BioChem

Optical coherence tomography (OCT) phantoms are essential tools for calibrating imaging systems, validating diagnostic algorithms, and bridging technological advancements with clinical applications. This review explores the development and application of materials used in OCT phantoms, emphasising their optical, mechanical, and biochemical fidelity to biological tissues. Gelatin-based phantoms (n = 1.35) offer controllable absorbance and scattering, with penetration depths (PDs) of 500–2000 µm and scattering coefficients (SCs) of 5–20 cm⁻¹ but are unstable at room temperature. Silicone phantoms (n = 1.41) are durable and stable, with SCs of 10–15 cm⁻¹, suitable for long-term studies. Polydimethylsiloxane (PDMS) phantoms (n = 1.41) provide manageable optical properties and are used in microfluidic applications. Polyvinyl alcohol (PVA) phantoms (n = 1.48) mimic soft tissue mechanics, with SCs of 5–15 cm⁻¹, but require freeze–thaw cycles. Fibrin phantoms (n = 1.38) simulate blood clotting, with SCs of 5–20 cm⁻¹. Scattering particles like polystyrene (n = 1.57) and titanium dioxide (TiO₂, n = 2.49) offer modifiable properties, while silica microspheres (SiO₂, n = 3.6) and gold nanoshells (n = 2.59) provide customisable optical characteristics. These materials and particles are crucial for simulating biological tissues, enhancing OCT imaging, and developing diagnostic applications. Despite progress, challenges persist in achieving submicron resolution, long-term stability, and cost-effective scalability. Full article

Personalized cancer vaccines are a promising immunotherapy targeting patient-specific tumor neoantigens, yet their design and efficacy remain challenging. Recent advances in artificial intelligence (AI) provide powerful tools to enhance multiple stages of cancer vaccine development. This review systematically evaluates AI applications in personalized cancer vaccine research over the past five years, focusing on four key areas: neoantigen discovery, codon optimization, untranslated region (UTR) sequence generation, and mRNA vaccine design. We examine AI model architectures (e.g., neural networks), datasets (from omics to high-throughput assays), and outcomes in improving vaccine development. In neoantigen discovery, machine learning and deep learning models integrate peptide–MHC binding, antigen processing, and T cell receptor recognition to enhance immunogenic neoantigen identification. For sequence optimization, deep learning models for codon and UTR design improve protein expression and mRNA stability beyond traditional methods. AI-driven strategies also optimize mRNA vaccine constructs and formulations, including secondary structures and nanoparticle delivery systems. We discuss how these AI approaches converge to streamline effective personalized vaccine development, while addressing challenges such as data scarcity, tumor heterogeneity, and model interpretability. By leveraging AI innovations, the future of personalized cancer immunotherapy may see unprecedented improvements in both design efficiency and clinical effectiveness. Full article

Metabolic engineering of the shikimate pathway offers a promising strategy for enhancing the production of aromatic compounds in microbial hosts. However, feedback inhibition of key enzymes, such as the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHP synthase), often limits the yield of target products. In this study, we focused on the DAHP synthase (AroF-I) from Pseudomonas putida. Through computational modeling and experimental validation, we identified specific amino-acid residues responsible for tyrosine-mediated feedback inhibition. By targeted mutagenesis, we engineered DAHP synthase variants that exhibit reduced sensitivity to feedback inhibition. The introduction of these engineered enzymes into a metabolically engineered Pseudomonas putida strain resulted in significantly increased production of p-coumaric acid. Our findings provide valuable insights into the regulation of the shikimate pathway and demonstrate the potential of protein engineering to improve microbial production of aromatic compounds. Full article

The Ebola virus (EBOV), a highly lethal pathogen causing hemorrhagic fever, poses a persistent public health threat, with devastating multi-organ complications and high transmission potential through bodily fluids. EBOV’s pathogenesis is marked by severe oxidative stress and immune dysregulation, where increased reactive oxygen species (ROS) levels foster cellular damage, hinder immune defenses, and facilitate viral replication. Through immune evasion and suppression of cellular stress responses, EBOV affects both innate and adaptive immunity, activating pyroptosis, PANoptosis, necroptosis, and lymphocyte apoptosis, thereby amplifying inflammation and disease severity. Recent research suggests that bioactive molecules, including quercetin, curcumin, eugenol, and p-anisaldehyde, may offer therapeutic potential due to their antioxidant, anti-inflammatory, and immunomodulatory effects. This review also underscores the potential of conventional treatments, including amiodarone, favipiravir, remdesivir, azithromycin, chloroquine, and nitazoxanide, as therapeutic agents against EBOV, thanks to their antiviral and anti-inflammatory properties, although their efficacy varies across experimental models. These natural compounds could enhance immune resilience by scavenging ROS, modulating inflammation, and mitigating immune dysregulation, presenting promising adjunctive strategies to support conventional EBOV therapies. Full article

