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Search Results (3,781)

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Keywords = small molecule targeting

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12 pages, 620 KiB  
Review
Manganese-Based Contrast Agents as Alternatives to Gadolinium: A Comprehensive Review
by Linda Poggiarelli, Caterina Bernetti, Luca Pugliese, Federico Greco, Bruno Beomonte Zobel and Carlo A. Mallio
Clin. Pract. 2025, 15(8), 137; https://doi.org/10.3390/clinpract15080137 - 25 Jul 2025
Abstract
Background/Objectives: Magnetic resonance imaging (MRI) is a powerful, non-invasive diagnostic tool capable of capturing detailed anatomical and physiological information. MRI contrast agents enhance image contrast but, especially linear gadolinium-based compounds, have been associated with safety concerns. This has prompted interest in alternative contrast [...] Read more.
Background/Objectives: Magnetic resonance imaging (MRI) is a powerful, non-invasive diagnostic tool capable of capturing detailed anatomical and physiological information. MRI contrast agents enhance image contrast but, especially linear gadolinium-based compounds, have been associated with safety concerns. This has prompted interest in alternative contrast agents. Manganese-based contrast agents offer a promising substitute, owing to manganese’s favorable magnetic properties, natural biological role, and strong T1 relaxivity. This review aims to critically assess the structure, mechanisms, applications, and challenges of manganese-based contrast agents in MRI. Methods: This review synthesizes findings from preclinical and clinical studies involving various types of manganese-based contrast agents, including small-molecule chelates, nanoparticles, theranostic platforms, responsive agents, and controlled-release systems. Special attention is given to pharmacokinetics, biodistribution, and safety evaluations. Results: Mn-based agents demonstrate promising imaging capabilities, with some achieving relaxivity values comparable to gadolinium compounds. Targeted uptake mechanisms, such as hepatocyte-specific transport via organic anion-transporting polypeptides, allow for enhanced tissue contrast. However, concerns remain regarding the in vivo release of free Mn2+ ions, which could lead to toxicity. Preliminary toxicity assessments report low cytotoxicity, but further comprehensive long-term safety studies should be carried out. Conclusions: Manganese-based contrast agents present a potential alternative to gadolinium-based MRI agents pending further validation. Despite promising imaging performance and biocompatibility, further investigation into stability and safety is essential. Additional research is needed to facilitate the clinical translation of these agents. Full article
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16 pages, 298 KiB  
Review
Small-Molecule Drugs in Pediatric Neuro-Oncology
by Stephanie Vairy and George Michaiel
Curr. Oncol. 2025, 32(8), 417; https://doi.org/10.3390/curroncol32080417 - 25 Jul 2025
Abstract
Advances in molecular diagnostics have enabled precision medicine approaches in pediatric neuro-oncology, with small-molecule drugs emerging as promising therapeutic candidates targeting specific genetic and epigenetic alterations in central nervous system (CNS) tumors. This review provides a focused overview of several small-molecule agents under [...] Read more.
Advances in molecular diagnostics have enabled precision medicine approaches in pediatric neuro-oncology, with small-molecule drugs emerging as promising therapeutic candidates targeting specific genetic and epigenetic alterations in central nervous system (CNS) tumors. This review provides a focused overview of several small-molecule agents under investigation or in early clinical use, including ONC201, tazemetostat, vorasidenib, CDK inhibitors, selinexor, and aurora kinase A inhibitors, among others. Highlighted are their mechanisms of action, pharmacokinetic properties, early efficacy data, and tolerability in pediatric populations. Despite encouraging preclinical and early-phase results, most agents face limitations due to study heterogeneity, lack of large-scale pediatric randomized trials, and challenges in drug delivery to the CNS. The review underscores the critical need for robust prospective clinical trials for the integration of these therapies into pediatric neuro-oncology care. Full article
(This article belongs to the Special Issue Clinical Outcomes and New Treatments in Pediatric Brain Tumors)
27 pages, 2494 KiB  
Review
Redox-Epigenetic Crosstalk in Plant Stress Responses: The Roles of Reactive Oxygen and Nitrogen Species in Modulating Chromatin Dynamics
by Cengiz Kaya and Ioannis-Dimosthenis S. Adamakis
Int. J. Mol. Sci. 2025, 26(15), 7167; https://doi.org/10.3390/ijms26157167 - 24 Jul 2025
Abstract
Plants are constantly exposed to environmental stressors such as drought, salinity, and extreme temperatures, which threaten their growth and productivity. To counter these challenges, they employ complex molecular defense systems, including epigenetic modifications that regulate gene expression without altering the underlying DNA sequence. [...] Read more.
