BioChem doi: 10.3390/biochem6020014

Authors: Chitaranjan Mahapatra

Voltage-gated sodium channels are central to electrical excitability, and Nav1.7 is a major therapeutic target implicated in pain disorders and sensory signaling. Within the channel pore, permeating Na+ ions experience dynamically fluctuating hydration and coordination environments that may influence local ion–protein interactions. Identifying chemically distinct coordination states from molecular dynamics (MD) simulations is an important prerequisite for future higher-level electronic structure investigations. In this study, we present a reproducible workflow for identifying and classifying Na+ hydration–coordination microstates in the Nav1.7 pore using explicit-solvent molecular dynamics simulations. A geometrically defined pore region was used to quantify pore hydration and Na+ inner-shell coordination based on a 3.2 Å Na–O distance criterion. Na+ configurations were classified according to ligand identity into water-only (W), mixed protein–water (PW), and protein-only (P) microstates. Analysis of a 2 ns proof-of-principle simulation revealed a persistently hydrated pore environment, with Na+ coordination dominated by water-rich states and a smaller but distinct population of protein-contact configurations. These observations demonstrate that local coordination environments are chemically heterogeneous and cannot be fully described by hydration number alone. Representative structures from each microstate class were extracted to provide candidate configurations for future quantum mechanical, Quantum Mechanics/Molecular Mechanics (QM/MM), or density functional theory investigations of ion–ligand interactions in confined pore environments. The present work establishes a transparent and reproducible microstate-selection framework and does not report quantum mechanical energies, free-energy landscapes, or converged microstate populations. More broadly, the workflow provides a practical strategy for reducing complex MD ensembles into chemically interpretable coordination states suitable for subsequent higher-level analysis.

BioChem doi: 10.3390/biochem6020013

Authors: Afsana Sharmin Bahar Uddin Mahmud

This study addresses two key challenges in computational pharmacology: identifying novel therapeutic uses for existing drugs and modeling drug safety-related characteristics. We propose a multi-relational biomedical knowledge graph that integrates gene, drug, and disease associations with adverse effect data, enabling joint modeling of therapeutic and safety-related properties. A Relational Graph Convolutional Network (R-GCN) is employed to learn relationally aware embeddings that capture complex biological interactions across heterogeneous entities. The framework is evaluated on two tasks: (1) drug–disease link prediction for drug repurposing and (2) prediction of drug side-effect burden based on adverse event patterns. The experimental results demonstrate that the R-GCN model outperforms baseline methods, achieving 94.63% accuracy in drug–disease link prediction, while embedding-based classifiers attain up to 97.14% F1-score in side-effect burden classification. Additionally, multi-hop relational reasoning enables the discovery of biologically plausible connections between drugs, genes, and diseases. These findings highlight the effectiveness of knowledge graph-based representation learning in jointly supporting therapeutic discovery and safety-related analysis. While side-effect burden is used as a surrogate measure rather than a direct indicator of drug quality, the proposed framework provides a scalable foundation for integrating real-world pharmacovigilance and regulatory data in future studies.

BioChem doi: 10.3390/biochem6020012

Authors: Zilong Zhao Yuhao Wang Dong Yan Ya Chen Jun Zhao

To improve the visible-light response and antibacterial performance of titanium dioxide, a TiO2/GO/CdS mesoporous nanocomposite was prepared via an ultrasound-assisted sol–gel method in this study. Systematic characterizations including XRD, XPS, SEM, TEM, BET, UV-Vis DRS and FTIR were carried out to analyze the structure, morphology and optical properties of the material. The results show that the composite exhibits a typical mesoporous structure with a specific surface area of 197.0962 m2/g and a pore size distribution of 2–14 nm. CdS is successfully doped into the TiO2 matrix and forms a heterostructure with GO. UV-Vis diffuse reflectance spectra indicate that the synergistic effect of CdS and GO significantly broadens the visible-light absorption range of TiO2 and suppresses the recombination of photogenerated carriers. Antibacterial tests using Escherichia coli as the target strain demonstrate that the TiO2/GO/CdS composite exhibits remarkably better visible-light photocatalytic bactericidal activity than pure TiO2 and the TiO2/GO composite. This work provides a new strategy for the modification of TiO2-based photocatalytic antibacterial materials, and the as-prepared composite shows promising application prospects in the antibacterial field.

BioChem doi: 10.3390/biochem6020011

Authors: Mayela del Ángel-Martínez Mauricio Salinas-Santander Michelle Giovanna Santoyo-Suárez Lesly González-Flores Omar Reyes-Torres Antonio Morlett-Chávez

Background: COVID-19 severity shows marked interindividual variability, suggesting a role for host genetic factors. Polymorphisms in genes involved in the renin–angiotensin system and inflammatory response, such as the angiotensin-converting enzyme (ACE) and the tumor necrosis factor-alpha (TNF-α), have been proposed as potential modulators of disease severity. Objectives: To evaluate the association between the ACE I/D (rs4646994) and TNF-α-308 G/A (rs1800629) polymorphisms and COVID-19 severity in a Mexican population. Methods: A total of 235 individuals with RT-PCR–confirmed SARS-CoV-2 infection were included. Patients were classified as hospitalized (severe, n = 155) or non-hospitalized (asymptomatic–mild, n = 80). Genotyping was performed by PCR–RFLP. Genotype distributions were analyzed using χ2 tests under dominant and recessive genetic models, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Results: The ACE I/D polymorphism showed a significant association with COVID-19 severity. Carriers of the I allele (ID + II) had a higher risk of hospitalization compared with DD homozygotes (OR = 2.78, 95% CI: 1.53–5.06, p = 0.001). After adjustment for sex, the association remained significant (adjusted OR = 2.55, 95% CI: 1.38–4.70, p = 0.003). Sex-stratified analysis revealed that this association was significant only in male patients. The DD genotype was more frequent among non-hospitalized individuals, suggesting a potential protective effect in this population. No significant association was observed between the TNF-α-308 G/A polymorphism. Conclusions: The ACE I/D polymorphism is associated with COVID-19 severity in a Mexican population, with a stronger association observed in males. These findings highlight the potential role of host genetic background and sex-specific effects in COVID-19 outcomes.

BioChem doi: 10.3390/biochem6020010

Authors: Masao Shimoda Bernard Yukihiro Hiraoka

Background: D-amino acids are increasingly recognized as bioactive molecules with diverse physiological and pathological roles in humans, particularly in the gut, kidneys, and nervous system. Advances in analytical techniques have revealed their widespread presence in biological fluids, including plasma, urine, cerebrospinal fluid, amniotic fluid, and saliva, challenging the long-standing assumption that D-amino acids are absent or biologically insignificant in mammals. Scope: This review systematically summarizes the current knowledge on D-amino acid sources, distribution, metabolic regulation, and biological functions, with emphasis on their roles in human physiology and disease. Key findings: Accumulating evidence indicates that major D-amino acids, including D-serine, D-aspartate, and D-alanine, are derived from multiple sources such as diet, intestinal microbiota, and endogenous racemization processes. Rather than being passive metabolic byproducts, D-amino acids are now understood to participate in host–microbe interactions, neurotransmission, and renal physiology. Importantly, a consistent trend across studies is their dual and concentration-dependent nature, exhibiting beneficial effects under physiological conditions but potential cytotoxic effects at elevated levels. Conclusions and perspectives: Overall, D-amino acids represent multifunctional biomolecules with tightly regulated physiological roles and context-dependent pathological implications. However, major gaps remain in understanding their quantitative dynamics, tissue-specific regulation, and microbiota-dependent metabolism. Future studies addressing these mechanisms will be essential for establishing their clinical utility as biomarkers and for developing D-amino acid-based therapeutic and nutritional strategies.

BioChem doi: 10.3390/biochem6020009

Authors: Manuel Aureliano Buyong Ma

As mentioned in the Editorial of the first edition of the Special Issue on “Feature Papers in BioChem”, biochemistry acts as a key cog in the “clock of the knowledge, permitting that wheels from several science areas move each other” [...]

BioChem doi: 10.3390/biochem6010008

Authors: Mst. Afsana Mimi Md. Mahmudul Hasan

The authors wish to correct the authorship of the published article [...]

BioChem doi: 10.3390/biochem6010007

Authors: Imane Nait Irahal Abderrahmane Thoume Asmaa Chbel Hicham Wahnou Fatima Abdou-Allah Ayoub Lafnoune Redouane Achagar Driss Benmessaoud Left Mustapha Zertoubi Noureddine Bourhim

Background: Diabetes mellitus is a global health challenge associated with chronic complications like diabetic nephropathy and diabetic foot infections. Diabetic nephropathy, mediated by hyperglycemia-induced activation of the polyol pathway, represents a primary cause of end-stage renal disease. Additionally, infections caused by multidrug-resistant bacteria like Enterococcus faecalis lead to amputations and contribute to morbidity in diabetic patients. Methods: In this study, we synthetized nitrogen-doped carbon dots (N-CDs) using succinic acid with either hexamethylenediamine (N-HCD) or ethylenediamine (N-ECD) and evaluated their potential therapeutic applications. Results: Both N-HCD and N-ECD demonstrated a significant reduction in aldose reductase (AR) and sorbitol dehydrogenase (SDH) in vitro, with a substantial reduction in polyol pathway enzymatic activity. Furthermore, these N-CDs exhibited antibacterial activity against E. faecalis in vitro. Conclusions: Taken together, our findings suggest that N-HCD and N-ECD represent promising candidates for addressing diabetes-related complications and warrant further investigation for potential drug delivery applications.

BioChem doi: 10.3390/biochem6010006

Authors: Gur Jai Pal Singh Anthony J. Hickey

The majority of approved drug products comprise formulations of either chemically synthesized small molecules or large molecular entities derived from living cells, commonly referred to as biologics. Over the past two decades, there has been remarkable growth in the approval of biologics for a variety of disorders, including respiratory diseases. The preference for biologics stems from their high target specificity, strong binding affinity, and favorable safety profiles. Most approved biologics are peptides or proteins, which are unsuitable for oral administration due to negligible bioavailability, resulting from their large molecular size, polarity, and susceptibility to enzymatic degradation in the gastrointestinal tract. Consequently, the majority of biologics are administered parenterally, delivering the drug systemically to reach target sites. However, achieving therapeutic concentrations of locally acting respiratory drugs in the lungs via systemic delivery often requires high doses, which increases the risk of adverse effects. For respiratory disorders, nasal and pulmonary drug deliveries are the preferred noninvasive routes. These routes bypass gastrointestinal and first-pass metabolism and deliver therapeutic agents directly to their local site of action. This approach enables a faster onset of action, reduces the required dose by orders of magnitude, and significantly lowers the risk of systemic adverse effects. These advantages have driven the successful development of inhaled formulations for certain rescue and maintenance medications that were originally administered orally or parenterally. Despite this, treatment options for respiratory diseases remain largely limited to small molecules, with only a single inhaled biologic approved in 1993, even though several parenterally administered biologics have since been approved for pulmonary disorders. The scarcity of inhaled biologics is primarily due to the inherent complexity of these drug substances, which impacts all stages of product development, including manufacturing, characterization, purification, stability, formulation design, delivery, and preclinical and clinical evaluations of safety and efficacy. Additionally, sponsors’ interest in developing inhaled biologics may be tempered by the lack of regulatory guidance addressing the multidisciplinary and intricate nature of their development. This article, together with the accompanying review, addresses both regulatory considerations and scientific challenges in the development of inhaled biologics. To the authors’ knowledge, these works represent seminal efforts to examine available regulatory guidance and the applicable literature across various phases of product development beyond safety and efficacy evaluations. We examined the formal regulatory expectations and summarized the requirements as they apply to inhaled products and inhaled biologic protein therapeutics. In parallel, we explored scientifically relevant considerations in the development of inhalation-specific protein therapeutics for which regulatory guidance remains limited, evolving, or absent. While they should not be considered definitive, it is hoped that these contributions will stimulate scientific and regulatory interest, ultimately promoting the identification and resolution of gaps to advance the development of locally acting biologics and address unmet patient needs.

BioChem doi: 10.3390/biochem6010005

Authors: Andrea Marzullo Cecilia Salzillo

Paediatric ovarian neoplasms are rare and histologically diverse tumours with distinct clinical behaviour and prognosis compared to their adult counterparts. This review synthesises current knowledge from an anatomical pathology perspective, emphasising diagnostic and therapeutic strategies. Paediatric ovarian tumours are classified into three main categories: germ cell tumours, sex cord-stromal tumours, and epithelial neoplasms. Germ cell tumours, the most frequent in children, include dysgerminoma, mature and immature teratoma, yolk sac tumour, and choriocarcinoma. Sex cord-stromal tumours encompass Sertoli-Leydig cell tumours, juvenile granulosa cell tumours, and adrenal-like stromal tumours, while epithelial tumours, rare in paediatric patients, include serous and mucinous adenocarcinomas or cystadenomas. Clinical presentation is often nonspecific, with abdominal pain, pelvic mass, or endocrine abnormalities. Diagnosis integrates imaging, serum tumour markers, and histopathology supported by immunohistochemistry. Treatment prioritises fertility-sparing surgery, with selective adjuvant chemotherapy based on histotype and stage. Despite generally favourable outcomes, the rarity of these tumours limits high-quality evidence, highlighting the need for referral centres and multicenter studies. Standardised diagnostic protocols and personalised therapeutic approaches are essential to optimising clinical outcomes and preserve long-term reproductive function.

