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26 pages, 6743 KiB  
Review
Nudibranchs as Sources of Marine Natural Products with Antitumor Activity: A Comprehensive Review
by Máximo Servillera, Mercedes Peña, Laura Cabeza, Héctor J. Pula, Jose Prados and Consolación Melguizo
Mar. Drugs 2025, 23(8), 319; https://doi.org/10.3390/md23080319 (registering DOI) - 3 Aug 2025
Abstract
Nudibranchs have garnered increasing interest in biomedical research due to their complex chemical defense mechanisms, many of which are derived from their diet, including sponges, cnidarians, tunicates, and algae. Their remarkable ability to sequester dietary toxins and synthesize secondary metabolites positions them as [...] Read more.
Nudibranchs have garnered increasing interest in biomedical research due to their complex chemical defense mechanisms, many of which are derived from their diet, including sponges, cnidarians, tunicates, and algae. Their remarkable ability to sequester dietary toxins and synthesize secondary metabolites positions them as a promising source of biologically active compounds with potential therapeutic applications, particularly in oncology. This study aimed to review and summarize the available literature on the bioactive potential of nudibranch-derived compounds, focusing mainly on their antitumor properties. Although research in this area is still limited, recent studies have identified alkaloids and terpenoids isolated from species such as Dolabella auricularia, Jorunna funebris, Dendrodoris fumata, and members of the genus Phyllidia. These compounds exhibit notable cytotoxic activity against human cancer cell lines, including those from colon (HCT-116, HT-29, SW-480), lung (A549), and breast (MCF7) cancer. These findings suggest that compounds derived from nudibranchs could serve as scaffolds for the development of more effective and selective anticancer therapies. In conclusion, nudibranchs represent a valuable yet underexplored resource for antitumor drug discovery, with significant potential to contribute to the development of novel cancer treatments. Full article
(This article belongs to the Special Issue Marine Natural Products as Anticancer Agents, 4th Edition)
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38 pages, 2079 KiB  
Article
Synthesis of Carboranyl-Containing β-Arylaliphatic Acids for Potential Application in BNCT
by Lana I. Lissovskaya and Ilya V. Korolkov
Molecules 2025, 30(15), 3250; https://doi.org/10.3390/molecules30153250 (registering DOI) - 2 Aug 2025
Abstract
One of the promising research areas involving carborane derivatives is boron neutron capture therapy (BNCT). Due to the high boron atom content in carborane molecules, these compounds are considered potential candidates for BNCT-based cancer treatment. Despite ongoing studies on various biologically active carboranyl-containing [...] Read more.
One of the promising research areas involving carborane derivatives is boron neutron capture therapy (BNCT). Due to the high boron atom content in carborane molecules, these compounds are considered potential candidates for BNCT-based cancer treatment. Despite ongoing studies on various biologically active carboranyl-containing compounds, the search continues for substances that meet the stringent requirements of effective BNCT agents. In this study, the synthesis of carboranyl-containing derivatives of β-arylaliphatic acids is described, along with the investigation of their reactivity with primary and secondary amines, as well as with metals and their hydroxides. The molecular structures of the synthesized compounds were confirmed using Fourier-transform infrared (FTIR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, elemental analysis, and mass spectrometry (LC-MS). Cytotoxicity of the water-soluble compound potassium 3-(2-isopropyl-1,2-dicarba-closo-dodecaboran-1-yl)-3-phenylpropanoate was evaluated using several cell lines, including HdFn and MCF-7. Full article
(This article belongs to the Section Organic Chemistry)
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35 pages, 7970 KiB  
Article
Heteroaryl-Capped Hydroxamic Acid Derivatives with Varied Linkers: Synthesis and Anticancer Evaluation with Various Apoptosis Analyses in Breast Cancer Cells, Including Docking, Simulation, DFT, and ADMET Studies
by Ekta Shirbhate, Biplob Koch, Vaibhav Singh, Akanksha Dubey, Haya Khader Ahmad Yasin and Harish Rajak
Pharmaceuticals 2025, 18(8), 1148; https://doi.org/10.3390/ph18081148 (registering DOI) - 1 Aug 2025
Viewed by 23
Abstract
Background/Objectives: Cancer suffers from unresolved therapeutic challenges owing to the lack of targeted therapies and heightened recurrence risk. This study aimed to investigate the new series of hydroxamate by structurally modifying the pharmacophore of vorinostat. Methods: The present work involves the synthesis [...] Read more.
