ChemBioChem最新文献

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are remarkable natural products with interesting chemical structures and potent bioactivities. RiPP pathways are abundant in all domains of life and harbor a large biosynthetic potential in the form of post-translationally acting enzymes. A relatively small number of RiPP biosynthetic gene clusters encode peptide arginases, a recently discovered maturase family capable of hydrolyzing arginine residues of RiPP core peptides to ornithines. In this study, members of the peptide arginase family (FlmR and OhkR), which are associated with uncharacterized precursors from orphan RiPP families, are identified. In vivo and in vitro activity of FlmR and OhkR with the five associated precursor peptides (FlmA1-3 and OhkA1-2) is demonstrated and kinetic studies to biochemically characterize the enzymes are performed. Furthermore, in silico structural analysis with AlphaFold 3 is used to predict precursor-arginase complexes, providing insights into how peptide arginases could bind their precursor substrates. In the case of OhkA-OhkR complexes, this analysis also allows a hypothesis as to which of the arginine residues of the core peptide is modified first, which is confirmed experimentally. This detailed biochemical and structural enzyme characterization is a prerequisite for the application of peptide arginases in peptide-based drug discovery platforms.

Trypanosoma cruzi, the etiologic agent of Chagas disease, is a protozoan parasite transmitted to humans via the feces of blood-sucking triatomine vectors such as Triatoma infestans. It has been shown that galactofuranose-containing oligosaccharides present in mucins of T. cruzi are involved in parasite adhesion to the T. infestans rectal ampoule, a key step in the differentiation programme from dividing epimastigote to nondividing mammal-infective metacyclic forms of the parasite. To further characterize this process, the α-benzyl glycoside of β-D-Galf(1 → 2)-β-D-Galf(1 → 4)-[β-D-Galp-(1 → 6)]-D-GlcNAc is synthesized and its alditol derivative is spectroscopically characterized. The tetrasaccharide component of this glycoside is a substructure of the O-linked pentasaccharide and hexasaccharide structures found in the T. cruzi epimastigote mucins. The tetrasaccharide glycoside inhibits parasite adhesion to the rectal ampoule of T. infestans, suggesting that some or all of the binding capacity of T. cruzi epimastigotes resides within this O-glycan tetrasaccharide substructure. Since T. cruzi mucin O-linked glycans are known to be acceptors for T. cruzi trans-sialidase, it is investigated whether the tetrasaccharide substructure acts as an acceptor substrate for this activity. The successful transfer of sialic acid to the tetrasaccharide glycoside indicates that further elaboration to the pentasaccharide and hexasaccharide structures is not essential for sialic acid transfer.

In the Chinese mythological narrative of Journey to the West, the Tightening Spell has the power to constrict Sun Wukong′s headband. In this context, Sun Wukong′s headband is used as a metaphor for the cyclic peptide Plecantide, while the descending spell symbolizes the incorporation of propargylalanine at the C-terminus. The observed constriction of the headband under the influence of the spell illustrates the concept that introducing propargylalanine at the C-terminus can stabilize the conformation of Plecantide by locking it into a more rigid structure. More details can be found in the Research Article by Pingzheng Zhou, Wu Su, Guiyang Yao, and co-workers (DOI: 10.1002/cbic.202500237).

Unbiased identification of drug-targets in live cells is essential for understanding the mechanism-of-action and potential off-target effects of drugs. The BioTAC system to measure these effects is previously developed. However, BioTAC has limitations, including lysine-directed biotinylation chemistry, and relatively long biotin labeling times. Herein, the development of the APEXTAC system, a small molecule guided proximity labeling platform based on the APEX2 peroxidase proximity labeling enzyme, is described as a complementary tool. A head-to-head comparison is performed between the APEXTAC system and the BioTAC system for (+)-JQ1 target-ID and demonstrated that APEXTAC can label E3-ligases via their ligands without requiring a proteasome inhibitor which can significantly perturb cell state. The APEXTAC system supports live cell target-ID across numerous molecules and targets, including components of the protein homeostasis machinery, without degradation of the labeling system, highlighting its potential application to the targeted protein degradation field.

Spatial metabolomics is transitioning from a descriptive mapping tool to a functional, system-level science. By visualizing the complex molecular signature of tissues and cells, spatial analytics is rapidly advancing the field to provide unprecedented insights into the metabolic underpinnings of health and disease. In this article, the latest high-resolution analytical technologies that drive this transformation are discussed, focusing on how progressive innovations in cellular chemical imaging, enabled by advanced analytics, allow the revelation of metabolic heterogeneity with unparalleled precision. Furthermore, the increasingly indispensable role of artificial intelligence is emphasized in navigating data complexity and the power of multiomics integration in creating comprehensive, multilayered biochemical mapping of biological systems, ranging from single cells to whole organisms.