BioChem doi: 10.3390/biochem6010004

Authors: Gur Jai Pal Singh Anthony J. Hickey

Following the discovery of therapeutic molecules and the identification of specific biological targets, preparation of regulatory dossiers entails extensive product development and characterization to support their safety, efficacy, and stability. We have examined the drug development and relevant regulatory considerations related to inhaled biological proteins in the accompanying article. This review focuses on the characterization of locally acting inhaled biological proteins. Drug product characterization is a regulatory requirement, and it ensures drug product safety, efficacy, stability, and usability by the target populations. Together, these two articles provide a comprehensive discussion based on our review and analysis of the available open literature. We have attempted to fill gaps and simulate discussion of challenges following sound scientific pathways. This approach has the prospect of addressing regulatory expectations leading to rapid solutions to unmet medical needs. The robustness of characterization strategies and the development of analytical methods used in the in vitro testing for the evaluation of drug product attributes is assured through application of the Design-of-Experiment (DOE) and Quality-by-Design (QBD) approaches. Drug product characterization entails a variety of in vitro studies evaluating drug products for purity and contamination, and determination of drug delivery by the intended route of administration. Measurement of the proportion of the labeled amount per dose and the form suitable for delivery to the intended target sites is central to this assessment. For respiratory Drug–Device combination products, the testing may vary with the product designs. However, determination of the single-dose content, delivered-dose uniformity, aerodynamic particle size distribution, and device robustness when used by the target populations is common to all combination products. Characterization of aerosol plumes is limited to inhalation aerosols that produce specific aerosol clouds upon actuation. The flow rate dependency of devices is also examined. Product characterization also includes safety-related product attributes such as degradation products and leachables. For inhaled biological proteins, safety-related in vitro testing includes additional testing to assure maintenance of the three-dimensional structural integrity and the sustained biological activity of the drug substance in the formulation, during aerosolization and upon deposition. This article discusses various tests employed for regulatory-compliant product characterization. In addition, the stability testing and handling of possible changes during product development and post-approval are discussed.

BioChem doi: 10.3390/biochem6010003

Authors: Maryam Rezvani Maria Manconi Nejat Düzgüneş

Background/Objectives: Lactic acid bacteria have long been recognized as pivotal microorganisms in food fermentation and health promotion. However, their significance has recently grown due to innovative applications in various fields, particularly at the intersection of biotechnology and nanotechnology. This study aimed to provide a comprehensive overview of these emerging applications. Methods: The latest scientific literature was drawn from online databases and thoroughly reviewed. The new nomenclature system based on the post-2020 reclassification was used for reports. Results: The current study highlighted the evolving role of lactic acid bacteria, beyond their traditional use as starter cultures for food fermentation, in newer challenges, including the production of high-value bioactive compounds through bioprocessing under optimal conditions to enhance the yield, underlining the involved genes and pathways. Furthermore, this review addressed the beneficial effects of lactic acid bacteria as probiotics, postbiotics, and paraprobiotics in the treatment of various diseases and disorders, their application in the production of functional foods, and the encapsulation of their bioproducts to produce advanced health-promoting functional ingredients. The potential use of lactic acid bacteria to synthesize metallic nanoparticles, minicells, and carbon dots was also explored, promising significant advancements in nanomedicine. Conclusions: This review could open a new horizon for leveraging the potential of lactic acid bacteria in biotechnology, food science, and nanomedicine. The multilateral perspective offered here would provide a foundation for future research and development to exploit the capabilities of lactic acid bacteria across these innovative fields.

BioChem doi: 10.3390/biochem6010002

Authors: Bruno F. E. Matarèse

The pharmaceutical industry faces a broken drug development pipeline, characterized by high costs, slow timelines and is prone to high failure rates. The convergence of Artificial Intelligence (AI) and quantum technologies is poised to fundamentally transform this landscape. AI excels in interpreting complex data, optimizing processes and designing drug candidates, while quantum systems enable unprecedented molecular simulation, ultra-sensitive sensing and precise physical control. This convergence establishes an integrated, self-learning ecosystem for the discovery, development, and delivery of therapeutics. This framework co-designs strategies from molecular targeting to formulation stability, compressing timelines and enhancing precision, which may enable safer, faster, and more adaptive medicines.

BioChem doi: 10.3390/biochem6010001

Authors: Ranbala Kumari Jasleen Kaur Mishi Wasson Deepika Trehan Pawan Vasudeva Niraj Kumar Nitu Kumari Usha Agrawal

Background: Proper storage of biofluids is critical to preserving their molecular integrity for downstream applications. This study investigates the effect of different storage temperatures on the stability of preservative-free urine samples over a two-year period. Methods: Urine samples were collected, aliquoted, and stored at −80 °C, −20 °C, 4 °C, and in lyophilized form. Samples were retrieved at 0, 6, 12, and 24 months for analysis. DNA, RNA, and protein were isolated and evaluated using agarose and polyacrylamide gel electrophoresis. Nucleic acid quality was assessed using Nanodrop spectrophotometry and Bioanalyzer profiles. Results: A significant increase in pH and a concurrent decline in protein concentration were observed within the first six months at −20 °C and 4 °C. These changes plateaued after six months. Samples stored at −80 °C and in lyophilized form showed minimal variation in pH and retained higher protein stability. DNA quality, based on 260/280 and 260/230 ratios and electrophoretic band integrity, was well-preserved under these two conditions. RNA quality remained stable for up to 12 months but declined thereafter. Conclusions: Storage at −80 °C or in lyophilized form offers optimal preservation of protein concentration and nucleic acid quality in preservative-free urine samples over extended storage durations. However, lyophilization offers a cost-effective and logistically practical alternative, as samples can be stored at room temperature without the requirement of ultra-low freezers.

BioChem doi: 10.3390/biochem5040044

Authors: Khalid Laaziri Abdelmajid Zyad Fatima Ezzahra Lahlimi Ouadii Abakarim Illias Tazi Ikram Brahim Nadia Lakhouaja Raja Hazime El Mostafa Mtairag Brahim Admou

Background/Objectives: Acute myeloid leukemia (AML) is the most common acute leukemia in adults, with over 50% of individuals succumbing to the disease annually. This study aimed to assess the correlation between human leukocyte antigen (HLA) genes and acute myeloid leukemia (AML) in an adult Moroccan cohort. We included 60 persons with acute myeloid leukemia (AML) who were eligible for hematopoietic stem cell transplantation and compared them to a control group of 90 healthy adults. Methods: Patients and controls were subjected to HLA class I and II typing utilizing either sequence-specific primers (SSP) or sequence-specific oligonucleotides (SSO) in polymerase chain reaction-based methodologies. Results: The AML categories were predominantly represented by AML2, AML3, and AML4, comprising 36.66%, 30%, and 16.66%, respectively. We identified a notable correlation between HLA-A*11 (p = 0.003) and HLA-B*27 (p = 0.005) with acute myeloid leukemia (AML), and for HLA class II allele groups, we detected an elevated frequency of HLA-DQB1*05 (p = 0.002) in adult AML patients. We identified a notable correlation between AML 2 and the allele groups examined, namely with HLA class I: HLA-A*11 (p = 0.0003) and HLA-B*27 (p = 0.00006). Conclusion: Our study suggests a potential association between specific HLA alleles and the development of AML specifically AML type 2 in adults. Further larger studies are needed to confirm these findings.

BioChem doi: 10.3390/biochem5040043

Authors: Abba Musa Abdullahi Shah Taha Sarmast Usama Ishaq Abdulrazak

Background: Microglial cells are the resident immune cells in the central nervous system (CNS) and constitute the brain’s innate immune system. They are the smallest of the glial cells and are derived from phagocytic white blood cells, fetal monocytes, which migrate from the blood into the brain during development. On the other hand, epilepsy is a chronic condition defined as recurrent unprovoked seizures, with at least two seizures occurring over 24 h apart. Methods: To determine the role of microglial activation in the pathogenesis of drug-resistant epilepsy, we systematically searched published data for biomarkers of microglial activation from main databases including PubMed, PubMed Central, Scopus, Embase, Google Scholar, and Medline. Two research registries were also searched: the Cochrane Registry and clinicaltrial.gov. Data was collected after applying inclusion and exclusion criteria and studies were appraised critically. Both Medical Subject Headings (MeSH) and regular keyword search strategies were employed. Results: Our systematic review shows significant elevation of biomarkers of microglial activation in patients with drug-resistant epilepsy, suggesting its role in the disease’s pathogenesis. Conclusions: Microglia cells are therefore considered as a special type of mononuclear phagocytes found in the CNS that plays important roles in both the brain’s immunity and homeostatic functions. The role of microglial activation in the pathogenesis of drug-resistant epilepsy is an active area of study, with potential therapies for drug-resistant epilepsy that target microglia currently being investigated.

BioChem doi: 10.3390/biochem5040042

Authors: Christian P. Ratti Alessandra Chiei Gallo Francesca Barei Alice Botta Matteo Cavara Eleonora Bono Lea Caron Valeria G. R. Ortolani Enrico Iemoli

Background/Objectives: Drug hypersensitivity reactions (DHRs) are an important cause of morbidity in hospitalized patients, but their epidemiology and management in the inpatient setting are not well defined. Mislabeling of drug allergies may lead to inappropriate treatment and reduced antimicrobial stewardship. This study aimed to characterize the clinical profile, diagnostics, and management of inpatients referred for suspected drug allergy in a tertiary care hospital. Methods: We retrospectively reviewed all adult inpatients (≥18 years) at Luigi Sacco Hospital (Milan, Italy) who received allergology consultation between 1 June 2022 and 31 May 2025. Data on demographics, reaction type, culprit drugs, investigations, and management were collected. Immediate reaction severity was graded using the United States Drug Allergy Registry (USDAR) scale; delayed reactions were classified as severe cutaneous adverse reactions (SCARs) or non-SCARs. Logistic regression identified predictors of severity. Results: Among 35,438 admissions, 334 patients (0.9%) were evaluated; median age was 65 years, 51.2% were female, 67.4% had atopic comorbidities, and 55.1% reported prior drug allergy. Immediate reactions occurred in 49.1%, delayed in 43.7%. Cutaneous involvement was present in 86.8%, anaphylaxis in 6.6%, and SCARs in 3.9%. Antibiotics—particularly β-lactams—were most often implicated. In multivariate analysis, antibiotic exposure and older age were linked to more severe immediate reactions, while the absence of atopy predicted SCARs. Desensitization was successfully performed in 16.2% of patients. Conclusions: DHRs in inpatients are frequent and often involve high-risk drugs. Structured inpatient allergology services and an “allergy stewardship” approach may reduce DHR-related risks, support optimal therapy, and improve antimicrobial use strategies in tertiary care settings.

BioChem doi: 10.3390/biochem5040041

Authors: Manuel Aureliano João Mateus David Manjua Rijo

Alzheimer’s disease (AD) signifies a devastating impact on the quality of life of patients and their families. At a biomolecular level, AD is characterized by the deposition of extracellular plaques of β-amyloid (Aβ), affecting language, spatial navigation, recognition abilities and memory. Among the selected 30 articles about polyoxometalates (POMs) and AD published from 2011 to 2025, pure POMs, hybrid POMs and POM nanoparticles can be found. The majority of POMs are polyoxotungstates (62%), the Keggin-type SiW11O39 being the most studied in AD. The main effect described is the inhibition of Aβ aggregates. Other effects include reversing the neurotoxicity induced by Aβ aggregates, decreasing ROS production and neuroinflammation, restoring memory and sequestering Zn2+ and Cu2+, among others, features that are well known to be associated with the pathology of AD. POMs have also shown the ability to induce the disaggregation of Aβ fibrils, particularly after irradiation, and to inhibit acetylcholinesterase activity at an nM range. Putting it all together, this review highlights a predominant trend in the exploration of POMs to act directly at the level of the formation and/or disaggregation of Aβ aggregates in the treatment of AD.

BioChem doi: 10.3390/biochem5040040

Authors: Akshata Yashwant Patne Imtiyaz Bagban Meghraj Vivekanand Suryawanshi

Alzheimer’s disease (AD), the leading cause of dementia, is defined by two pathological hallmarks, amyloid-β (Aβ) plaques and hyperphosphorylated tau tangles—both now structurally resolved at near-atomic precision thanks to cryo-EM. Despite decades of research, effective disease-modifying therapies remain elusive, underscoring the need for innovative interdisciplinary approaches. This review synthesizes recent advances in structural biology and nanotechnology, highlighting their synergistic potential in revolutionizing AD diagnosis and treatment. Cryo-EM and NMR have revolutionized our understanding of Aβ/tau polymorphs, revealing structural vulnerabilities ripe for therapeutic targeting—yet clinical translation remains bottlenecked by the blood–brain barrier (BBB). Concurrently, nanotechnology offers groundbreaking tools, including nanoparticle-based drug delivery systems for blood–brain barrier (BBB) penetration, quantum dot biosensors for early Aβ detection, and CRISPR-nano platforms for APOE4 gene editing. We discuss how integrating these disciplines addresses critical challenges in AD management—from early biomarker detection to precision therapeutics—and outline future directions for translating these innovations into clinical practice.

