ChemBioChem最新文献

The last decade has witnessed tremendous progress in the field of biocatalysis. One of the most frequently utilized enzymes in diverse biocatalytic applications is NAD(P)-dependent glucose dehydrogenases (GDHs). Traditionally, these enzymes are employed for their role in regenerating NAD(P)H in various enzymatic reactions utilizing glucose. However, recent studies have expanded the scope of GDHs beyond cofactor regeneration, highlighting their potential as biocatalysts in diverse chemical transformations. GDHs have demonstrated versatility in catalyzing key reactions in the synthesis of various drug molecules and intermediates, including ketone reduction to produce alcohols, imine reduction of C=N bonds to yield amines, reduction of aldehydes to alcohols, and dehydrogenation of cyclohexanol derivatives. This review highlights recent advancements in elucidating the multifunctional roles of NAD(P)-dependent glucose dehydrogenases (GDHs) in biocatalysis, with an emphasis on their growing applications and significant potential in small molecule synthesis.

Beyond the pivotal genetic roles of DNA, its duplex structures as chiral scaffolds interacting with metal complexes give rise to DNA hybrid catalysts for a set of aqueous-phase enantioselective reactions. Besides DNA duplex, DNA quadruplexes including G-quadruplex and i-motif show tunable structures with variable non-canonical base pairs. In this concept, based on the interaction between metal species and DNA, we classify the construction strategies of quadruplex DNA hybrid catalysts into supramolecular, covalent and coordinative modes. Furthermore, we analyze the relationship between DNA quadruplexes and their enantioselective catalytic performance. Finally, we summarize the current challenges and look forward to the future directions in DNA-based enantioselective catalysis.

Conjugation of ubiquitin (Ub) and structurally related ubiquitin-like proteins (Ubls), essential for many cellular processes, employs multi-step reactions orchestrated by specific E1, E2 and E3 enzymes. The E1 enzyme activates the Ub/Ubl C-terminus in an ATP-dependent process that results in the formation of a thioester linkage with the E1 active site cysteine. The thioester-activated Ub/Ubl is transferred to the active site of an E2 enzyme which then interacts with an E3 enzyme to promote conjugation to the target substrate. The E1-E2-E3 enzymatic cascades utilize labile intermediates, extensive conformational changes, and vast combinatorial diversity of short-lived protein-protein complexes to conjugate Ub/Ubl to various substrates in a regulated manner. In this review, we discuss various chemical tools and methods used to study the consecutive steps of Ub/Ubl activation and conjugation, which are often too elusive for direct studies. We focus on methods developed to probe enzymatic activities and capture and characterize stable mimics of the transient intermediates and transition states, thereby providing insights into fundamental mechanisms in the Ub/Ubl conjugation pathways.

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.

An increasingly effective strategy to identify synthetically useful enzymes is to sample the diversity already present in Nature. Here, we construct and assay a panel of phylogenetically diverse aromatic prenyltransferases (PTs). These enzymes catalyze a variety of C-C bond forming reactions in natural product biosynthesis and are emerging as tools for synthetic chemistry and biology. Homolog screening was further empowered through substrate-multiplexed screening, which provides direct information on enzyme specificity. We perform a head-to-head assessment of the model members of the PT family and further identify homologs with divergent sequences that rival these superb enzymes. This effort revealed the first bacterial O-Tyr PT and, together, provide valuable benchmarking for future synthetic applications of PTs.

Diabetes is a metabolic disorder characterized by insufficient endogenous insulin production or impaired sensitivity to insulin. In recent years, a class of incretin-based hypoglycemic drugs, glucagon-like peptide-1 receptor agonists (GLP-1RAs), have attracted great attention in the management of type 2 diabetes mellitus (T2DM) due to their benefits, including stable glycemic control ability, a low risk of hypoglycemia, and weight reduction for patients. However, like other peptide drugs, GLP-1RAs face challenges such as instability, susceptibility to enzymatic degradation, and immunogenicity, which severely limit their clinical application. In recent years, various strategies have been developed to improve the bioavailability and therapeutic efficacy of GLP-1RAs, including structural modification and carrier-mediated delivery. This article briefly introduces the research and application status of several common GLP-1RAs and their limitations. Taking exendin-4 as an example, we focus on the research progress of improving bioavailability and therapeutic efficacy based on structural modification and carrier delivery strategies, aiming to provide reference for the development of new GLP-1RAs treatment systems.

