Search Results (57)

COASY-related disorders (CRDs) are a spectrum of autosomal recessive conditions caused by the dysfunction of CoA synthase, an enzyme responsible for the final steps of CoA synthesis. Clinical manifestations of CRDs are highly variable, ranging from perinatal lethal pontocerebellar hypoplasia to childhood-onset neurodegenerative brain iron accumulation, which is often recognized after clinical regression. Recent reports have described a few individuals with CRD who screened positive for carnitine palmitoyltransferase-I deficiency by newborn screening (NBS). However, heterogeneous clinical presentations, conflicting biochemical/molecular sequencing of CPT1A, and a lack of metabolic characterization have led to lengthy, costly diagnostic journeys. To address some of these aspects, this investigation retrospectively evaluated NBS acylcarnitine patterns in five CRD cases using Collaborative Laboratory Integrated Reports (CLIR). A total of 25 metabolites/ratios were identified to deviate significantly from reference ranges and were primarily composed of elevated free carnitine and reduced long-chain acylcarnitine levels. While low acylcarnitine concentrations are often not reported due to a lack of lower reference cutoffs, ratios involving these metabolites relative to short-chain acylcarnitines could aid in identifying CRD cases via NBS. When comparing this pattern to CPT-Ia cases, we confirmed a nearly identical acylcarnitine pattern between these, and thus support the need to consider CRD in cases with NBS results suggestive of CPT-Ia. This study is the first case series to characterize NBS patterns in patients with CRD and highlights the unique opportunity for early detection, particularly in cases that are neonatally asymptomatic and have unremarkable confirmatory biochemical results. Full article

In order to understand the dynamic interaction process among species, enzymes, and metabolites during the fermentation process of Baobaoqu, which is a representative Daqu starter for Chinese baijiu, the intimate connection between the progression of microbial communities and the diversities and activities of enzymes was examined by metagenomics, metatranscriptomics and metaproteomics. It was found that while 5211 species of microorganisms were detected by metagenomics, only 1774 active species were detected by metatranscriptomics, which indicated that only a small proportion (34.04%) were active. The metabolic routes associated with the breakdown of substrates and synthesis of metabolites were redesigned, and the special functional microorganisms for lactate, pyrazines and phenylethyl alcohol production were isolated. It was found that the progression of the microbial community was highly coupled with the components of enzymes and flavor substrates, precisely corresponding to the three stages of the Baobaoqu fermentation process, and were regulated by multiple physical factors. During the Baobaoqu-making process of the fermentation, microorganisms with different functions work together to complete metabolism in different stages. These findings will aid us in gaining a deeper and clearer understanding of the “species–enzyme–metabolite” system within the Daqu starter culture, thus offering valuable perspectives for developing artificial synthetic communities and the production of high-quality Baobaoqu. Full article

Thiamine (vitamin B1) is key in maintaining cellular health and energy metabolism. Thiamine is required for proper functioning of enzymes involved in glucose metabolism, which is critical for providing energy to cells. This energy is essential for various cellular processes, including DNA repair mechanisms. In addition, it is a prerequisite for the functioning of key enzymes in the biosynthesis of pentose sugars, which are essential in the synthesis of nucleic acids. Additionally, thiamine has antioxidant properties that help reduce oxidative stress in cells; thus, by relieving this stress, thiamine indirectly supports the maintenance of DNA integrity. Ensuring adequate thiamine intake through diet or supplements can support overall cellular health and potentially aid in DNA repair processes. This review aims to highlight the essential role of vitamin B1 in supporting metabolic health, especially given that deficiencies can develop in patients with disease-related malnutrition as well as in those with an inadequate diet. Full article

Enzymes, as nature’s precision biocatalysts, hold transformative potential across industrial, environmental, and biomedical sectors. However, their instability, solvent sensitivity, and limited reusability in their free form necessitate advanced immobilization strategies to enhance their robustness and scalability. This review critically examines cutting-edge advancements in enzyme immobilization, focusing on the integration of artificial intelligence (AI), novel nanomaterials, and dynamic carrier systems to overcome the traditional limitations of mass transfer, enzyme leakage, and cost inefficiency. Key innovations such as metal–organic frameworks (MOFs), magnetic nanoparticles, self-healing hydrogels, and 3D-printed scaffolds are highlighted for their ability to optimize enzyme orientation, stability, and catalytic efficiency under extreme conditions. Moreover, AI-driven predictive modeling and machine learning emerge as pivotal tools for rationalizing nanomaterial synthesis, multi-enzyme cascade design, and toxicity assessment, while microfluidic systems enable precise biocatalyst fabrication. This review also explores emerging carrier-free strategies, including cross-linked enzyme aggregates (CLEAs) and DNA-directed immobilization, which minimize diffusion barriers and enhance substrate affinity. Despite progress, challenges persist in regards to eco-friendly nanomaterial production, industrial scalability, and real-world application viability. Future directions emphasize sustainable hybrid material design, AI-aided lifecycle assessments, and interdisciplinary synergies between synthetic biology, nanotechnology, and data analytics. By connecting laboratory innovation with industrial needs, this work provides a forward-thinking framework to harness immobilized enzymes for achieving global sustainability goals, particularly in bioremediation, bioenergy, and precision medicine. Full article

