in Issue 1, 2020 (DOI: 10.1002/cbic.201900498).

Free Access

Cover Feature: Characterisation of the Dynamic Interactions between Complex N-Glycans and Human CD22 (ChemBioChem 1-2/2020)

  • Pages: 3
  • First Published: 30 December 2019
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Recognition and binding of host sialoglycans by human CD22. On resting B-cells, the cis interaction of h-CD22 with sialoglycans exposed on the same plasma membrane results in the formation of CD22 homo-oligomers. Conversely, trans interactions allow the recruitment of CD22 to the B-cell receptor complex, thereby inhibiting its signaling. In their full paper, S. Martín-Santamaría, R. Marchetti, A. Silipo, et al. on page 129 in Issue 1, 2020 (DOI: 10.1002/cbic.201900295) deepen the molecular insights into the binding mode and the conformation behavior of complex-type N-glycans bound to h-CD22. These new findings will enable the design of novel therapeutics with the aim of tackling autoimmune disorders and B-cell malignancies.

Free Access

Cover Feature: Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation (ChemBioChem 1-2/2020)

  • Pages: 4
  • First Published: 30 December 2019
Description unavailable

The Staudinger reduction provides a bio-orthogonal and generalizable approach to small-molecule-triggered protein activation. We have developed three genetically encoded caged lysine analogues that can be rapidly activated with phosphines in order to control protein function in mammalian cells. This was applied to the conditional control of protein translocation and triggering SUMOylation, an important post-translational modification, of a caged target protein. More information can be found in the full paper by A. Deiters et al. on page 141 in Issue 1, 2020 (DOI: 10.1002/cbic.201900464).

Editorial

Free Access

ChemBioChem@20—Some Reflections

  • Pages: 5-6
  • First Published: 26 November 2019
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Looking back, looking forward: In 2000, ChemBioChem debuted. The chemistry of carbohydrates, nucleic acids, peptides, proteins, natural products and other small molecules had reached a level that allowed biological questions to be probed. Today, there is no end in sight to studying biological matter with chemical tools or making use of biological methods to produce chemicals.

Reviews

Factors Governing the Thermal Stability of Lasso Peptides

  • Pages: 7-18
  • First Published: 27 June 2019
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The lariat-knot-resembling topology is only maintained by steric means for class II lasso peptides. At high temperatures, this fold either remains intact or unthreads to yield a branched-cyclic peptide. This review summarizes the current knowledge about the factors that dictate the stability of lasso peptides when heated.

Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms

  • Pages: 19-32
  • First Published: 15 November 2019
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New chemical tools: Advances in bioorthogonal chemical reporters have afforded new tools to explore the targets and functions of specific metabolites in diverse microbes. Here we summarize the development and application of metabolite chemical reporters to study fundamental pathways in bacteria as well as microbiota mechanisms in health and disease.

Minireviews

Very Important Paper

Advances in DNA Origami–Cell Interfaces

  • Pages: 33-44
  • First Published: 06 November 2019
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Biological curiosity or real-world applications: DNA nanotechnology could soon be hailed as the greatest thing since splicing genes, but does this field, which is still in its infancy, actually show promise in real-world applications? Examples of what occurs once DNA nanostructures reach their target site, and those that utilise clever design to accomplish desired functions are reviewed.

Open Access

Small-Molecule Inhibition of Glucose Transporters GLUT-1–4

  • Pages: 45-52
  • First Published: 25 September 2019
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Targeting aerobic glycolysis by means of glucose uptake inhibition may be a new approach for the treatment of proliferative diseases such as cancer and inflammatory disorders. This Minireview provides an overview of the most potent and advanced inhibitors of glucose uptake by glucose transporters GLUT-1–4 and sheds light on their potential for therapeutic applications.

Communications

A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer: An ATPase-Mimicking Nucleoapzyme

  • Pages: 53-58
  • First Published: 25 March 2019
Description unavailable

Artificial DNAzymes: A series of nucleoapzymes consisting of the bis-Zn2+-pyridyl-salen-type complex conjugated to the ATP aptamer at different positions and in variable conjugation modes reveal ATPase-mimicking functions, catalyzing the hydrolysis of ATP to ADP. Molecular dynamics simulations suggest that the distance separating the catalytic site from the ATP linked to ATP aptamer binding site guides the relative activities of the nucleoapzymes.