Metal complexes activated by light can combat infections by triggering the photodynamic inactivation of bacteria. Herein, we report six mixed-ligand nickel(II) complexes with the formulation [Ni(NN)₂(L)] (1-6), where NN represents an N,N-donor phenanthroline ligand, specifically 1,10-phenanthroline (phen in 1, 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 3, 4), and dipyrido[3,2-a:2',3'-c]phenazine (dppz in 5, 6), while L is an O,O donor bidentate ligand derived from catechol (cat^2-, in 1, 3, 5) or esculetin (esc^2-, in 2, 4, 6). The paramagnetic d⁸ octahedral complexes demonstrated good dark and photostability in the solution phase and exhibited significant light absorption in the visible (400-700 nm) region. When exposed to low-energy visible light, these complexes demonstrated significant photodynamic inactivation activity against both Gram-(+) Staphylococcus aureus (S. aureus) and Gram-(-) Escherichia coli (E. coli) bacteria. This resulted in minimum inhibitory concentration (MIC) values ranging from 0.31-9.49 μM. The activity was caused by the cell-damaging singlet oxygen species produced by the complexes under light exposure. Notably, the complexes showed no bacterial inhibition activity under dark conditions. This study marks the first examples of Ni(II) complexes designed for light-triggered antibacterial activity, illuminating the path for Ni(II)-based non-macrocyclic complexes for antibacterial PDT applications.

Alpha-helical membrane proteins perform numerous critical functions essential for the survival of living organisms. Traditionally, these proteins are extracted from membranes using detergent solubilization and reconstitution into liposomes or nanodiscs. However, these processes often obscure the effects of nanoconfinement and the native environment on the structure and conformational heterogeneity of the target protein. We demonstrate that pulsed dipolar electron spin resonance spectroscopy, combined with the Gd³⁺-nitroxide spin pair, enables the selective observation of the vitamin B₁₂ importer BtuCD-F in its native cellular envelope. Despite the high levels of non-specific labeling in the envelope, this orthogonal approach combined with the long phase-memory time for the Gd³⁺ spin enables the observation of the target protein complex at a few micromolar concentrations with high resolution. In the native envelope, vitamin B₁₂ induces a distinct conformational shift at the BtuCD-BtuF interface, which is not observed in the micelles. This approach offers a general strategy for investigating protein-protein and protein-ligand/drug interactions and conformational changes of the alpha-helical membrane proteins in their native envelope context.

This study aims to investigate the potential role of antioxidants in oxidative stress and its consequent impact on the mechanical properties of neuronal cells, particularly the stress induced by amyloid-beta (1-42) (Aβ₄₂) aggregates. A key aspect of our research involved using scanning ion-conductance microscopy (SICM) to assess the mechanical properties (Young's modulus) of neuronal cells under oxidative stress. Reactive oxygen species (ROS) level was measured in single-cell using the electrochemical method by low-invasive Pt nanoelectrode. We investigated the effects of the low molecular weight antioxidant N-acetylcysteine (NAC) and the antioxidant enzyme superoxide dismutase 1 (SOD1) on the physiological and mechanical properties of neuronal cells using SICM. Using electrochemical method and SICM, NAC effectively reduces oxidative stress and restores Young's Modulus in SH-SY5Y cells exposed to hydrogen peroxide and Aβ₄₂ oligomers. Our study first examined the influence of SOD1 on intracellular ROS levels in the presence of Aβ oligomers. The investigation into the effects of SOD1 and its nanoparticle form SOD1 on SH-SY5Y cells reveals impacts on mechanical properties and oxidative stress. The combined use of SICM and electrochemical measurements provided a comprehensive understanding of how oxidative stress, including that triggered by the Aβ oligomers affects the mechanical properties of cells.

Glycosphingolipids (GSL) are functionally important components of the cell membrane and recognition of their glycan "head" by the immune system is a key part of normal and pathological processes. Recognition of glycolipid antigens on a living cell, their structure, "context" (microenvironment and clustering), presentation including orientation and distance from the plasma membrane, as well as molecular dynamics are important. GSL antigens are targets for the development of anticancer vaccines and therapeutic antibodies, therefore, control of the presentation of their glycans by synthetic methods opens up new possibilities in medicine. In this work, we synthesized 13 GSL analogues as function-spacer-lipids (FSLs) with the same head (blood group A tetrasaccharide, ABO system) but each either differing in the structure of the lipid tail, or the length of the region between the head and the tail, or cluster organization of the head (from 2 to 4 tetrasaccharides in a cluster). The insertion of these FSLs into an artificial and erythrocyte membranes was compared, and their interaction with antibodies was studied, including erythrocyte agglutination. The results give further insight into knowledge of the membrane presentation of GSLs (some results can be extrapolated to glycoproteins) and factors involved in their interaction with antibodies.