This study employed shotgun metagenomics to investigate microbial dynamics, phage-bacteria interactions, and functional genes throughout a three-month apple vinegar fermentation process. A total of 5621 microbial species were identified, revealing three distinct phases: (i) Enterobacteria and non-Saccharomyces species dominated the initial substrate; (ii) S. cerevisiae and Leuconostoc pseudomesenteroides prevailed in the intermediate phase; and (iii) acetic acid bacteria (Acetobacter ghanesis and Gluconobacter spp.), alongside non-Saccharomyces species (Pichia kudriavzevii and Malassezia restricta), dominated the final stages. Bacteriophage analysis revealed the presence of phages targeting spoilage bacteria, such as Pseudomonas and Erwinia, suggesting a role in regulating microbial stability and enhancing fermentation control. Functional metagenomic analysis highlighted key pathways associated with microbial growth and metabolite production, including carbohydrate and amino acid metabolism, energy production, and glycan biosynthesis. Enzymes involved in stress adaptation and secondary metabolism, including oxidative phosphorylation and phenolic compound synthesis, demonstrated microbial resilience and their potential role in shaping the product’s sensory and functional properties. Moreover, Enterobacteriaceae species were associated with pectin degradation during the early stages, aiding substrate breakdown. These findings are crucial for microbial and phage management in fermentation technology, offering valuable insights for innovation in the vinegar industry. Full article

Autism spectrum disorder (ASD) is a genetically heterogeneous syndrome characterized by repetitive, restricted, and stereotyped behaviors, along with persistent difficulties with social interaction and communication. Despite its increasing prevalence globally, the underlying pathogenic mechanisms of this complex neurodevelopmental disorder remain poorly understood. Therefore, the identification of reliable biomarkers could play a crucial role in enabling early screening and more precise classification of ASD subtypes, offering valuable insights into its physiopathology and aiding the customization of treatment or early interventions. Biogenic amines, including serotonin, histamine, dopamine, epinephrine, norepinephrine, and polyamines, are a class of organic compounds mainly produced by the decarboxylation of amino acids. A substantial portion of the genetic variation observed in ASD has been linked to genes that are either directly or indirectly involved in the metabolism of biogenic amines. Their potential involvement in ASD has become an area of growing interest due to their pleiotropic activities in the central nervous system, where they act as both neurotransmitters and neuromodulators or hormones. This review examines the role of biogenic amines in ASD, with a particular focus on genetic alterations in the enzymes responsible for their synthesis and degradation. Full article

Background: Ischemic heart disease remains the leading cause of death worldwide, with coronary microvascular dysfunction (CMD) as a key complication after ST-elevation myocardial infarction (STEMI). Endothelial dysfunction contributes to CMD, impairing vascular tone and increasing inflammation. While angiotensin-converting enzyme (ACE) inhibitors and angiotensin II receptor blockers (ARBs) aid vascular health, their efficacy may improve with therapeutic ultrasound, which enhances drug delivery and endothelial response. This study explores the combined effects of ultrasound and pharmacological treatment on the ACE axis and inflammation in endothelial and renal cells. Methods: Human umbilical vein endothelial cells (HUVECs) and human renal proximal tubular epithelial cell line RPTEC/TERT1 were treated with captopril, losartan, and dexamethasone, alone or combined with low-frequency ultrasound (LFU). Cell viability and wound-healing assays assessed cellular function, while nitric oxide (NO) and reactive oxygen species (ROS) assays were used to evaluate redox signaling. Gene expression related to the ACE axis, inflammation, and vascular and renal cell function was analyzed via qPCR. Results: Captopril and losartan combined with LFU improved endothelial cell viability, wound healing, and NO production at various concentrations, whereas only losartan with LFU enhanced cell viability and wound healing in renal cells. Dexamethasone with LFU increased ROS levels and had variable effects on RPTEC/TERT1 cell survival. Gene expression analysis showed that LFU alone reduced pro-inflammatory markers VCAM-1, ICAM-1, and PTGS2 in captopril-treated HUVECs and similarly affected CYP4F2 in losartan-treated HUVECs. LFU also decreased PTGS2 expression at higher dexamethasone concentrations. In RPTEC/TERT1 cells, LFU alone did not impact SGLT2 or GGT1 expression, but captopril with LFU downregulated GGT1, and dexamethasone with LFU upregulated SGLT2 at higher concentrations. Conclusions: This study demonstrates that LFU enhances the effects of RAS inhibitors by promoting NO synthesis and reducing oxidative stress, while its combination with dexamethasone may have variable, potentially cytotoxic effects on renal cells. Gene expression patterns suggest LFU’s anti-inflammatory potential and its role in modulating drug efficacy. Full article