Evaluation of the Interaction between Bax and Hsp70 in Cells by Using a FRET System Consisting of a Fluorescent Amino Acid and YFP as a FRET Pair

  • Pages: 59-63
  • First Published: 17 June 2019
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Understanding interactions: To elucidate how organelle-targeting substances affect the Bax–Hsp70 interaction, a FRET system of Hsp70-YFP and ANAP-Bax was employed. Our results reveal that brefeldin A, chlorpromazine and apoptozole promote dissociation of the Bax/Hsp70 complex but bafilomycin A1, raptinal and Az-TPP-O3 have no influence on the interaction of Bax with Hsp70.

Very Important Paper

Analysis of Site-Specific Phosphorylation of PTEN by Using Enzyme-Catalyzed Expressed Protein Ligation

  • Pages: 64-68
  • First Published: 17 June 2019
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Specific phosphorylation: By subtiligase-catalyzed ligation of C-terminal phosphopeptide segments of the phospholipid phosphatase PTEN to PTEN′s recombinant core, four monophosphorylated semisynthetic PTEN proteins were synthesized. Analysis of these phosphorylated forms allows precise measurement of the autoinhibition mediated by each of these modifications and the importance of Tyr379 in PTEN regulation.

Probing for Thiol-Mediated Uptake into Bacteria

  • Pages: 69-73
  • First Published: 11 October 2019
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In or out? Cyclic oligochalcogenides (COCs), inhibit, rather than mediate, uptake into bacteria. This conclusion, resulting from the synthesis and evaluation of a series of COC–antibiotic conjugates, supports that COCs penetrate mammalian cells along nontrivial uptake pathways involving dynamic covalent exchange chemistry, mobility along disulfide tracks, and adaptive micellar pores.

Self-Assembly of Proteinaceous Shells around Positively Charged Gold Nanomaterials Enhances Colloidal Stability in High-Ionic-Strength Buffers

  • Pages: 74-79
  • First Published: 15 September 2019
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Engineered electrostatic interactions enable the self-assembly of a lumazine synthase variant on differently sized and shaped gold nanomaterials. The resulting complexes possess dramatically enhanced colloidal stability in high-ionic-strength buffers owing to the formation of a protective ≈4-nm-thick proteinaceous shell around the core particle.

Very Important Paper

Direct Enzymatic Synthesis of a Deep-Blue Fluorescent Noncanonical Amino Acid from Azulene and Serine

  • Pages: 80-83
  • First Published: 12 September 2019
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Into the wild blue yonder: The substrate scope of the tryptophan synthase β-subunit is expanded to accept the non-indole nucleophile azulene and synthesize the blue fluorescent noncanonical amino acid β-(1-azulenyl)-l-alanine (AzAla). AzAla is synthesized on the gram scale in a one-step enzymatic synthesis.

In Vitro Biosynthesis of Peptides Containing Exotic Azoline Analogues

  • Pages: 84-87
  • First Published: 15 September 2019
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FIT for purpose: The reprogrammed flexible in vitro translation (FIT) system for PatD reveals remarkable stereo-, chemo-, and regioversatility for modifiable residues in post-translational cyclodehydration catalyzed by a YcaO protein. This allows in vitro biosynthesis of peptides with diverse kinds of exotic azolines in the backbones.

Open Access

A Genetically Encoded Diazirine Analogue for RNA–Protein Photo-crosslinking

  • Pages: 88-93
  • First Published: 28 October 2019
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UV irradiation is widely used in molecular biology to covalently crosslink RNA with RNA-binding proteins; however, the yield of this process is usually low. We show that site-selective labeling of an RNA-binding protein with a diazirine-based unnatural amino acid gives higher yields of the photo-crosslinking product under milder irradiation conditions.

Construction and Characterization of a Mirror-Image l-DNA i-Motif

  • Pages: 94-97
  • First Published: 28 October 2019
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Through the looking glass: l-Type i-motif DNA give the same performance as the corresponding natural DNA in terms of thermodynamic properties, but exhibited mirror-image chirality and strong enzymatic resistance, potentially opening the way to the development of new DNA materials of pharmaceutical and biological interest.

Laccase-Mediated Catalyzed Fluorescent Reporter Deposition for Live-Cell Imaging

  • Pages: 98-102
  • First Published: 25 September 2019
Description unavailable

No added oxidants: Laccase can be used as a reporter enzyme to carry out catalyzed reporter deposition for fluorescent labeling of cells. When laccase is targeted to cells with an antibody, it can covalently deposit a fluorescently labeled ferulic acid derivative on the surface of cells. This method enables the amplified fluorescent labeling of live cells without the need for hydrogen peroxide.

Open Access

A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

  • Pages: 103-107
  • First Published: 08 October 2019
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Freezing interactions for identification: A new crosslinking reagent, with a sulfoxide fragmentation group and a click site, is reported for crosslink enrichment. Due to special cleavable properties, the reagent can be used for MS2 and potentially for MS3 experiments.

