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Themed collection RSC Chemical Biology Transparent Peer Review Collection

45 items
Open Access Review Article

Direct targeting of TDP-43, from small molecules to biologics: the therapeutic landscape

Given the therapeutic interest of targeting TDP-43, this review focuses on the current landscape of strategies, ranging from biologics to small molecules, that directly target TDP-43. Regions targeted are shown on the 3D structure of RNA-bound TDP-43.

Graphical abstract: Direct targeting of TDP-43, from small molecules to biologics: the therapeutic landscape
Open Access Review Article

Wnt signaling activation: targets and therapeutic opportunities for stem cell therapy and regenerative medicine

Overview of the Wnt signaling pathway and targets of Wnt activators.

Graphical abstract: Wnt signaling activation: targets and therapeutic opportunities for stem cell therapy and regenerative medicine
Open Access Review Article

Recent developments and applications of quantitative proteomics strategies for high-throughput biomolecular analyses in cancer research

Various quantitative strategies can be utilized in mass spectrometry (MS)-based proteomic investigations. Here we explore recent applications of quantitative MS-based strategies and the resulting advances in the areas of prostate, pancreatic, breast and ovarian cancer research.

Graphical abstract: Recent developments and applications of quantitative proteomics strategies for high-throughput biomolecular analyses in cancer research
Open Access Review Article

19 F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery

19 F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens.

Graphical abstract: 19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery
Open Access Review Article

Reactive oxygen species, proinflammatory and immunosuppressive mediators induced in COVID-19: overlapping biology with cancer

Mitochondria-targeted drugs inhibit cancer and COVID-19 mechanisms.

Graphical abstract: Reactive oxygen species, proinflammatory and immunosuppressive mediators induced in COVID-19: overlapping biology with cancer
Open Access Review Article

Optical chemosensors for the detection of proximally phosphorylated peptides and proteins

This review details optical detection methods for proximal multi-site phosphorylation, a critical post-translational modification in protein biology.

Graphical abstract: Optical chemosensors for the detection of proximally phosphorylated peptides and proteins
Open Access Review Article

Nanobodies as in vivo, non-invasive, imaging agents

In vivo imaging has become in recent years an incredible tool to study biological events and has found critical applications in diagnostic medicine.

Graphical abstract: Nanobodies as in vivo, non-invasive, imaging agents
Open Access Review Article

Investigation of the biological functions of heparan sulfate using a chemoenzymatic synthetic approach

Heparan sulfate (HS) is a highly sulfated polysaccharide playing essential physiological and pathophysiological roles in the animal kingdom.

Graphical abstract: Investigation of the biological functions of heparan sulfate using a chemoenzymatic synthetic approach
Open Access Review Article

Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection

Crosslinker-modified nucleic acid probes are promising substitutes for regular oligonucleotide probes in hybridization-based assays, as they allow a more selective and efficient detection of nucleic acid targets and nucleic acid biomarkers.

Graphical abstract: Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection
Open Access Review Article

Design and synthesis of metabolic chemical reporters for the visualization and identification of glycoproteins

This review details a brief history of the synthesis and characterization of metabolic chemical reporters used to study glycosylation before describing recent applications and finishing with considerations and limitations of reporter molecules.

Graphical abstract: Design and synthesis of metabolic chemical reporters for the visualization and identification of glycoproteins
Open Access Review Article

Modulators of protein–protein interactions as antimicrobial agents

This review describes recent efforts towards the modulation of protein–protein interactions in infectious bacteria.

Graphical abstract: Modulators of protein–protein interactions as antimicrobial agents
Open Access Review Article

Biological functions of supramolecular assemblies of small molecules in the cellular environment

Supramolecular assemblies of small molecules, exhibiting emergent properties, are becoming a new and dynamic molecular platform for biological functions and for developing novel therapeutic approaches.

Graphical abstract: Biological functions of supramolecular assemblies of small molecules in the cellular environment
Open Access Review Article

DNA folds threaten genetic stability and can be leveraged for chemotherapy

Alternative DNA structures (including G-quadruplexes and DNA junctions) represent promising targets for combinatorial chemotherapeutic treatments aiming at fostering genomic instability and impeding DNA repair.

Graphical abstract: DNA folds threaten genetic stability and can be leveraged for chemotherapy
Open Access Review Article

Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors

The 20S proteasome is a valuable target for the treatment of a number of diseases including cancer, neurodegenerative disease, and parasitic infection.

Graphical abstract: Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors
Open Access Review Article

The chemical biology of IL-12 production via the non-canonical NFkB pathway

Interleukin-12 (IL-12) has emerged as an attractive cytokine for cancer therapy because it has direct anti-cancer effects and additionally plays a critical role in enhancing checkpoint inhibitors.

