ChemBioChem最新文献

Heme is involved in many critical processes in pathogenic bacteria as iron acquisition by these microorganisms is achieved by either direct uptake of heme or use of heme-binding proteins called hemophores. Exploring the underlying mechanisms on a molecular level can open new avenues in understanding the host-pathogen interactions. Any imbalance of the heme concentration has a direct impact on the bacterial growth and survival. Thus, heme-regulated proteins that are involved in heme homeostasis poise to be promising targets for research. Similarly, naturally occurring compounds, including cysteine-rich peptides from either plant secondary metabolites or venom toxins from vertebrates and invertebrates, have been studied for their therapeutic potential. NCR247 is such a cysteine-rich peptide, known to be crucial for nitrogenase activity in M. truncatula and its symbiotic relation with S. meliloti. NCR247-derived peptides were suggested to serve as high-affinity heme-binding molecules with remarkable heme-capturing properties. A comprehensive biochemical and computational analysis of NCR247-derived peptides, however, redefines their heme-binding capacity and consequently their potential therapeutic role.

Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by pruritus and impaired skin barrier function. Advances in drug delivery systems have transformed AD treatment by enhancing drug stability, bioavailability, and targeted delivery. Drug delivery systems such as liposomes, hydrogels, and microneedles enable deeper skin penetration, prolonged drug retention, and controlled release, reducing side effects and treatment frequency. Liposomes improve drug absorption and stability, while hydrogels offer high water content and responsive drug release. Microneedles facilitate painless, localized drug delivery, enhancing patient compliance. These systems address the limitations of traditional therapies like topical corticosteroids and systemic immunosuppressants, which are associated with adverse effects and poor patient adherence. Recent innovations include Janus kinase (JAK) inhibitors and biologics targeting immune pathways, demonstrating significant efficacy in reducing inflammation and symptoms. Drug delivery systems offer a safer, more efficient alternative for delivering these advanced therapies. By improving therapeutic outcomes and patient experience, drug delivery systems represent a crucial advancement in AD management.

RNA exhibits remarkable capacity as a functional polymer, with broader catalytic and ligand-binding capability than previously thought. Despite this, the low side chain diversity present in nucleic acids (two purines and two pyrimidines) relative to proteins (20+ side chains of varied charge, polarity, and chemical functionality) limits the capacity of functional RNAs to act as environmentally responsive polymers, as is possible for peptide-based receptors and catalysts. Here we show that incorporation of the modified nucleobase 2-thiouridine (2sU) into functional (aptamer and ribozyme) RNAs produces functionally inactivated polymers that can be activated by oxidative treatment. 2-thiouridine lacksthe 2-position oxygen found in uridine, altering its hydrogen bonding pattern. This limits critical interactions (e. g., G-U wobble pairs) that allow for proper folding. Oxidative desulfurization of the incorporated 2-thiouridine moieties to uridine relieves this inability to fold properly, enabling recovery of function. This demonstration of expanded roles for RNA as environmentally responsive functional polymers challenges the notion that they are not known to be redox-sensitive. Harnessing redox switchability in RNA could regulate cellular activities such as translation, or allow switching RNA between a "template" and a "catalytic" state in "RNA World" scenarios or in synthetic biology.

Adeno-associated virus (AAV) has emerged as a powerful and effective tool for the delivery of exogenous genes into various cells or tissues. To improve the gene delivery efficiency, as well as the safety and specificity of AAV's cell-targeting capabilities, extensive investigations have been conducted into its molecular biological characteristics, including capsid structure, cellular tropism, and the mechanisms underlying its entry, replication, DNA packaging, and capsid assembly. Significant differences exist between human and non-human primate AAVs regarding tissue targeting and transduction efficiency. These differences are primarily attributed to the amino acid sequences of AAV capsid proteins, the structural characteristics of these proteins, and the interactions of AAV with surface factors on host cells, such as cell surface receptors, signaling molecules, and associated proteins. This review primarily focuses on several key aspects of AAV, including its genome, coat proteins and their structures, genome replication, virus assembly, and the role of helper viruses. Additionally, it examines the utilization of recombinant adeno-associated viruses (rAAV), detailing their production methods, mechanisms of cell entry and trafficking, and various serotypes. The review further interprets the role of rAAV by analyzing its current applications in research and therapy.