Plants are constantly exposed to environmental stressors such as drought, salinity, and extreme temperatures, which threaten their growth and productivity. To counter these challenges, they employ complex molecular defense systems, including epigenetic modifications that regulate gene expression without altering the underlying DNA sequence. This review comprehensively examines the emerging roles of reactive oxygen species (ROS) and reactive nitrogen species (RNS) as central signaling molecules orchestrating epigenetic changes in response to abiotic stress. In addition, biotic factors such as pathogen infection and microbial interactions are considered for their ability to trigger ROS/RNS generation and epigenetic remodeling. It explores how ROS and RNS influence DNA methylation, histone modifications, and small RNA pathways, thereby modulating chromatin structure and stress-responsive gene expression. Mechanistic insights into redox-mediated regulation of DNA methyltransferases, histone acetyltransferases, and microRNA expression are discussed in the context of plant stress resilience. The review also highlights cutting-edge epigenomic technologies such as whole-genome bisulfite sequencing (WGBS), chromatin immunoprecipitation sequencing (ChIP-seq), and small RNA sequencing, which are enabling precise mapping of stress-induced epigenetic landscapes. By integrating redox biology with epigenetics, this work provides a novel framework for engineering climate-resilient crops through the targeted manipulation of stress-responsive epigenomic signatures. Full article
(This article belongs to the Section Molecular Biology)
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15 pages, 1064 KiB  
Article
Targeting RARγ Decreases Immunosuppressive Macrophage Polarization and Reduces Tumor Growth
by Jihyeon Park, Jisun Oh, Sang-Hyun Min, Ji Hoon Yu, Jong-Sup Bae and Hui-Jeon Jeon
Molecules 2025, 30(15), 3099; https://doi.org/10.3390/molecules30153099 - 24 Jul 2025
Abstract
Tumor-associated macrophages (TAMs) play a critical role in the tumor microenvironment (TME), interacting with cancer cells and other components to promote tumor growth. Given the influence of TAMs on tumor progression and resistance to therapy, regulating the activity of these macrophages is crucial [...] Read more.
Tumor-associated macrophages (TAMs) play a critical role in the tumor microenvironment (TME), interacting with cancer cells and other components to promote tumor growth. Given the influence of TAMs on tumor progression and resistance to therapy, regulating the activity of these macrophages is crucial for improving cancer treatment outcomes. TAMs often exhibit immunosuppressive phenotypes (commonly referred to as M2-like macrophages), which suppress immune responses and contribute to drug resistance. Therefore, inhibiting immunosuppressive polarization offers a promising strategy to impede tumor growth. This study revealed retinoic acid receptor gamma (RARγ), a nuclear receptor, as a key regulator of immunosuppressive polarization in THP-1 macrophages. Indeed, the inhibition of RARγ, either by a small molecule or gene silencing, significantly reduced the expression of immunosuppressive macrophage markers. In a three-dimensional tumor spheroid model, immunosuppressive macrophages enhanced the proliferation of HCT116 colorectal cancer cells, which was significantly hindered by RARγ inhibition. These findings suggest that targeting RARγ reprograms immunosuppressive macrophages and mitigates the tumor-promoting effects of TAMs, highlighting RARγ as a promising therapeutic target for developing novel anti-cancer strategies. Full article
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14 pages, 7293 KiB  
Article
Components of Mineralocorticoid Receptor System in Human DRG Neurons Co-Expressing Pain-Signaling Molecules: Implications for Nociception
by Shaaban A. Mousa, Xueqi Hong, Elsayed Y. Metwally, Sascha Tafelski, Jan David Wandrey, Jörg Piontek, Sascha Treskatsch, Michael Schäfer and Mohammed Shaqura
Cells 2025, 14(15), 1142; https://doi.org/10.3390/cells14151142 - 24 Jul 2025
Abstract
The mineralocorticoid receptor (MR), traditionally associated with renal function, has also been identified in various extrarenal tissues, including the heart, brain, and dorsal root ganglion (DRG) neurons in rodents. Previous studies suggest a role for the MR in modulating peripheral nociception, with MR [...] Read more.