Graphical abstract: The chemical biology of IL-12 production via the non-canonical NFkB pathway
Open Access Review Article

Matters of class: coming of age of class III and IV lanthipeptides

In this review, we give a concise overview of the known biosynthetic princples of class III and IV lanthipeptide synthtases.

Graphical abstract: Matters of class: coming of age of class III and IV lanthipeptides
Open Access Communication

Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor

A rationally designed stapled JAZ peptide selectively inhibited MYCs, master-regulators of the jasmonate signaling in Arabidopsis thaliana. It is proposed as a novel chemical tool for the analysis of MYC related jasmonate signaling.

Graphical abstract: Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor
Open Access Communication

Tranylcypromine specificity for monoamine oxidase is limited by promiscuous protein labelling and lysosomal trapping

Chemical proteomics and cellular imaging reveal lysosomal trapping of tranylcypromine which can be largely reverted by the addition of lysosomotropic drugs.

Graphical abstract: Tranylcypromine specificity for monoamine oxidase is limited by promiscuous protein labelling and lysosomal trapping
Open Access Communication

Synthetic hyperacetylation of nucleosomal histones

A chemical catalyst system enabling high-yielding and comprehensive lysine acetylation of nucleosomal histones was developed as an epigenetics tool.

Graphical abstract: Synthetic hyperacetylation of nucleosomal histones
Open Access Paper

Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain

The significant improvement in the binding affinity of the stapled peptide to the PSD-95 GK domain is mostly contributed by the reduction in the entropy penalty of the stapled peptide due to the restriction in the α-helical structure by stapling in the free state.

Graphical abstract: Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain
Open Access Paper

Deciphering the substrate recognition mechanisms of the heparan sulfate 3-O-sulfotransferase-3

Co-crystallization and biochemical analyses with structurally defined oligosaccharides show the low reactivity of HS 3-OST-3 toward 6-O-sulfated substrates is due to inhibition of enzyme activity by 6-O-sulfated oligosaccharides.

Graphical abstract: Deciphering the substrate recognition mechanisms of the heparan sulfate 3-O-sulfotransferase-3
Open Access Paper

Members of the Legionella pneumophila Sde family target tyrosine residues for phosphoribosyl-linked ubiquitination

During infection, Legionella pneumophila translocates hundreds of effectors into host cells. Among these, the Sde family effector SdeC catalyzes atypical ubiquitination of host targets at tyrosine, not only serine, residues.

Graphical abstract: Members of the Legionella pneumophila Sde family target tyrosine residues for phosphoribosyl-linked ubiquitination
Open Access Paper

A cell permeable bimane-constrained PCNA-interacting peptide

A small, inherently fluorescent macrocyclic peptide constrained with a bimane-linker is cell permeable, and binds the human sliding clamp protein, PCNA, in a 310-helical conformation with nanomolar affinity.

Graphical abstract: A cell permeable bimane-constrained PCNA-interacting peptide
Open Access Paper

Glycan–protein interactions determine kinetics of N-glycan remodeling

Atomistic glycoprotein simulations reveal a site-specific availability of glycan substrates in time-resolved mass spectrometry of maturating enzyme kinetics.

Graphical abstract: Glycan–protein interactions determine kinetics of N-glycan remodeling
Open Access Paper

The two domains of human galectin-8 bind sialyl- and fucose-containing oligosaccharides in an independent manner. A 3D view by using NMR

NMR, ITC, and MD data show that the two domains of human galectin-8 independently recognize sialyl- and fucosyl-containing glycans.

Graphical abstract: The two domains of human galectin-8 bind sialyl- and fucose-containing oligosaccharides in an independent manner. A 3D view by using NMR
Open Access Paper

Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens

Click handle-containing antigens can be used to study uptake, processing and presentation by immune cells.

Graphical abstract: Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens
Open Access Paper

A two-trick pony: lysosomal protease cathepsin B possesses surprising ligase activity

Cathepsin B is an important protease within the lysosome, where it helps recycle proteins to maintain proteostasis.

Graphical abstract: A two-trick pony: lysosomal protease cathepsin B possesses surprising ligase activity
Open Access Paper

Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein

This study provides a mechanistic description of how the membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein.

Graphical abstract: Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein
Open Access Paper

Metathramycin, a new bioactive aureolic acid discovered by heterologous expression of a metagenome derived biosynthetic pathway

Heterologous expression of an aromatic polyketide biosynthetic gene cluster recovered from a New Zealand soil metagenome library resulted in the discovery of new bioactive aureolic acids.

Graphical abstract: Metathramycin, a new bioactive aureolic acid discovered by heterologous expression of a metagenome derived biosynthetic pathway
Open Access Paper

Identifying cysteine residues susceptible to oxidation by photoactivatable atomic oxygen precursors using a proteome-wide analysis

Evaluation of O(3P)-mediated cysteine oxidation in the proteome of a cell using dibenzothiophene-S-oxide derivatives as O(3P)-precursors.