Evidence found in the literature indicates that dimeric flavonoids constitute important therapeutic options against cancer. Using these molecules to prevent cancer progression might be a novel and promising therapeutic approach with advantages like fewer side effects, easy access in nature, overall health benefits and overcoming drug resistance. Cancer is a complex disease and still not understood, but there are some common mechanisms and biological characteristics underlying tumor progression that have been scrutinized over the years. This information was summarized in a conceptual framework designated as hallmarks of cancer. Dimeric flavonoids exert biological effects in several pathways involved in cancer hallmarks including cell growth, cell cycle, apoptosis, metastasis and metabolism. Full article

Isoquinoline derivatives exhibit a range of biological properties, including antibacterial activity, and are thus attractive as a scaffold for developing broad-spectrum antibacterial compounds. A series of six isoquinoline-based compounds were synthesized using the reaction of 6,7-dimethoxy-1-methyl-3,4-dihydroisoquinoline with dimethyl acetylenedicarboxylate (DMAD) to provide the tricyclic (2Z)-[2-oxo-5,6-dihydropyrrolo[2,1,a]isoquinolin-3-ylidene]-2-ethanoate. The [2 + 3] cycloaddition of DMAD with C-6 and C-7 substituted 1-methyl-3,4-dihydroisoquinolines proceeded using aryl ethers or unsubstituted compounds, but not with amine, amide or nitro moieties at the C-7 position. Compounds 8d and 8f were found to have antibacterial properties against some Gram-positive pathogens (Staphylococcus aureus—8d = 16 µg/mL, 8f = 32 µg/mL; Streptococcus pneumoniae—8f = 32 µg/mL; and Enterococcus faecium—8d = 128 µg/mL, 8f = 64 µg/mL). Evaluation of their cytotoxic properties against mammalian cell lines revealed some cytotoxic effects (8b and 8d, 125 µM, 24 h, HEp-2 cells) and (8a, 8b, 8d = 125 µM, 8f = 62.5 µM, 24 h, McCoy B cells), suggesting limitations in their antibacterial applications without further development. Full article

Background/Objectives: Plant-derived compounds are increasingly valued in drug discovery for their therapeutic potential. This study aims to examine the antimicrobial, antioxidant, and anticancer properties of kombucha beverages fermented with Gardenia jasminoides (GJ) and various types of Camellia sinensis teas: matcha green tea (MGT), organic green tea (OGT), and decaffeinated green tea (DGT). Methods: Two experimental designs were employed: (1) using black tea as a base substrate, infusing the four teas post-fermentation over 0–14 days, and (2) directly fermenting tea–herb combinations over 0–21 days. Antioxidant activity was assessed via the DPPH assay. Microbial dynamics were analyzed through total mesophilic bacteria and Lactobacillus counts. Antimicrobial potential was evaluated against E. coli, S. aureus, and S. enteritidis over 24 h. Cytotoxicity assays were conducted on Caco-2 and U251 cell lines to assess anticancer effects, with pH-adjusted controls used to differentiate bioactivity from acidity. Results: In the first experiment, GJ kombucha displayed the highest antioxidant potential (IC50: 14.04 µg/mL), followed by MGT (IC₅₀: 32.85 µg/mL) and OGT (IC₅₀: 98.21 µg/mL). In the second setup, unfermented GJ kombucha initially showed high antioxidant activity (IC₅₀: 12.94 µg/mL), improving during fermentation to reach an IC₅₀ of 18.26 µg/mL by day 21. Microbial analysis indicated moderate increases in total mesophilic bacteria and Lactobacillus in GJ kombucha after 14 days, while MGT, OGT, and DGT exhibited higher increments. GJ kombucha consistently demonstrated the highest antimicrobial activity against E. coli, S. aureus, and S. enteritidis, with significant inhibitory effects observed by 24 h. Cytotoxicity assays showed that GJ kombucha reduced Caco-2 cell viability to 20% at 800 µg/mL after 14 days, while U251 cells maintained 50% viability at the same concentration. Conclusions: This study highlights the antimicrobial, antioxidant, and anticancer potential of GJ kombucha, with fermentation enhancing bioactive metabolite production. Optimizing fermentation conditions, identifying specific bioactive compounds, expanding cytotoxicity testing, and exploring broader therapeutic applications of kombucha could maximize its health benefits and establish it as a natural antimicrobial and anticancer agent. Full article

