Journal Description
BioChem
BioChem
is an international, peer-reviewed, open access journal on biochemistry published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, EBSCO and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 21.7 days after submission; acceptance to publication is undertaken in 6.5 days (median values for papers published in this journal in the second half of 2024).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
Latest Articles
HCC in MASLD and ALD: Biochemical Pathways, Epidemiology, Diagnosis, and Treatment
BioChem 2025, 5(3), 19; https://doi.org/10.3390/biochem5030019 - 25 Jun 2025
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality globally, with metabolic-dysfunction-associated steatohepatitis (MASH) and alcohol-related liver disease (ALD) emerging as major etiologies. This review explores the epidemiological trends, pathogenesis, and clinical management of HCC arising from MASH and ALD, highlighting both
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Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality globally, with metabolic-dysfunction-associated steatohepatitis (MASH) and alcohol-related liver disease (ALD) emerging as major etiologies. This review explores the epidemiological trends, pathogenesis, and clinical management of HCC arising from MASH and ALD, highlighting both the shared and distinct mechanisms. MASH-HCC is driven by metabolic dysregulation, including obesity, insulin resistance, and lipotoxicity, with genetic polymorphisms such as PNPLA3 and TM6SF2 playing critical roles in disease progression. ALD-HCC, in contrast, is propelled by the toxic byproducts of ethanol metabolism, including acetaldehyde and reactive oxygen species, which induce chronic inflammation, and fibrosis. Both conditions also involve immune dysregulation, gut dysbiosis, and increased intestinal permeability, contributing to hepatic carcinogenesis. The review emphasizes that, while there is consensus regarding the screening of HCC in cirrhosis patients, there is lack of consensus on screening strategies for non-cirrhotic MASH patients who are also at risk for HCC. This underscores the importance of the early detection of cirrhosis using advanced diagnostic tools such as transient elastography and fibrosis scores. Current therapeutic approaches, ranging from surgical resection, liver transplantation, and locoregional therapies to systemic therapies like immune checkpoint inhibitors, are discussed, with an emphasis on the need for personalized treatment strategies. Finally, the review highlights future research priorities, including the development of novel biomarkers, exploration of the gut–liver axis, and deeper investigation of the interplay between genetic predisposition and environmental factors. By synthesizing these insights, the review aims to inform multidisciplinary approaches to reduce the global burden of MASH- and ALD-related HCC and improve patient outcomes.
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(This article belongs to the Special Issue Feature Papers in BioChem, 2nd Edition)
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Advances in Structural Biology for Anesthetic Drug Mechanisms: Insights into General and Local Anesthesia
by
Hanxiang Liu, Zheng Liu, Huixian Zhou, Rongkai Yan, Yuzhen Li, Xiaofeng Zhang, Lingyu Bao, Yixin Yang, Jinming Zhang and Siyuan Song
BioChem 2025, 5(2), 18; https://doi.org/10.3390/biochem5020018 - 12 Jun 2025
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Anesthesia is a cornerstone of modern medicine, enabling surgery, pain management, and critical care. Despite its widespread use, the precise molecular mechanisms of anesthetic action remain incompletely understood. Recent advancements in structural biology, including cryo-electron microscopy (Cryo-EM), X-ray crystallography, and computational modeling, have
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Anesthesia is a cornerstone of modern medicine, enabling surgery, pain management, and critical care. Despite its widespread use, the precise molecular mechanisms of anesthetic action remain incompletely understood. Recent advancements in structural biology, including cryo-electron microscopy (Cryo-EM), X-ray crystallography, and computational modeling, have provided high-resolution insights into anesthetic–target interactions. This review examines key molecular targets, including GABA_A receptors, NMDA receptors, two-pore-domain potassium (K2P) channels (e.g., TREK-1), and voltage-gated sodium (Nav) channels. General anesthetics modulate GABA_A and NMDA receptors, affecting inhibitory and excitatory neurotransmission, while local anesthetics primarily block Nav channels, preventing action potential propagation. Structural studies have elucidated anesthetic binding sites and gating mechanisms, providing a foundation for drug optimization. Advances in computational drug design and AI-assisted modeling have accelerated the development of safer, more selective anesthetics, paving the way for precision anesthesia. Future research aims to develop receptor-subtype-specific anesthetics, Nav1.7-selective local anesthetics, and investigate the neural mechanisms of anesthesia-induced unconsciousness and postoperative cognitive dysfunction (POCD). By integrating structural biology, AI-driven drug discovery, and neuroscience, anesthesia research is evolving toward safer, more effective, and personalized strategies, enhancing clinical outcomes and patient safety.