The intersection of DNA/RNA nanotechnology and single-molecule solid-state nanopore sensing enables precise detection of low-abundance biomolecules. However, a significant challenge persists that nucleic acid molecules readily fold during nanopore translocation, which gives rise to ambiguous current signatures, reduces the number of usable data points, and compromises detection accuracy. Herein, a recent advancement by the Platnich group is highlighted, wherein urea is employed as a noncovalent modulator to participate in the isothermal assembly of MS2 bacteriophage RNA with DNA barcodes. This modulator stably binds to the RNA:DNA hybrids through supramolecular interactions after removal of free urea by buffer exchange. Nanopore assays showed a ≈50% reduction in fold-shift events in the urea-treated group. Atomic force microscopy characterization shows that the persistence length of the hybrids is enhanced by ≈40%. This strategy provides a new noncovalent regulatory tool for nucleic acid nanotechnology and pushes the nanopore sensing technology toward the precision detection of low-abundance RNA.

In this work, we develop a platform for multimerizing peptides/miniproteins using various polyvalent thioester cores derived from easy-to-synthesize N-hydroxysuccinimide esters. We employed native chemical ligation to attach multiple copies of peptide/miniprotein around a fixed multi-armed thioester core in a one-pot fashion, leading to the first-generation multimers. Further, using a reverse thioether ligation strategy, we synthesized second-generation branched homo/hetero multimers. The reactions proceed under an aqueous environment that closely mimics physiological conditions, forming multimeric products with yields ranging from 30% to 90%. The general utility of this strategy is showcased by the synthesis of multimeric linear and bicyclic peptides, bicyclic peptide-cell penetrating peptide conjugates, and multimeric miniproteins which show picomolar affinity against SARS-CoV-2 receptor binding domain. We believe that this modular approach of generating multimeric molecules should find broad applicability in peptide chemistry and chemical biology.

In recent years, nanozymes have increasingly attracted the attention of researchers due to their low cost, high stability, and straightforward preparation when compared with natural enzymes. Furthermore, the biocompatibility of nanozymes has been enhanced through surface adsorption, hence broadening their application scope. In this work, Co₃O₄ nanozyme was adsorbed with diverse DNA, and the catalytic performance was significantly boosted compared with the pure Co₃O₄ nanozyme. Peroxidase-like activity assays revealed three key findings. First, the adsorption of single-stranded DNA proved to be more effective than that of double-stranded DNA. Second, the 50-nucleotide single-stranded DNA sequence yielded the stronger catalytic signal. Ultimately, guanine rich nucleotide exhibited the higher catalytic efficiency in single-stranded DNA and cytosine-guanine rich nucleotide exhibited the stronger catalytic efficiency in double-stranded DNA. The kinetic results of its catalytic activity showed that the catalysis of the adsorbed Co₃O₄ nanozyme followed the Michaelis–Menten kinetics. In parallel, the K_m value of 50-nucleotide single-stranded DNA adsorption was the lowest of diverse DNA, which was 6.11 mM and 54.8% of the pure Co₃O₄ nanozyme. These findings establish DNA adsorption as an effective strategy for enhancing the catalytic activity of Co₃O₄ nanozymes, presenting significant potential for applications in medical diagnostics and antioxidant-related fields.

No specific vaccines or therapeutics are currently available for the prevention or treatment of Zika virus infections. The viral protease NS2B-NS3 is essential for the replication of Zika and other orthoflaviviruses, making it a target for antiviral drug development. Traditional discovery of competitive inhibitors has relied on substrate recognition sequences, typically yielding multibasic peptides. Herein, a de novo strategy is presented for identifying competitive inhibitors using peptide phage display in combination with Bi(III)-mediated in situ formation of bicyclic peptides. In an initial screening, phages displaying a library of randomized peptide-bismuth bicycles are eluted by interrupting the phage-target interactions at low pH. This approach yields a small number of peptides biased toward the active site, characterized by dibasic motifs, but only one low-ranking sequence shows modest inhibitory activity. To enhance specificity, a second screening campaign employs competitive phage elution using the dibasic boronate inhibitor CN-714 that covalently binds to the catalytically active serine residue S135 of NS2B-NS3. This strategy enriches a larger pool of competitive inhibitors sharing the characteristic dibasic substrate recognition motif. The most potent peptide-bismuth bicycle identified and synthesized features a completely novel sequence, exhibits an inhibition constant of 3.9 µM and displays remarkable proteolytic stability over 24 h.

Viral macrodomains, which hydrolyze mono-ADP-ribosylated proteins to evade host immunity, represent emerging antiviral targets, yet their druggability remains underexplored. GS-441524, the active metabolite of remdesivir, has been identified as an inhibitor of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus) macrodomain (Nsp3b). Herein, the structure–activity relationship governing macrodomain recognition by the ribosylated moiety using a panel of nucleoside analogs, revealing that phosphate configuration and nucleobase identity critically modulate binding affinity. GS-441524 derivatives exhibit up to 200-fold higher affinity compared to adenosine-based ligands. A novel sulfamoyl derivative demonstrates superior inhibitory potency, attributable to its occupation of the phosphate subsite and formation of a stabilizing hydrogen-bond network. These findings provide molecular insights into Nsp3b–ligand interactions and establish a rational framework for the development of high-affinity, structure-guided inhibitors targeting viral macrodomains.