The mineralocorticoid receptor (MR), traditionally associated with renal function, has also been identified in various extrarenal tissues, including the heart, brain, and dorsal root ganglion (DRG) neurons in rodents. Previous studies suggest a role for the MR in modulating peripheral nociception, with MR activation in rat DRG neurons by its endogenous ligand, aldosterone. This study aimed to determine whether MR, its protective enzyme 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2), its endogenous ligand aldosterone, and the aldosterone-synthesizing enzyme CYP11B2 are expressed in human DRG neurons and whether they colocalize with key pain-associated signaling molecules as potential targets for genomic regulation. To this end, we performed mRNA transcript profiling and immunofluorescence confocal microscopy on human and rat DRG tissues. We detected mRNA transcripts for MR, 11β-HSD2, and CYP11B2 in human DRG, alongside transcripts for key thermosensitive and nociceptive markers such as TRPV1, the TTX-resistant sodium channel Nav1.8, and the neuropeptides CGRP and substance P (Tac1). Immunofluorescence analysis revealed substantial colocalization of MR with 11β-HSD2 and CGRP, a marker of unmyelinated C-fibers and thinly myelinated Aδ-fibers, in human DRG. MR immunoreactivity was primarily restricted to small- and medium-diameter neurons, with lower expression in large neurons (>70 µm). Similarly, aldosterone colocalized with CYP11B2 and MR with nociceptive markers including TRPV1, Nav1.8, and TrkA in human DRG. Importantly, functional studies demonstrated that prolonged intrathecal inhibition of aldosterone synthesis within rat DRG neurons, using an aldosterone synthase inhibitor significantly downregulated pain-associated molecules and led to sustained attenuation of inflammation-induced hyperalgesia. Together, these findings identify a conserved peripheral MR signaling axis in humans and highlight its potential as a novel target for pain modulation therapies. Full article
(This article belongs to the Section Cells of the Nervous System)
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12 pages, 2911 KiB  
Article
A pH-Sensitive Glutathione Responsive Small-Molecule Probe TZ2 Sensitizes Lung Cancer Cells to Chemotherapy by Targeting Tumor Microenvironment
by Changle Zhong, Minghan Lu, Guanhao Pan, Xintong You, Yan Peng, Shulan Zeng and Guohai Zhang
Molecules 2025, 30(15), 3081; https://doi.org/10.3390/molecules30153081 - 23 Jul 2025
Viewed by 76
Abstract
The tumor microenvironment plays an important role in tumor incidence, metastasis, and chemotherapy resistance. Novel therapeutic strategies targeting the tumor microenvironment have become a research focus in the field of biomedicine. In this study, we developed a smart small-molecule probe, TZ2, featuring [...] Read more.
The tumor microenvironment plays an important role in tumor incidence, metastasis, and chemotherapy resistance. Novel therapeutic strategies targeting the tumor microenvironment have become a research focus in the field of biomedicine. In this study, we developed a smart small-molecule probe, TZ2, featuring pH/GSH dual-responsive characteristics. TZ2 exhibits a unique pH-dependent reaction mechanism: GSH is preferentially covalently modified with maleimide groups in acidic microenvironments (pH < 7), while specifically activating nucleophilic substitutions under alkaline conditions (pH > 7). It is worth noting that TZ2 effectively eliminates intracellular glutathione (GSH) in a time and concentration-dependent manner, demonstrating significant GSH depletion ability in various tumor cell lines. Pharmacodynamic studies have shown that TZ2 not only inhibits the cell cycle by regulating the expression of cell cycle-related proteins, but also effectively suppresses the cloning ability of cancer cells. Furthermore, TZ2 significantly increases the sensitivity of drug-resistant cancer cells to cisplatin. By integrating microenvironment modulation, real-time monitoring, and synergistic therapy, TZ2 provides a novel molecular tool and theoretical basis for tumor theranostics integration. Full article
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34 pages, 800 KiB  
Review
The Role of miRNAs and Extracellular Vesicles in Adaptation After Resistance Exercise: A Review
by Dávid Csala, Zoltán Ádám and Márta Wilhelm
Curr. Issues Mol. Biol. 2025, 47(8), 583; https://doi.org/10.3390/cimb47080583 - 23 Jul 2025
Viewed by 56
Abstract
Resistance exercise can enhance or preserve muscle mass and/or strength. Modifying factors are secreted following resistance exercise. Biomarkers like cytokines and extracellular vesicles, especially small extracellular vesicles, are released into the circulation and play an important role in cell-to-cell and inter-tissue communications. There [...] Read more.
