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Search Results (651)

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23 pages, 4589 KiB  
Review
The Novel Achievements in Oncological Metabolic Radio-Therapy: Isotope Technologies, Targeted Theranostics, Translational Oncology Research
by Elena V. Uspenskaya, Ainaz Safdari, Denis V. Antonov, Iuliia A. Valko, Ilaha V. Kazimova, Aleksey A. Timofeev and Roman A. Zubarev
Med. Sci. 2025, 13(3), 107; https://doi.org/10.3390/medsci13030107 (registering DOI) - 1 Aug 2025
Abstract
Background/Objectives. This manuscript presents an overview of advances in oncological radiotherapy as an effective treatment method for cancerous tumors, focusing on mechanisms of action within metabolite–antimetabolite systems. The urgency of this topic is underscored by the fact that cancer remains one of the [...] Read more.
Background/Objectives. This manuscript presents an overview of advances in oncological radiotherapy as an effective treatment method for cancerous tumors, focusing on mechanisms of action within metabolite–antimetabolite systems. The urgency of this topic is underscored by the fact that cancer remains one of the leading causes of death worldwide: as of 2022, approximately 20 million new cases were diagnosed globally, accounting for about 0.25% of the total population. Given prognostic models predicting a steady increase in cancer incidence to 35 million cases by 2050, there is an urgent need for the latest developments in physics, chemistry, molecular biology, pharmacy, and strict adherence to oncological vigilance. The purpose of this work is to demonstrate the relationship between the nature and mechanisms of past diagnostic and therapeutic oncology approaches, their current improvements, and future prospects. Particular emphasis is placed on isotope technologies in the production of therapeutic nuclides, focusing on the mechanisms of formation of simple and complex theranostic compounds and their classification according to target specificity. Methods. The methodology involved searching, selecting, and analyzing information from PubMed, Scopus, and Web of Science databases, as well as from available official online sources over the past 20 years. The search was structured around the structure–mechanism–effect relationship of active pharmaceutical ingredients (APIs). The manuscript, including graphic materials, was prepared using a narrative synthesis method. Results. The results present a sequential analysis of materials related to isotope technology, particularly nucleus stability and instability. An explanation of theranostic principles enabled a detailed description of the action mechanisms of radiopharmaceuticals on various receptors within the metabolite–antimetabolite system using specific drug models. Attention is also given to radioactive nanotheranostics, exemplified by the mechanisms of action of radioactive nanoparticles such as Tc-99m, AuNPs, wwAgNPs, FeNPs, and others. Conclusions. Radiotheranostics, which combines the diagnostic properties of unstable nuclei with therapeutic effects, serves as an effective adjunctive and/or independent method for treating cancer patients. Despite the emergence of resistance to both chemotherapy and radiotherapy, existing nuclide resources provide protection against subsequent tumor metastasis. However, given the unfavorable cancer incidence prognosis over the next 25 years, the development of “preventive” drugs is recommended. Progress in this area will be facilitated by modern medical knowledge and a deeper understanding of ligand–receptor interactions to trigger apoptosis in rapidly proliferating cells. Full article
(This article belongs to the Special Issue Feature Papers in Section Cancer and Cancer-Related Diseases)
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22 pages, 1588 KiB  
Article
Scaffold-Free Functional Deconvolution Identifies Clinically Relevant Metastatic Melanoma EV Biomarkers
by Shin-La Shu, Shawna Benjamin-Davalos, Xue Wang, Eriko Katsuta, Megan Fitzgerald, Marina Koroleva, Cheryl L. Allen, Flora Qu, Gyorgy Paragh, Hans Minderman, Pawel Kalinski, Kazuaki Takabe and Marc S. Ernstoff
Cancers 2025, 17(15), 2509; https://doi.org/10.3390/cancers17152509 - 30 Jul 2025
Viewed by 180
Abstract
Background: Melanoma metastasis, driven by tumor microenvironment (TME)-mediated crosstalk facilitated by extracellular vesicles (EVs), remains a major therapeutic challenge. A critical barrier to clinical translation is the overlap in protein cargo between tumor-derived and healthy cell EVs. Objective: To address this, we developed [...] Read more.
