ChemBioChem最新文献

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.

Biosensors and microdevices using living cells have gained significant attention in recent years, including methods for cell immobilization on antibody-coated surfaces. Random antibody fixation may lead to suboptimal exposure of recognition sites, reducing interaction efficiency. In contrast, aligned antibody immobilization enhances antigen recognition and binding capacity during cell immobilization. Site incorporation of azido-phenylalanine (AzF) into antibodies facilitates site-specific conjugation, enabling aligned antibody immobilization. In this study, we expressed and purified anti-mCherry variable domains of heavy-chain-only antibodies (VHHs), incorporating AzF at the C-terminus using an unnatural amino acid system to ensure its placement away from the antigen-binding site for mCherry. Anti-mCherry VHH-AzF was conjugated to dibenzylcyclooctyne (DBCO)-coated glass via click chemistry, followed by incubation with HeLa cells expressing mCherry on their surfaces (mCherry-coated cells). This resulted in increased immobilization of mCherry-coated cells on the VHH-coated glass, whereas normal HeLa cells did not adhere.

The spatiotemporal control of biomolecular functions via light-triggered bond cleavage has emerged as a powerful approach in chemical biology and cell biology. In this concept review, three major modalities of photo-cleavable systems—proteins, small molecules, and metal complexes—are classified and discussed, highlighting their design principles, biological applicability, and remaining challenges. Emphasis is placed on recent efforts to address key design challenges—such as balancing functional performance, biological compatibility, and optical responsiveness—across different molecular modalities, offering perspectives for the next generation of photo-responsive tools for biological research.

The effects of the substitution of a guanine (G) base by the oxidative lesion 8-oxo-7,8-dihydroguanine (OG) on the affinity of the DNA aptamer selected against L-argininamide (L-Rm) are studied. Results indicate that, depending on the position of the modified base located in the recognition site, the substitution of only one G by OG could either reduce, not affect, or increase such an affinity. In addition, attempts are carried out to promote chemical crosslinks between the aptamer and its target following selective oxidation of OG. Results show that such crosslinks could be produced with a high efficacy through nucleophilic addition of L-argininamide, presumably onto the C5 position of the oxidized OG base inserted into the aptamer in any position, and that no crosslink is generated for the original aptamer (not containing any OG). However, such reaction being very efficient, crosslinks are also produced between L-argininamide and oligonucleotides (including scramble sequences) that are not supposed to bind to that amino acid. Such an effect could be explained by the electrostatic interactions between the negatively charged oligonucleotides and the protonated amino acid, which favor the formation of crosslinks upon OG oxidation. Efforts to decrease formation of such nonspecific crosslinks are only partly successful.

Transcription factors (TFs) are important gene regulators whose abnormal expression or function is involved in the occurrence of various diseases. The emergence of transcription factor-targeted proteolysis-targeting chimeras (TF-PROTACs) using DNA with a specific sequence as the targeting ligand of TFs provides a promising strategy to overcome the difficulties of using small molecules to inhibit TFs without well-defined ligand-binding pockets. A smart nanomachine is reported to realize near-infrared (NIR) light-triggered release and activation of TF-PROTAC using upconversion nanoparticles loaded with caged TF-PROTAC targeting the transcriptional factor NF-κB. The release of the active TF degrader (dNF-κB) under 980 nm NIR irradiation is demonstrated in a controlled manner, enabling precise control of the degradation of the transcriptional factor NF-κB p65 in live cells. The construction of the NIR-responsive nanomachine makes it possible to load and release various TF-PROTACs to degrade different transcriptional factors on demand with spatial and temporal resolution.

Genomic DNA stores genetic information and regulates functions of various biological processes. Genetic diseases can be caused by abnormal gene expression. Genetic manipulation requires sequence-selective recognition of double-stranded DNAs, various chemical approaches for double-duplex invasion have been developed. In the previous research, a photo-induced double-duplex invasion (pDDI) is introduced that uses artificial nucleotides, 3-cyanovinylcarbazole nucleoside (^CNVK) as photo-crosslinker and 5-cyanouridine (^CU) as inter-probe photo-crosslinking inhibitor. In this study, while investigating the invasion mechanism of the pDDI, the invasion independence of pDDI probes is discovered and proposed a photo-induced duplex invasion (pDI) that achieves fast invasion using only ^CNVK while still maintaining a high invasion efficiency. This rapid pDI approach provides a powerful new tool for site-specific manipulation of genomic DNA.