Graphical abstract: Identifying cysteine residues susceptible to oxidation by photoactivatable atomic oxygen precursors using a proteome-wide analysis
Open Access Paper

Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate

A revision is proposed to the biosynthetic pathway to the well-known red pigment prodigiosin via a new thioester intermediate.

Graphical abstract: Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate
Open Access Paper

Mechanism-based inhibitors of SIRT2: structure–activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration

Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. Here, we developed small peptide-based inhibitors of its activity in living cells in culture.

Graphical abstract: Mechanism-based inhibitors of SIRT2: structure–activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration
Open Access Paper

Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein

Rad4/XPC DNA damage sensor protein specifically binds to a photocleavable NPOM-DNA adduct, and this recognition is abolished upon photo-cleavage of NPOM.

Graphical abstract: Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein
Open Access Paper

Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications

Using protein semi-synthesis, segmentally isotope-labelled variants of nucleosome-binding protein HMGN1 were generated with site-specific posttranslational modifications to explore their structural and functional effects.

Graphical abstract: Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications
Open Access Paper

In vivo modulation of ubiquitin chains by N-methylated non-proteinogenic cyclic peptides

Cyclic peptides containing unnatural amino acids can modulate Lys-48 ubiquitin chains in cells and animals.

Graphical abstract: In vivo modulation of ubiquitin chains by N-methylated non-proteinogenic cyclic peptides
Open Access Paper

Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme

Cyclodipeptide synthases recognize a minimalistic substrate to produce cyclic dipeptides in a tRNA-independent manner.

Graphical abstract: Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme
Open Access Paper

Finding and characterizing a catalytic antibody light chain, H34, capable of degrading the PD-1 molecule

Programmed cell death 1 (PD-1) is an immune checkpoint regulating T-cell function. A catalytic antibody light chain, H34, could enzymatically degrade the PD-1 molecule. In addition, it inhibited the binding of PD-1 with PD-L1.

Graphical abstract: Finding and characterizing a catalytic antibody light chain, H34, capable of degrading the PD-1 molecule
Open Access Paper

In silico peptide-directed ligand design complements experimental peptide-directed binding for protein–protein interaction modulator discovery

Using the protein–protein interaction of Mcl-1/Noxa, two methods for efficient modulator discovery are directly compared.

Graphical abstract: In silico peptide-directed ligand design complements experimental peptide-directed binding for protein–protein interaction modulator discovery
Open Access Paper

Fluorescent macrolide probes – synthesis and use in evaluation of bacterial resistance

Macrolide fluorescent probes illuminate the interactions between antibiotics and bacteria, providing new insight into mechanisms of resistance.

Graphical abstract: Fluorescent macrolide probes – synthesis and use in evaluation of bacterial resistance
Open Access Paper

Cyclic peptide scaffold with ability to stabilize and deliver a helical cell-impermeable cargo across membranes of cultured cancer cells

A new helix-loop-helix peptide scaffold with dual ability to transport cargo across cancer cell membranes and disrupt mitochondrial membrane function.

Graphical abstract: Cyclic peptide scaffold with ability to stabilize and deliver a helical cell-impermeable cargo across membranes of cultured cancer cells
Open Access Paper

Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors

We identified potent, functionalisable BMX inhibitors and revealed their covalent mode of binding to BMX by X-ray crystallography.

Graphical abstract: Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors
Open Access Paper

A thorough analysis and categorization of bacterial interrupted adenylation domains, including previously unidentified families

In-depth study of intriguing bacterial interrupted adenylation domains from seven distinct families and six different types.

Graphical abstract: A thorough analysis and categorization of bacterial interrupted adenylation domains, including previously unidentified families
Open Access Paper

Antibacterial activity of a dual peptide targeting the Escherichia coli sliding clamp and the ribosome

Bifunctional peptides targeting both the translation and the replication machineries have been developed and shown to act as new antimicrobials.

Graphical abstract: Antibacterial activity of a dual peptide targeting the Escherichia coli sliding clamp and the ribosome
Open Access Paper

Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism

Investigation of the downstream effects of NMT inhibition identified novel defense mechanism against chemical toxicity in fungal pathogen Z. tritici.

Graphical abstract: Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism
Open Access Paper

A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor

UDP-N-acetylglucosamine pyrophosphorylase (UAP1) catalyses the last step in eukaryotic biosynthesis of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), converting UTP and GlcNAc-1P to the sugar nucleotide.

Graphical abstract: A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor
45 items

About this collection

In the interest of transparency and open science, RSC Chemical Biology is the first Royal Society of Chemistry journal to offer our authors the option of transparent peer review, where the editor’s decision letter, reviewers’ comments and authors’ response for all versions of the manuscript are published alongside the article under an Open Access Creative Commons licence (CC-BY). Authors are asked if they would like to take up this option at the revision stages. Reviewer comments will remain anonymous unless the individual chooses to sign their report.

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