Background: Melanoma metastasis, driven by tumor microenvironment (TME)-mediated crosstalk facilitated by extracellular vesicles (EVs), remains a major therapeutic challenge. A critical barrier to clinical translation is the overlap in protein cargo between tumor-derived and healthy cell EVs. Objective: To address this, we developed Scaffold-free Functional Deconvolution (SFD), a novel computational approach that leverages a comprehensive healthy cell EV protein database to deconvolute non-oncogenic background signals. Methods: Beginning with 1915 proteins (identified by MS/MS analysis on an Orbitrap Fusion Lumos Mass Spectrometer using the IonStar workflow) from melanoma EVs isolated using REIUS, SFD applies four sequential filters: exclusion of normal melanocyte EV proteins, prioritization of metastasis-linked entries (HCMDB), refinement via melanocyte-specific databases, and validation against TCGA survival data. Results: This workflow identified 21 high-confidence targets implicated in metabolic-associated acidification, immune modulation, and oncogenesis, and were analyzed for reduced disease-free and overall survival. SFD’s versatility was further demonstrated by surfaceome profiling, confirming enrichment of H7-B3 (CD276), ICAM1, and MIC-1 (GDF-15) in metastatic melanoma EV via Western blot and flow cytometry. Meta-analysis using Vesiclepedia and STRING categorized these targets into metabolic, immune, and oncogenic drivers, revealing a dense interaction network. Conclusions: Our results highlight SFD as a powerful tool for identifying clinically relevant biomarkers and therapeutic targets within melanoma EVs, with potential applications in drug development and personalized medicine. Full article
(This article belongs to the Section Methods and Technologies Development)
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17 pages, 2178 KiB  
Article
Enabling Early Prediction of Side Effects of Novel Lead Hypertension Drug Molecules Using Machine Learning
by Takudzwa Ndhlovu and Uche A. K. Chude-Okonkwo
Drugs Drug Candidates 2025, 4(3), 35; https://doi.org/10.3390/ddc4030035 - 29 Jul 2025
Viewed by 191
Abstract
Background: Hypertension is a serious global health issue affecting over one billion adults and leading to severe complications if left unmanaged. Despite medical advancements, only a fraction of patients effectively have their hypertension under control. Among the factors that hinder adherence to [...] Read more.
Background: Hypertension is a serious global health issue affecting over one billion adults and leading to severe complications if left unmanaged. Despite medical advancements, only a fraction of patients effectively have their hypertension under control. Among the factors that hinder adherence to hypertensive drugs are the debilitating side effects of the drugs. The lack of adherence results in poorer patient outcomes as patients opt to live with their condition, instead of having to deal with the side effects. Hence, there is a need to discover new hypertension drug molecules with better side effects to increase patient treatment options. To this end, computational methods such as artificial intelligence (AI) have become an exciting option for modern drug discovery. AI-based computational drug discovery methods generate numerous new lead antihypertensive drug molecules. However, predicting their potential side effects remains a significant challenge because of the complexity of biological interactions and limited data on these molecules. Methods: This paper presents a machine learning approach to predict the potential side effects of computationally synthesised antihypertensive drug molecules based on their molecular properties, particularly functional groups. We curated a dataset combining information from the SIDER 4.1 and ChEMBL databases, enriched with molecular descriptors (logP, PSA, HBD, HBA) using RDKit. Results: Gradient Boosting gave the most stable generalisation, with a weighted F1 of 0.80, and AUC-ROC of 0.62 on the independent test set. SHAP analysis over the cross-validation folds showed polar surface area and logP contributing the largest global impact, followed by hydrogen bond counts. Conclusions: Functional group patterns, augmented with key ADMET descriptors, offer a first-pass screen for identifying side-effect risks in AI-designed antihypertensive leads. Full article
(This article belongs to the Section In Silico Approaches in Drug Discovery)
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27 pages, 1813 KiB  
Review
The Review on Adverse Effects of Energy Drinks and Their Potential Drug Interactions
by Lukasz Dobrek
Nutrients 2025, 17(15), 2435; https://doi.org/10.3390/nu17152435 - 25 Jul 2025
Viewed by 676
Abstract
Background: Energy drinks (EDs) are non-alcoholic, functional beverages sold worldwide in more than 165 countries. These products are very popular and often consumed by children, teenagers, and young adults to improve physical performance, reduce drowsiness, and improve memory and concentration with increased intellectual [...] Read more.
Background: Energy drinks (EDs) are non-alcoholic, functional beverages sold worldwide in more than 165 countries. These products are very popular and often consumed by children, teenagers, and young adults to improve physical performance, reduce drowsiness, and improve memory and concentration with increased intellectual effort. However, their consumption is associated with an increased risk of various health consequences. Objectives: The purpose of this non-systematic review was to discuss the components of EDs and their effects, summarize the AEs reported in the literature associated with the consumption of EDs, and briefly characterize the possible ED-related drug interactions. Methods: Scientific evidence was extracted by searching the databases PubMed and Google Scholar. In addition, the reference lists of the retrieved papers were reviewed and cross-referenced to reveal additional relevant scientific evidence. Results: The most common ingredients in EDs are caffeine, taurine, glucuronolactone, B vitamins, the vitamin-like compound inositol, and sweeteners (sugar, fructose, glucose–fructose syrup or artificial sweeteners). Although it is difficult to conclusively prove a cause-and-effect relationship between the consumption of EDs and the observed pathophysiological abnormalities, most scientific evidence (mostly clinical case reports) indicates that both occasional and especially chronic use of EDs is associated with the occurrence of numerous adverse effects (AEs). Among these, the best documented AEs are those on the cardiovascular system. It should also be noted that the components of EDs (primarily caffeine) may have drug interactions; therefore, EDs may be an important factor influencing the safety of pharmacotherapy in patients consuming EDs. Conclusions: Consuming energy drinks lead to various health problems and may interfere with pharmacotherapy due to the potential development of drug interactions. Due to the widespread availability of EDs, their suggestive advertising aimed at the youngest customers, and ambiguous regulations, new legislative policies are required to limit the widespread consumption of such products and their negative health effects. Full article
(This article belongs to the Special Issue Food Security, Food Insecurity, and Nutritional Health)
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29 pages, 2729 KiB  
Article
Computational Evaluation and Multi-Criteria Optimization of Natural Compound Analogs Targeting SARS-CoV-2 Proteases
by Paul Andrei Negru, Andrei-Flavius Radu, Ada Radu, Delia Mirela Tit and Gabriela Bungau
Curr. Issues Mol. Biol. 2025, 47(7), 577; https://doi.org/10.3390/cimb47070577 - 21 Jul 2025
Viewed by 337
Abstract
The global impact of the COVID-19 crisis has underscored the need for novel therapeutic candidates capable of efficiently targeting essential viral proteins. Existing therapeutic strategies continue to encounter limitations such as reduced efficacy against emerging variants, safety concerns, and suboptimal pharmacodynamics, which emphasize [...] Read more.