Resistance exercise can enhance or preserve muscle mass and/or strength. Modifying factors are secreted following resistance exercise. Biomarkers like cytokines and extracellular vesicles, especially small extracellular vesicles, are released into the circulation and play an important role in cell-to-cell and inter-tissue communications. There is increasing evidence that physical activity itself promotes the release of extracellular vesicles into the bloodstream, suggesting the importance of vesicles in mediating systemic adaptations following exercise. Extracellular vesicles contain proteins, nucleic acids like miRNAs, and other molecules targeting different cell types and tissues of distant organs. Therefore, extracellular vesicles and encapsulated miRNAs are fine tuners of protein synthesis and are important in the adaptation after resistance training. However, there is a lack of strong data supporting the precise mechanisms of these processes. In this literature review, we collected publications related to miRNA and extracellular vesicle profile changes induced by resistance exercise. To the best of our knowledge, the changes in human extracellular vesicle and microRNA profiles following resistance exercise have not been reviewed yet. We aimed to assess the shortcomings and difficulties characterizing this research area, to summarize the existing results to date, and to propose possible solutions that could help standardize the implementation of future investigations. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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21 pages, 2774 KiB  
Article
Design, Synthesis, and Anticancer Evaluation of New Small-Molecule EGFR Inhibitors Targeting NSCLC and Breast Cancer
by Belgin Sever, Masami Otsuka, Mikako Fujita and Halilibrahim Ciftci
Int. J. Mol. Sci. 2025, 26(15), 7065; https://doi.org/10.3390/ijms26157065 - 22 Jul 2025
Viewed by 107
Abstract
EGFR is the most frequently altered driver gene in non-small-cell lung cancer (NSCLC), and its overexpression is also associated with breast cancer. In the present study, we synthesized 18 new compounds (B-1, B-2, B-6, B-7, and BP-1 [...] Read more.
EGFR is the most frequently altered driver gene in non-small-cell lung cancer (NSCLC), and its overexpression is also associated with breast cancer. In the present study, we synthesized 18 new compounds (B-1, B-2, B-6, B-7, and BP-114). The cytotoxicity of these compounds was evaluated in A549 NSCLC and MCF-7 breast cancer cells, as well as in Jurkat cells and PBMCs (healthy). The most potent compounds were further examined for their ability to induce apoptosis in A549 and MCF-7 cells, as well as their EGFR inhibitory activity. Molecular docking was conducted at the ATP-binding site of EGFR, and key pharmacokinetic and toxicity parameters were predicted in silico. B-2 demonstrated the strongest cytotoxicity against A549 and MCF-7 cells (IC50 = 2.14 ± 0.83 μM and 8.91 ± 1.38 μM, respectively), displaying selective cytotoxicity between Jurkat cells and PBMCs (SI = 23.2). B-2 induced apoptosis in A549 and MCF-7 cells at rates of 16.8% and 4.3%, respectively. B-2 inhibited EGFR by 66% at a 10 μM concentration and showed a strong binding affinity to the ATP-binding site of EGFR. Furthermore, B-2 exhibited drug-like characteristics and was not identified as carcinogenic, genotoxic, or mutagenic. B-2 shows promise as an apoptosis inducer and EGFR inhibitor for future anti-NSCLC and anti-breast cancer research. Full article
(This article belongs to the Special Issue Design of Bioactive Agents and Interaction with Biological Systems)
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26 pages, 4405 KiB  
Review
Nanocarriers for Combination Therapy in Pancreatic Ductal Adenocarcinoma: A Comprehensive Review
by Iris Pontón and David Sánchez-García
Nanomaterials 2025, 15(15), 1139; https://doi.org/10.3390/nano15151139 - 22 Jul 2025
Viewed by 212