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Open AccessEditorial
Feature Papers in BioChem
by
Manuel Aureliano and Buyong Ma
BioChem 2025, 5(2), 17; https://doi.org/10.3390/biochem5020017 - 11 Jun 2025
Abstract
Biochemistry, or the chemistry of life, is an interdisciplinary science that uses strategies and methods from all exact and natural sciences [...]
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(This article belongs to the Special Issue Feature Papers in BioChem)
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Open AccessReview
Single-Cell Transcriptomics in Spinal Cord Studies: Progress and Perspectives
by
Maiweilan Maihemuti, Mst. Afsana Mimi, S. M. Sohag and Md. Mahmudul Hasan
BioChem 2025, 5(2), 16; https://doi.org/10.3390/biochem5020016 - 10 Jun 2025
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized neuroscience by enabling the analysis of cellular heterogeneity and dynamic molecular processes at the single-cell resolution. In spinal cord research, scRNA-seq provides critical insights into cell type diversity, developmental trajectories, and pathological mechanisms. This review summarizes recent
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Single-cell RNA sequencing (scRNA-seq) has revolutionized neuroscience by enabling the analysis of cellular heterogeneity and dynamic molecular processes at the single-cell resolution. In spinal cord research, scRNA-seq provides critical insights into cell type diversity, developmental trajectories, and pathological mechanisms. This review summarizes recent progress in the application of scRNA-seq to spinal cord development, injury, and neurodegenerative diseases and discusses the current challenges and future directions. Relevant studies focusing on the key applications of scRNA-seq, including advances in spatial transcriptomics and multi-omics integration, were retrieved from PubMed and the Web of Science. scRNA-seq has enabled the identification of distinct spinal cord cell populations and revealed the gene regulatory networks driving development. Injury models have revealed the temporal dynamics of immune and glial responses, alongside potential regenerative processes. In neurodegenerative conditions, scRNA-seq highlights cell-specific vulnerabilities and molecular changes. The integration of spatial transcriptomics and computational tools, such as machine learning, has further improved the resolution of spinal cord biology. However, challenges remain in terms of data complexity, sample acquisition, and clinical translation. Single-cell transcriptomics is a powerful approach for understanding spinal cord biology. Its integration with emerging technologies will advance both basic research and clinical applications, supporting personalized and regenerative therapy. Addressing these technical and analytical barriers is essential to fully realize the potential of scRNA-seq in spinal cord science.
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(This article belongs to the Special Issue Feature Papers in BioChem, 2nd Edition)
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Open AccessReview
The Mini-TRH Test, Dopamine Transmission, and Schizophrenia Symptoms
by
Johan Spoov
BioChem 2025, 5(2), 15; https://doi.org/10.3390/biochem5020015 - 9 Jun 2025
Abstract
Studies in animals and humans suggested that the tonic dopamine inhibition of prolactin release may be estimated by submaximal prolactin stimulation by thyrotropin-releasing hormone (TRH), the mini-TRH test. Because patients with schizophrenia may be more vulnerable to stress-induced elevations of prolactin, great care
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Studies in animals and humans suggested that the tonic dopamine inhibition of prolactin release may be estimated by submaximal prolactin stimulation by thyrotropin-releasing hormone (TRH), the mini-TRH test. Because patients with schizophrenia may be more vulnerable to stress-induced elevations of prolactin, great care was taken to avoid stress-induced increases in prolactin, including applying local anaesthesia before blood extraction in our psychotic patients. Basal prolactin levels were in the reference range in all psychotic patients studied by us and were not higher in male patients than in normal men. Results of the mini-TRH test suggested that in acute patients with non-affective psychoses, everyday memory problems, non-paranoid delusions, and first-rank symptoms, but not other Comprehensive Psychopathological Rating Scale (CPRS) positive symptoms, could correlate with decreasing dopamine transmission in lactotrophs. In acute patients with first-episode schizophrenia, increasing negative disorganisation symptoms might correlate with increasing dopamine transmission. In first-episode patients, a hypersensitivity of the TRH response was detected, which could indicate that variability in the basal prolactin levels may confound the interpretation of the mini-TRH response. To avoid that, a smaller dose of TRH was recommended in first-episode patients. Studies using other estimates of basal dopamine release suggested that striatal dopamine transmission reflected delusions and hallucinations but not other Positive and Negative Symptom Scale (PANSS) positive symptoms. Including a wide range of symptoms in the PANSS positive scale may reduce its specificity for assessing basal dopamine transmission, although the scale remains useful for tracking treatment response.