The global impact of the COVID-19 crisis has underscored the need for novel therapeutic candidates capable of efficiently targeting essential viral proteins. Existing therapeutic strategies continue to encounter limitations such as reduced efficacy against emerging variants, safety concerns, and suboptimal pharmacodynamics, which emphasize the potential of natural-origin compounds as supportive agents with immunomodulatory, anti-inflammatory, and antioxidant benefits. The present study significantly advances prior molecular docking research through comprehensive virtual screening of structurally related analogs derived from antiviral phytochemicals. These compounds were evaluated specifically against the SARS-CoV-2 main protease (3CLpro) and papain-like protease (PLpro). Utilizing chemical similarity algorithms via the ChEMBL database, over 600 candidate molecules were retrieved and subjected to automated docking, interaction pattern analysis, and comprehensive ADMET profiling. Several analogs showed enhanced binding scores relative to their parent scaffolds, with CHEMBL1720210 (a shogaol-derived analog) demonstrating strong interaction with PLpro (−9.34 kcal/mol), and CHEMBL1495225 (a 6-gingerol derivative) showing high affinity for 3CLpro (−8.04 kcal/mol). Molecular interaction analysis revealed that CHEMBL1720210 forms hydrogen bonds with key PLpro residues including GLY163, LEU162, GLN269, TYR265, and TYR273, complemented by hydrophobic interactions with TYR268 and PRO248. CHEMBL1495225 establishes multiple hydrogen bonds with the 3CLpro residues ASP197, ARG131, TYR239, LEU272, and GLY195, along with hydrophobic contacts with LEU287. Gene expression predictions via DIGEP-Pred indicated that the top-ranked compounds could influence biological pathways linked to inflammation and oxidative stress, processes implicated in COVID-19’s pathology. Notably, CHEMBL4069090 emerged as a lead compound with favorable drug-likeness and predicted binding to PLpro. Overall, the applied in silico framework facilitated the rational prioritization of bioactive analogs with promising pharmacological profiles, supporting their advancement toward experimental validation and therapeutic exploration against SARS-CoV-2. Full article
(This article belongs to the Special Issue Novel Drugs and Natural Products Discovery)
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14 pages, 929 KiB  
Article
Possible Association Between Concomitant Use of SSRIs with NSAIDs and an Increased Risk of Adverse Events Among People with Depressive Disorders: Data Mining of FDA Adverse Event Reporting System
by Yi Zhang, Xiaoyu Liu, Jianru Wu, Xuening Zhang, Fenfang Wei, Limin Li, Hongqiao Li, Xinru Wang, Bei Wang, Wenyu Wu and Xiang Hong
Pharmaceuticals 2025, 18(7), 1062; https://doi.org/10.3390/ph18071062 - 18 Jul 2025
Viewed by 352
Abstract
Background: Depression, a major global health issue, is commonly treated with selective serotonin reuptake inhibitors (SSRIs). Given the link between depression and inflammation, nonsteroidal anti-inflammatory drugs (NSAIDs) may have adjunctive benefits. Clinically, SSRIs and NSAIDs are often co-prescribed for comorbid pain or [...] Read more.