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers worldwide, characterized by late diagnosis, aggressive progression, and poor response to conventional monotherapies. Combination therapies have emerged as a promising approach to overcome multidrug resistance (MDR), enhance efficacy, and target the complex tumor [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers worldwide, characterized by late diagnosis, aggressive progression, and poor response to conventional monotherapies. Combination therapies have emerged as a promising approach to overcome multidrug resistance (MDR), enhance efficacy, and target the complex tumor microenvironment (TME). Nanoparticle-based drug delivery systems (DDSs) have gained significant attention for their ability to co-deliver multiple agents with controlled release profiles. This review comprehensively examines nanoparticle-based platforms developed for PDAC combination therapies, focusing on small-molecule drugs. The systems discussed are drawn from studies published between 2005 and 2025. Full article
(This article belongs to the Special Issue Nanoparticles for Multiple Drug Release)
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30 pages, 775 KiB  
Review
Epigenetic Therapies in Endocrine-Related Cancers: Past Insights and Clinical Progress
by Dhruvika Varun, Maria Haque, Jorja Jackson-Oxley, Rachel Thompson, Amber A. Kumari, Corinne L. Woodcock, Anna E. Harris, Srinivasan Madhusudan, Emad Rakha, Catrin S. Rutland, Nigel P. Mongan and Jennie N. Jeyapalan
Cancers 2025, 17(15), 2418; https://doi.org/10.3390/cancers17152418 - 22 Jul 2025
Viewed by 155
Abstract
In hormone-dependent cancers, front-line treatment options include surgery and therapies that target hormone dependance. These therapies are effective initially but fail in tumors that recur, develop resistance or present at an advanced stage. Consequently, new therapeutic avenues are urgently needed. Increasing evidence implicates [...] Read more.
In hormone-dependent cancers, front-line treatment options include surgery and therapies that target hormone dependance. These therapies are effective initially but fail in tumors that recur, develop resistance or present at an advanced stage. Consequently, new therapeutic avenues are urgently needed. Increasing evidence implicates epigenetic modulators in tumor initiation, progression and therapeutic response, making them attractive biomarkers for patient stratification and targets for intervention. Over the past two decades, the discovery and development of small-molecule inhibitors directed against key epigenetic regulators have accelerated. This review provides a comprehensive overview of the major epigenetic targets, the inhibitors developed against them and the clinical trials currently underway in endocrine-related cancers. While epigenetic agents have shown limited benefits as monotherapies, their use in combination regimens is emerging as a strategy to overcome resistance and enhance the efficacy of existing treatments. We summarize the current landscape of combination trials, highlight early signs of clinical activity and discuss the opportunities and challenges inherent in integrating epigenetic drugs into the management of advanced endocrine-related cancers. Full article
(This article belongs to the Special Issue Epigenetics in Endocrine-Related Cancer)
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20 pages, 1400 KiB  
Review
Novel Therapeutics and the Path Toward Effective Immunotherapy in Malignant Peripheral Nerve Sheath Tumors
by Joshua J. Lingo, Elizabeth C. Elias and Dawn E. Quelle
Cancers 2025, 17(14), 2410; https://doi.org/10.3390/cancers17142410 - 21 Jul 2025
Viewed by 250
Abstract
Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are a deadly subtype of soft tissue sarcoma for which effective therapeutic options are lacking. Currently, the best treatment for MPNSTs is complete surgical resection with wide negative margins, but this is often complicated by the tumor [...] Read more.
Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are a deadly subtype of soft tissue sarcoma for which effective therapeutic options are lacking. Currently, the best treatment for MPNSTs is complete surgical resection with wide negative margins, but this is often complicated by the tumor size and location and/or the presence of metastases. Radiation or chemotherapy may be combined with surgery, but patient responses are poor. Targeted treatments, including small-molecule inhibitors of oncogenic proteins such as mitogen-activated protein kinase kinase (MEK), cyclin-dependent kinases 4 and 6 (CDK4/6), and Src-homology 2 domain-containing phosphatase 2 (SHP2), are promising therapeutics for MPNSTs, especially when combined together, but they have yet to gain approval. Immunotherapeutic approaches have been revolutionary for the treatment of some other cancers, but their utility as single agents in sarcoma is limited and not approved for MPNSTs. The immunosuppressive niche of MPNSTs is thought to confer inherent treatment resistance, particularly to immunotherapies. Remodeling an inherently “cold” tumor microenvironment into a “hot” immune milieu to bolster the anti-tumor activity of immunotherapies is of great interest throughout the cancer community. This review focuses on novel therapeutics that target dysregulated factors and pathways in MPNSTs, as well as different types of immunotherapies currently under investigation for this disease. We also consider how certain therapeutics may be combined to remodel the MPNST immune microenvironment and thereby generate a durable anti-tumor immune response to immunotherapy. Full article
(This article belongs to the Special Issue Next-Generation Cancer Therapies)
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23 pages, 4463 KiB  
Review
Stargardt’s Disease: Molecular Pathogenesis and Current Therapeutic Landscape
by Kunal Dayma, Kalpana Rajanala and Arun Upadhyay
Int. J. Mol. Sci. 2025, 26(14), 7006; https://doi.org/10.3390/ijms26147006 - 21 Jul 2025
Viewed by 163
Abstract
Stargardt’s disease (STGD1) is an autosomal recessive juvenile macular degeneration caused by mutations in the ABCA4 gene, impairing clearance of toxic retinoid byproducts in the retinal pigment epithelium (RPE). This leads to lipofuscin accumulation, oxidative stress, photoreceptor degeneration, and central vision loss. Over [...] Read more.
Stargardt’s disease (STGD1) is an autosomal recessive juvenile macular degeneration caused by mutations in the ABCA4 gene, impairing clearance of toxic retinoid byproducts in the retinal pigment epithelium (RPE). This leads to lipofuscin accumulation, oxidative stress, photoreceptor degeneration, and central vision loss. Over 1200 pathogenic/likely pathogenic ABCA4 variants highlight the genetic heterogeneity of STGD1, which manifests as progressive central vision loss, with phenotype influenced by deep intronic variants, modifier genes, and environmental factors like light exposure. ABCA4 variants also show variable penetrance and geographical prevalence. With no approved treatment, investigational therapies target different aspects of disease pathology. Small-molecule therapies target vitamin A dimerization (e.g., ALK-001), inhibit lipofuscin accumulation (e.g., soraprazan), or modulate the visual cycle (e.g., emixustat hydrochloride). Gene therapy trials explore ABCA4 supplementation including strategies like RNA exon editing (ACDN-01) and bioengineered ambient light-activated OPSIN. RORA gene therapy (Phase 2/3) addresses oxidative stress, inflammation, lipid metabolism, and complement system dysregulation. Trials like DRAGON (Phase 3, tinlarebant), STARLIGHT (phase 2, bioengineered OPSIN) show promise, but optimizing efficacy remains challenging. With the key problem of establishing genotype–phenotype correlations, the future of STGD1 therapy may rely on approaches targeting oxidative stress, lipid metabolism, inflammation, complement regulation, and genetic repair. Full article
(This article belongs to the Special Issue Molecular Research in Retinal Degeneration)
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20 pages, 1292 KiB  
Review
AI-Driven Polypharmacology in Small-Molecule Drug Discovery
by Mena Abdelsayed
Int. J. Mol. Sci. 2025, 26(14), 6996; https://doi.org/10.3390/ijms26146996 - 21 Jul 2025
Viewed by 234
Abstract
Polypharmacology, the rational design of small molecules that act on multiple therapeutic targets, offers a transformative approach to overcome biological redundancy, network compensation, and drug resistance. This review outlines the scientific rationale for polypharmacology, highlighting its success across oncology, neurodegeneration, metabolic disorders, and [...] Read more.
