ChemBioChem最新文献

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.

Cysteine sulfenyl iodides (Cys–SIs) have long been recognized as important intermediates in the oxidative modification of cysteine thiols since 1950s, implicated in pathways such as hydrolysis to cysteine sulfenic acid (Cys–SOH) and electrophilic aromatic substitution with an indole ring of tryptophan to form Cys–Trp thioether linkages. Despite their proposed significance in both biological and chemical contexts, direct examination of Cys–SIs has been precluded by their intrinsic instability. Herein, the first isolation of a small-molecule Cys–SI, stabilized using a nanosized molecular cradle at the N-terminus of cysteine, is reported. The structure of the isolable Cys–SI is determined by X-ray crystallography, and its reactivity is investigated with a range of nucleophiles. Hydrolysis to Cys–SOH and reaction with an indole derivative provide direct chemical evidence for long-standing mechanistic proposals. Furthermore, rapid formation of sulfenamides with amines and high-yield adduct formation with dimedone, a canonical sulfenic-acid probe, reveal that Cys–SI possesses even greater electrophilicity than Cys–SOH. These results deliver a structurally defined reference for Cys–SI and inform mechanisms of iodine-mediated protein oxidation and peptide modification.

Bispecific antibodies (BsAbs) are engineered immunoglobulins that can simultaneously recognize two distinct antigens or two distinct epitopes on the same antigen. They exhibit cooperative therapeutic effects surpassing those of natural monoclonal antibodies, such as bridging the immune cells and tumor cells to stimulate targeted immune response, or blocking codependent signaling pathways. These advantages make them attractive therapeutic reagents for various diseases such as cancers, immunodeficiency syndromes, and ophthalmic disorders. However, the unique structural characteristics of BsAbs pose various challenges to their preparation. In the past few decades, various types of BsAbs have been designed and prepared through genetic engineering or chemical conjugation strategies, many of which have been approved as drugs or entered clinical trials. This review provides a systematic summary of these strategies and their corresponding principles, and focuses on the application of modern genetic engineering and chemical conjugation methods in the generation of BsAbs.