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(This article belongs to the Special Issue Feature Papers in BioChem, 2nd Edition)
Open AccessArticle
Formulation and In Vitro Characterization of Cellulose-Based Propranolol Hydrochloride Sustained Release Matrix Tablets
by
Aashish Khadka, Bhupendra Raj Giri, Rishiram Baral, Shailendra Shakya and Ashwinee Kumar Shrestha
BioChem 2025, 5(2), 14; https://doi.org/10.3390/biochem5020014 - 30 May 2025
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Background/Objectives: Propranolol HCl (PPH), a nonselective beta-adrenergic receptor blocker, is employed as an anti-hypertensive, anti-anginal, anti-arrhythmic, and anti-migraine agent. Given its utility in chronic conditions, developing a sustained-release dosage form becomes imperative to optimize therapeutic outcomes while enhancing patient adherence and minimizing side
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Background/Objectives: Propranolol HCl (PPH), a nonselective beta-adrenergic receptor blocker, is employed as an anti-hypertensive, anti-anginal, anti-arrhythmic, and anti-migraine agent. Given its utility in chronic conditions, developing a sustained-release dosage form becomes imperative to optimize therapeutic outcomes while enhancing patient adherence and minimizing side effects. In this study, we employed a widely adopted matrix-based system to develop PPH sustained-release (PPH-SR) matrix tablets, ensuring the uniform dispersion of the drug within the polymeric matrix to regulate its release rate. Methods: Utilizing cellulose-based polymers, specifically HPMC K100M and ethyl cellulose (EC), as matrix formers, nine different formulations were prepared at varying drug-to-polymer ratios. We employed a wet granulation method, followed by compression of the dried granules, to fabricate round-shaped biconvex PPH-SR tablets. Results: Among these different formulations, formulation 2 (F2), comprising 40 mg PPH and 50 mg HPMC K100M (along with other excipients), showed excellent flowability, as evidenced by Carr’s index and angle of repose values of 12.50 and 28.50, respectively. Additionally, the mechanical properties of F2 tablets showed a hardness of 12.34 ± 0.91 KP, an average weight of 200.45 ± 1.87 mg, with a friability of 0.20%, and a content uniformity of 98.36%. Moreover, in vitro release characteristics of F2 tablets demonstrated a sustained-release behavior, with 94.3 ± 10.2% drug release over 24 h. A comparative analysis with marketed tablets yielded similarity and dissimilarity factors of 64 and 8, respectively. Furthermore, the release profile of F2 exhibited a high degree of linearity with the Korsmeyer–Peppas model (R2 of 0.977), showcasing its reliability and predictability. Conclusions: In essence, this in-house developed PPH sustained-release formulation can improve patient adherence, reduce side effects, and improve therapeutic outcomes. These results align with our objective of enhancing the therapeutic efficacy of PPH and affirm the broader relevance of innovative formulation strategies in addressing the challenges of chronic disease management.
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Open AccessReview
Factors Influencing Late Breast Toxicity After Radiotherapy: A Scoping Review
by
Riccardo Ray Colciago, Chiara Chissotti, Federica Ferrario, Ilenia Manno, Matteo Mombelli, Giulia Rossano, Lorenzo De Sanctis and Stefano Arcangeli
BioChem 2025, 5(2), 13; https://doi.org/10.3390/biochem5020013 - 30 May 2025
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Radiation therapy offers well-established benefits in enhancing loco-regional control, distant disease control, and breast-cancer-specific survival. However, it is not without its challenges, particularly in breast cancer patients, where advances in systemic therapies and other treatment modalities have significantly improved survival outcomes. As radiation
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Radiation therapy offers well-established benefits in enhancing loco-regional control, distant disease control, and breast-cancer-specific survival. However, it is not without its challenges, particularly in breast cancer patients, where advances in systemic therapies and other treatment modalities have significantly improved survival outcomes. As radiation oncologists, our responsibility is to deliver the most effective treatments while minimizing toxicity for each patient. This scoping review aims to retrieve and assess the literature on factors associated with increased radiation-induced late breast toxicity. Specifically, we seek to identify both non-modifiable variables and those that can be influenced by the choices made by radiation oncologists. This review highlights which clinical decisions could directly impact late breast toxicity following adjuvant radiation therapy after breast-conserving surgery.