Background/Objectives: Cancer suffers from unresolved therapeutic challenges owing to the lack of targeted therapies and heightened recurrence risk. This study aimed to investigate the new series of hydroxamate by structurally modifying the pharmacophore of vorinostat. Methods: The present work involves the synthesis of 15 differently substituted 2H-1,2,3-triazole-based hydroxamide analogs by employing triazole ring as a cap with varied linker fragments. The compounds were evaluated for their anticancer effect, especially their anti-breast cancer response. Molecular docking and molecular dynamics simulations were conducted to examine binding interactions. Results: Results indicated that among all synthesized hybrids, the molecule VI(i) inhibits the growth of MCF-7 and A-549 cells (GI50 < 10 μg/mL) in an antiproliferative assay. Compound VI(i) was also tested for cytotoxic activity by employing an MTT assay against A549, MCF-7, and MDA-MB-231 cell lines, and the findings indicate its potent anticancer response, especially against MCF-7 cells with IC50 of 60 µg/mL. However, it experiences minimal toxicity towards the normal cell line (HEK-293). Mechanistic studies revealed a dual-pathway activation: first, apoptosis (17.18% of early and 10.22% of late apoptotic cells by annexin V/PI analysis); second, cell cycle arrest at the S and G2/M phases. It also promotes ROS generation in a concentration-dependent manner. The HDAC–inhibitory assay, extended in silico molecular docking, and MD simulation experiments further validated its significant binding affinity towards HDAC 1 and 6 isoforms. DFT and ADMET screening further support the biological proclivity of the title compounds. The notable biological contribution of VI(i) highlights it as a potential candidate, especially against breast cancer cells. Full article
(This article belongs to the Section Medicinal Chemistry)
27 pages, 2602 KiB  
Article
Folate-Modified Albumin-Functionalized Iron Oxide Nanoparticles for Theranostics: Engineering and In Vitro PDT Treatment of Breast Cancer Cell Lines
by Anna V. Bychkova, Maria G. Gorobets, Anna V. Toroptseva, Alina A. Markova, Minh Tuan Nguyen, Yulia L. Volodina, Margarita A. Gradova, Madina I. Abdullina, Oksana A. Mayorova, Valery V. Kasparov, Vadim S. Pokrovsky, Anton V. Kolotaev and Derenik S. Khachatryan
Pharmaceutics 2025, 17(8), 982; https://doi.org/10.3390/pharmaceutics17080982 - 30 Jul 2025
Viewed by 298
Abstract
Background/Objectives: Magnetic iron oxide nanoparticles (IONPs), human serum albumin (HSA) and folic acid (FA) are prospective components for hybrid nanosystems for various biomedical applications. The magnetic nanosystems FA-HSA@IONPs (FAMs) containing IONPs, HSA, and FA residue are engineered in the study. Methods: [...] Read more.