Background: Depression, a major global health issue, is commonly treated with selective serotonin reuptake inhibitors (SSRIs). Given the link between depression and inflammation, nonsteroidal anti-inflammatory drugs (NSAIDs) may have adjunctive benefits. Clinically, SSRIs and NSAIDs are often co-prescribed for comorbid pain or inflammatory conditions. However, both drug classes pose risks of adverse effects, and their interaction may lead to clinically significant drug–drug interactions. Objectives: This study analyzed FDA Adverse Event Reporting System (FAERS) data (2004–2024) to assess gastrointestinal bleeding, thrombocytopenia, and acute kidney injury (AKI) potential risks linked to SSRIs (citalopram, escitalopram, fluoxetine, paroxetine, fluvoxamine, and sertraline) and NSAIDs (propionic/acetic/enolic acid derivatives, COX-2 inhibitors) in depression patients, alone and combined. Methods: Disproportionality analysis (crude reporting odds ratios, cROR) identified possible associations; drug interactions were evaluated using Ω shrinkage, additive, multiplicative, and combination risk ratio (CRR) models. Results: Gastrointestinal bleeding risk was potentially elevated with citalopram (cROR = 2.81), escitalopram (2.27), paroxetine (2.17), fluvoxamine (3.58), sertraline (1.69), and propionic acid NSAIDs (3.17). Thrombocytopenia showed a potential correlation with fluoxetine (2.11) and paroxetine (2.68). AKI risk may be increased with citalopram (1.39), escitalopram (1.36), fluvoxamine (3.24), and COX-2 inhibitors (2.24). DDI signal analysis suggested that citalopram in combination with propionic acid derivatives (additive model = 0.01, multiplicative model = 1.14, and CRR = 3.13) might increase the risk of bleeding. Paroxetine combined with NSAIDs (additive model = 0.014, multiplicative model = 2.65, and CRR = 2.99) could potentially increase the risk of thrombocytopenia. Sertraline combined with NSAIDs (Ω025 = 0.94, multiplicative model = 2.14) might be associated with an increasing risk of AKI. Citalopram combined with propionic acid derivatives (Ω025 = 1.08, multiplicative model = 2.17, and CRR = 2.42) could be associated with an increased risk of acute kidney injury. Conclusions: Certain combinations of SSRIs and NSAIDs might further elevate these risks of gastrointestinal bleeding, thrombocytopenia, and acute kidney injury in patients with depression. Given the potential drug–drug interactions, heightened clinical vigilance is advised when prescribing SSRIs and NSAIDs in combination to patients with depression. Full article
(This article belongs to the Special Issue Therapeutic Drug Monitoring and Adverse Drug Reactions: 2nd Edition)
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31 pages, 25018 KiB  
Article
VPS26A as a Prognostic Biomarker and Therapeutic Target in Liver Hepatocellular Carcinoma: Insights from Comprehensive Bioinformatics Analysis
by Hye-Ran Kim and Jongwan Kim
Medicina 2025, 61(7), 1283; https://doi.org/10.3390/medicina61071283 - 16 Jul 2025
Viewed by 206
Abstract
Background and Objectives: VPS26A, a core component of the retromer complex, is pivotal to endosomal trafficking and membrane protein recycling. However, its expression profile, prognostic significance, and clinical relevance in liver hepatocellular carcinoma (LIHC) remain unexplored. This study investigates the prognostic potential of [...] Read more.
Background and Objectives: VPS26A, a core component of the retromer complex, is pivotal to endosomal trafficking and membrane protein recycling. However, its expression profile, prognostic significance, and clinical relevance in liver hepatocellular carcinoma (LIHC) remain unexplored. This study investigates the prognostic potential of VPS26A by extensively analyzing publicly available LIHC-related databases. Materials and Methods: Multiple databases, including TIMER, UALCAN, HPA, GSCA, KM Plotter, OSlihc, MethSurv, miRNet, OncomiR, LinkedOmics, GeneMANIA, and STRING, were used to evaluate VPS26A expression patterns, prognostic implications, correlations with tumor-infiltrating immune cells (TIICs), epigenetic modifications, drug sensitivity, co-expression networks, and protein–protein interactions in LIHC. Results: VPS26A was significantly overexpressed at both the mRNA and protein levels in LIHC tissues compared to that in normal tissues. This upregulation was strongly associated with a poor prognosis. Furthermore, VPS26A expression was both positively and negatively correlated with various TIICs. Epigenetic analysis indicated that VPS26A is regulated by promoter and regional DNA methylation. Additionally, VPS26A influences the sensitivity of LIHC cells to a broad range of anticancer agents. Functional enrichment and co-expression analyses revealed that VPS26A serves as a central regulator of the LIHC transcriptomic landscape, with positively correlated gene sets linked to poor prognosis. Additionally, VPS26A contributes to the molecular architecture governing vesicular trafficking, with potential relevance to diseases involving defects in endosomal transport and autophagy. Notably, miRNAs targeting VPS26A-associated gene networks have emerged as potential prognostic biomarkers for LIHC. VPS26A was found to be integrated into a highly interconnected signaling network comprising proteins in cancer progression, immune regulation, and cellular metabolism. Conclusions: Overall, VPS26A may serve as a potential prognostic biomarker and therapeutic target in LIHC. This study provides novel insights into the molecular mechanisms underlying LIHC progression, and highlights the multifaceted role of VPS26A in tumor biology. Full article
(This article belongs to the Section Oncology)
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17 pages, 3753 KiB  
Article
LSA-DDI: Learning Stereochemistry-Aware Drug Interactions via 3D Feature Fusion and Contrastive Cross-Attention
by Shanshan Wang, Chen Yang and Lirong Chen
Int. J. Mol. Sci. 2025, 26(14), 6799; https://doi.org/10.3390/ijms26146799 - 16 Jul 2025
Viewed by 252
Abstract
Accurate prediction of drug–drug interactions (DDIs) is essential for ensuring medication safety and optimizing combination-therapy strategies. However, existing DDI models face limitations in handling interactions related to stereochemistry and precisely locating drug interaction sites. These limitations reduce the prediction accuracy for conformation-dependent interactions [...] Read more.