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Open AccessReview
From Microbes to Molecules: Synthetic Biology Approaches for Advanced Materials Design
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Roshini Ramachandran, Frank Macabenta, Grace Bettencourt and Shulammite Feng
BioChem 2025, 5(2), 12; https://doi.org/10.3390/biochem5020012 - 28 May 2025
Abstract
Traditional materials synthesis often involves energy-intensive processes with significant waste generation and limited control over material properties. This review examines synthetic biology as a sustainable alternative for designing advanced materials with enhanced precision and versatility. It explores microbial biomineralization, detailing how microorganisms influence
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Traditional materials synthesis often involves energy-intensive processes with significant waste generation and limited control over material properties. This review examines synthetic biology as a sustainable alternative for designing advanced materials with enhanced precision and versatility. It explores microbial biomineralization, detailing how microorganisms influence the formation of mineral deposits and participate in key biogeochemical cycles. It highlights recent research advancements in using a wide variety of microorganisms for the synthesis of inorganic materials such as metal and metal oxide nanoparticles, quantum dots, magnetic nanoparticles, and thin films. The review also discusses the production and properties of various biopolymers. Important factors that can influence the size, morphology, and uniformity of these biomaterials are covered in detail. Emphasis is placed on advancements utilizing synthetic biology tools, such as protein engineering and genome editing, and recent research for creating smart and responsive materials. Considering the present limitations of synthetic biology, challenges related to scale-up, yield, and uniformity are discussed, and suggestions for future research are detailed.
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(This article belongs to the Special Issue Feature Papers in BioChem, 2nd Edition)
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Protein Ligases: Nature’s Gift for Protein/Peptide Synthesis
by
Yvonne Ritsema, Huapeng Li and Qingfei Zheng
BioChem 2025, 5(2), 11; https://doi.org/10.3390/biochem5020011 - 7 May 2025
Cited by 1
Abstract
Proteins are structurally and functionally diverse biomacromolecules that serve a variety of essential activities to ensure complex biological homeostasis. The desire to elucidate and enhance these biological functions has been at the forefront of research for many decades. However, generating active proteins via
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Proteins are structurally and functionally diverse biomacromolecules that serve a variety of essential activities to ensure complex biological homeostasis. The desire to elucidate and enhance these biological functions has been at the forefront of research for many decades. However, generating active proteins via recombinant expression or through chemical total synthesis each has limitations in terms of yield and functionality. Nature has provided a solution to this problem through evolving protein ligases that catalyze the formation of amide bonds between peptides/proteins, which can be exploited by protein engineers to develop robust functional proteins. Here, we summarize the biochemical mechanisms and applications of multiple cysteine-based protein ligases, especially focusing on how they have been utilized for protein therapeutics and engineering, as well as how they inspired chemists to develop efficient methodologies for protein synthesis (e.g., native chemical ligation).
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Open AccessArticle
Mammarenavirus Z Protein Myristoylation and Oligomerization Are Not Required for Its Dose-Dependent Inhibitory Effect on vRNP Activity
by
Haydar Witwit and Juan C. de la Torre
BioChem 2025, 5(2), 10; https://doi.org/10.3390/biochem5020010 - 29 Apr 2025
Abstract
Background/Objectives: N-Myristoyltransferase inhibitors (NMTi) represent a novel antiviral strategy against mammarenaviruses such as Lassa and Junin viruses. The Z matrix protein inhibits viral ribonucleoprotein (vRNP) activity in a dose-dependent manner. Here, we investigated whether Z-mediated vRNP inhibition depends on Z myristoylation or
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Background/Objectives: N-Myristoyltransferase inhibitors (NMTi) represent a novel antiviral strategy against mammarenaviruses such as Lassa and Junin viruses. The Z matrix protein inhibits viral ribonucleoprotein (vRNP) activity in a dose-dependent manner. Here, we investigated whether Z-mediated vRNP inhibition depends on Z myristoylation or oligomerization. Methods: We used HEK293T cells transfected with wild-type (WT) or G2A-mutated Z constructs in LCMV minigenome (MG) assays. Cells were treated with the NMTi IMP-1088 and the proteasome inhibitor MG132. Z protein expression, vRNP activity, and VLP production were analyzed by immunofluorescence, western blotting, and colocalization analyses. Results: IMP-1088 treatment led to proteasome-mediated degradation of Z, reducing its inhibition of vRNP activity, which was restored by MG132. The non-myristoylated Z G2A mutant retained vRNP inhibitory activity but showed impaired oligomerization and budding capacity. These findings demonstrate that Z-mediated vRNP inhibition is independent of myristoylation and oligomerization. Conclusions: Z myristoylation and oligomerization are not required for its inhibitory vRNP activity. Targeting Z myristoylation with NMTi impairs virus assembly and budding without affecting Z-mediated inhibition of vRNP activity, supporting the development of NMTi as a promising broad-spectrum antiviral strategy against mammarenaviruses.