BioChem doi: 10.3390/biochem5040039

Authors: Eric Zanderigo Phyllis Schram Owen Rogers Mikayla McLaughlin Colin A. Smith Alison L. O’Neil

Background/Objectives: Approximately 20% of familial ALS (fALS) cases are linked to mutations in Cu/Zn superoxide dismutase (SOD1). Through a gain function, SOD1 misfolding exerts a toxic effect on motor neurons, leading to their degradation and ALS symptomology in both fALS cases and sporadic ALS (sALS) cases with no known genetic cause. To further our understanding of SOD1-ALS etiology, identifying motor neuron-specific SOD1 post-translational modifications (PTMs) and studying their structural influence is necessary. To this end, we have conducted a study on the influence of the deamidation of Asn53, a PTM proximal to key stabilizing motifs in SOD1, which has scarcely been addressed in the literature to date. Methods: Deamidation to N53 was identified by tandem mass spectrometry of SOD1 immunoprecipitated from motor neuron (MN) cultures derived from wild-type (WT) human induced pluripotent stem cells (iPSCs). WT SOD1 and N53D SOD1, a mutant mimicking the deamidation, were expressed in Escherichia coli and purified for in vitro analyses. Differences between species were measured by experiments probing metal cofactors, relative monomer populations, and aggregation propensity. Furthermore, molecular dynamics experiments were conducted to model and determine the influence of the PTM on SOD1 structure. Results: In contrast to WT, N53D SOD1 showed non-native incorporation of metal cofactors, coordinating more Zn2+ cofactors than total Zn-binding sites, and more readily adopted monomeric forms, unfolded, and aggregated with heating, possibly while releasing coordinated metals. Conclusions: Deamidation to N53 in SOD1 encourages the adoption of non-native conformers, and its detection in WT MN cultures suggests relevance to sALS pathophysiology.

BioChem doi: 10.3390/biochem5040038

Authors: Cecilia Salzillo Andrea Marzullo

RASopathies are a heterogeneous group of genetic syndromes caused by germline mutations in genes encoding proteins of the RAS/MAPK pathway, which are essential in the regulation of cell proliferation, differentiation and survival. Although characterized by common phenotypic manifestations such as craniofacial dysmorphism, congenital heart defects, and growth retardation, an aspect of great clinical relevance is the increased risk of sudden cardiac death, especially in relation to hypertrophic cardiomyopathy (HCM) and ventricular arrhythmias. Pathogenic variants in genes such as RAF1, RIT1, PTPN11, BRAF and SHOC2 have been associated with phenotypes with increased incidence of HCM, sometimes with early onset and a rapidly evolving course. The literature highlights the importance of early identification of patients at risk; however, specific surveillance protocols and follow-up strategies are defined in expert guidelines. This literature review aims to provide an updated overview of the main RASopathies with cardiac involvement, highlighting the genotype-phenotype correlations, the pathogenic mechanisms underlying sudden cardiac death, and current diagnosis, monitoring, and prevention strategies. The aim is to promote greater clinical awareness and encourage a multidisciplinary approach aimed at reducing mortality in these rare genetic conditions.

BioChem doi: 10.3390/biochem5040037

Authors: Mike Tabone

Skeletal muscle is increasingly recognized as a dynamic endocrine organ whose secretome—particularly myokines—serves as a central hub for the coordination of systemic metabolic health, inflammation, and tissue adaptation. This review integrates molecular, cellular, and physiological evidence to elucidate how myokine signaling translates mechanical and metabolic stimuli from exercise into biochemical pathways that regulate glucose homeostasis, lipid oxidation, mitochondrial function, and immune modulation. We detail the duality and context-dependence of cytokine and myokine actions, emphasizing the roles of key mediators such as IL-6, irisin, SPARC, FGF21, and BAIBA in orchestrating cross-talk between muscle, adipose tissue, pancreas, liver, bone, and brain. Distinctions between resistance and endurance training are explored, highlighting how each modality shapes the myokine milieu and downstream metabolic outcomes through differential activation of AMPK, mTOR, and PGC-1α axes. The review further addresses the hormetic role of reactive oxygen species, the importance of satellite cell dynamics, and the interplay between anabolic and catabolic signaling in muscle quality control and longevity. We discuss the clinical implications of these findings for metabolic syndrome, sarcopenia, and age-related disease, and propose that the remarkable plasticity of skeletal muscle and its secretome offers a powerful, multifaceted target for lifestyle interventions and future therapeutic strategies. An original infographic is presented to visually synthesize the complex network of myokine-mediated muscle–organ interactions underpinning exercise-induced metabolic health.

BioChem doi: 10.3390/biochem5040036

Authors: Kisook Jung Narae Kim Chaelin Park Jaewook Kim

Background/Objectives: Ginsenosides, one of the most pharmaceutically valuable chemical compounds in Panax ginseng, are synthesized with several enzymes, including UGTs. UGTs determine absorbability and physiological function upon consumption. Thus, understanding the functional residues of ginsenoside biosynthesis-associated UGTs is crucial for enhancing the production of valuable ginsenoside varieties. Methods: We collected the UGT homologs of high sequence similarity from two rate-limiting steps of the biosynthetic pathway. The 3D structures of these proteins were predicted using the AlphaFold3 model. The ligand-binding interactions of these UGTs were examined using SwissDock and CB-Dock2. Enzyme kinetics were analyzed with MPEK. Using these tools, we performed in silico mutagenic analyses to identify the functional residues of UGTs in detail. Results: We elucidated the molecular mechanisms of experimentally verified functional residues in UGTs, many of which were associated with optimal ligand interaction angles that expose target carbons. We also identified putatively important amino acid residues that mediate ligand interactions and modulate reaction kinetics by more than 25%. In this study, residues at positions 62, 224, 397, and 398 were shown to significantly influence enzyme kinetics. Conclusions: Our study provides the first structural analysis of the functional residues of ginsenoside biosynthetic UGTs based on their 3D structures. We identified several key amino acid residues essential for proper ginsenoside biosynthesis: (1) residues determining ligand interactions, (2) residues modulating ligand binding angles, and (3) residues affecting reaction kinetics. Our findings demonstrate an effective approach to identifying functional residues in plant enzymes and present valuable UGT candidates for future experimental validation.

BioChem doi: 10.3390/biochem5040035

Authors: Charles F. Manful Eric Fordjour Emmanuel Ikumoinein Lord Abbey Raymond Thomas

Oxidative stress and inflammation are deeply interconnected processes implicated in the onset and progression of numerous chronic diseases. Despite promising mechanistic insights, conventional antioxidant and anti-inflammatory therapies such as NSAIDs, corticosteroids, and dietary antioxidants have shown limited and inconsistent success in long-term clinical applications due to challenges with efficacy, safety, and bioavailability. This review explores the molecular interplay between redox imbalance and inflammatory signaling and highlights why conventional therapeutic translation has often been inconsistent. It further examines emerging strategies that aim to overcome these limitations, including mitochondrial-targeted antioxidants, Nrf2 activators, immunometabolic modulators, redox enzyme mimetics, and advanced delivery platforms such as nanoparticle-enabled delivery. Natural polyphenols, nutraceuticals, and regenerative approaches, including stem cell-derived exosomes, are also considered for their dual anti-inflammatory and antioxidant potential. By integrating recent preclinical and clinical evidence, this review underscores the need for multimodal, personalized interventions that target the redox-inflammatory axis more precisely. These advances offer renewed promise for addressing complex diseases rooted in chronic inflammation and oxidative stress.

BioChem doi: 10.3390/biochem5040034

Authors: Yue Liang Peng Zhao Haoran Shi Feiyan Xue

Background: Cadmium (Cd) pollution poses a significant environmental challenge. Microbially induced carbonate precipitation (MICP), an advanced bioremediation approach, relies on the co-precipitation of soluble metals with the microbial hydrolysate from urea. This study isolated a urease-producing strain and evaluated its Cd remediation potential. Methods: The isolated strain UA7 was identified through 16S rDNA gene sequencing. Urease production was enhanced by optimizing the culture conditions, including temperature, dissolved oxygen levels—which were affected by the rotational speed and the design of the Erlenmeyer flask, and the concentration of urea added. Its Cd remediation efficacy was assessed both in water and soil. Results: UA7 was identified as Lysinibacillus sp., achieving peak urease activity of 188 U/mL. The immobilization rates of soluble Cd reached as high as 99.61% and 63.37%, respectively, at initial concentrations of 2000 mg/L in water and 50 mg/kg in soil. The mechanism of Cd immobilization by strain UA7 via MICP was confirmed by the microstructure of the immobilized products with attached bacteria, characteristic absorption peaks, and the formed compound Ca0.67Cd0.33CO3, which were analyzed using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD). The Cd-remediation effect of strain UA7, which reduces lodging in wheat plants, prevents the thinning and yellowing of stems and leaves, and hinders the transition of soluble Cd to the above-ground parts of the plant, was also demonstrated in a pot experiment. Conclusions: Therefore, Lysinibacillus sp. UA7 exhibited high potential for efficiently remediating contaminated Cd.

BioChem doi: 10.3390/biochem5040033

Authors: Víctor Coca-Ruiz

The global transition to a circular bioeconomy is accelerating the demand for sustainable, high-performance materials. Filamentous fungi represent a promising solution, as they function as living foundries that transform low-value biomass into advanced, self-assembling materials. While mycelium-based composites have proven potential, progress has been predominantly driven by empirical screening of fungal species and substrates. To unlock their full potential, a paradigm shift from empirical screening to rational design is required. This review introduces a conceptual framework centered on the biochemical programming of the fungal cell wall. Viewed through a materials science lens, the cell wall is a dynamic, hierarchical nanocomposite whose properties can be deliberately tuned. We analyze the contributions of its principal components—the chitin–glucan structural scaffold, the glycoprotein functional matrix, and surface-active hydrophobins—to the bulk characteristics of mycelium-derived materials. We then identify biochemical levers for controlling these properties. External factors such as substrate composition and environmental cues (e.g., pH) modulate cell wall architecture through conserved signaling pathways. Complementing these, an internal synthetic biology toolkit enables direct genetic and chemical intervention. Strategies include targeted engineering of biosynthetic and regulatory genes (e.g., CHS, AGS, GCN5), chemical genetics to dynamically adjust synthesis during growth, and modification of surface chemistry for specialized applications like tissue engineering. By integrating fungal cell wall biochemistry, materials science, and synthetic biology, this framework moves the field from incidental discovery toward the intentional creation of smart, functional, and sustainable mycelium-based materials—aligning material innovation with the imperatives of the circular bioeconomy.

BioChem doi: 10.3390/biochem5030032

Authors: Tuan Minh Dao Taseef Rahman

Proteins are dynamic macromolecules whose functions are intricately linked to their structural flexibility. Recent breakthroughs in deep learning have enabled accurate prediction of static protein structures. However, understanding protein function is more complex. It often requires access to a diverse ensemble of conformations. Traditional sampling techniques exist to help with this. These include molecular dynamics and Monte Carlo simulations. These techniques can explore conformational landscapes. However, they have limitations as they are often limited by high computational cost and suffer from slow convergence. In response, deep generative models (DGMs) have emerged as a powerful alternative for efficient and scalable protein conformation sampling. Leveraging architectures such as variational autoencoders, normalizing flows, generative adversarial networks, and diffusion models, DGMs can learn complex, high-dimensional distributions over protein conformations directly from data. This survey on generative models for protein conformation sampling provides a comprehensive overview of recent advances in this emerging field. We categorize existing models based on generative architecture, structural representation, and target tasks. We also discuss key datasets, evaluation metrics, limitations, and opportunities for integrating physics-based knowledge with data-driven models. By bridging machine learning and structural biology, DGMs are poised to transform our ability to model, design, and understand dynamic protein behavior.

BioChem doi: 10.3390/biochem5030031

Authors: Chiara Castellani Erica De Martino Paolo Scapato

Osteoporosis is a common skeletal disease that leads to increased bone fragility, associated with increased risk of fracture and consequent significant morbidity and mortality, and is a global public health problem. It results from a chronic imbalance in bone remodeling, where bone resorption by osteoclasts exceeds bone formation by osteoblasts. Aging, hormonal changes, comorbidities, and drugs influence the process that leads to osteoporosis. In this review, we delve into the pathogenesis of primary and secondary osteoporosis after a summary of the normal physiology of bone homeostasis. Primary osteoporosis includes postmenopausal osteoporosis, driven largely by estrogen deficiency, and age-related (senile) osteoporosis, associated with reduced bone formation. An insight into male osteoporosis and osteoporosis treatment is also provided. Secondary osteoporosis can derive from underlying conditions, such as endocrine disorders, chronic inflammatory and genetic diseases, or prolonged use of glucocorticoids. Clinically, osteoporosis is often unacknowledged, underlining the importance of early risk assessment and diagnosis. A thorough understanding of the disease, its subtypes, and its underlying pathogenetic mechanisms is essential for early diagnosis and individualized treatment, all targeted to effective fracture prevention.