Accurate prediction of drug–drug interactions (DDIs) is essential for ensuring medication safety and optimizing combination-therapy strategies. However, existing DDI models face limitations in handling interactions related to stereochemistry and precisely locating drug interaction sites. These limitations reduce the prediction accuracy for conformation-dependent interactions and the interpretability of molecular mechanisms, potentially posing risks to clinical safety. To address these challenges, we introduce LSA-DDI, a Spatial-Contrastive-Attention-Based Drug–Drug Interaction framework. Our 3D feature extraction method captures the spatial structure of molecules through three features—coordinates, distances, and angles—and fuses them to enhance the model of molecular spatial structures. Concurrently, we design and implement a Dynamic Feature Exchange (DFE) mechanism that dynamically regulates the flow of information across modalities via an attention mechanism, achieving bidirectional enhancement and semantic alignment of 2D topological and 3D spatial structure features. Additionally, we incorporate a dynamic temperature-regulated multiscale contrastive learning framework that effectively aligns multiscale features and enhances the model’s generalizability. Experiments conducted on public drug databases under both warm-start and cold-start scenarios demonstrated that LSA-DDI achieved competitive performance, with consistent improvements over existing methods. Full article
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18 pages, 20761 KiB  
Article
Integrated Meta-Analysis Identifies Keratin Family Genes and Associated Genes as Key Biomarkers and Therapeutic Targets in Metastatic Cutaneous Melanoma
by Sumaila Abubakari, Yeşim Aktürk Dizman and Filiz Karaman
Diagnostics 2025, 15(14), 1770; https://doi.org/10.3390/diagnostics15141770 - 13 Jul 2025
Viewed by 429
Abstract
Background/Objectives: Cutaneous melanoma is one of the aggressive forms of skin cancer originating from melanocytes. The high incidence of melanoma metastasis continues to rise, partly due to the complex nature of the molecular mechanisms driving its progression. While melanomas generally arise from melanocytes, [...] Read more.
Background/Objectives: Cutaneous melanoma is one of the aggressive forms of skin cancer originating from melanocytes. The high incidence of melanoma metastasis continues to rise, partly due to the complex nature of the molecular mechanisms driving its progression. While melanomas generally arise from melanocytes, we investigated whether aberrant keratinocyte differentiation pathways—like cornified envelope formation—discriminate primary melanoma from metastatic melanoma, revealing novel biomarkers in progression. Methods: In the present study, we retrieved four datasets (GSE15605, GSE46517, GSE8401, and GSE7553) associated with primary and metastatic melanoma tissues and identified differentially expressed genes (DEGs). Thereafter, an integrated meta-analysis and functional enrichment analysis of the DEGs were performed to evaluate the molecular mechanisms involved in melanoma metastasis, such as immune cell deconvolution and protein-protein interaction (PPI) network construction. Hub genes were identified based on four topological methods, including ‘Betweenness’, ‘MCC’, ‘Degree’, and ‘Bottleneck’. We validated the findings using the TCGA-SKCM cohort. Drug-gene interactions were evaluated using the DGIdb, whereas structural druggability was assessed using the ProteinPlus and AlphaFold databases. Results: We identified a total of eleven hub genes associated with melanoma progression. These included members of the keratin gene family (e.g., KRT5, KRT6A, KRT6B, etc.). Except for the gene CDH1, all the hub genes were downregulated in metastatic melanoma tissues. From a prognostic perspective, these hub genes were associated with poor prognosis (i.e., unfavorable). Using the Human Protein Atlas (HPA), immunohistochemistry evaluation revealed mostly undetected levels in metastatic melanoma. Additionally, the cornified envelope formation was the most enriched pathway, with a gene ratio of 17/33. The tumor microenvironment (TME) of metastatic melanomas was predominantly enriched in NK cell–associated signatures. Finally, several hub genes demonstrated favorable druggable potential for immunotherapy. Conclusions: Through integrated meta-analysis, this study identifies transcriptional, immunological, and structural pathways to melanoma metastasis and highlights keratin family genes as promising biomarkers for therapeutic targeting. Full article
(This article belongs to the Section Pathology and Molecular Diagnostics)
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25 pages, 4620 KiB  
Review
Network Pharmacology as a Tool to Investigate the Antioxidant and Anti-Inflammatory Potential of Plant Secondary Metabolites—A Review and Perspectives
by Anna Merecz-Sadowska, Arkadiusz Sadowski, Hanna Zielińska-Bliźniewska, Karolina Zajdel and Radosław Zajdel
Int. J. Mol. Sci. 2025, 26(14), 6678; https://doi.org/10.3390/ijms26146678 - 11 Jul 2025
Viewed by 334
Abstract
Plant secondary metabolites possess significant antioxidant and anti-inflammatory properties, but their complex polypharmacological mechanisms remain poorly understood. Network pharmacology has emerged as a powerful systems-level approach for investigating multi-target interactions of natural products. This review systematically analyzes network pharmacology applications in elucidating the [...] Read more.