Deploying Fluorescent Nucleoside Analogues for High-Throughput Inhibitor Screening

  • Pages: 108-112
  • First Published: 10 November 2019
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An advantageous alternative: We present the development of nucleoside-based environment-sensitive fluorophore (ESF) probes that are applicable to competitive-binding analyses. Use of the ESF probes is illustrated by application to a high-throughput fragment-based screen for identification of leads for inhibitor development against a clinically relevant glycosyltransferase from the C. difficile TcdB toxin.

Full Papers

Open Access

N-Hydroxysuccinimide-Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates

  • Pages: 113-119
  • First Published: 29 October 2019
Description unavailable

Creating links: Building blocks equipped with an N-hydroxysuccinimide and an ethynylphosphonamidate residue can be used as selective amine–thiol linkers with defined configuration. The high selectivity for cysteine can solve current issues of succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate associated with homo-crosslinking side products under physiological conditions.

A Quencher-Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue

  • Pages: 120-128
  • First Published: 24 September 2019
Description unavailable

Finding mismatches: Fluorescent 5-(perylenylethynyl)uracil (PeU) is incorporated into serinol nucleic acid (SNA) strands, and a quencher-free linear SNA probe with three PeU is synthesized. In the single-stranded form, fluorescence is quenched, relative to that if the SNA is hybridized to RNA. The probe discriminates target RNA from RNA with a single-base mismatch.

Characterisation of the Dynamic Interactions between Complex N-Glycans and Human CD22

  • Pages: 129-140
  • First Published: 16 May 2019
Description unavailable

Molecular clues about dynamic recognition of complex-type N-glycans by human CD22. We highlight the importance of the sialic acid galactose moieties in the recognition process and study the conformational behaviour of complex biantennary glycans in depth throughout their binding to h-CD22. We also analyse the molecular basis of CD22 homo-oligomer formation on B-cell surfaces.

Very Important Paper

Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation

  • Pages: 141-148
  • First Published: 30 October 2019
Description unavailable

Wrestling SUMO onto proteins: We report three genetically encoded groups to activate protein function through an optimized phosphine-based small-molecule trigger. We demonstrate rapid and tunable control of protein SUMOylation and protein localization.

Solution Structure and Dynamics of the Small Protein HVO_2922 from Haloferax volcanii

  • Pages: 149-156
  • First Published: 04 June 2019
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It takes two: We present a high-resolution NMR solution structure of the HVO_2922 small protein from H. volcanii. The isolated protein forms a symmetrical dimer, which is stabilized by intramonomer electrostatic interactions. Dimerization is crucial for the protein stability and most probably for its functionality.

A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition

  • Pages: 157-162
  • First Published: 17 May 2019
Description unavailable

Characterizing the conformational changes of a DNA aptamer: A DNA aptamer that binds cAMP was isolated by using SELEX. Diverse spectroscopic and electrophoretic analyses reveal its parallel G-quadruplex conformation, as well as its adaptive recognition of high concentrations of cAMP.

Structural and Functional Characterization of 4-Hydroxyphenylacetate 3-Hydroxylase from Escherichia coli

  • Pages: 163-170
  • First Published: 02 June 2019
Description unavailable

More than a FAD: The structural and functional characterization of HpaB from E. coli, which is a FAD-dependent 4-hydroxyphenylacetate 3-monooxygenase, is reported. This enzyme enjoys a relatively broad substrate specificity that is useful for the conversion of diverse phenolic compounds into their corresponding catechols.

Vicinal Diol-Tethered Nucleobases as Targets for DNA Redox Labeling with Osmate Complexes

  • Pages: 171-180
  • First Published: 17 June 2019
Description unavailable

Tag, you're Os! A new approach for redox labeling of DNA is reported based on the enzymatic incorporation of a vicinal diol-labeled nucleotide into DNA followed by osmylation of the diol. The results show that a cyclic cis-diol is a better target for osmylation than that of the flexible aliphatic ones (alkyl- or alkynyl-linked).

Stabilization of Hydroxynitrile Lyases from Two Variants of Passion Fruit, Passiflora edulis Sims and Passiflora edulis Forma flavicarpa, by C-Terminal Truncation

  • Pages: 181-189
  • First Published: 27 September 2019
Description unavailable

Yellow versus purple: Hydroxynitrile lyase (HNL) from yellow passion fruit shows much better thermostability, pH stability, and organic tolerance than that of the HNL from purple passion fruit. The nonglycosylated and C-truncated mutant could improve the stability and reusability properties similar to that of glycosylated natural HNL.