BioChem doi: 10.3390/biochem5030030

Authors: João Gomes Joana Brandão Silva César Vinícius José Hugo Ribeiro

Introduction: Anemia, characterized by a reduction in hemoglobin concentration, is a widespread health concern globally, impacting individuals across various demographics. Iron deficiency, often compounded by inadequate folic acid levels, is a primary driver. This review aims to consolidate current evidence and offer a practical recommendation regarding the role of folic acid 1 mg + iron (ferrous sulfate) 90 mg supplementation in both preventing and treating anemia. Objective: We aimed to provide a comprehensive review and recommendation regarding the use of folic acid 1 mg + iron (ferrous sulfate) 90 mg supplementation in the prevention and treatment of anemia in adults, based on current evidence and clinical experience. Methods: A thorough literature review was conducted, encompassing studies, guidelines, and meta-analyses related to iron deficiency, anemia, and folic acid supplementation. This review incorporated data from sources such as the World Health Organization (WHO), the European Hematology Association (EHA), and Cochrane Database. Clinical experience of the authors was also taken into account. Results: Anemia, a prevalent hematological condition, affects a significant portion of the global population. The risk factors for iron deficiency and iron deficiency anemia include age, menstruation, pregnancy, dietary restrictions, chronic diseases, and inflammatory conditions. Accurate diagnosis of anemia involves reticulocyte count, morphological classification, and identification of the underlying etiology. Oral iron salts, particularly ferrous sulfate, are the first-line treatment for uncomplicated iron deficiency anemia, with lower doses or alternate-day dosing improving tolerability. Adequate folic acid availability is crucial for erythropoiesis, and supplementation is safe and enhances treatment response, especially in mixed deficiency anemia. A fixed-dose combination of folic acid 1 mg + iron (ferrous sulfate) 90 mg is effective and well-tolerated for the treatment of iron deficiency anemia, mixed nutritional anemia, and iron deficiency without anemia in adults. Conclusions: Based on extensive scientific evidence and clinical experience, the combination of folic acid 1 mg + iron (ferrous sulfate) 90 mg is a valuable therapeutic option for the prevention and treatment of anemia. This combination should be indicated for iron and folic acid deficiency during pregnancy, lactation, and the postpartum period and for the prophylaxis and treatment of anemia during pregnancy and in adults in general. This approach enables correction of folate deficiencies, optimizing treatment response and ensuring sufficient folic acid levels, particularly in cases of incomplete adherence or missed doses, and is critical during pregnancy to minimize the risk of neural tube defects.

BioChem doi: 10.3390/biochem5030029

Authors: Rahul Jain Bipneet Singh Palak Grover Jahnavi Ethakota Sakshi Bai Gurleen Kaur Merritt Bern

IgG4-related disease (IgG4-RD) is a subacute, progressive, multisystemic autoinflammatory condition which presents with nonspecific symptoms like weight loss, fatigue and myalgia, and is marked by lymphoplasmacytic infiltrates rich in IgG4-positive plasma cells. IgG4-RD can involve various organs including the pancreas, bile ducts, thyroid, salivary and lacrimal glands, retroperitoneum, kidneys, lungs and CNS, often mimicking malignancy. A rigorous literature review was conducted. Articles on IgG4 disease, CD-19 and the MITIGATE trials were studied and included in the review. Glucocorticoids remain first-line therapy, but adverse effects and relapses are common. Rituximab, an anti-CD20 agent, is effective but may leave CD20-negative plasmablasts intact, contributing to relapse. In contrast, CD19-targeting therapies like inebilizumab offer more comprehensive B-cell depletion, including plasmablasts, potentially reducing relapses, fibrosis progression and long-term organ damage. MITIGATE trials showed promise in the use of an anti-CD-19 agent in preventing IgG4 disease flares and prolonging the time to first flare.

BioChem doi: 10.3390/biochem5030028

Authors: Pokphazz Christjaroon Orli Wagon Artiene H. Tatian

Background/Objectives: Pemphigus is a rare blistering disease characterized by a chronic course, associated with significant mortality and morbidity. This review article aims to delve into three Pemphigus subtypes: Pemphigus Vulgaris, Pemphigus Foliaceus and Paraneoplastic Pemphigus, including the safety and efficacy of their treatment options. Methods: A thorough literature search was conducted using PubMed, EMBASE, Medline and Cochrane Library to collate data on pharmaceutical treatments of Pemphigus. Studies were selected based on predefined inclusion criteria, which included English language, peer-reviewed articles published in the date range January 2000 to May 2025. Eligible studies involved adults diagnosed with Pemphigus Vulgaris, Pemphigus Foliaceus or Paraneoplastic Pemphigus who were treated with Glucocorticoids, Mycophenolate mofetil, azathioprine or rituximab. The focus was on identifying adverse effects, complete remission and relapse rates. Results: The analysis revealed that glucocorticoid is the first-line treatment for Pemphigus. However, low remission rates of 34% along with steroid-related adverse effects indicate the use of Mycophenolate and azathioprine as steroid-sparing adjuvant therapies. Emerging treatments with rituximab have demonstrated 90% remission rates, indicating promising results with a comparatively mild side effect profile. Conclusions: The findings highlight the importance of ongoing evaluation of treatment modalities for Pemphigus subtypes to optimise remission rates and minimise adverse effects. Ultimately, studies often fail to isolate specific Pemphigus subtypes owing to the scarcity of literature. There is also a crucial need to address the lack of a standardised grading system for the side effects of glucocorticoids and long-term safety data for rituximab in further longitudinal research.

BioChem doi: 10.3390/biochem5030027

Authors: Yonghong Zhang Shu Xiao Hongsheng Miao Changrui Lu Qi Zhao Zhiyu Shao Ting Chen

Background: Insulin-degrading enzyme (IDE) has become an essential target for the clinical treatment of various important diseases, including type 2 diabetes, Alzheimer’s disease, and breast cancer, owing to its diverse substrate specificity. Particularly in cancer therapy, IDE inhibitors have received significant attention. Methods: We evaluated the in vitro inhibitory activity (IC50) of ethyl 2-(3,5-dioxo-2-p-tolyl-1,2,4-thiadiazolidin-4-yl) acetate (1) against wild-type IDE. The mechanism of action was investigated using Lineweaver–Burk double reciprocal plots and molecular docking analyses. Additionally, we examined the structure–activity relationship, cytotoxicity, selectivity, and effects on cell migration to assess its potential druggability. Based on molecular docking results, we prepared the mutant protein T142A and compared its inhibitory effects with those of the wild-type and mutant proteins. Results: Compound 1 exhibited an inhibitory effect on IDE (IC50 = 3.60 μM). This compound exerts its inhibitory effect through competitive binding to the catalytic site of IDE. Compound 1 demonstrated selective cytotoxicity toward cancer cells compared to normal cells, effectively inhibiting IDE at concentrations ≤ 10 μM. At a concentration of 3.6 μM, the inhibitory effect of the compound on cancer cell migration was significantly stronger than that observed in normal cells. Although the T142A mutant retained catalytic hydrolysis activity with a similar Km value, its reaction rate was markedly lower than that of the wild-type enzyme. Conclusions: Compound 1 exhibits a competitive inhibitory effect on IDE, selectively targeting IDE with greater toxicity toward cancer cells compared to normal cells. It also inhibits cancer cell migration. Notably, 1 demonstrates significantly stronger inhibitory activity against the T142A mutant than the wild-type IDE, indicating that the Thr142 residue plays a crucial role in the interaction between the IDE hydrophobic pocket and 1. These findings suggest that 1 holds potential as a chemotherapeutic agent for treating IDE-related cancers, including breast, prostate, and pancreatic cancers.

BioChem doi: 10.3390/biochem5030026

Authors: Yana Gvozdeva Petya Georgieva

Colon cancer ranks among the most prevalent and lethal cancers worldwide. Lifestyle and dietary factors—such as high consumption of processed foods, red meat, and alcohol, coupled with sedentary behavior—are key contributors to its development. Despite the availability of standard treatments like surgery, chemotherapy, and radiotherapy, colon cancer remains a significant cause of cancer-related deaths. These conventional approaches are often limited by severe side effects, toxicity, recurrence, and the emergence of drug resistance, highlighting the urgent need for alternative therapeutic strategies. Essential oils are a potential cancer-treatment candidate owing to their diverse composition and favorable safety profile. Numerous studies have revealed essential oils’ promising cytotoxic, antioxidant, and anti-inflammatory effects, supporting their potential role in cancer prevention and treatment. Nevertheless, applying volatile oils to the colon faces several limitations, mainly due to their low bioavailability. Furthermore, conditions within the gastrointestinal tract also contribute to the reduced therapeutic efficacy of essential oils. Novel and promising strategies have been developed to overcome the limitations associated with the application of essential oils. The utilization of targeted drug delivery systems has improved the stability of essential oils and enhanced their therapeutic potential in colon cancer treatment. Moreover, even though essential oils cannot replace conventional chemotherapy, they can mitigate some of its adverse effects and improve the efficacy of associated chemotherapy drugs. This review explores the potential of essential oils and their bioactive compounds in colon cancer therapy and highlights current advancements in micro- and nanoencapsulation techniques for their targeted delivery to the colon.

BioChem doi: 10.3390/biochem5030025

Authors: Mariagrazia Piscione Maria Carmela Di Marcantonio Barbara Pala Gabriella Mincione

The growing success of oncologic therapies has led to a significant improvement in patient survival; however, this has been accompanied by an increasing incidence of cardiovascular adverse events, particularly cancer therapy-related cardiac dysfunction (CTRCD). Among these, left ventricular impairment represents a major concern due to its potential to compromise both cardiac and oncologic outcomes. This review provides an in-depth overview of the cardiotoxic adverse events associated with several classes of anticancer agents. Particular focus is given to the molecular mechanisms involved in myocardial injury, such as oxidative stress, mitochondrial dysfunction, calcium dysregulation, endothelial reticulum stress, autophagy, and apoptosis. In parallel, established and emerging cardioprotective strategies, from conventional to newer therapeutic approaches, are explored. The role of advanced imaging modalities, as well as cardiac biomarkers, is discussed in the context of early detection and monitoring of subclinical cardiac injury. Finally, the integration of pharmacogenomics and epigenetics is considered as a promising avenue to personalize risk stratification and preventive therapy. By elucidating the complex interplay between cancer treatments and cardiovascular health, this review underscores the importance of a multidisciplinary, precision medicine approach to optimizing the care of patients undergoing potentially cardiotoxic therapies.

BioChem doi: 10.3390/biochem5030024

Authors: Tayo Alex Adekiya

Prostate cancer continues to be the most common cause of cancer-related disease and mortality among men worldwide, especially in the advanced stages, notably metastatic castration-resistant prostate cancer (mCRPC), which poses significant treatment challenges. Docetaxel, a widely used chemotherapeutic agent, has long served as the standard treatment, offering survival benefits and mitigation. However, its clinical impact is frequently undermined by the development of chemoresistance, which is a formidable challenge that leads to treatment failure and disease progression. The mechanisms driving docetaxel resistance are diverse and complex, encompassing modifications in androgen receptor signaling, drug efflux transporters, epithelial-mesenchymal transition (EMT), microtubule alterations, apoptotic pathway deregulation, and tumor microenvironmental influences. Recent evidence suggests that extracellular RNAs influence drug responses, further complicating the resistance landscape. This review offers a broad discussion on the mechanisms of resistance and explores novel therapeutic approaches to address them. These include next-generation taxanes, targeted molecular inhibitors, immunotherapies, and combination regimens that can be designed to counteract specific resistance pathways. By broadening our understanding of docetaxel resistance, this review highlights potential strategies to improve therapeutic efficacy and the potential to enhance outcomes in patients with advanced treatment-resistant prostate cancer.

BioChem doi: 10.3390/biochem5030023

Authors: Dhienda C. Shahannaz Tadahisa Sugiura Brandon E. Ferrell

Background: Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) hold transformative potential for cardiovascular regenerative medicine, yet their clinical application is hindered by suboptimal mitochondrial maturation and metabolic inefficiencies. This systematic review evaluates targeted strategies for optimizing mitochondrial function, integrating metabolic preconditioning, substrate selection, and pathway modulation to enhance energy production and cellular resilience. Additionally, we examine the role of extracellular matrix stiffness and mechanical stimulation in mitochondrial adaptation, given their influence on metabolism and maturation. Methods: A comprehensive analysis of recent advancements in iPSC-CM maturation was conducted, focusing on metabolic interventions that enhance mitochondrial structure and function. Studies employing metabolic preconditioning, lipid and amino acid supplementation, and modulation of key signaling pathways, including PGC-1α, AMPK, and mTOR, were reviewed. Computational modeling approaches predicting optimal metabolic shifts were assessed, alongside insights into reactive oxygen species (ROS) signaling, calcium handling, and the impact of electrical pacing on energy metabolism. Results: Evidence indicates that metabolic preconditioning with fatty acids and oxidative phosphorylation enhancers improves mitochondrial architecture, cristae density, and ATP production. Substrate manipulation fosters a shift toward adult-like metabolism, while pathway modulation refines mitochondrial biogenesis. Computational models enhance precision, predicting interventions that best align iPSC-CM metabolism with native cardiomyocytes. The synergy between metabolic and biomechanical cues offers new avenues for accelerating maturation, bridging the gap between in vitro models and functional cardiac tissues. Conclusions: Strategic metabolic optimization is essential for overcoming mitochondrial immaturity in iPSC-CMs. By integrating biochemical engineering, predictive modeling, and biomechanical conditioning, a robust framework emerges for advancing iPSC-CM applications in regenerative therapy and disease modeling. These findings pave the way for more physiologically relevant cell models, addressing key translational challenges in cardiovascular medicine.

