BioChem, Volume 5, Issue 3 (September 2025) – 14 articles

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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 K_m 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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article