Vanillin, an aromatic aldehyde, is one of the most popular flavors worldwide, extensively used in the food, cosmetics, pharmaceutical, and agrochemical industries. Despite its widespread use, less than 1% of the total vanillin production is natural, with the majority being synthesized chemically. While chemical synthesis can help to meet the growing demand for vanillin, a strong market trend has rapidly developed for products created from natural ingredients, including natural vanillin. Given the labor-intensive process of extracting vanillin from vanilla pods, there is a critical need for new metabolic engineering platforms to support the biotechnological production of nature-identical vanillin. This review highlights the significance of vanillin in various markets, its diverse applications, and the current state of bio-engineered production using both prokaryotic and eukaryotic biological systems. Although recent advancements have demonstrated successful vanillin production through biocatalytic approaches, our focus was to provide a current and innovative overview of vanillin bioengineering across various host systems with special consideration placed on microalgae, which are emerging as promising platforms for vanillin production through metabolic engineering. The use of these systems to support the biotechnological production of vanillin, while leveraging the photosynthetic capabilities of microalgae to capture CO₂ and convert it into biomass, can significantly reduce the overall carbon footprint. Full article

Background/Objectives: Juvenile idiopathic arthritis (JIA) is a chronic childhood disease that often persists into the reproductive years. JIA may impact long-term fertility due to the prolonged exposure to immunosuppressive therapies. Methods: A total of 35 adult JIA female patients of childbearing age and 20 age-matched healthy controls were studied to test their anti-Müllerian hormone (AMH) serum levels as a biomarker of ovarian reserve. Demographic characteristics, disease duration, previous and current treatments, disease activity (DAS44), and a health assessment questionnaire (HAQ) were recorded. Results: JIA patients had a mean age of 22.3 ± 2.9 years, a disease duration of 12.3 ± 6.1 years, and a DAS44 of 1.24 ± 0.61. No differences were found in AMH serum levels between JIA and controls (5.78 ± 2.37 ng/mL vs. 6.60 ± 2.68 ng/mL, respectively; p = 0.17). Among the patients, 22 (62.9%) were receiving a stable dose of methotrexate (MTX) and 19 (54.3%) a dose of TNFα inhibitors. No difference in AMH serum levels was observed between JIA patients who were or were not exposed to MTX (p = 0.29) or to TNFα inhibitors (p = 0.50). Conclusions: Ovarian reserve as assessed by AMH serum levels appears to be comparable between those with JIA and age-matched controls and does not appear to be influenced by disease characteristics or prior/concomitant exposure to immunosuppressive drugs. Full article

The elderly population is growing worldwide. Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed, but their adverse events can pose significant risks. Different NSAID molecules can exhibit varying risk profiles. This study aims to evaluate the cardiovascular, gastrointestinal, and renal safety profiles of ibuprofen, naproxen, acemetacin, diclofenac, celecoxib, and etoricoxib in elderly patients. A comprehensive literature search was conducted in PubMed and Cochrane Library. For the selection of articles, we used Medical Subject Headings (MeSH) terms “aged” sequentially and together with “ibuprofen”, “diclofenac”, “naproxen”, “acemetacin”, “celecoxib”, and “etoricoxib”. To assess the quality and interest of the articles, four independent reviewers screened titles and abstracts to identify potentially eligible studies. Strength of Recommendation Taxonomy (SORT) was used to rate the quality of individual studies and to establish recommendation strengths (RS). From 2086 articles identified, 39 studies met the inclusion criteria. Twenty studies analyzed cardiovascular safety, fourteen gastrointestinal safety, and four renal safety. When CV risk is the main concern celecoxib or naproxen are a good first choice (RS B). In high GI risk addition of PPI to naproxen or celecoxib use should be recommended (RS A). When renal function is on focus, celecoxib remains as first line of therapy (RS A). Diclofenac in the geriatric population should be avoided (RS B). Celecoxib is a good choice for elderly patients for whom it is difficult to direct pain treatment based on a single known risk factor (RS B). Full article