BioChem doi: 10.3390/biochem5030022

Authors: Charli Fox Lavannya M. Pandit

Chronic thromboembolic pulmonary hypertension (CTEPH) is a rare, progressive form of pre-capillary pulmonary hypertension characterized by persistent, organized thromboemboli in the pulmonary vasculature, leading to vascular remodeling, elevated pulmonary artery pressures, right heart failure, and significant morbidity and mortality if untreated. Despite advances, CTEPH remains underdiagnosed due to nonspecific symptoms and overlapping features with other forms of pulmonary hypertension. Basic Methodology: This review synthesizes data from large international registries, epidemiologic studies, translational research, and multicenter clinical trials. Key methodologies include analysis of registry data to assess incidence and risk factors, histopathological examination of lung specimens, and molecular studies investigating endothelial dysfunction and inflammatory pathways. Diagnostic modalities and treatment outcomes are evaluated through observational studies and randomized controlled trials. Recent Advances and Affected Population: Research has elucidated that CTEPH arises from incomplete resolution of pulmonary emboli, with subsequent fibrotic transformation mediated by dysregulated TGF-β/TGFBI signaling, endothelial dysfunction, and chronic inflammation. Affected populations are typically older adults, often with prior venous thromboembolism, splenectomy, or prothrombotic conditions, though up to 25% have no history of acute PE. The disease burden is substantial, with delayed diagnosis contributing to worse outcomes and higher societal costs. Microvascular arteriopathy and PAH-like lesions in non-occluded vessels further complicate the clinical picture. Conclusions: CTEPH is now recognized as a treatable disease, with multimodal therapies—surgical endarterectomy, balloon pulmonary angioplasty, and targeted pharmacotherapy—significantly improving survival and quality of life. Ongoing research into molecular mechanisms and biomarker-driven diagnostics promises earlier identification and more personalized management. Multidisciplinary care and continued translational investigation are essential to further reduce mortality and optimize outcomes for this complex patient population.

BioChem doi: 10.3390/biochem5030021

Authors: Vitor Marcelo Soares Campos Angela Theresa Zuffo Yabrude Renata Delarue Toniolo Lima Fernanda Wagner Henrique Nunes Pereira Oliva

Background/Objectives: Passiflora (passionflower), traditionally used for anxiety and insomnia, is primarily known for GABAergic modulation. However, evidence suggests broader neuropharmacological actions. This review aimed to systematically explore non-GABAergic mechanisms of Passiflora. Methods: We performed a systematic review following PRISMA Guidelines (PROSPERO: CRD420251028681). PubMed/Medline, PsycINFO, Embase, Web of Science, and Scopus were searched for original research on non-GABA neurobiological mechanisms of Passiflora species (P. incarnata, P. edulis, P. caerulea, P. actinia, P. foetida). Studies were screened and assessed for eligibility, and data on design, Passiflora preparation, mechanisms, and main findings were extracted. Results: Thirteen studies revealed diverse non-GABAergic actions. Passiflora modulates opioidergic and nicotinic cholinergic systems (relevant to analgesia), monoaminergic pathways (affecting dopamine, norepinephrine, serotonin), and the glutamatergic system (offering neuroprotection via NMDA receptor inhibition). It also exhibits significant anti-inflammatory and antioxidant effects (reducing cytokines, activating Nrf2) and modulates the HPA axis (reducing stress hormones). Other mechanisms include gut microbiota modulation and metabolic effects. Conclusions: Passiflora’s therapeutic potential extends beyond GABA, involving multiple neurotransmitter systems and neuroprotective, anti-inflammatory, antioxidant, and HPA axis-regulating activities. This multi-target profile likely contributes to its clinical efficacy in conditions like anxiety, pain, and stress, potentially with a favorable side-effect profile. Further research, including mechanistic studies and clinical trials with relevant biomarkers, is needed to fully elucidate its complex pharmacology.

BioChem doi: 10.3390/biochem5030020

Authors: Tayo Alex Adekiya

Background: Transcription factor pancreatic and duodenal homeobox 1 (PDX1) plays a central role in pancreatic development and insulin regulation. However, its role in breast cancer remains largely unexplored. Objective: This study investigated the effects of PDX1 knockdown and overexpression on MCF7 breast cancer cell proliferation and responsiveness to paclitaxel and doxorubicin. Methods: PDX1 knockdown and overexpression models were established in MCF7 cells. Cell viability was assessed using the XTT assay following exposure to paclitaxel (5–100 nM) or doxorubicin (125–10 µM). Gene and protein expression levels were analyzed by qRT-PCR and western blotting. Results: PDX1 knockdown in MCF7 cells led to a significant increase in proliferation compared to the scrambled control, with approximately 3.22-fold at 72 h, whereas PDX1 overexpression markedly reduced proliferation by about 2.4-fold at 72 h when compared with the control. Upon treatment with paclitaxel or doxorubicin, knockdown cells showed higher viability, indicating reduced drug sensitivity. In contrast, PDX1-overexpressing cells exhibited a significant decrease in viability after treatment with both drugs, demonstrating enhanced sensitivity. Conclusions: PDX1 exhibits tumor-suppressive properties in MCF7 cells and modulates drug response, suggesting that it may serve as a biomarker or therapeutic target in hormone receptor-positive breast cancer.

BioChem doi: 10.3390/biochem5030019

Authors: Sheel Patel Fares Kasem Dylan Flaherty Ashutosh Barve

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.

BioChem doi: 10.3390/biochem5020018

Authors: Hanxiang Liu Zheng Liu Huixian Zhou Rongkai Yan Yuzhen Li Xiaofeng Zhang Lingyu Bao Yixin Yang Jinming Zhang Siyuan Song

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.

BioChem doi: 10.3390/biochem5020017

Authors: Manuel Aureliano Buyong Ma

Biochemistry, or the chemistry of life, is an interdisciplinary science that uses strategies and methods from all exact and natural sciences [...]

BioChem doi: 10.3390/biochem5020016

Authors: Mst. Mimi Md. Hasan

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.

BioChem doi: 10.3390/biochem5020015

Authors: Johan Spoov

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.

BioChem doi: 10.3390/biochem5020014

Authors: Aashish Khadka Bhupendra Raj Giri Rishiram Baral Shailendra Shakya Ashwinee Kumar Shrestha

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.

BioChem doi: 10.3390/biochem5020013

Authors: Riccardo Ray Colciago Chiara Chissotti Federica Ferrario Ilenia Manno Matteo Mombelli Giulia Rossano Lorenzo De Sanctis Stefano Arcangeli

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.

BioChem doi: 10.3390/biochem5020012

Authors: Roshini Ramachandran Frank Macabenta Grace Bettencourt Shulammite Feng

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.

BioChem doi: 10.3390/biochem5020011

Authors: Yvonne Ritsema Huapeng Li Qingfei Zheng

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).

BioChem doi: 10.3390/biochem5020010

Authors: Haydar Witwit Juan C. de la Torre

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.

BioChem doi: 10.3390/biochem5020009

Authors: Prachi Atre Syed A. A. Rizvi

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.

BioChem doi: 10.3390/biochem5020008

Authors: Berkay Baydogan Aslihan Kucuk Bensu Kozan Merve Erdal Burcin Irem Abas Ozge Cevik

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.

BioChem doi: 10.3390/biochem5020007

Authors: Manuel Aureliano M. Cancela Ana Costa Célia Antunes

The XXI SPB National Congress of Biochemistry 2021 was held at the University of Évora in Portugal on 14–16 October 2021 [...]

BioChem doi: 10.3390/biochem5020006

Authors: Mukhit Kulmaganbetov

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.

BioChem doi: 10.3390/biochem5020005

Authors: Hyunseung Kong

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.

BioChem doi: 10.3390/biochem5010004

Authors: William Merre Ricardo Andrade Cyril Perot Alexia Chandor-Proust Caroline Ranquet

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.

BioChem doi: 10.3390/biochem5010003

Authors: Martin Ndayambaje Hicham Wahnou Abdallah Naya Mounia Oudghiri

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.

BioChem doi: 10.3390/biochem5010002

Authors: Inês Lopes Isabel Meireles Rafaela Rocha Rui Medeiros Fátima Cerqueira

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.

BioChem doi: 10.3390/biochem5010001

Authors: Matthew J. A. Phillips Alison T. Ung Elizabeth J. Harry Jason Ashmore Andrew M. McDonagh

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.

BioChem doi: 10.3390/biochem4040018

Authors: Gayathree Thenuwara Xu Cui Zhen Yao Bilal Javed Azza Silotry Naik Furong Tian

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.

BioChem doi: 10.3390/biochem4040017

Authors: Arnold William Tazon Fatima Awwad Fatma Meddeb-Mouelhi Isabel Desgagné-Penix

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.

BioChem doi: 10.3390/biochem4040016

Authors: Clara Di Mario Maria Rita Gigante Angelina Barini Luca Petricca Antonella Barini Antonio Bianchi Stefano Alivernini Barbara Tolusso Elisa Gremese

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.

BioChem doi: 10.3390/biochem4040015

Authors: Carolina Costa Diana Soares Ana Borges Ana Gonçalves José Paulo Andrade Hugo Ribeiro

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).

BioChem doi: 10.3390/biochem4030014

Authors: Nonjabulo Ntombikhona Magwaza Aganze Gloire-Aimé Mushebenge Samuel Chima Ugbaja Nonkululeko Avril Mbatha Rene B. Khan Hezekiel M. Kumalo

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.

BioChem doi: 10.3390/biochem4030013

Authors: Gênifer Erminda Schreiner Elizandra Gomes Schmitt Gabriela Escalante Brittes Laura Smolski dos Santos Luana Tamires Maders Itamar Luís Gonçalves Sílvia Muller de Moura Sarmento Nessana Dartora Vanusa Manfredini

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.

BioChem doi: 10.3390/biochem4030012

Authors: Sila Ozlem Sener Rateep Nasim Talat Nasim

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.

BioChem doi: 10.3390/biochem4030011

Authors: María Paula López María Camila Jiménez Julián Esteban Contreras Laura Rojas Susana Fiorentino José Iglesias

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.

BioChem doi: 10.3390/biochem4030010

Authors: Maryam Rezvani

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.

BioChem doi: 10.3390/biochem4030009

Authors: Stamatia Spyrou Myrto G. Bellou Angelos Papanikolaou Konstantina Nakou Vasiliki G. Kontogianni Alexandra V. Chatzikonstantinou Haralambos Stamatis

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%.

BioChem doi: 10.3390/biochem4020008

Authors: Trevena N. Youssef Sherri L. Christian Rick Rideout Aaron Adamack Pierre Thibault Eric Bonneil Travis D. Fridgen Joseph Banoub

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.

BioChem doi: 10.3390/biochem4020007

Authors: Alhaji H. Janneh

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.

BioChem doi: 10.3390/biochem4020006

Authors: Triet M. Pham Morgan G. Howard Shane M. Carey Lindsey R. Baker Edward L. D’Antonio

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a human pathogenic virus that encodes for a helicase (SC2Hel) that is essential for viral replication. SC2Hel has the ability to unravel dsRNA or dsDNA in an NTP-dependent manner from the 5′ to 3′ directionality. The standard helicase assay from studies involving SARS-CoV and SARS-CoV-2 have relied on the concept of fluorescence resonance energy transfer. Adding to the collection of helicase assays, herein, we have developed a novel tetrazolium-based colorimetric assay system for the detection of ADP that is produced via SC2Hel activity. This SC2Hel assay combines three enzyme-coupled steps involving the ADP-dependent Thermococcus litoralis glucokinase (TlGlcK), Leuconostoc mesenteroides glucose-6-phosphate dehydrogenase (LmG6PDH), and Clostridium kluyveri diaphorase (CkDIA). Iodonitrotetrazolium chloride (INT), a colorimetric tetrazolium reagent, was used in the final step of the assay that converted into INT-formazan during reduction. INT-formazan in the assay’s buffered solution at pH 7.6 exhibited an intense colorimetric response at a wavelength maximum of 505 nm. The assay exhibited excellent performance characteristics as it revealed a Z’ factor of 0.87 and it has the potential to be further adopted into high-throughput screening studies for therapeutic drug discovery research.