The threat posed by bacteria resistant to common antibiotics creates an urgent need for novel antimicrobials. Non-ribosomal peptide natural products that bind Lipid II, such as vancomycin, represent a promising source for such agents. The fungal defensin plectasin is one of a family of ribosomally produced miniproteins that also exert antimicrobial activity via Lipid II binding. Made up entirely of canonical amino acids, these molecules are potentially more susceptible to degradation by protease enzymes than non-ribosomal counterparts. Here, we report the development of proteomimetic variants of plectasin through the systematic incorporation of artificial backbone connectivity in the domain. An iterative secondary-structure-based design scheme yields a variant with a tertiary fold indistinguishable from the prototype natural product, potent activity against Gram positive bacteria, and low mammalian cell toxicity. Backbone modification is shown to improve oxidative folding efficiency of the disulfide-rich scaffold as well as resistance to proteolytic hydrolysis. These results broaden the scope of design strategies toward protein mimetics as well as folds and biological functions possible in such agents.

The heme enzymes of the cytochrome P450 superfamily (CYPs) catalyse the selective hydroxylation of unactivated C-H bonds in organic molecules. There is great interest in applying these enzymes as biocatalysts with a focus on self-sufficient CYP 'fusion' enzymes, comprising a single polypeptide chain with the electron transfer components joined to the heme domain. Here we elucidate the function of the self-sufficient CYP116B46 fusion enzyme, from the thermophilic bacterium Tepidiphilus thermophilus. We demonstrate that it efficiently hydroxylates aromatic organic acids, exemplified by oxidation of 2-hydroxyphenylacetic acid to homogentisic acid (2,5-dihydroxyphenylacetic acid), an important metabolite in bacterial catabolism. In line with the thermophilic nature of the source bacterium, activity increased at higher temperatures, (50 °C), with a catalytic preference for NADPH over NADH. While self-sufficient fusion enzymes simplify biocatalysis; engineered peroxygenase activity is also a key advance in the application of these enzymes as biocatalysts as it eliminates the need for electron transfer partner proteins and nicotinamide cofactors. We demonstrate that a T278E mutation in the heme domain of CYP116B46, confers peroxygenase activity. This engineered peroxygenase enzyme is stable to elevated temperatures and catalytic concentrations of hydrogen peroxide, with an observed optimal activity resulting in a total turnover number of ~650.

Protein degradation is pivotal for all biochemical aspects of cellular function. In mammalian cells, protein degradation is mediated mainly by the ubiquitin proteasome system (UPS) and the autophagic-lysosomal system (ALS). Over the last two decades, different types of targeted protein degradation approaches have been developed including proteolysis targeting chimeras (PROTACs) and lysosome targeting chimeras (LYTACs), which employ the UPS to degrade intracellular proteins and the ALS to degrade extracellular and membrane proteins respectively. Nevertheless, Current targeted membrane protein degradation approaches face some inherent challenges including limited target protein degradation efficacy and cell type specific applicability. Herein, we highlight some recent developments of novel targeted membrane protein degradation modalities that exhibit wide-applicability and high protein degradation efficiency. These novel membrane protein degraders hold tremendous promise as new pharmacological and biochemical tools in targeting membrane and secretory proteins for lysosomal degradation.

Smart shape-memory DNA hydrogels, which can respond to various types of external stimuli and undergo macroscopic shape deformations, have shown great potential in various applications. By constructing free-standing films, the deformation and response properties of these hydrogels can be further enhanced, and visualized deformation can be achieved. However, DNA hydrogels that can exhibit rapid and high-degree shape deformations, such as the inverse shape deformations, are still lacking. Herein, free-standing oligoadenine strand-functionalized polyacrylamide hydrogel films were developed that can exhibit reversible and high degree of inverse shape deformation upon cyclic pH changes. The oligoadenine strands exhibit a pH-stimulated reversible conformational transition between a flexible single-stranded state and parallel duplex A-motif structures, resulting in their role change in the film from negatively charged side chains to "head-to-head" crosslinking structures, driving a high degree of inverse shape deformation with a relative bending angle change of 223.7 % of the film, which is more than 5 times that of a film driven by pH-responsive i-motif structures, facilitating the development of bilayer hydrogel film actuators with potential in flexible sensors and robots.

The cover image shows interactions of polypyridyl-Zn(II)-curcumin complexes with key SARS-CoV-2 viral proteins, including spike protein, Angiotensin-converting enzyme II, nucleocapsid protein, main protease protein, and RNA-dependent RNA polymerase protein. These findings indicates possible applications of polypyridyl-Zn(II)-curcumin complexes as anti SARS-CoV-2 agents. More details can be found in article 10.1002/cbic.202400612 by Samya Banerjee and co-workers.

The front cover shows the structure of lipase A from Candida antarctica with auroras in the background. Like this light display of Nature in the sky, enzymes sometimes unfold their power in unexpected forms, thus enriching the scope of applications. By engineering the active site, the catalytic properties of the lipase can be further improved so that the enzyme begins its infinite journey through space and time typified by the enantioselective esterification of (R)-tertiary alcohols, which has been difficult to achieve. More details can be found in article 10.1002/cbic.202400082 by Shuji Akai, Harald Gröger, and co-workers.