ChemBioChem最新文献

Nanozymes exhibiting natural enzyme-mimicking catalytic activities as antibacterial agents present several advantages, including high stability, low cost, broad-spectrum antibacterial activity, ease of preparation and storage, and minimal bacterial resistance. Consequently, they have attracted significant attention in recent years. However, the rapid expansion of antimicrobial nanozyme research has resulted in pioneering reviews that do not comprehensively address emerging concerns and enhancement strategies within this field. This paper first summarizes the factors influencing the intrinsic activity of nanozymes; subsequently, we outline new research considerations for designing antibacterial nanozymes with enhanced functionality and biosafety features such as degradable, imageable, targeted, and bacterial-binding nanozymes as well as those capable of selectively targeting pathogenic bacteria while sparing normal cells and probiotics. Furthermore, we review novel enhancement strategies involving external physical stimuli (light or ultrasound), the introduction of extrinsic small molecules, and self-supplying H₂O₂ to enhance the activity of antibacterial nanozymes under physiological conditions characterized by low concentrations of H₂O₂ and O₂. Additionally, we present non-redox nanozymes that operate independently of highly toxic reactive oxygen species (ROS) alongside those designed to combat less common pathogenic bacteria. Finally, we discuss current issues, challenges faced in the field, and future prospects for antibacterial nanozymes.

DNA logic gates with dynamic nanostructures have made a profound impact on cancer diagnosis and treatment. Through programming the dynamic structure changes of DNA nanodevices, precise molecular recognition with signal amplification and smart therapeutic strategies have been reported. This enhances the specificity and sensitivity of cancer theranostics, and improves diagnosis precision and treatment outcomes. This review explores the basic components of dynamic DNA nanostructures and corresponding DNA logic gates, as well as their applications for cancer diagnosis and therapies. The dynamic DNA nanostructures would contribute to cancer early detection and personalized treatment.

Modular type I polyketide synthases (PKSs) are remarkable molecular machines that can synthesize structurally complex polyketide natural products with a wide range of biological activities. In these molecular machines, ketosynthase (KS) domains play a central role, typically by catalyzing decarboxylative Claisen condensation for polyketide chain extension. Noncanonical KS domains with catalytic functions rather than Claisen condensation have increasingly been evidenced, further demonstrating the capability of type I PKSs for structural diversity. This review provides an overview of the reactions involving unusual KS activities, including PKS priming, acyl transfer, Dieckmann condensation, Michael addition, aldol-lactonization bicyclization, C-N bond formation and decarbonylation. Insights into these reactions can deepen the understanding of PKS-based assembly line chemistry and guide the efforts for rational engineering of polyketide-related molecules.

The chemokine-like receptor 1 (CMKLR1) is activated by the adipokine and chemoattractant protein chemerin. Cryo-EM structures of chemerin-9-CMKLR1-Gi have been published, where chemerin-9 is the nonapeptide of the C terminus of chemerinS157. Chemerin-9 is as active as the full-length protein in Ca²⁺-release but shows differences in equilibrium read-outs. An equally potent cyclic chemerin-9 variant (cC9) was reported previously. Now, we have built a computational model of CMKLR1 to investigate the binding mode of cC9 and chemerinS157 in comparison to chemerin-9. Differences were investigated using CMKLR1 variants. Double-mutant cycle analysis identified CMKLR1-F2.53 as the relevant position for Phe8-binding of cC9. Energy contribution revealed slight differences in Phe8-binding to CMKLR1-F2.53 and space for larger residues. This was confirmed as the chemerin-9 variant with 1-naphthyl-L-alanine at position 8 showed a 4-fold increased potency of 2 nM (pEC₅₀=8.6±0.15). While chemerin-9 and cC9 share their interactions at the CMKLR1, chemerinS157 tolerates most mutations of CMKLR1 in the deep binding site. The computational model of chemerinS157 suggests a β-sheet interaction between the N-terminal CMKLR1-segment I25VVL28 and the β-sheet D108KVLGRLVH116 of ChemS157, which was confirmed experimentally. Our data add to the knowledge by identifying the binding mode of chemerinS157 and cC9 at CMKLR1, facilitating the future structure-based drug design.