Background/Objectives: Magnetic iron oxide nanoparticles (IONPs), human serum albumin (HSA) and folic acid (FA) are prospective components for hybrid nanosystems for various biomedical applications. The magnetic nanosystems FA-HSA@IONPs (FAMs) containing IONPs, HSA, and FA residue are engineered in the study. Methods: Composition, stability and integrity of the coating, and peroxidase-like activity of FAMs are characterized using UV/Vis spectrophotometry (colorimetric test using o-phenylenediamine (OPD), Bradford protein assay, etc.), spectrofluorimetry, dynamic light scattering (DLS) and electron magnetic resonance (EMR). The selectivity of the FAMs accumulation in cancer cells is analyzed using flow cytometry and confocal laser scanning microscopy. Results: FAMs (dN~55 nm by DLS) as a drug delivery platform have been administered to cancer cells (human breast adenocarcinoma MCF-7 and MDA-MB-231 cell lines) in vitro. Methylene blue, as a model photosensitizer, has been non-covalently bound to FAMs. An increase in photoinduced cytotoxicity has been found upon excitation of the photosensitizer bound to the coating of FAMs compared to the single photosensitizer at equivalent concentrations. The suitability of the nanosystems for photodynamic therapy has been confirmed. Conclusions: FAMs are able to effectively enter cells with increased folate receptor expression and thus allow antitumor photosensitizers to be delivered to cells without any loss of their in vitro photodynamic efficiency. Therapeutic and diagnostic applications of FAMs in oncology are discussed. Full article
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13 pages, 1600 KiB  
Article
LIMK2-1 Is a Phosphorylation-Dependent Inhibitor of Protein Phosphatase-1 Catalytic Subunit and Myosin Phosphatase Holoenzyme
by Andrea Kiss, Emese Tóth, Zsófia Bodogán, Mohamad Mahfood, Zoltán Kónya and Ferenc Erdődi
Int. J. Mol. Sci. 2025, 26(15), 7347; https://doi.org/10.3390/ijms26157347 - 30 Jul 2025
Viewed by 139
Abstract
The C-kinase-activated protein phosphatase-1 (PP1) inhibitor of 17 kDa (CPI-17) is a specific inhibitor of the PP1 catalytic subunit (PP1c) and the myosin phosphatase (MP) holoenzyme. CPI-17 requires the phosphorylation of Thr38 in the peptide segment 35ARV(P)TVKYDRREL46 for inhibitory activity. CPI-17 [...] Read more.
The C-kinase-activated protein phosphatase-1 (PP1) inhibitor of 17 kDa (CPI-17) is a specific inhibitor of the PP1 catalytic subunit (PP1c) and the myosin phosphatase (MP) holoenzyme. CPI-17 requires the phosphorylation of Thr38 in the peptide segment 35ARV(P)TVKYDRREL46 for inhibitory activity. CPI-17 regulates myosin phosphorylation in smooth muscle contraction and the tumorigenic transformation of several cell lines via the inhibition of MP. A phosphospecific antibody (anti-CPI-17pThr38) against the phosphorylation peptide was used to determine the phosphorylation levels in cells. We found that phospho-CPI-17 and its closely related proteins are not present in HeLa and MCF7 cells after inducing phosphorylation by inhibiting phosphatases with calyculin A. In contrast, cross-reactions of proteins in the 40–220 kDa range with anti-CPI-17pThr38 were apparent. Searching the protein database for similarities to the CPI-17 phosphorylation sequence revealed several proteins with 42–75% sequence identities. The LIMK2-1 isoform emerged as a possible PP1 inhibitor. Experiments with Flag-LIMK2-1 overexpressed in tsA201 cells proved that LIMK2-1 interacts with PP1c isoforms and is phosphorylated predominantly by protein kinase C. Phosphorylated LIMK2-1 inhibits PP1c and the MP holoenzyme with similar potencies (IC50 ~28–47 nM). In conclusion, our results suggest that LIMK2-1 is a novel phosphorylation-dependent inhibitor of PP1c and MP and may function as a CPI-17-like phosphatase inhibitor in cells where CPI-17 is present but not phosphorylated upon phosphatase inhibition. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Macromolecules)
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12 pages, 1508 KiB  
Article
Impact of Copper Nanoparticles on Keratin 19 (KRT19) Gene Expression in Breast Cancer Subtypes: Integrating Experimental and Bioinformatics Approaches
by Safa Taha, Ameera Sultan, Muna Aljishi and Khaled Greish
Int. J. Mol. Sci. 2025, 26(15), 7269; https://doi.org/10.3390/ijms26157269 - 27 Jul 2025
Viewed by 414
Abstract
This study investigates the effects of copper nanoparticles (CuNPs) on KRT19 gene expression in four breast cancer cell lines (MDA-MB-231, MDA-MB-468, MCF7, and T47D), representing triple-negative and luminal subtypes. Using cytotoxicity assays, quantitative RT-PCR, and bioinformatics tools (STRING, g:Profiler), we demonstrate subtype-specific, dose-dependent [...] Read more.