BioChem doi: 10.3390/biochem4020005

Authors: Guillem Santamaria Francisco R. Pinto

Metabolites are at the end of the gene–transcript–protein–metabolism cascade. As such, metabolomics is the omics approach that offers the most direct correlation with phenotype. This allows, where genomics, transcriptomics and proteomics fail to explain a trait, metabolomics to possibly provide an answer. Complex phenotypes, which are determined by the influence of multiple small-effect alleles, are an example of these situations. Consequently, the interest in metabolomics has increased exponentially in recent years. As a newer discipline, metabolomic bioinformatic analysis pipelines are not as standardized as in the other omics approaches. In this review, we synthesized the different steps that need to be carried out to obtain biological insight from annotated metabolite abundance raw data. These steps were grouped into three different modules: preprocessing, statistical analysis, and metabolic pathway enrichment. We included within each one of them the different state-of-the-art procedures and tools that can be used depending on the characteristics of the study, providing details about each method’s characteristics and the issues the reader might encounter. Finally, we introduce genome-scale metabolic modeling as a tool for obtaining pseudo-metabolomic data in situations where their acquisition is difficult, enabling the analysis of the resulting data with the modules of the described workflow.

BioChem doi: 10.3390/biochem4020004

Authors: Karine Minari Vitor Hugo Balasco Serrão Júlio César Borges

Heat Shock Protein 90 (Hsp90) acts as a crucial molecular chaperone, playing an essential role in activating numerous signaling proteins. The intricate mechanism of Hsp90 involving ATPase-coupled conformational changes and interactions with cochaperone proteins has been elucidated through biochemical and structural analyses, revealing its activation mechanism and its diverse set of “client” proteins. Despite recent advancements, certain aspects of Hsp90’s ATPase-coupled mechanism remain contentious, and the specific nature of the alterations induced by Hsp90 in client proteins remains largely undiscovered. In this review, we explore the current understanding of Hsp90’s structure and function, drawing insights from single-particle cryoEM studies. Structural studies on Hsp90 using cryoEM have provided valuable insights into the structural dynamics and interactions of this molecular chaperone. CryoEM structures have been instrumental in understanding the ATPase-coupled conformational changes that Hsp90 undergoes during its chaperone cycle. We also highlight recent progress in elucidating the structure of the ATP-bound state of the complete dimeric chaperone. Furthermore, we delve into the roles played by the multitude of cochaperones that collaborate with Hsp90, providing a glimpse into their biochemical mechanisms through the newly obtained cryoEM structures of Hsp90 cochaperone complexes.

BioChem doi: 10.3390/biochem4010003

Authors: Hicham Wahnou Youness Limami Mounia Oudghiri

Arthritis, a global health burden comprising osteoarthritis and rheumatoid arthritis, demands advanced therapeutic approaches. In this context, flavonoids, a diverse group of naturally occurring compounds abundant in fruits, vegetables, and medicinal plants, have emerged as promising candidates for mitigating the inflammatory processes associated with arthritic conditions. This review aims, first, to provide a comprehensive exploration of the potential of flavonoids, focusing on specific compounds such as quercetin, epigallocatechin-3-gallate (EGCG), apigenin, luteolin, fisetin, silibinin, kaempferol, naringenin, and myricetin. The second section of this review delves into the anti-arthritic activities of these flavonoids, drawing insights from clinical trials and scientific studies. Each flavonoid is scrutinized individually to elucidate its mechanisms of action and therapeutic efficacy in the context of both osteoarthritis and rheumatoid arthritis. The third section of this review highlights the challenges associated with harnessing flavonoids for anti-inflammatory purposes. Bioavailability limitations pose a significant hurdle, prompting the exploration of innovative strategies such as the use of nanoparticles as delivery vehicles. In response to these challenges, the fourth section focuses on the emerging field of flavonoid-based nanoparticles. This includes detailed discussions on quercetin, EGCG, fisetin, and naringenin-based nanoparticles, highlighting formulation strategies and preclinical evidence supporting their potential in arthritis management. The targeted delivery to inflammatory sites and the exploration of synergistic combinations with other compounds are also discussed as promising avenues to enhance the therapeutic impact of flavonoids. This review consolidates current knowledge on flavonoids and their nanoformulations as potential therapeutic interventions for osteoarthritis and rheumatoid arthritis. By addressing challenges and presenting future research directions, this review aims to contribute to the advancement of innovative and effective strategies for alleviating the global burden of arthritis.

BioChem doi: 10.3390/biochem4010002

Authors: Lisa Landino Lydia Boike Taylor Lain

Muscle lactate dehydrogenase (LDH-A) catalyzes the reduction of pyruvate to lactate, the end product of anaerobic glycolysis. LDH-A is overexpressed in many cancers prior to and even when tumors receive adequate oxygen, and lactate has multiple cellular roles. We assessed the effect of singlet oxygen and hypochlorous acid (HOCl) on mammalian LDH-A. Oxidants induced distinct patterns of protein crosslinks observed by SDS-PAGE under reducing conditions. LDH-A cysteines were detected using fluorescein-modified maleimide to assess their oxidation and accessibility. Singlet oxygen initially increased cysteine exposure, but higher doses resulted in their oxidation in addition to non-reducible covalent crosslinks. LDH-A cysteines were oxidized by micromolar HOCl (1–10 equivalents over enzyme) but were resistant to millimolar H2O2, chloramines and Angeli’s salt. HOCl oxidation inhibited LDH-A activity and yielded inter-chain disulfides observed by nonreducing SDS-PAGE. Disulfide reduction did not restore LDH-A activity that was lost due to HOCl oxidation. An irreversible conformational change induced by HOCl was detected by native gel electrophoresis and tryptophan fluorescence. In the absence of pyruvate, LDH-A enhanced NADH oxidation resulting in H2O2 formation. Singlet oxygen, but not HOCl, initiated this superoxide-dependent chain reaction. Once damaged by both singlet oxygen or HOCl, LDH-A had decreased NADH oxidation activity.

BioChem doi: 10.3390/biochem4010001

Authors: Evelynn Vergauwen Michiel R. L. Tubeeckx Annemie Houben Sandra Van Vlierberghe Marc Demolder Guido R. Y. De Meyer Patrick Pauwels Tomas Menovsky

The current standard technique for vascular grafting in cerebral revascularization surgery employs the interposition of an autologous blood vessel. Technical complications have necessitated the development of a synthetic alternative, but classical biomaterials are not suited for small caliber vascular grafting due to the resulting neointimal hyperplasia and thrombosis. The electrospinning of polymers is a promising technique for the development of small vascular grafts. The in vivo performance and efficacy of electrospun polyurethane (ePU) grafts with an internal diameter of <1.5 mm have thus far not been evaluated. We developed a novel ePU graft, with a diameter of 1.25 mm, for implantation into the infrarenal aorta of rats. The patency rates of grafts after a 4-month period were equal to those reported in other studies using larger ePU graft diameters and equal or higher than in studies employing other biomaterials. We observed some loss in flow velocity throughout the grafts, which suggests a decreased elasticity of the graft compared to that of the native rat aorta. However, the grafts demonstrated good neo-endothelialization and minimal neointimal hyperplasia. Their porosity promoted cellular infiltration, as observed under tissue slide examination. Our results show that ePU vascular grafts with an internal diameter of <1.5 mm are promising candidates for vascular grafting in cerebral revascularization surgery.

BioChem doi: 10.3390/biochem3040013

Authors: Inês B. Santos Juan Garrido-Maraver Carolina Gonçalves Bruna I. Oliveira Álvaro A. Tavares

Signaling pathways that integrate a large set of inputs (both extra- and intracellular) to control cell proliferation are essential during both development and adult stages to guarantee organism homeostasis. Mobs are small adaptor proteins that participate in several of these signaling pathways. Here, we review recent advances unravelling Mob4 cellular functions, a highly conserved non-catalytic protein, that plays a diversity of roles in cell proliferation, sperm cell differentiation and is simultaneously involved in synapse formation and neural development. In addition, the gene is often overexpressed in a large diversity of tumors and is linked to poor clinical outcomes. Nevertheless, Mob4 molecular functions remain poorly defined, although it integrates the core structure of STRIPAK, a kinase/phosphatase protein complex, that can act upstream of the Hippo pathway. In this review we focus on the recent findings of Mob4 functions, that have begun to clarify its critical role on cell proliferation and the development of tissues and individuals.

BioChem doi: 10.3390/biochem3040012

Authors: Bibiana Correia Maria Inês Sousa João Ramalho-Santos

Diapause-like features can be extended to naïve mouse embryonic stem cells (mESCs) to induce paused pluripotency by using INK128 (mTi), a mammalian target of rapamycin (mTOR) inhibitor. As a core integrative pathway, mTOR senses diverse stimuli and translates these cues to coordinate several processes. We have previously shown that the withdrawal of leucine and arginine from the culture medium of naïve mESCs can induce features of a paused-pluripotent state, including reduced cell proliferation, cell cycle arrest, and reductions in glycolytic and oxidative metabolism. However, surprisingly, although mTi did indeed provoke a paused-like state, this was distinct from and less pronounced than what resulted from leucine and arginine removal, and, according to our results, these features did not seem to necessarily be mTOR-driven. Therefore, this possibility should be considered in further experiments, and mTOR inhibition when using INK128 should always be confirmed and not merely assumed when INK128 is present in the culture medium.

BioChem doi: 10.3390/biochem3040011

Authors: Elizabeth Fitriana Sari Ali I. Mohammed Antonio Celentano Michael John McCullough Nicola Cirillo

A betel quid (BQ) chewing habit has been strongly associated with the development of several oral mucosal diseases. In order to investigate whether individual components of BQ mixtures have distinct physio-pathological effects on oral mucosal cells, we examined the impact of areca nut (AN), Piper betle leaf (Leaf), Piper betle stem inflorescence (SI), areca husk (Husk) and the complete BQ mixture on the growth of oral keratinocytes (OKF-6) and primary oral fibroblasts (MMF-1). Based on their known chemical properties, we selected BQ samples from Banda Aceh (BA) and West Papua (WP) regions for our in vitro study. We used a fluorescein diacetate assay (FDA) to assess the cell viability of BQ components on OKF-6 and MMF-1 cells. The cytotoxic effect of WP-AN on the OKF-6 cell line was observed at a concentration of 100 μg/mL, resulting in a 50% reduction in cell viability (IC50) after a 2-day incubation. Similarly, BA-AN exhibited cytotoxic effect, although at a higher concentration (500 μg/mL). WP-SI also displayed cytotoxic effects at a concentration of 500 μg/mL following 2 days of incubation. In contrast, Leaf, BQ mixture and husk extracts did not show any cytotoxic effects even after 3 days of incubation. No cytotoxic effects were observed at any concentration of BQ components when exposed to MMF-1 cells. Regarding cell proliferation, MMF-1 cells exposed to BA-AN and WP-AN showed increased growth on day 1, followed by decreased growth on day 2, in a dose- and time-dependent manner. Overall, our study indicates that BQ components induce distinctive cytotoxic effects on stromal and epithelial cells from the oral cavity.

BioChem doi: 10.3390/biochem3030010

Authors: Denis Sergeevich Naberezhnov Alexander Andreevich Alferov Yuriy Borisovich Kuzmin Nikolay Evgenievich Kushlinskii

The isothermal amplification of nucleic acids refers to processes that quickly increase the amount of DNA at a constant temperature. These methods are mainly developed as alternatives to PCR for cases in which the application of a thermal cycler is not possible or the assay method must be as rapid as possible. We have developed a new method of isothermal amplification based on the formation of hairpins at the ends of DNA fragments containing palindromic sequences and increased by the hydrolysis of one or both DNA strands by restriction endonuclease, known as hairpin-assisted isothermal reaction (HAIR). The key steps in HAIR are the formation of a self-complementary hairpin and the DNA breakage introduced by nickase. The end hairpins facilitate primer-free amplification, the amplicon strand cleavage by nickase produces additional 3′ ends that serve as new amplification points, and the amount of DNA can increase exponentially. The rate of amplification in HAIR is more than five times the rate of loop-mediated isothermal amplification (LAMP), and the total amount of DNA product of HAIR is more than double the amount of the LAMP product.

BioChem doi: 10.3390/biochem3030009

Authors: Rafaella S. Coelho Sandra M. Rocha Cláudio J. Maia

Oncologic disease is a significant global health issue that causes thousands of deaths annually, and it has a significant impact on the quality of life of patients. Prostate cancer (PCa) is the second most diagnosed cancer and the fourth leading cause of cancer-related death in men in the Western world. Delineation of pathogenetic pathways and key driver molecular alterations involved in PCa development has provided a roadmap for the evaluation of biomarkers in predicting disease outcome and to identify potential therapeutic targets. Chemotherapeutic agents introduced from the 1990s include the taxanes (paclitaxel, docetaxel, and cabazitaxel), which are the anticancer drugs used most frequently for PCa treatment. This review presents the current knowledge about the onset and development of PCa, the state of the art of the use of taxane-based therapy, and their combination with targeting different transmembrane oncoproteins in PCa. The silencing of some transmembrane proteins can improve taxane sensitivity, and therefore may be a mechanism to improve the effectiveness of these drugs in PCa treatment. This combined therapy needs to be explored as a potential therapeutic agent for reducing cell proliferation, migration, and invasiveness in PCa.