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Open AccessReview
Advances in Oral Solid Drug Delivery Systems: Quality by Design Approach in Development of Controlled Release Tablets
by
Prachi Atre and Syed A. A. Rizvi
BioChem 2025, 5(2), 9; https://doi.org/10.3390/biochem5020009 - 25 Apr 2025
Abstract
Oral solid drug delivery continues to be the gold standard in pharmaceutical formulations, owing to its cost-effectiveness, ease of administration, and high patient compliance. Tablets, the most widely used dosage form, are favored for their precise dosing, simplicity, and economic advantages. Among these,
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Oral solid drug delivery continues to be the gold standard in pharmaceutical formulations, owing to its cost-effectiveness, ease of administration, and high patient compliance. Tablets, the most widely used dosage form, are favored for their precise dosing, simplicity, and economic advantages. Among these, controlled release (CR) tablets stand out for their ability to maintain consistent drug levels, enhance therapeutic efficacy, and reduce dosing frequency, thereby improving patient adherence and treatment outcomes. A well-designed CR system ensures a sustained and targeted drug supply, optimizing therapeutic performance while minimizing side effects. This review delves into the latest advancements in CR formulations, with a particular focus on hydrophilic matrix systems, which regulate drug release through mechanisms such as swelling, diffusion, and erosion. These systems rely on a variety of polymers as drug-retarding agents to achieve tailored release profiles. Recent breakthroughs in crystal engineering and polymer science have further enhanced drug solubility and bioavailability, addressing critical challenges associated with poorly soluble drugs. In terms of manufacturing, direct compression has emerged as the most efficient method for producing CR tablets, streamlining production while ensuring consistent drug release. The integration of the Quality by Design framework has been instrumental in optimizing product performance by systematically linking formulation and process variables to patient-centric quality attributes. The advent of cutting-edge technologies such as artificial intelligence and 3D printing is revolutionizing the field of CR formulations. AI enables predictive modeling and data-driven optimization of drug release profiles, while 3D printing facilitates the development of personalized medicines with highly customizable release kinetics. These innovations are paving the way for more precise and patient-specific therapies. However, challenges such as regulatory hurdles, patent constraints, and the need for robust in vivo validation remain significant barriers to the widespread adoption of these advanced technologies. This succinct review underscores the synergistic integration of traditional and emerging strategies in the development of CR matrix tablets. It highlights the potential of hydrophilic and co-crystal matrix systems, particularly those produced via direct compression, to enhance drug bioavailability, improve patient adherence, and deliver superior therapeutic outcomes. By bridging the gap between established practices and innovative approaches, this field is poised to address unmet clinical needs and advance the future of oral drug delivery.
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(This article belongs to the Special Issue Drug Delivery: Latest Advances and Prospects)
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Open AccessArticle
Hydrogels Made with Tilapia Fish Skin Increase Collagen Production and Have an Effect on MMP-2/MMP-9 Enzymes in Burn Treatment
by
Berkay Baydogan, Aslihan Kucuk, Bensu Kozan, Merve Erdal, Burcin Irem Abas and Ozge Cevik
BioChem 2025, 5(2), 8; https://doi.org/10.3390/biochem5020008 - 22 Apr 2025
Cited by 1
Abstract
Background/Objectives: Burns are a prevalent health concern that manifest on the skin’s surface or within organs due to various traumas and necessitate prompt intervention. The healing process of the skin involves a sequence of time-dependent events, commencing with the activation of growth
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Background/Objectives: Burns are a prevalent health concern that manifest on the skin’s surface or within organs due to various traumas and necessitate prompt intervention. The healing process of the skin involves a sequence of time-dependent events, commencing with the activation of growth factors and culminating in the expression of various genes. To expedite the healing process of burn wounds, there is a need to develop biodegradable materials and new technologies that are compatible with the skin. Methods: In this study, the roles of tilapia (TL, Oreochromis niloticus) fish skin in burn wound treatment processes were investigated. TL or TL-alginate hydrogels (AGTL) were applied to a burn wound created in Sprague Dawley rats for 7 and 14 days. Following the administration of treatment, the levels of hydroxyproline, a critical element in tissue reorganization, along with the gene expression levels of COL1A1, COL3A1, MMP-2, and MMP-9, and the protein expression levels of MMP-2 and MMP-9 were evaluated. Results: Wound closure processes were faster in AGTL-groups compared to TL-groups, and hydroxyproline levels were found to be higher. While the increase in MMP-2 levels was less, the increase in MMP-9 gene and protein levels was greater in the AGTL-group. Concurrently, COL1A1 levels decreased over 14 days, while COL3A1 levels increased in the AGTL-group. Conclusions: Consequently, it was determined that the biological substances in the TL structure, in conjunction with alginate, were effective in the healing and reorganization of the wound tissue. This finding suggests that tilapia may provide a valuable source of insights for future studies aimed at developing effective wound dressings for wound tissues.