This study investigates the effects of copper nanoparticles (CuNPs) on KRT19 gene expression in four breast cancer cell lines (MDA-MB-231, MDA-MB-468, MCF7, and T47D), representing triple-negative and luminal subtypes. Using cytotoxicity assays, quantitative RT-PCR, and bioinformatics tools (STRING, g:Profiler), we demonstrate subtype-specific, dose-dependent KRT19 suppression, with epithelial-like cell lines showing greater sensitivity. CuNPs, characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM) with a mean size of 179 ± 15 nm, exhibited dose-dependent cytotoxicity. Bioinformatics analyses suggest KRT19′s potential as a biomarker for CuNP-based therapies, pending in vivo and clinical validation. These findings highlight CuNPs’ therapeutic potential and the need for further studies to optimize their application in personalized breast cancer treatment. Full article
(This article belongs to the Special Issue Nanoparticles for Cancer Treatment)
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19 pages, 3605 KiB  
Article
Luminescent Properties and Cytotoxic Activity of 2-phenylbenzoxazole Fluorosulfate Derivatives
by Nadezhda V. Danilenko, Mariia O. Lutsuk, Alexey A. Ryadun, Dmitry I. Pavlov, Evgenii V. Plotnikov, Daria D. Eskova, Yulia D. Klimenko, Andrei S. Potapov and Andrei I. Khlebnikov
Int. J. Mol. Sci. 2025, 26(15), 7261; https://doi.org/10.3390/ijms26157261 - 27 Jul 2025
Viewed by 231
Abstract
The synthesis of 2-phenylbenzoxazole fluorosulfate derivatives was carried out using the SuFEx reaction. To study the anticancer properties of the obtained compounds, the cell lines PC-3 (obtained from prostate adenocarcinoma), BT-474, and MCF-7 (both obtained from breast carcinoma) were used. The cytotoxicity on [...] Read more.
The synthesis of 2-phenylbenzoxazole fluorosulfate derivatives was carried out using the SuFEx reaction. To study the anticancer properties of the obtained compounds, the cell lines PC-3 (obtained from prostate adenocarcinoma), BT-474, and MCF-7 (both obtained from breast carcinoma) were used. The cytotoxicity on murine 3T3L1 embryonic was also investigated. Among the tested compounds, the ortho-substituted fluorosulfate derivative (BOSo) exhibited significant cytotoxicity against MCF-7 cells. The biological findings are consistent with molecular docking results, which revealed a structural similarity between BOSo and known inhibitors of hER and HER2 receptors—tamoxifen and SYR127063. Therefore, BOSo shows promise as a potential therapeutic agent with antiproliferative properties. The photoluminescent characteristics of the fluorosulfate derivatives were examined in the solid state, in acetonitrile solution and in PBS, with the highest quantum yields reaching up to 64% for the para-fluorosulfate derivative in acetonitrile. Overall, these compounds demonstrate considerable potential for the development of new multifunctional molecular tools that combine biological activity with fluorescent properties. Full article
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20 pages, 2015 KiB  
Article
Origanum majorana Extracts: A Preliminary Comparative Study on Phytochemical Profiles and Bioactive Properties of Valuable Fraction and By-Product
by Simone Bianchi, Rosaria Acquaviva, Claudia Di Giacomo, Laura Siracusa, Leeyah Issop-Merlen, Roberto Motterlini, Roberta Foresti, Donata Condorelli and Giuseppe Antonio Malfa
Plants 2025, 14(15), 2264; https://doi.org/10.3390/plants14152264 - 23 Jul 2025
Viewed by 287
Abstract
Origanum majorana L. (O. majorana) (Lamiaceae) is an aromatic Mediterranean plant widely used in food, cosmetics, and traditional medicine due to its aroma and rich content of bioactive compounds. While its leaves and flowers are commonly utilized, lignified stems are often [...] Read more.