BioChem doi: 10.3390/biochem3030008

Authors: Rick M. Rideout Trevena N. Youssef Aaron T. Adamack Rince John Alejandro M. Cohen Travis D. Fridgen Joseph H. Banoub

Despite decades of research on fish otoliths and their capacity to serve as biochronological recorders, much remains unknown about their protein composition, the mechanisms by which proteins are incorporated into the otolith matrix, or the potential for using otolith proteins to provide insight into aspects of fish life history. We examined the protein composition of Atlantic cod (Gadus morhua) otoliths using a state-of-the-art shotgun proteomics approach with liquid chromatography coupled to an electrospray ionization-orbitrap tandem mass spectrometer. In addition to previously known otolith matrix proteins, we discovered over 2000 proteins not previously identified in cod otoliths and more than 1500 proteins not previously identified in any fish otoliths. These included three novel proteins (Somatolactin, F-actin-capping protein subunit beta, Annexin) primarily involved in binding calcium ions and likely mediating crystal nucleation. However, most of the otolith proteins were not necessarily related to otolith formation but rather to other aspects of fish physiology. For example, we identified sex-related biomarkers for males (SPATA6 protein) and females (Vitellogenin-2-like protein). We highlight some noteworthy classes of proteins having diverse functions; however, the primary goal here is not to discuss each protein separately. The number and diverse roles of the proteins discovered in the otoliths suggest that proteomics could reveal critical life history information from archived otolith collections that could be invaluable for understanding aspects of fish biology and population ecology. This proof-of-concept methodology paper provides a novel methodology whereby otolith proteomics can be further explored.

BioChem doi: 10.3390/biochem3020007

Authors: Hyunju Han Jin-Kyu Kang Keun Jae Ahn Chang-Gu Hyun

Dimethyl sulfoxide (DMSO), an amphipathic molecule composed of one highly polar sulfinyl group and two nonpolar methyl groups, is considered an excellent solvent due to its capability to dissolve many polar and nonpolar compounds. Therefore, DMSO is widely used to solubilize drugs for therapeutic applications. DMSO is reported to possess anti-inflammatory, anticancer, and antioxidative capacities, and the anti-inflammatory efficacy of DMSO has been intensively studied in various cell lines and animal models. An in vitro model of mouse macrophage RAW 264.7 cells has been widely used, among several experimental designs, for evaluation during the development of new anti-inflammatory drugs. DMSO, which is used to dissolve samples, is also prone to experimental errors because of its anti-inflammatory properties. Therefore, we systematically confirmed the cytotoxic and anti-inflammatory effects of DMSO and the related signaling pathways in RAW 264.7 cells. The results show that DMSO at 0.25% to 1.5% did not result in cellular toxicity, with results comparable to the control group where DMSO is absent; at concentrations 2.0%, however, it inhibited the viability of RAW264.7 cells (13.25%). The results demonstrate that pretreatment with DMSO profoundly attenuates the lipopolysaccharide (LPS)-stimulated levels of nitric oxide (NO) and prostaglandin (PG)E2, as well as the levels of pro-inflammatory cytokines, cyclooxygenase-2 (COX-2) protein, and inducible nitric oxide synthase (iNOS). Collectively, the DMSO pretreatments appear to notably alleviate LPS-induced damage by reducing phosphorylation of p38, c-Jun N-terminal kinase (JNK), and extracellular signal-regulated kinase proteins (ERKs), nuclear factor-kappa-B (NF-κB) in addition to NF-κB/p65 nuclear translocation. Taken together, the results clearly show that DMSO attenuates the inflammatory response in LPS-induced RAW264.7 cells by regulating the activation of the MAPK and NF-κB signaling pathways. These results contribute to potentially reducing experimental errors or misjudgments when using the LPS-induced RAW 264.7 macrophage cell model for evaluation during the development of new anti-inflammatory drugs.

BioChem doi: 10.3390/biochem3020006

Authors: Carla Nunes João Laranjinha

Nitric oxide (•NO), a diffusible free radical, is an intercellular messenger, playing a crucial role in several key brain physiological processes, including in neurovascular coupling (NVC). In the brain, glutamatergic activation of the neuronal nitric oxide synthase (nNOS) enzyme constitutes its main synthesis pathway. However, when oxygen (O2) supply is compromised, such as in stroke, ischemia, and aging, such •NO production pathway may be seriously impaired. In this context, evidence suggests that, as already observed in the gastric compartment, the reduction of nitrite by dietary compounds (such as ascorbate and polyphenols) or by specific enzymes may occur in the brain, constituting an important rescuing or complementary mechanism of •NO production. Here, using microsensors selective for •NO, we show that nitrite enhanced the •NO production in a concentration-dependent manner and in the presence of ascorbate evoked by N-methyl-D-aspartate (NMDA) and glutamate stimulation of rat hippocampal slices. Additionally, nitrite potentiated the •NO production induced by oxygen-glucose deprivation (OGD). Overall, these observations support the notion of a redox interaction of ascorbate with nitrite yielding •NO upon neuronal glutamatergic activation and given the critical role of NO as the direct mediator of neurovascular coupling may represents a key physiological mechanism by which •NO production for cerebral blood flow (CBF) responses to neuronal activation is sustained under hypoxic/acidic conditions in the brain.

BioChem doi: 10.3390/biochem3020005

Authors: Ryo Doge Yuki Nishino Akiko Saito

Flavan-3-ol derivatives are polyphenolic compounds with multifunctional properties. One of the flavan-3-ol derivatives, green tea catechin epigallocatechin gallate, is known to have anticancer activity as one of its multifunctional properties. We have studied the synthesis of flavan-3-ol derivatives and conducted structure-activity relationship studies; we found that the fluorinated derivatives exhibited high toxicity against HeLa and A549 cells. It was confirmed that the cytotoxicity was affected by the conformation of the flavan-3-ol skeleton and that the 2,3-cis form was dominant. The addition of fluorinated compounds increased the amount of intracellular mitochondrial superoxide, abolished the membrane potential of mitochondria, and, interestingly, formed granular aggregates containing mitochondria. When the level of LC3-II, a marker of autophagy induction, was confirmed, it suggested that the addition of the fluorinated compounds promoted autophagy. These results suggest that the novel highly cytotoxic fluorinated flavan-3-ol compound synthesized in this study promotes autophagy and induces cell death by triggering mitochondrial dysfunction. We believe that these results suggest the possibility of conferring more functionality through structural transformations of flavan-3-ol derivatives.

BioChem doi: 10.3390/biochem3010004

Authors: Lidia La Barbera Chiara Rizzo Giulia Grasso Federica Macaluso Federica Camarda Francesco Ciccia Giuliana Guggino

Modern “omics” sciences, including metabolomics and microbiomics, are currently being applied to inflammatory autoimmune diseases, such as rheumatoid arthritis (RA), to investigate the interplay between microbiota, metabolic function, and the immune system. In recent decades, robust evidence has suggested that disruption of the normal composition of the microbiome, known as dysbiosis, in the gut and mouth of RA patients contributes to immune dysregulation and alterations in the metabolic pathways, shaping the pathogenesis of the disease and playing a central role in the risk and progression of RA. Metabolic pathways can be influenced by various agents such as the surrounding environment, lifestyle, and exposure to microbiota imbalance. In turn, the body’s metabolic homeostasis influences the immune response, making metabolomics helpful not only to understand pathogenesis pathways, but also to improve early disease detection and therapeutic chances. Combined gut microbiome and metabolome studies set out to unravel the interactions between these two entities, providing insights to discover new treatment targets and potential biomarkers to prevent joint damage. The purpose of this review is to summarize the main recent findings that suggest promising new research directions for the pathogenesis of RA.

BioChem doi: 10.3390/biochem3010003

Authors: Raffaella Gallo

Eukaryotic cells are intracellularly divided into several compartments that provide spatiotemporal control over biochemical reactions. Phase separation of proteins and RNA is emerging as an important mechanism underlying the formation of intracellular compartments that are not delimited by membranes. These structures are also known as biomolecular condensates and have been shown to serve a myriad of cellular functions, such as organization of cytoplasm and nucleoplasm, stress response, signal transduction, gene regulation, and immune response. Here, the author will summarize our current understanding of intracellular phase separation, its biological functions, and how this phenomenon is regulated in eukaryotic cells. Additionally, the author will review recent evidence of the role of biomolecular condensates in the development of pathophysiological conditions, with special emphasis on cancer and immune signaling.

BioChem doi: 10.3390/biochem3010002

Authors: Olga M. Rodríguez Martínez Michelle A. Narváez Ramos Angeliz A. Soto Acevedo Carolina C. Colón Colón Darlene Malavé Ramos Coral Castro Rivera Miguel E. Castro Rosario

An acidic extracellular pH value (pHe) is characteristic of many cancers, in contrast to the physiologic pHe found in most benign cells. This difference in pH offers a unique opportunity to design and engineer chemicals that can be employed for pH-selective reactions in the extracellular fluid of cancer cells. The viability of human skin melanoma and corresponding fibroblasts exposed to CaS dispersions is reported. The viability of melanoma cells decreases with CaS dispersion concentration and reaches 57% at 3%, a value easily distinguishable from melanoma control experiments. In contrast, the viability of benign fibroblasts remains nearly constant within experimental error over the range of dispersion concentrations studied. The CaS dispersions facilitate vinculin delocalization in the cytoplasmic fluid, a result consistent with improved focal adhesion kinase (FAK) regulation in melanoma cells. Thermodynamic considerations are consistent with the formation of H2S from CaS in the presence of protons. The thermodynamic prediction is verified in independent experiments with solid CaS and acidic aqueous solutions. The amount of H2S formed decreases with pH. An activation energy for the process of (30 ± 10) kJ/mol in the temperature range of 280 to 330 K is estimated from initial rate measurements as a function of temperature. The total Gibbs energy minimization approach was employed to establish the distribution of sulfides—including H2S in the gas and aqueous phases—from the dissociation of CaS as a function of pH to mimic physiologically relevant pH values. Theoretical calculations suggest that partially protonated CaS in solution can be stable until the sulfur atom bonds to two hydrogen atoms, resulting in the formation of Ca2+ and H2S, which can be solvated and/or released to the gas phase. Our results are consistent with a model in which CaS is dissociated in the extracellular fluid of melanoma cells selectively. The results are discussed in the context of the potential biomedical applications of CaS dispersions in cancer therapies.

BioChem doi: 10.3390/biochem3010001

Authors: Johanna Mattay

It is commonly understood that RNA-binding proteins crucially determine the fate of their target RNAs. Vice versa, RNAs are becoming increasingly recognized for their functions in protein regulation and the dynamics of RNA-protein complexes. Long non-coding RNAs are emerging as potent regulators of proteins that exert unknown RNA-binding properties and moonlighting functions. A vast array of RNA- and protein-centric techniques have been developed for the identification of protein and RNA targets, respectively, including unbiased protein mass spectrometry and next-generation RNA sequencing as readout. Determining true physiological RNA and protein targets is challenging as RNA–protein interaction is highly dynamic, tissue- and cell-type-specific, and changes with the environment. Here I review current techniques for the analysis of RNA–protein interactions in living cells and in vitro. RNA-centric techniques are presented on the basis of cross-linking or the use of alternative approaches. Protein-centric approaches are discussed in combination with high-throughput sequencing. Finally, the impact of mutations in RNA–protein complexes on human disease is highlighted.

BioChem doi: 10.3390/biochem2040019

Authors: Elisângela Gomes De Lima Oliveira Simone Araújo Vieira Fernando Antônio Gomes Da Silva Mateus Matiuzzi Da Costa Anderson S. L. Gomes Helinando P. De Oliveira

The development of composites with antibacterial activity represents an important strategy to avoid side effects such as increasing bacterial resistance to antibiotics. In particular, the green synthesis of metal nanoparticles avoids the use of hazardous chemical compounds and introduces the intrinsic beneficial properties of plant-derived compounds. Herein, the reduction of gold salt into metal nanoparticles was provided by the action of a cationic polymer derived from tannin (Tanfloc®). Comparative activity of antibacterial agents (pure Tanfloc and Au NPs—Tanfloc) at different concentrations were evaluated in terms of the antibiofilm activity, kill-time assays and inhibition haloes confirming the antibacterial activity of the Tanfloc that is reinforced by the incorporation of reduced gold nanoparticles, resulting in the complete elimination of S. aureus from an initial concentration of 108 CFU/mL after 120 min of reaction of Au NPs + Tanfloc solution in association with strong inhibition of the biofilm formation attributed to the Tanfloc.