This study aims to design improved inhibitors targeting the thymidylate kinase (TMK) of Mycobacterium tuberculosis (Mtb), the causative agent of infectious disease tuberculosis that is associated with high morbidity and mortality in developing countries. TMK is an essential enzyme for the synthesis of bacterial DNA. We have performed computer-aided molecular design of MtbTMK inhibitors by modification of the reference crystal structures of the lead micromolar inhibitor TKI1 1-(1-((4-(3-Chlorophenoxy)quinolin-2-yl)methyl)piperidin-4-yl)-5-methylpyrimidine-2,4(1H,3H)-dione bound to TMK of Mtb strain H37Rv (PDB entries: 5NRN and 5NR7) using the computational approach MM-PBSA. A QSAR model was prepared for a training set of 31 MtbTMK inhibitors with published inhibitory potencies (${\mathrm{I}\mathrm{C}}_{50}^{\mathrm{e}\mathrm{x}\mathrm{p}}$) and showed a significant correlation between the calculated relative Gibbs free energies of the MtbTMK–TKIx complex formation and the observed potencies. This model was able to explain approximately 95% of the variation in the in vitro inhibition data and validated our molecular model of MtbTMK inhibition for the subsequent design of new TKI analogs. Furthermore, we have confirmed the predictive capacity of this complexation QSAR model by generating a 3D QSAR PH4 pharmacophore-based model. A satisfactory correlation was also obtained for the validation PH4 model of MtbTMK inhibition (R² = 0.84). We have extended the hydrophobic m-chloro-phenoxyquinolin-2-yl group of TKI1 that can occupy the entry into the thymidine binding cleft of MtbTMK by alternative larger hydrophobic groups. Analysis of residue interactions at the enzyme binding site made it possible to select suitable building blocks to be used in the preparation of a virtual combinatorial library of 28,900 analogs of TKI1. Structural information derived from the complexation model and the PH4 pharmacophore guided the in silico screening of the library of analogs and led to the identification of new potential MtbTMK inhibitors that were predicted to be effective in the low nanomolar concentration range. The QSAR complexation model predicted an inhibitory concentration ${\mathrm{I}\mathrm{C}}_{50}^{\mathrm{p}\mathrm{r}\mathrm{e}}$ of 9.5 nM for the best new virtual inhibitor candidate TKI 13_1, which represents a significant improvement in estimated inhibitory potency compared to TKI1. Finally, the stability of the MtbTMK–inhibitor complexes and the flexibility of the active conformation of the inhibitors were assessed by molecular dynamics for five top-ranking analogs. This computational study resulted in the discovery of new MtbTMK inhibitors with predicted enhanced inhibitory potencies, which also showed favorable predicted pharmacokinetic profiles. Full article

Phallus echinovolvatus is a well-known edible and medicinal fungus with significant economic value. However, the available whole-genome information is lacking for this species. The chromosome-scale reference genome (Monop) and two haploid genomes (Hap1 and Hap2) of P. echinovolvatus, each assembled into 11 pseudochromosomes, were constructed using Illumina, PacBio-HiFi long-read sequencing, and Hi-C technology. The Monop had a size of 36.54 Mb, with 10,251 predicted protein-coding genes and including 433 carbohydrate-active enzyme genes, 385 cytochrome P450 enzyme genes, and 42 gene clusters related to secondary metabolite synthesis. Phylogenetic and collinearity analysis revealed a close evolutionary relationship between P. echinovolvatus and Clathrus columnatus in the core Phallales clade. Hap1 and Hap2 had sizes of 35.46 Mb and 36.11 Mb, respectively. Collinear relationships were not observed for 15.38% of the genes in the two haplotypes. Hap1 had 256 unique genes, and Hap2 had 370 unique genes. Our analysis of the P. echinovolvatus genome provides insights into the genetic basis of the mechanisms underlying the metabolic effects of bioactive substances and will aid ongoing breeding efforts and studies of genetic mechanisms. Full article