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-2, created an incomparable global health crisis. Due to its highly virulent nature, identifying potential therapeutic agents against this lethal virus is crucial. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. To expedite the search for potential therapeutic candidates, this review delved into computational studies. Recent investigations have harnessed computational methods to identify promising inhibitors targeting PLpro, aiming to suppress the viral activity. Molecular docking techniques were employed by researchers to explore the binding sites for antiviral drugs within the catalytic region of PLpro. The review elucidates the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Through comprehensive all-atom molecular dynamics (MD) simulations, the stability of drug–PLpro complexes was assessed, providing dynamic insights into their interactions. By evaluating binding energy estimates from MD simulations, stable drug–PLpro complexes with potential antiviral properties were identified. This review offers a comprehensive overview of the potential drug/lead candidates discovered thus far against PLpro using diverse in silico methodologies, encompassing drug repurposing, structure-based, and ligand-based virtual screenings. Additionally, the identified drugs are listed based on their chemical structures and meticulously examined according to various structural parameters, such as the estimated binding free energy (ΔG), types of intermolecular interactions, and structural stability of PLpro–ligand complexes, as determined from the outcomes of the MD simulations. Underscoring the pivotal role of targeting SARS-CoV-2 PLpro in the battle against COVID-19, this review establishes a robust foundation for identifying promising antiviral drug candidates by integrating molecular dynamics simulations, structural modeling, and computational insights. The continual imperative for the improvement of existing drugs and exploring novel compounds remains paramount in the global efforts to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, underscoring the interdisciplinary synergy crucial to this endeavor. Full article

Background: Levels of chronic inflammation, oxidative stress, and neurotransmitter availability are altered in depressed patients and can be used as biological markers. This study aimed to analyze these markers in female Wistar rats under chronic inflammation induced by E. coli lipopolysaccharide (LPS), treated with aqueous extract of A. gratissima and rutin, the major flavonoid of its extract. Methods: Thirty female Wistar rats under a chronic inflammatory regimen induced by 1 mg/kg i.p. of LPS were divided into six experimental groups: control (1), treated with fluoxetine 5 mg/kg (2), rutin at 50 mg/kg (3) or 100 mg/kg (4), aqueous extract of A. gratissima 100 mg/kg (5), and co-treatment with 50 mg/kg of extract and 10 mg/kg of rutin (6). Treatments were administered by gavage for 15 days. Results: Oxidative damage to proteins and lipids was lower in group 6 compared to group 2. Pro- and anti-inflammatory cytokines increased in group 1 but not in group 2, indicating a relationship with depression. Similar effects were observed in the treated groups, showing no significant differences from group 2. Neurotransmitter levels of dopamine and serotonin were low in group 1, and all treatments effectively increased them. Additionally, A. gratissima extract at 100 ppm increased locomotor activity in planarians. Conclusions: This study demonstrates the effectiveness of the LPS induction model in subacute experimental designs and the potential antidepressant effect of the treatments due to their antioxidant and anti-inflammatory properties, and ability to increase neurotransmitter levels. Full article

Pulmonary arterial hypertension (PAH) is a progressive disorder caused by the narrowing of small blood vessels in the lungs, which, in the absence of therapies, leads to right heart failure and premature death. No cure for this devastating disorder is known. Current management therapies aim to improve symptoms, and hence, there is a need to identify novel therapeutic interventions. The major objectives of this review are to critically evaluate current treatment strategies and highlight the challenges and prospects of established drugs and natural products for the resolution of PAH. Full article

Colorectal cancer (CRC) is a prevalent and deadly tumor worldwide. Understanding the molecular mechanisms underlying CRC development will improve treatment outcomes and patient survival. Natural molecules and metabolites from plants, such as Tillandsia usneoides, reduce tumor growth by modulating glucose metabolism and increasing reactive oxygen species (ROS). To shed light on the mechanism involved in the anti-tumor effects of T. usneoides, we evaluated the cytotoxic effect of the ethanolic extract of this plant on the colon cancer cell line SW480 through the activation of the peroxisome proliferator-activated receptor gamma (PPARγ), a nuclear receptor that plays a role on lipid metabolism and inflammation in cancer cells. To this end, we assessed the activation of PPARγ by T. usneoides extract in transactivation luciferase assays, as well as the cytotoxic effect of this extract on the SW480 cell line after knocking down PPARγ using shRNA. Our findings indicate that the T. usneoides extract exhibits cytotoxic effects on the SW480 cell line, potentially in the same way as PPARγ activator, pioglitazone, i.e., by increasing reactive oxygen species (ROS). In addition, both T. usneoides extract and pioglitazone exert lipogenic properties in the SW480 cells. Taken together, these results demonstrate that the T. usneoides extract decreases the viability of the colon cancer cell line SW480, at least in part, through the activation of PPARγ. This suggests the potential for further use of this plant in the treatment of other chronic diseases. Full article