Very Important Paper

Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae

  • Pages: 190-199
  • First Published: 18 September 2019
Description unavailable

Go with your gut: Two unusual class II lanthipeptide synthetases and a SAM-dependent C-terminal methyltransferase are encoded in a novel lanthipeptide biosynthetic gene cluster (lah) from L. bacterium C6A11. These enzymes were biochemically characterized, setting the stage for further exploration of the final products and their physiological functions in gut microbiota.

Sequential Two-Step Stereoselective Amination of Allylic Alcohols through the Combination of Laccases and Amine Transaminases

  • Pages: 200-211
  • First Published: 12 September 2019
Description unavailable

Enantioselective generation of allylic amines: Two-step amination of racemic (3E)-4-(het)arylbut-3-en-2-alcohols through a sequential cascade is described. The approach consists of oxidation mediated by laccase T. versicolor/TEMPO to form the corresponding ketone intermediates, followed by asymmetric bio-transamination by amine transaminases. Sixteen amine enantiomer pairs were obtained with 94 to >99 % ee.

Very Important Paper

Modulation of Pharmacologically Relevant Properties of Piperidine Derivatives by Functional Groups in an Equatorial or Axial β-Position to the Amino Group

  • Pages: 212-234
  • First Published: 06 September 2019
Description unavailable

A set of amine basicity and lipophilicity data for β-substituted piperidine derivatives provide enhanced insight into the stereospecific modulation of pharmacologically relevant properties by small substituents and prototypic functional groups, establishing a valuable reference base for molecular design.

Open Access

Acyldepsipeptide Probes Facilitate Specific Detection of Caseinolytic Protease P Independent of Its Oligomeric and Activity State

  • Pages: 235-240
  • First Published: 05 September 2019
Description unavailable

Antibiotic potential: Caseinolytic protease P (ClpP) is a peptidase that can gain proteolytic activity together with an ATPase. Acyldepsipeptides (ADEPs) mimic those, and thereby induce the activation of ClpP. The detection of ClpP has been realized with active-site-directed probes such as D3. Following SAR studies, we developed an ADEP photoprobe that is able to detect ClpP in its inactive form as well.

Very Important Paper

Open Access

Thermodynamic and Structural Behavior of α-Galactosylceramide and C6-Functionalized α-GalCer in 2D Layers at the Air–Liquid Interface

  • Pages: 241-247
  • First Published: 22 September 2019
Description unavailable

Robust under pressure: α-Galactosylceramide (KRN7000) and analogues thereof are used in novel immunotherapies, but little is known about the influence of structural modifications on the physical properties of the conjugates. By investigating 2D monolayers at the air–liquid interface, this study shows that KRN7000 can be modified at C6 without changing its highly ordered sub-gel structures.

Two-Step Bioorthogonal Activity-Based Protein Profiling of Individual Human Proteasome Catalytic Sites

  • Pages: 248-255
  • First Published: 09 October 2019
Description unavailable

Norbornene-modified proteasome inhibitors were developed for selective labeling of each of the six active sites of human constitutive proteasomes and immunoproteasomes. With these, β1i, β2,i β5c, and β5i can be selectively visualized in living Raji cells and cell extracts by inverse-electron-demand Diels–Alder ligation, thus adding to the proteasome probe toolbox we and others have generated over the past decades.

Very Important Paper

Open Access

Analysis of the Substrate Specificity of the SMYD2 Protein Lysine Methyltransferase and Discovery of Novel Non-Histone Substrates

  • Pages: 256-264
  • First Published: 15 October 2019
Description unavailable

SMYD2 methylates different histone and non-histone proteins. We investigated its substrate specificity and discovered several novel peptide and protein substrates, many of which are methylated more strongly than the p53 protein, the best SMYD2 substrate described so far. Our data will aid in understanding the role of SMYD2 in development and cancer.

Open Access

Practical Synthesis of Cap-4 RNA

  • Pages: 265-271
  • First Published: 18 October 2019
Description unavailable

Highly methylated mRNA caps are encountered in Trypanosoma. A solid-phase-based chemoenzymatic approach makes these RNAs synthetically accessible, thereby facilitating the study of the metabolism of, and essential biological functions mediated by these unique structural features found in this important class of human pathogenic parasites.

Very Important Paper

In Vivo Expression of Genetic Information from Phosphoramidate–DNA

  • Pages: 272-278
  • First Published: 23 December 2019
Description unavailable

The path of more resistance: Genetic information can be stored in a chemically altered DNA carrying several acid-labile phosphoramidate linkages. The modified gene was assembled from complementary single-stranded DNA fragments and successfully induced resistance to the antibiotic trimethoprim in bacteria.