Dextran is an exopolysaccharide (EPS) with multifunctional applications in the food and pharmaceutical industries, primarily synthesized from Leuconostoc mesenteroides. Dextran can be produced from dextrin through Gluconobacter oxydans fermentation, utilizing its dextran dextrinase activity. This study examined how jar fermentor conditions impact the growth and enzyme activity of G. oxydans, with a focus on the effects of pH on dextran synthesis via bioconversion (without pH control, pH 4.5, and pH 5.0; Jp-UC, Jp-4.5, and Jp-5.0). After 72 h, the cell density (O.D. at 600 nm) was 7.2 for Jp-4.5, 6.5 for Jp-5.0, and 3.7 for Jp-UC. Flow property analysis, indicating dextran production, showed that Jp-4.5 had the highest viscosity (30.99 mPa·s). ¹H-NMR analysis confirmed the formation of α-1,6 glycosidic bonds in bioconversion products, with bond ratios ranging from ~1:0.17 to ~1:2.84. The distribution of molecular weights varied from 1.3 × 10³ Da to 5.1 × 10⁴ Da depending on pH. The hydrolysis rates to glucose differed with pH, with the slowest rate at pH 4.5 (53.96%). These results suggest that the production of dextran by G. oxydans is significantly influenced by the pH conditions. This dextran could function as a slowly digestible carbohydrate, aiding in postprandial glycemic regulation and mitigating chronic metabolic diseases like diabetes. Full article

The formation of atroposelective biaryl compounds in plants and fungi is well understood; however, polyketide aglycone synthesis and dimerization in bacteria remain unclear. Thus, the biosynthetic gene cluster (BGC) responsible for antibacterial setomimycin production from Streptomyces nojiriensis JCM3382 was examined in comparison with the BGCs of spectomycin, julichromes, lincolnenins, and huanglongmycin. The setomimycin BGC includes post-polyketide synthase (PKS) assembly/cycling enzymes StmD (C-9 ketoreductase), StmE (aromatase), and StmF (thioesterase) as key components. The heterodimeric TcmI-like cyclases StmH and StmK are proposed to aid in forming the setomimycin monomer. In addition, StmI (P-450) is predicted to catalyze the biaryl coupling of two monomeric setomimycin units, with StmM (ferredoxin) specific to the setomimycin BGC. The roles of StmL and StmN, part of the nuclear transport factor 2 (NTF-2)-like protein family and unique to setomimycin BGCs, could particularly interest biochemists and combinatorial biologists. α-Glucosidase, a key enzyme in type 2 diabetes, hydrolyzes carbohydrates into glucose, thereby elevating blood glucose levels. This study aimed to assess the α-glucosidase inhibitory activity of EtOAc extracts of JCM 3382 and setomimycin. The JCM 3382 EtOAc extract and setomimycin exhibited greater potency than the standard inhibitor, acarbose, with IC₅₀ values of 285.14 ± 2.04 μg/mL and 231.26 ± 0.41 μM, respectively. Molecular docking demonstrated two hydrogen bonds with maltase-glucoamylase chain A residues Thr205 and Lys480 (binding energy = −6.8 kcal·mol⁻¹), two π–π interactions with Trp406 and Phe450, and one π–cation interaction with Asp542. Residue-energy analysis highlighted Trp406 and Phe450 as key in setomimycin’s binding to maltase-glucoamylase. These findings suggest that setomimycin is a promising candidate for further enzymological research and potential antidiabetic therapy. Full article