Plant secondary metabolites possess significant antioxidant and anti-inflammatory properties, but their complex polypharmacological mechanisms remain poorly understood. Network pharmacology has emerged as a powerful systems-level approach for investigating multi-target interactions of natural products. This review systematically analyzes network pharmacology applications in elucidating the antioxidant and anti-inflammatory mechanisms of plant metabolites, evaluating concordance between computational predictions and experimental validation. A comprehensive literature search was conducted across major databases (2015–2025), focusing on network pharmacology studies with experimental validation. Analysis revealed remarkable convergence toward common molecular mechanisms, despite diverse chemical structures. For antioxidant activities, the Nrf2/KEAP1/ARE pathway emerged as the most frequently validated mechanism, along with PI3K/AKT, MAPK, and NF-κB signaling. Anti-inflammatory mechanisms consistently involved NF-κB, MAPK, and PI3K/AKT pathways. Key targets, including AKT1, TNF-α, COX-2, NFKB1, and RELA, were repeatedly identified. Flavonoids, phenolic acids, and terpenoids dominated as bioactive compounds. Molecular docking studies supported predicted interactions, with experimental validation showing good concordance for pathway modulation and cytokine regulation. Network pharmacology provides a valuable framework for investigating the complex bioactivities of plant metabolites. The convergence toward common regulatory hubs suggests that natural compounds achieve protective effects by modulating central nodes that integrate redox balance and inflammatory responses. Despite limitations, including database dependency, integrating network pharmacology with experimental validation accelerates mechanistic understanding in natural-product drug discovery. Full article
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19 pages, 1938 KiB  
Article
Identification of Pharmacophore Groups with Antimalarial Potential in Flavonoids by QSAR-Based Virtual Screening
by Adriana de Oliveira Fernandes, Valéria Vieira Moura Paixão, Yria Jaine Andrade Santos, Eduardo Borba Alves, Ricardo Pereira Rodrigues, Daniela Aparecida Chagas-Paula, Aurélia Santos Faraoni, Rosana Casoti, Marcus Vinicius de Aragão Batista, Marcel Bermudez, Silvio Santana Dolabella and Tiago Branquinho Oliveira
Drugs Drug Candidates 2025, 4(3), 33; https://doi.org/10.3390/ddc4030033 - 4 Jul 2025
Viewed by 406
Abstract
Background/Objectives: Severe malaria, mainly caused by Plasmodium falciparum, remains a significant therapeutic challenge due to increasing drug resistance and adverse effects. Flavonoids, known for their wide range of bioactivities, offer a promising route for antimalarial drug discovery. The aim of this [...] Read more.
Background/Objectives: Severe malaria, mainly caused by Plasmodium falciparum, remains a significant therapeutic challenge due to increasing drug resistance and adverse effects. Flavonoids, known for their wide range of bioactivities, offer a promising route for antimalarial drug discovery. The aim of this study was to elucidate key structural features associated with antimalarial activity in flavonoids and to develop accurate, interpretable predictive models. Methods: Curated databases of flavonoid structures and their activity against P. falciparum strains and enzymes were constructed. Molecular fingerprinting and decision tree analyses were used to identify key pharmacophoric groups. Subsequently, molecular descriptors were generated and reduced to build multiple classification and regression models. Results: These models demonstrated high predictive accuracy, with test set accuracies ranging from 92.85% to 100%, and R2 values from 0.64 to 0.97. Virtual screening identified novel flavonoid candidates with potential inhibitory activity. These were further evaluated using molecular docking and molecular dynamics simulations to assess binding affinity and stability with Plasmodium proteins (FabG, FabZ, and FabI). The predicted active ligands exhibited stable pharmacophore interactions with key protein residues, providing insights into binding mechanisms. Conclusions: This study provides highly predictive models for antimalarial flavonoids and enhances the understanding of structure–activity relationships, offering a strong foundation for further experimental validation. Full article
(This article belongs to the Section In Silico Approaches in Drug Discovery)
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26 pages, 3510 KiB  
Article
Comparative Transcriptomics Study of Curcumin and Conventional Therapies in Translocation, Clear Cell, and Papillary Renal Cell Carcinoma Subtypes
by Moses Owoicho Abah, Deborah Oganya Ogenyi, Angelina V. Zhilenkova, Freddy Elad Essogmo, Ikenna Kingsley Uchendu, Yvan Sinclair Ngaha Tchawe, Akaye Madu Pascal, Natalia M. Nikitina, Onoja Solomon Oloche, Maria Pavliv, Alexander S. Rusanov, Varvara D. Sanikovich, Yuliya N. Pirogova, Leonid N. Bagmet, Aleksandra V. Moiseeva and Marina I. Sekacheva
Int. J. Mol. Sci. 2025, 26(13), 6161; https://doi.org/10.3390/ijms26136161 - 26 Jun 2025
Viewed by 1049
Abstract
Currently, there is no standard treatment for renal cell carcinoma (RCC) that is free of side effects and resistance. Additionally, limited information exists on how curcumin affects the gene expression profiles of patients with translocation renal cell carcinoma (tRCC) and papillary renal cell [...] Read more.