Flavin-dependent enzymes catalyze a panoply of chemical transformations essential for living organisms. Through oxygen activation, flavoenzymes could generate diverse flavin-oxygen species that mediate numerous redox and non-redox transformations. In this review, we highlight the extensive oxygen activation chemistry at two sites of the flavin cofactor: C4a and N5 sites. Oxygen activation at the C4a site generates flavin-C4aOO(H) species for various monooxygenation reactions, while activation at the N5 site produces negatively charged flavin-N5OOH species, which act as highly reactive nucleophiles or bases. The selective oxygen activation at either the C4a or N5 site depends on the nature of substrates and is controlled by the active site architecture. These insights have expanded our understanding of oxygen activation chemistry in flavoenzymes and will serve as a foundation for future efforts in enzyme engineering and redesign.

Linkers with disulfide bonds are the only cleavable linkers that utilize physiological thiol gradients as a trigger to initiate the intracellular drug release cascade. Herein, we present a novel concept exploiting the thiol gradient phenomena to design a new class of cleavable linker with no disulfide bond. To support the concept, an electron-deficient sulfonamide-based cleavable linker amenable to conjugation of drug molecules with targeting agents, was developed. Modulating the electron-withdrawing nature of the aryl sulfonamide was critical to the balance between the stability and drug release. Favorable stability and payload release in human serum under physiologically relevant thiol concentrations was demonstrated with two potent cytotoxics. Intracellular payload release was further validated in cell-based assay in context of antibody-drug conjugate generated from monoclonal antibody and sulfonamide containing linker. To support the proposed release mechanism, possible downstream by-products formed from the drug-linker adduct were characterized.

The diazo group is an important functional group in organic synthesis because it confers high reactivity to the compounds and has been applied in various chemical reactions, such as the Sandmeyer reaction, Wolff rearrangement, cyclopropanation, and C-N bond formation with active methylene compounds. Previously, we revealed that 3-diazoavenalumic acid (3-DAA), which is potentially produced by several actinomycete species and contains an aromatic diazo group, is a biosynthetic intermediate of avenalumic acid. In this study, we aimed to construct a production system for phenyldiazene derivatives by adding several active methylene compounds to the culture of a 3-DAA-producing recombinant actinomycete. First, acetoacetanilide and its derivatives, which have an active methylene and are raw materials for arylide yellow dyes, were individually added to the culture of a 3-DAA-producing actinomycete. When their metabolites were analyzed, each expected compound with a phenyldiazenyl moiety was detected in the culture extract. Moreover, we established a one-pot in vitro enzymatic production system for the same phenyldiazene derivatives using a highly reactive diazotase, CmaA6. These results showed that the diazo group of natural products is an attractive tool for expanding the structural diversity of natural products both in vivo and in vitro.

Olivetolic acid (OA) is an essential precursor in the cannabinoid biosynthesis. It is produced through a unique interaction between the two proteins, olivetol synthase (CsOLS) and olivetolic acid cyclase (CsOAC). When the OA biosynthesis is transferred to Saccharomyces cerevisiae, olivetol (OL) is produced as a side product, even with a high enhancement of copy number of CsOAC. In order to increase the OA titer while decreasing the OL titer in S. cerevisiae, rational design was applied to CsOAC using in silico approaches such as protein-ligand docking to find potential protein variants. In vivo screening and also testing different approaches for both proteins was applied to identify the best performing variants of CsOAC. Four variants were identified that gave the desired properties. The best CsOAC variant, G82 A/L92Y, resulted in a 1.7-fold increase in OA production and a shift in the ratio between the two products towards OA.

Cancer has long been a significant threat to human life and health. The advent of immune checkpoint blockade strategies has reversed cancer-induced immune suppression, advanced the development of immunotherapy, and offered new hope in the fight against cancer. Aptamers, which possess the same specificity and affinity as antibodies, are advantageous due to their synthetic accessibility and ease of modification, providing novel insights for immune checkpoint research. In this review, we outline the key aptamers currently developed for immune checkpoints such as CTLA-4, PD-1, PD-L1 and Siglec-15. We explore their potential in therapeutic strategies, including functionalizing or engineering aptamers for covalent binding, valency control, and nanostructure assembly, as well as investigating molecular mechanisms such as glycosylated protein functions and cell-cell interactions. Finally, the future applications of aptamers in immunotherapy are discussed.

Isocyanates are versatile electrophiles that can react with a wide range of nucleophiles to afford important organic structures. Although the reactions between isocyanates and alcohols, amines and organometallic reagents have been well established, the synthesis of amides through the decarboxylative condensation of carboxylic acids and isocyanates is less appreciated. In this review, the synthesis of isocyanates and its application on amide synthesis through the condensation with carboxylic acids are summarized and discussed. It is our hope that this review will attract more attention to this less mentioned transformation and inspire new developments in the fields of organic synthesis, polymer synthesis and chemical biology.