Silver nanoparticles have unique physical, chemical, and biological properties that make them attractive for medical applications. They have gained attention in dentistry for their potential use in caries management. This study reviews the different synthesis methods of silver nanoparticles and the application of them for caries management. Silver nanoparticles are tiny silver and are typically less than 100 nanometres in size. They have a high surface area-to-volume ratio, making them highly reactive and allowing them to interact with bacteria and other materials at the molecular level. Silver nanoparticles have low toxicity and biocompatibility. Researchers have employed various methods to synthesise silver nanoparticles, including chemical, physical, and biological methods. By controlling the process, silver nanoparticles have defined sizes, shapes, and surface properties for wide use. Silver nanoparticles exhibit strong antibacterial properties, capable of inhibiting a broad range of bacteria, including antibiotic-resistant strains. They inhibit the growth of cariogenic bacteria, such as Streptococcus mutans. They can disrupt bacterial cell membranes, interfere with enzyme activity, and inhibit bacterial replication. Silver nanoparticles can inhibit biofilm formation, reducing the risk of caries development. Additionally, nano silver fluoride prevents dental caries by promoting tooth remineralisation. They can interact with the tooth structure and enhance the deposition of hydroxyapatite, aiding in repairing early-stage carious lesions. Silver nanoparticles can also be incorporated into dental restorative materials such as composite resins and glass ionomer cements. The incorporation can enhance the material’s antibacterial properties, reducing the risk of secondary caries and improving the longevity of the restoration. Full article

This study explores the reasons behind the variations in the enantioselectivity of the sulfoxidation of methyl phenyl sulfide by marine-derived vanadium-dependent haloperoxidases (VHPOs). Twelve new VHPOs of marine organisms were overexpressed, purified, and tested for their ability to oxidize sulfide. Most of these marine enzymes exhibited nonenantioselective behavior, underscoring the uniqueness of AnVBPO from the brown seaweed Ascophyllum nodosum and CpVBPO from the red seaweed Corallina pilulifera, which produce (R)- and (S)-sulfoxides, respectively. The enantioselective sulfoxidation pathway is likely due to direct oxygen transfer within the VHPO active site. This was demonstrated through molecular docking and molecular dynamics simulations, which revealed differences in the positioning of sulfide within AnVBPO and CpVBPO, thus explaining their distinct enantioselectivities. Nonenantioselective VHPOs probably follow a different oxidation pathway, initiating with sulfide oxidation to form a positively charged radical. Further insights were gained from studying the catalytic effect of VO₄³⁻ on H₂O₂-driven sulfoxidation. This research improves the understanding of VHPO-mediated sulfoxidation and aids in developing biocatalysts for sulfoxide synthesis. Full article

Antibiotic resistance is a major problem and a major global health concern. In total, there are 16 million deaths yearly from infectious diseases, and at least 65% of infectious diseases are caused by microbial communities that proliferate through the formation of biofilms. Antibiotic overuse has resulted in the evolution of multidrug-resistant (MDR) microbial strains. As a result, there is now much more interest in non-antibiotic therapies for bacterial infections. Among these revolutionary, non-traditional medications is quorum sensing inhibitors (QSIs). Bacterial cell-to-cell communication is known as quorum sensing (QS), and it is mediated by tiny diffusible signaling molecules known as autoinducers (AIs). QS is dependent on the density of the bacterial population. QS is used by Gram-negative and Gram-positive bacteria to control a wide range of processes; in both scenarios, QS entails the synthesis, identification, and reaction to signaling chemicals, also known as auto-inducers. Since the usual processes regulated by QS are the expression of virulence factors and the creation of biofilms, QS is being investigated as an alternative solution to antibiotic resistance. Consequently, the use of QS-inhibiting agents, such as QSIs and quorum quenching (QQ) enzymes, to interfere with QS seems like a good strategy to prevent bacterial infections. This review sheds light on QS inhibition strategy and mechanisms and discusses how using this approach can aid in winning the battle against resistant bacteria. Full article

Cytochrome P450 (CYP450) is a group of enzymes that play an essential role in Phase I metabolism, with 57 functional genes classified into 18 families in the human genome, of which the CYP1, CYP2, and CYP3 families are prominent. Beyond drug metabolism, CYP enzymes metabolize endogenous compounds such as lipids, proteins, and hormones to maintain physiological homeostasis. Thus, dysregulation of CYP450 enzymes can lead to different endocrine disorders. Moreover, CYP450 enzymes significantly contribute to fatty acid metabolism, cholesterol synthesis, and bile acid biosynthesis, impacting cellular physiology and disease pathogenesis. Their diverse functions emphasize their therapeutic potential in managing hypercholesterolemia and neurodegenerative diseases. Additionally, CYP450 enzymes are implicated in the onset and development of illnesses such as cancer, influencing chemotherapy outcomes. Assessment of CYP450 enzyme expression and activity aids in evaluating liver health state and differentiating between liver diseases, guiding therapeutic decisions, and optimizing drug efficacy. Understanding the roles of CYP450 enzymes and the clinical effect of their genetic polymorphisms is crucial for developing personalized therapeutic strategies and enhancing drug responses in diverse patient populations. Full article