Currently, there is no standard treatment for renal cell carcinoma (RCC) that is free of side effects and resistance. Additionally, limited information exists on how curcumin affects the gene expression profiles of patients with translocation renal cell carcinoma (tRCC) and papillary renal cell carcinoma (pRCC). The pathways responsible for metastasis in tRCC are still not well understood, and there is no established treatment or reliable biomarker to predict outcomes for metastatic tRCC. Primary clinical data from patients were retrieved from the TCGA database and analyzed using cBioPortal, stitch, string, R and Python. Various analyses were performed, including differential gene expression, protein-protein interaction (PPI) network analysis, drug-targeted gene analysis, gene ontology (GO), enrichment analyses, and systematic searches to assess the impact of curcumin on the transcriptomic profiles of tRCC, pRCC, and clear cell renal cell carcinoma (ccRCC). No significant impact of sensitive genes on survival in KIRC and KIRP was found, though a trend suggested they may delay disease progression. The combination of curcumin with sunitinib showed promise in overcoming drug resistance in ccRCC by inducing ferroptosis, reducing iron, and increasing ADAMTS18 expression. This study, leveraging data from the TCGA database and other databases explored the impact of curcumin on transcriptomic profiles in tRCC, pRCC, and clear cell RCC (ccRCC). Gene analysis revealed immune and metabolic differences, with KIRC showing a stronger immune response. This study is the first to propose that future research into the miR-148/ADAMTS18 genes and the ferroptosis pathway in tRCC and pRCC could lead to the development of new therapies and the identification of novel therapeutic targets, potentially overcoming drug resistance and metastasis. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
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33 pages, 9434 KiB  
Article
Structure-Based Discovery of Orthosteric Non-Peptide GLP-1R Agonists via Integrated Virtual Screening and Molecular Dynamics
by Mansour S. Alturki, Reem A. Alkhodier, Mohamed S. Gomaa, Dania A. Hussein, Nada Tawfeeq, Abdulaziz H. Al Khzem, Faheem H. Pottoo, Shmoukh A. Albugami, Mohammed F. Aldawsari and Thankhoe A. Rants’o
Int. J. Mol. Sci. 2025, 26(13), 6131; https://doi.org/10.3390/ijms26136131 - 26 Jun 2025
Viewed by 734
Abstract
The development of orally bioavailable non-peptidomimetic glucagon-like peptide-1 receptor agonists (GLP-1RAs) offers a promising therapeutic avenue for the treatment of type 2 diabetes mellitus (T2DM) and obesity. An extensive in silico approach combining structure-based drug design and ligand-based strategies together with pharmacokinetic properties [...] Read more.
The development of orally bioavailable non-peptidomimetic glucagon-like peptide-1 receptor agonists (GLP-1RAs) offers a promising therapeutic avenue for the treatment of type 2 diabetes mellitus (T2DM) and obesity. An extensive in silico approach combining structure-based drug design and ligand-based strategies together with pharmacokinetic properties and drug-likeness predictions is implemented to identify novel non-peptidic GLP-1RAs from the COCONUT and Marine Natural Products (CMNPD) libraries. More than 700,000 compounds were screened by shape-based similarity filtering in combination with precision docking against the orthosteric site of the GLP-1 receptor (PDB ID: 6X1A). The docked candidates were further assessed with the molecular mechanics MM-GBSA tool to check the binding affinities; the final list of candidates was validated by running a 500 ns long MD simulation. Twenty final hits were identified, ten from each database. The hits contained compounds with reported antidiabetic effects but with no evidence of GLP-1 agonist activity, including hits 1, 6, 7, and 10. These findings proposed a novel mechanism for these hits through GLP-1 activity and positioned the other hits as potential promising scaffolds. Among the studied compounds—especially hits 1, 5, and 9—possessed strong and stable interactions with critical amino acid residues such as TRP-203, PHE-381, and GLN-221 at the active site of the 6X1A-substrate along with favorable pharmacokinetic profiles. Moreover, the RMSF and RMSD plots further suggested the possibility of stable interactions. Specifically, hit 9 possessed the best docking score with a ΔG_bind value of −102.78 kcal/mol, surpassing even the control compound in binding affinity. The ADMET profiling also showed desirable drug-likeness and pharmacokinetic characteristics for hit 9. The pipeline of computational integration underscores the potential of non-peptidic alternatives in natural product libraries to pursue GLP-1-mediated metabolic therapy into advanced preclinical validation. Full article
(This article belongs to the Special Issue Small Molecule Drug Design and Research: 3rd Edition)
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23 pages, 3705 KiB  
Article
Revealing the Multi-Target Mechanisms of Fespixon Cream in Diabetic Foot Ulcer Healing: Integrated Network Pharmacology, Molecular Docking, and Clinical RT-qPCR Validation
by Tianbo Li, Dehua Wei, Jiangning Wang and Lei Gao
Curr. Issues Mol. Biol. 2025, 47(7), 485; https://doi.org/10.3390/cimb47070485 - 25 Jun 2025
Viewed by 712
Abstract
Objective: This study aims to elucidate the potential mechanisms by which Fespixon cream promotes diabetic foot ulcer (DFU) healing using network pharmacology, molecular docking, and RT-qPCR validation in clinical tissue samples. Methods: Active components of Fespixon cream were screened from the Traditional Chinese [...] Read more.