Origanum majorana L. (O. majorana) (Lamiaceae) is an aromatic Mediterranean plant widely used in food, cosmetics, and traditional medicine due to its aroma and rich content of bioactive compounds. While its leaves and flowers are commonly utilized, lignified stems are often discarded. This study compared hydroalcoholic extracts from the leaves and flowers (valuable fraction, VF) and stems (by-product, BP). Phytochemical analysis revealed qualitatively similar profiles, identifying 20 phenolic compounds, with Rosmarinic acid and Salvianolic acid B as the most and second most abundant, respectively. Antioxidant activity was evaluated in vitro using DPPH (IC50 [µg/mL]: VF 30.11 ± 3.46; BP 31.72 ± 1.46), H2O2 (IC50 [µg/mL]: VF 103.09 ± 4.97; BP 119.55 ± 10.58), and O2•− (IC50 [µg/mL]: VF 0.71 ± 0.062; BP 0.79 ± 0.070). Both extracts (20 µg/mL) fully restored oxidative balance in hemin-stressed AC16 cardiomyocytes, without altering the expression of catalase, heme-oxygenase 1, superoxide dismutase 2, or ferritin. Anti-inflammatory activity in LPS-stimulated RAW 264.7 macrophages showed that VF (IC50 400 µg/mL) reduced NO release to control levels, while BP achieved a ~60% reduction. Cytotoxicity was assessed on cancer cell lines: CaCo-2 (IC50 [µg/mL]: VF 154.1 ± 6.22; BP 305.2 ± 15.94), MCF-7 (IC50 [µg/mL]: VF 624.6 ± 10.27; BP 917.9 ± 9.87), and A549 (IC50 [µg/mL]: VF 720.8 ± 13.66; BP 920.2 ± 16.79), with no cytotoxicity on normal fibroblasts HFF-1 (IC50 > 1000 µg/mL for both extracts). Finally, both extracts slightly inhibited only CYP1A2 (IC50 [µg/mL]: VF 497.45 ± 9.64; BP 719.72 ± 11.37) and CYP2D6 (IC50 [µg/mL]: VF 637.15 ± 14.78, BP 588.70 ± 11.01). These results support the potential reuse of O. majorana stems as a sustainable source of bioactive compounds for nutraceutical and health-related applications. Full article
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37 pages, 20768 KiB  
Article
Design, Synthesis, and Testing of 1,2,3-Triazolo-Quinobenzothiazine Hybrids for Cytotoxic and Immunomodulatory Activity
by Klaudia Giercuszkiewicz-Haśnik, Magdalena Skonieczna, Beata Morak-Młodawska and Małgorzata Jeleń
Int. J. Mol. Sci. 2025, 26(14), 6920; https://doi.org/10.3390/ijms26146920 - 18 Jul 2025
Viewed by 372
Abstract
Phenothiazines, mainly known for their antipsychotic activity, have recently attracted attention as potential compounds with anticancer and immunomodulatory activity In this study, 20 new quinobenzothiazines (MJ1MJ20) were synthesized and their effects on normal cell lines (BEAS-2B, NHDF) and cancer [...] Read more.