Polypharmacology, the rational design of small molecules that act on multiple therapeutic targets, offers a transformative approach to overcome biological redundancy, network compensation, and drug resistance. This review outlines the scientific rationale for polypharmacology, highlighting its success across oncology, neurodegeneration, metabolic disorders, and infectious diseases. Emphasis is placed on how polypharmacological agents can synergize therapeutic effects, reduce adverse events, and improve patient compliance compared to combination therapies. We also explore how computational methods—spanning ligand-based modeling, structure-based docking, network pharmacology, and systems biology—enable target selection and multi-target ligand prediction. Recent advances in artificial intelligence (AI), particularly deep learning, reinforcement learning, and generative models, have further accelerated the discovery and optimization of multi-target agents. These AI-driven platforms are capable of de novo design of dual and multi-target compounds, some of which have demonstrated biological efficacy in vitro. Finally, we discuss the integration of omics data, CRISPR functional screens, and pathway simulations in guiding multi-target design, as well as the challenges and limitations of current AI approaches. Looking ahead, AI-enabled polypharmacology is poised to become a cornerstone of next-generation drug discovery, with potential to deliver more effective therapies tailored to the complexity of human disease. Full article
(This article belongs to the Special Issue Techniques and Strategies in Drug Design and Discovery, 3rd Edition)
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14 pages, 2021 KiB  
Review
New Advances in Small Molecules Targeted at Viral Capsid–Genome Binding
by Jiamei Li, Chengfeng Zhang, Benteng Li and Yuqing Wu
Int. J. Mol. Sci. 2025, 26(14), 6979; https://doi.org/10.3390/ijms26146979 - 20 Jul 2025
Viewed by 214
Abstract
The capsid protein plays a crucial role in the viral life cycle. By interacting with the viral genome, it facilitates the assembly of the nucleocapsid, ultimately leading to the formation of the viral particle. Therefore, interfering with or disrupting the interaction between the [...] Read more.
The capsid protein plays a crucial role in the viral life cycle. By interacting with the viral genome, it facilitates the assembly of the nucleocapsid, ultimately leading to the formation of the viral particle. Therefore, interfering with or disrupting the interaction between the capsid protein and viral genome can effectively inhibit viral replication and infection. This review focuses on elucidating the binding mechanisms between the capsid protein and the viral genome, as well as their potential applications as therapeutic targets. In particular, it summarizes the research progress on small-molecule drugs targeting the capsid–genome binding sites of dengue virus, HBV, and SARS-CoV-2. Notably, this review provides a detailed discussion on the mechanisms by which these small-molecule inhibitors interfere with the capsid–genome interaction, aiming to offer inspiration for the future development of novel antiviral drugs targeting the capsid–genome binding. Full article
(This article belongs to the Special Issue Latest Review Papers in Macromolecules 2025)
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21 pages, 2552 KiB  
Review
The Impact of Fusobacterium nucleatum and the Genotypic Biomarker KRAS on Colorectal Cancer Pathogenesis
by Ahmed Dewan, Ivan Tattoli and Maria Teresa Mascellino
Int. J. Mol. Sci. 2025, 26(14), 6958; https://doi.org/10.3390/ijms26146958 - 20 Jul 2025
Viewed by 339
Abstract
Fusobacterium nucleatum and activating mutations in the Kirsten rat sarcoma virus oncogene homolog (KRAS) are increasingly recognized as cooperative drivers of colorectal cancer (CRC). F. nucleatum promotes tumorigenesis via adhesion to epithelial cells, modulation of the immune microenvironment, and delivery of virulence factors, [...] Read more.
Fusobacterium nucleatum and activating mutations in the Kirsten rat sarcoma virus oncogene homolog (KRAS) are increasingly recognized as cooperative drivers of colorectal cancer (CRC). F. nucleatum promotes tumorigenesis via adhesion to epithelial cells, modulation of the immune microenvironment, and delivery of virulence factors, while KRAS mutations—present in 60% of CRC cases—amplify proliferative signaling and inflammatory pathways. Here, we review the molecular interplay by which F. nucleatum enhances KRAS-driven oncogenic cascades and, conversely, how KRAS mutations reshape the tumor niche to favor bacterial colonization. We further discuss the use of KRAS as a prognostic biomarker and explore promising non-antibiotic interventions—such as phage therapy, antimicrobial peptides, and targeted small-molecule inhibitors—aimed at selectively disrupting F. nucleatum colonization and virulence. This integrated perspective on microbial–genetic crosstalk offers novel insights for precision prevention and therapy in CRC. Full article
(This article belongs to the Section Molecular Microbiology)
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