Objective: This study aims to elucidate the potential mechanisms by which Fespixon cream promotes diabetic foot ulcer (DFU) healing using network pharmacology, molecular docking, and RT-qPCR validation in clinical tissue samples. Methods: Active components of Fespixon cream were screened from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and relevant literature, and their corresponding targets were standardized using the Universal Protein Resource (UniProt) database. Diabetic foot ulcer (DFU)-related targets were retrieved and filtered from the GeneCards database and the Online Mendelian Inheritance in Man (OMIM) database. The intersection of drug and disease targets was identified, and a protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. The interaction network was visualized using Cytoscape version 3.7.2 software. The potential mechanisms of the shared targets were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis using R software packages, and results were visualized through Bioinformatics online tools. Molecular docking was performed to validate the binding between key active compounds of Fespixon cream and core DFU targets using AutoDock Vina version 1.1.2 and PyMOL software. Furthermore, RT-qPCR analysis was performed on wound edge tissue samples from DFU patients treated with Fespixon cream to experimentally verify the mRNA expression levels of predicted hub genes. Results: Network pharmacology analysis identified eight active compounds in Fespixon cream, along with 153 potential therapeutic targets related to diabetic foot ulcer (DFU). Among these, 21 were determined as core targets, with the top five ranked by degree value being RAC-αserine/threonine-protein kinase (AKT1), Cellular tumor antigen p53 (TP53), Tumor necrosis factor (TNF), Interleukin-6 (IL6), and Mitogen-activated protein kinase 1 (MAPK1). GO enrichment analysis indicated that the targets of Fespixon cream were primarily involved in various biological processes related to cellular stress responses. KEGG pathway enrichment revealed that these targets were significantly enriched in pathways associated with diabetic complications, atherosclerosis, inflammation, and cancer. Molecular docking confirmed stable binding interactions between the five major active compounds—quercetin, apigenin, rosmarinic acid, salvigenin, and cirsimaritin—and the five core targets (AKT1, TP53, TNF, IL6, MAPK1). Among them, quercetin exhibited the strongest binding affinity with AKT1. RT-qPCR validation in clinical DFU tissue samples demonstrated consistent expression trends with computational predictions: AKT1 was significantly upregulated, while TP53, TNF, IL6, and MAPK1 were markedly downregulated in the Fespixon-treated group compared to controls (p < 0.001), supporting the proposed multi-target therapeutic mechanism. Conclusions: Our study reveals the potential mechanisms by which Fespixon cream exerts therapeutic effects on DFUs. The efficacy of Fespixon cream in treating DFUs is attributed to the synergistic actions of its bioactive components through multiple targets and multiple signaling pathways. Full article
(This article belongs to the Section Molecular Pharmacology)
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12 pages, 1336 KiB  
Article
Evaluating Genomic and Clinical Risk Factors for Alzheimer’s Disease in Individuals with Hypertension
by Elizabeth Kim, Kevin Zhang, Miski Abdi, Wei Tse Li, Ruomin Xin, Jessica Wang-Rodriguez and Weg M. Ongkeko
Biomedicines 2025, 13(6), 1508; https://doi.org/10.3390/biomedicines13061508 - 19 Jun 2025
Viewed by 532
Abstract
Background/Objectives: Alzheimer’s disease (AD) is a progressive neurodegenerative condition whose growing prevalence has become an increasingly important public health concern as the population ages. The lack of a definitive cure elevates the importance of identifying risk factors that are crucial for prevention efforts. [...] Read more.
Background/Objectives: Alzheimer’s disease (AD) is a progressive neurodegenerative condition whose growing prevalence has become an increasingly important public health concern as the population ages. The lack of a definitive cure elevates the importance of identifying risk factors that are crucial for prevention efforts. Hypertension (HTN) and obesity have emerged as two highly widespread, interrelated conditions that have independently been associated with AD risk. Despite extensive research into AD pathology, the impact of obesity in a hypertensive population is not well explored. This study aims to investigate how obesity and blood pressure control within a hypertensive population may interact with genomic risk and environmental factors to influence AD incidence. Methods: A retrospective cohort of matched AD and normal patients diagnosed with HTN and taking anti-HTN drugs (n = 1862) from the All of Us database was analyzed. In this hypertensive cohort, obesity was significantly associated with increased AD risk. Genome-wide association studies (GWASs) were conducted on hypertensive AD individuals (n = 1030) and identified six single nucleotide variants (SNVs) that were associated with AD development in this population. Results: Obesity and Area Deprivation Index, a measure of socioeconomic status, were significantly associated with elevated AD risk within the hypertensive cohort. GWAS analysis identified six SNVs significantly associated with AD development among the hypertensive cohort. Conclusions: Our findings suggest that among hypertensive individuals, comorbid obesity and the Area Deprivation Index confer greater AD risk. These results highlight the critical need for obesity prevention and management strategies as part of Alzheimer’s risk reduction efforts. Full article
(This article belongs to the Section Neurobiology and Clinical Neuroscience)
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