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(This article belongs to the Special Issue Feature Papers in BioChem)
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Open AccessEditorial
Selected Papers from the XXI SPB National Congress of Biochemistry 2021
by
Manuel Aureliano, M. Leonor Cancela, Ana R. Costa and Célia M. Antunes
BioChem 2025, 5(2), 7; https://doi.org/10.3390/biochem5020007 - 10 Apr 2025
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The XXI SPB National Congress of Biochemistry 2021 was held at the University of Évora in Portugal on 14–16 October 2021 [...]
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Open AccessReview
Advancements in Retinal Tissue-Mimicking Optical Coherence Tomography Phantoms: Materials, Properties, and Applications
by
Mukhit Kulmaganbetov
BioChem 2025, 5(2), 6; https://doi.org/10.3390/biochem5020006 - 9 Apr 2025
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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
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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.
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Open AccessReview
Advances in Personalized Cancer Vaccine Development: AI Applications from Neoantigen Discovery to mRNA Formulation
by
Hyunseung Kong
BioChem 2025, 5(2), 5; https://doi.org/10.3390/biochem5020005 - 31 Mar 2025
Abstract
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
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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.
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(This article belongs to the Special Issue Feature Papers in BioChem, 2nd Edition)
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Open AccessArticle
Overproduction of Phenolic Compounds in Pseudomonas putida KT2440 Through Endogen Deregulation of the Shikimate Pathway
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William Merre, Ricardo Andrade, Cyril Perot, Alexia Chandor-Proust and Caroline Ranquet
BioChem 2025, 5(1), 4; https://doi.org/10.3390/biochem5010004 - 11 Mar 2025
Cited by 1
Abstract
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
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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.
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(This article belongs to the Special Issue Feature Papers in BioChem)
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Open AccessReview
Therapeutic Management of Ebola Virus: Targeting Oxidative Stress and Inflammatory Pathways
by
Martin Ndayambaje, Hicham Wahnou, Abdallah Naya and Mounia Oudghiri
BioChem 2025, 5(1), 3; https://doi.org/10.3390/biochem5010003 - 11 Feb 2025
Abstract
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
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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.
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(This article belongs to the Special Issue Targeting Oxidative Stress and Inflammation: Emerging Mechanisms and Therapeutics)
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Open AccessReview
An Overview of the Therapeutic Potential of Dimeric Flavonoids for Targeting Cancer Hallmarks
by
Inês Lopes, Isabel Meireles, Rafaela Rocha, Rui Medeiros and Fátima Cerqueira
BioChem 2025, 5(1), 2; https://doi.org/10.3390/biochem5010002 - 14 Jan 2025
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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
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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.
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Open AccessArticle
Synthesis and Investigation of Tricyclic Isoquinoline Derivatives as Antibacterial Agents
by
Matthew J. A. Phillips, Alison T. Ung, Elizabeth J. Harry, Jason Ashmore and Andrew M. McDonagh
BioChem 2025, 5(1), 1; https://doi.org/10.3390/biochem5010001 - 31 Dec 2024
Cited by 1
Abstract
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
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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.
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(This article belongs to the Special Issue Feature Papers in BioChem)
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Open AccessArticle
Evaluating the Health Implications of Kombucha Fermented with Gardenia jasminoides Teas: A Comprehensive Analysis of Antioxidant, Antimicrobial, and Cytotoxic Properties
by
Gayathree Thenuwara, Xu Cui, Zhen Yao, Bilal Javed, Azza Silotry Naik and Furong Tian
BioChem 2024, 4(4), 350-370; https://doi.org/10.3390/biochem4040018 - 15 Dec 2024
Cited by 1
Abstract
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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),
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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.
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