Gastrointestinal diseases have been among the main concerns of medical and scientific societies for a long time. Several studies have emphasized the critical role of oxidative stress in the pathogenesis of the most common gastrointestinal diseases. To provide a comprehensive overview of gastrointestinal diseases caused by oxidative stress, their biological aspects, molecular mechanisms and specific pathways, the results of the most recent published articles from the online databases were studied considering both the upper and lower parts of the digestive tract. The results revealed that although the oxidative stress in each part of the digestive system manifests itself in a specific way, all these diseases arise from the imbalance between the generation of the reactive intermediates (especially reactive oxygen species) and the antioxidant defense system. Annual incidence and mortality statistics of gastrointestinal diseases worldwide emphasize the urgent need to find an effective and non-invasive treatment method to overcome these life-threatening problems. Therefore, in the next step, a variety of nanomedicurfines developed to treat these diseases and their effect mechanisms were investigated precisely. Furthermore, the most important nanomedicines responsive to endogenous and exogenous stimuli were evaluated in detail. This review could pave the way to open a new horizon in effectively treating gastrointestinal diseases. Full article

In the present work, methanolic extracts from thyme and dittany plants were prepared and characterized in terms of their polyphenolic content through analytical and spectrophotometric techniques. Rosmarinic acid, thymol and carvacrol were found to be the main components of the extracts, which were further biologically assessed for their antioxidant, anti-tyrosinase, anti-lipase and antibacterial activity against Gram-negative and Gram-positive bacteria. As found, thyme extracts exhibited superior antioxidant activity (SC₅₀ at 33.9 μg mL⁻¹), while dittany extracts inhibited the microbial growth to a great extent against Bacillus subtilis strain (MIC at 0.5 mg mL⁻¹) and E. coli strain (MIC at 2 mg mL⁻¹). Furthermore, the thyme extract was proven to strongly inhibit the activity of lipase from Candida rugosa (IC₅₀ at 63.9 μg mL⁻¹), comparable to the standard inhibitor orlistat, while its inhibitory effect against mushroom tyrosinase was weak. On the other hand, the dittany extract presented an inhibitory effect against the tested lipase (IC₅₀ over 500 μg mL⁻¹) and an activation effect against tyrosinase (at concentrations > 500 μg mL⁻¹). Additionally, molecular docking studies of the main compounds of the extracts showed that rosmarinic acid plays a crucial role on the inhibitory activity of the extracts against lipase, while thymol has a stronger effect on inhibiting tyrosinase. Furthermore, both extracts were employed in the preparation of gelatin-deep eutectic solvent (DES) hydrogels that were further studied for their antioxidant and antibacterial activity. The results showed that the incorporation of the extracts offered antibacterial properties to the biopolymer-based hydrogels and enhanced the antioxidant activity of gelatin up to 85%. Full article

Otoliths of the fish’s inner ear serve as a natural chronological recorder because of their continuous formation marked by daily, monthly, and annual increments. Despite their importance, the comprehensive protein content of otoliths remains not fully identified. Using the label-free shotgun proteomics method with one-dimensional liquid chromatography coupled to electrospray ionization-orbitrap tandem mass spectrometry, we quantified a broad range of proteins, with individual otoliths containing between 1341 and 1839 proteins. The identified proteins could potentially serve as a blueprint for fish growth from embryo to adult. We quantified eleven heat-shock proteins (HSPs) in both sexes and several proteins impacted by endocrine disruptors, indicating the otolith’s capacity to reflect environmental stress, potentially linked to climate change effects and altering of hormonal and neuroendocrine functions. Our bioinformatic ontology analysis confirmed the presence of proteins critical for various biological processes, including structural and enzymatic proteins. Protein–protein interaction (PPI) mapping also identified key interactions between the identified proteins. These findings significantly advance our understanding of otolith proteomics, offering a solid foundation for future work. Most of the identified proteins deposited daily and influenced by the environment were not implicated in the biomineralization of otolith, raising the potential for the otolith proteome to recreate details of fish life history at previously unrealized levels. Full article

Glioblastoma is the most common and aggressive type of malignant brain tumor with a poor prognosis due to the lack of effective treatment options. Therefore, new treatment options are required. Sphingolipids are essential components of the cell membrane, while complement components are integral to innate immunity, and both play a critical role in regulating glioblastoma survival signaling. This review focuses on recent studies investigating the functional roles of sphingolipid metabolism and complement activation signaling in glioblastoma. It also discusses how targeting these two systems together may emerge as a novel therapeutic approach. Full article