BioChem doi: 10.3390/biochem2040018

Authors: Mariana Olívia Santana dos Santos Mariana Maciel Nepomuceno José Erivaldo Gonçalves Ana Catarina Leite Véras Medeiros Rafaella Miranda Machado Caroline Pontes da Silva Santos Maria José Cremilda Ferreira Alves Aline do Monte Gurgel Idê Gomes Dantas Gurgel

The 2019 oil spill was considered the largest environmental disaster in the Brazilian Northeastern coast. It was associated with mostly ineffective government actions, thus intensifying historical vulnerabilities faced by local populations. We aimed to analyze the environmental conflicts and injustices and the socio-environmental, economic, and health vulnerabilities arising from the oil spill, considering the COVID-19 pandemic, impacting artisanal fishing communities of the Northeastern coast. A document-based, qualitative, cross-sectional research was carried out between September 2019 and October 2022, in open access secondary databases, and using field diaries from research of the Environmental Health and Work Laboratory (LASAT) of the Aggeu Magalhães Institute of the Oswaldo Cruz Foundation. The disaster caused situations of injustice and environmental conflicts that had negative repercussions in the territories with socioeconomic impacts, on the environment, and on the health of the population. The entire marine environment was affected, resulting in physical and chemical alterations. The health vulnerabilities faced by local people were intensified, influencing the social determination of the health–disease process. The local economy was extremely affected, generating job insecurity and several socio-cultural problems. It is essential to build environmental and health diagnoses for remedial measures in disasters such as the oil spill.

BioChem doi: 10.3390/biochem2040017

Authors: Elzbieta Wanowska Alexis McFeely Joanna Sztuba-Solinska

Epitranscriptome refers to post-transcriptional modifications to RNA and their associated regulatory factors that can govern changes in an organism’s cells in response to various environmental stimuli. Recent studies have recognized over 170 distinct chemical signatures in RNA, and the list keeps expanding. These modifications are hypothesized to have roles beyond simply fine-tuning the structure and function of RNA, as studies have linked them to various infectious and noninfectious diseases in humans. Dedicated cellular machinery comprising of RNA-binding proteins (RBPs) that can write, erase, and read these modifications drives the regulation of the epitranscriptomic code, and as such influences RNA metabolism and homeostasis. Equally, perturbations in the function of RBPs may disrupt RNA processing, further implicating them in pathogenesis. As such, the mechanisms underlying RNA modifications and their association with RBPs are emerging areas of interest within the field of biomedicine. This review focuses on understanding epitranscriptomic modifications, their effects on RNA–RBPs interactions, and their influence on cellular processes.

BioChem doi: 10.3390/biochem2040016

Authors: Miloslav Milichovský

The bilayer’s formations of amphiphilic molecules or polyions of different ionogenity comprise the basic building units of most organic biological and non-biological systems. A theory has evolved to explain their behaviour during the creation of those organized structures, such as anisotropic liquid crystal (LC) in lyotropic (especially hydrotropic) systems and polyelectrolyte multilayer (PEM) assemblies. Particular attention has been paid to the temperature and the important role of water in the formation and behaviour of the bilayers. A novel insight into the formation of hydrotropic liquid LC systems and their thermotropic behaviour is presented. In this context, the systems PEM assemblies are also discussed. Essentially, a structuralised form of water fills out continuous and discontinuous, i.e., confined, nano-spaces among hydrophilic interfaces of bilayers, controlling their supramolecular structure through a system of attractive and repulsive hydration forces. The character of those sophisticated bonding hydration systems is predestined by the composition and type of these hydrophilic interface groups. The miscellaneous complexity of the bilayer’s aqueous systems suggests the need to study these examples in greater detail. Therefore, the bilayer’s processes connected with disruption as far as destruction of bilayers are mentioned, i.e., the processes with the highest potential to combat bacteria, fungi, and viruses, such as in a situation where a person exhales a breath of micro-droplets containing virus nanoparticles (e.g., the COVID-19 virus).

BioChem doi: 10.3390/biochem2040015

Authors: Mariana Marques João Nunes Bárbara Ustymenko Luísa Fialho Luís Martins Anthony J. Burke Cesar Filho Alexandre C. Craveiro Ana R. Costa Sandra Branco Célia M. Antunes

Skin is one of the organs most tested for toxicity and safety evaluation during the process of drug research and development and in the past has usually been performed in vivo using animals. Over the last few years, non-animal alternatives have been developed and validated epidermis models for human and rat skin are already available. Our goal was to develop a histotypical canine skin analog, suitable for non-animal biocompatibility and biosafety assessment. Canine keratinocytes were seeded in an air-lift culture using an adapted version of the CELLnTEC protocol. Corrosion and irritation protocols were adapted from human EpiSkinTM. For histological analysis, sample biopsies were fixed in neutral-buffered formalin, and paraffin slices were routinely processed and stained with hematoxylin and eosin. A canine multilayer and stratified epidermal-like tissue (cEpiderm), confirmed by histological analysis, was obtained. The cEpiderm tissue exhibited normal morphological and functional characteristics of epidermis, namely impermeability and an adequate response to stressors. The cEpiderm is a promising canine skin model for non-animal safety testing of veterinary pharmaceuticals and/or cosmetics, significantly contributing to reducing undesirable in vivo approaches. cEpiderm is therefore a valid canine skin model and may be made commercially available either as a service or as a product.

BioChem doi: 10.3390/biochem2030014

Authors: Ricardo Silva David F. Carrageta Marco G. Alves Pedro F. Oliveira

The incidence of male infertility has been increasing over the years and is now becoming a serious health problem. This trend has been followed by an increase in metabolic diseases, which are known to induce clear alterations in testicular metabolism, although the underlying mechanismremain unclear. Testicular metabolism displays several unique features, with testicular somatic cells being central in providing the conditions needed for spermatogenesis, including its nutritional and hormonal support. In addition to glucose and lactate, the two main energy sources used by the testis, glycogen is also present in testicular cells. Glycogen metabolism is a potential source of glucose to both testicular somatic (namely Sertoli and Leydig cells) and germ cells. Many of the enzymes involved in the pathways of the synthesis and degradation of glycogen were identified in these cells, emphasising the relevance of this complex carbohydrate. Glycogen, however, has other non-canonical functions in testicular cells; besides its role as a source of energy, it is also associated with events such as cellular differentiation and apoptosis. In this review, we address the relevance of testicular glycogen metabolism, focusing on its role in Sertoli and Leydig cells and spermatogenesis. In addition, all the available information on the role of glycogen and related pathways in male infertility cases is discussed. Our discussion highlights that glycogen metabolism has been somewhat overlooked in testis and its contribution to spermatogenesis may be underestimated.

BioChem doi: 10.3390/biochem2030013

Authors: Biplab K. Maiti José J. G. Moura

Metalloenzymes are the most proficient nature catalysts that are responsible for diverse biochemical transformations introducing excellent selectivity and performing at high rates, using intricate mutual relationships between metal ions and proteins. Inspired by nature, chemists started using naturally occurring proteins as templates to harbor non-native metal catalysts for the sustainable synthesis of molecules for pharmaceutical, biotechnological and industrial purposes. Therefore, metalloenzymes are the relevant targets for the design of artificial biocatalysts. The search and development of new scaffolds capable of hosting metals with high levels of selectivity could significantly expand the scope of bio-catalysis. To meet this challenge, herein, three native scaffolds: [1Fe-4Cys] (rubredoxin), [3Fe-4S] (ferredoxin), and [S2MoS2CuS2MoS2]-ORP (orange protein) protein scaffolds are case studies describing templates for the synthesis of non-native monomeric to mixed metal–sulfur clusters, which mimic native Ni containing metalloenzymes including [Ni-Fe] Hydrogenase and [Ni-Fe] CO Dehydrogenase. The non-native metal-substituted metalloproteins are not only useful for catalysis but also as spectroscopic probes.

BioChem doi: 10.3390/biochem2030012

Authors: Aninda Sundar Dey

Three forms of methylated cytosines are present in the eukaryotic genome: 3-methylcytosine, 4-methylcytosine and 5-methylcytosine. 3-methylcytosines create methyl lesions, which impair local DNA function and flexibility, resulting in replication and transcription error. On the other hand, 5-methylcytosine is usually present at the gene promoter which blocks transcription and translation. Fe(II)/2OG-dependent nucleic acid-modifying enzymes are the class of enzymes responsible for the demethylation of these modified cytosines. ALKBH2 and 3 remove 3-methylcytosine via a one-step direct demethylation process. On the other hand, active demethylation of 5mC is initiated by Ten-Eleven Translocation (TET)-family dioxygenases. Via oxidative demethylation, TET1-3 converts 5mC into 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Remarkably, recent findings demonstrate that ALKBH2,3 possess oxidative demethylation properties, along with direct demethylation. On the other hand, the TET family of enzymes possess direct demethylation properties along with oxidative demethylation. Here we review the importance of methylated cytosines in human DNA, their origin, function and removal. In addition, we discuss the recent findings of extraordinary flexibility of Fe(II)/2OG-dependent nucleic acid-modifying enzymes ALKBH2,3 and TET family of enzymes in cytosine demethylation, as well as their impact on epigenetics.

BioChem doi: 10.3390/biochem2020011

Authors: Márcio Simão Natércia Conceição Susana Imaginário João Amaro Maria Leonor Cancela

The Molecular Genetics Mobile Lab or “Laboratório itinerante de Genética Molecular” (Lab-it) was funded in 2008 by Leonor Cancela to promote the learning of molecular genetics which had been introduced at that time into high school biology programms. The project aimed to introduce hands-on laboratory activities in molecular genetics to complement the theoretical concepts taught in school. These included the development of experimental protocols based on theoretical scenarios focusing on themes of forensics sciences, biomedical applications, diagnostic methods, and ecological research using basic molecular biology techniques, such as DNA extraction, polymerase chain reaction (PCR), electrophoresis, and restriction enzyme application. In these scenarios, the students execute all the procedures with the help of the Lab-it instructor and using the Lab-it equipment, followed by a discussion of the results with all the participants and the school teacher. These approaches help the students to consolidate the concepts of molecular biology and simultaneously promote discussions on new advances in the area and choices for university careers. In addition to practical sessions, Lab-it also promotes seminars on topics of interest to the students and teachers. Since 2008, 18 high schools have participated in the region of Algarve, averaging each year about 400 students participating in practical activities. In 2021, despite the COVID pandemic, 9 schools and 379 students were involved in Lab-it practical sessions and 99% of them considered the activity to contribute to better understanding the molecular biology methods approached in theoretical classes and expressed high interest in those sessions.

BioChem doi: 10.3390/biochem2020010

Authors: Custódia Fonseca Manuel Aureliano

In this contribution, we provide an overview of gold compound applications against viruses or parasites during recent years. The special properties of gold have been the subject of intense investigation in recent years, which has led to the development of its chemistry with the synthesis of new compounds and the study of its applicability in various areas such as catalysis, materials, nanotechnology and medicine. Herein, thirteen gold articles with applications in several viruses, such as hepatitis C virus (HCV), influenza A virus (H1N1), vesicular stomatitis virus (VSV), coronavirus (SARS-CoV and SARS-CoV-2), Dengue virus, and several parasites such as Plasmodium sp., Leishmania sp., Tripanossoma sp., Brugia sp., Schistosoma sp., Onchocerca sp., Acanthamoeba sp., and Trichomonas sp. are described. Gold compounds with anti-viral activity include gold nanoparticles with the ligands mercaptoundecanosulfonate, 1-octanethiol and aldoses and gold complexes with phosphine and carbene ligands. All of the gold compounds with anti-parasitic activity reported are gold complexes of the carbene type. Auranofin is a gold drug already used against rheumatoid arthritis, and it has also been tested against virus and parasites.

BioChem doi: 10.3390/biochem2020009

Authors: Deena Fayyad Jessica L. Kelts Tristan H. Nielson Ibiere Lovelyn Epelle Nicodemus C. Monear Miguel T. G. Strawn Benjamin N. Woerner Besa Xhabija

Objectives: The emergence of coronavirus disease 2019 (COVID-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global health calamity unprecedented in the modern world. The disease spread worldwide, and to date, there have been over 230 million confirmed cases of COVID-19, including approximately 4.7 million deaths. Mutant variants of the virus have raised concerns about additional pandemic waves and threaten to reverse our progress thus far to limit the spread of the virus. These variants include Alpha, Beta, and Delta (first reported in December 2020 in the United Kingdom, South Africa, and India, respectively) and Gamma (reported in January 2021 in Brazil). In some cases, countries have even reported a rise in daily cases higher than the first wave in March 2020. Given the rapidly evolving nature of COVID-19 and subsequent new findings and updates each day, this review article aims to comprehensively summarize the etiology, pathophysiology, and clinical features of SARS-CoV-2 infection. Methods: A systematic review of the literature was performed in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to gain insight into the transmissibility, pathogenesis, entry factors, and immune response of COVID-19. Specifically, Pubmed and Google Scholar databases were searched to identify any relevant articles. References within the included articles were reviewed. Published articles related to search criteria from the onset of the COVID-19 pandemic to March 2022 were included. Results: Viral transmissibility is predominantly affected by the modes of transmission, various mutations on the nucleocapsid protein and endoRNAse, gender, age, and other factors. The pathophysiological mechanism is generally unknown, although the clinical manifestations such as headache, loss of smell and taste, vomiting, diarrhea, multiorgan failure, and dermatological and cardiovascular complications are well documented. The progression of infection depends on the immunopathological response and the innate/adaptive immunity. Conclusion: Our review has summarized the latest knowledge about SARS-CoV2. However, as the pandemic continues to spread across the continents, there is an urgent need for more research on potentially emerging coronaviruses and the development of a universal coronaviruses vaccine to put the pandemic behind us.