Phenothiazines, mainly known for their antipsychotic activity, have recently attracted attention as potential compounds with anticancer and immunomodulatory activity In this study, 20 new quinobenzothiazines (MJ1MJ20) were synthesized and their effects on normal cell lines (BEAS-2B, NHDF) and cancer cell lines (HCT116, MCF7, A549, SH-SY5Y, U2OS) were investigated. The studies included cytotoxicity assessment, analysis of the expression of genes (BCL2, AIFM2, MDM2) and pro-inflammatory cytokines (IL6, IL8) using the RT-qPCR method, and prediction of biological activity using the PASS platform. The results indicate that the compounds MJ19 and MJ20 have the greatest effect on the induction of pro-inflammatory (IL6, IL8) and antiapoptotic (BCL2, MDM2) genes, suggesting their potential use in therapies for inflammatory and autoimmune diseases. Gene expression analysis showed that compound MJ2 in BEAS-2B cells significantly induced the expression of AIFM2, a protein responsible for protecting against ferroptosis, while moderately increasing the expression of BCL2 and MDM2, suggesting a potential role for MJ2 in the modulation of protective mechanisms of healthy cells, e.g., avoiding apoptosis death. These results emphasize the potential of quinobenzothiazines as multifunctional bioactive compounds, which require further studies to determine their mechanisms of action and specificity. Full article
(This article belongs to the Special Issue Techniques and Strategies in Drug Design and Discovery, 3rd Edition)
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19 pages, 2360 KiB  
Article
Novel N-Alkyl 3-(3-Benzyloxyquinoxalin-2-yl) Propanamides as Antiproliferative Agents: Design, Synthesis, In Vitro Testing, and In Silico Mechanistic Study
by Samar A. Abubshait
Molecules 2025, 30(14), 3025; https://doi.org/10.3390/molecules30143025 - 18 Jul 2025
Viewed by 468
Abstract
A series of eleven new N-alkyl 3-(3-benzyloxyquinoxalin-2-yl) propanamides were prepared based on the azide coupling of 3-(3-benzyloxyquinoxalin-2-yl) propanhydrazide with a variety of primary and secondary amines and the consequent conjunction of a broad spectrum of lipophile and hydrophile characters to a quinoxaline [...] Read more.
A series of eleven new N-alkyl 3-(3-benzyloxyquinoxalin-2-yl) propanamides were prepared based on the azide coupling of 3-(3-benzyloxyquinoxalin-2-yl) propanhydrazide with a variety of primary and secondary amines and the consequent conjunction of a broad spectrum of lipophile and hydrophile characters to a quinoxaline ring system. 3-(3-benzyloxyquinoxalin-2-yl) propanhydrazide was produced in a two-step reaction of methyl 3-(3-oxo-3,4-dihydroquinoxalin-2-yl) propanoate with benzyl chloride followed by the hydrazinolysis of the corresponding ester. The antiproliferative activity of the compounds was tested in various cancer cell lines, including PC-3, Hela, HCT-116, and MCF-7; they showed a wide spectrum of activity for most of the tested compounds. Compound 6k exhibited the highest activity, which was comparable to that of doxorubicin, with IC50 (µM) values of 12.17 ± 0.9, 9.46 ± 0.7, 10.88 ± 0.8, and 6.93 ± 0.4 µM compared to 8.87 ± 0.6, 5.57 ± 0.4, 5.23 ± 0.3, and 4.17 ± 0.2 µM for doxorubicin against Hela, HCT-116, and MCF-7, respectively. The in silico mechanistic study revealed the inhibition of HDAC-6 through the binding of the unique zinc finger ubiquitin-binding domain (HDAC6 Zf-UBD). The docking results showed a specific binding pattern that emphasized the crucial role of the quinoxaline ring and its substituents. The newly developed derivatives were evaluated for antitumor effects against four cancer cell lines PC-3, HeLa, HCT-116, and MCF-7. This research led to the identification of a quinoxaline-based scaffold exhibiting broad-spectrum antiproliferative activity and a distinct mechanism involving binding to HDAC6 Zf-UBD. The findings highlight its potential for further optimization and preclinical studies to support future anticancer drug development. Full article
(This article belongs to the Special Issue Molecular Docking in Drug Discovery, 2nd Edition)
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22 pages, 8519 KiB  
Article
RNA-Seq Analysis of MCF-7 Breast Cancer Cells Treated with Methyl Gallate Isolated from the Rhizomes of Nymphaea Odorata L. Shows Upregulation of Apoptosis, Autophagy, and Unfolded Protein Canonical Pathways
by Nishikant A. Raut, Pinal N. Kanabar, Mark Maienschein-Cline, Nina S. Los, Zarema Arbieva, Temitope O. Lawal, Shitalben Patel and Gail B. Mahady
Molecules 2025, 30(14), 3022; https://doi.org/10.3390/molecules30143022 - 18 Jul 2025
Viewed by 313
Abstract
The effects of a methanol extract of Nymphaea odorata (MeNO) rhizomes, its fractions and the active compound (methyl gallate, MeG) were investigated in estrogen receptor-positive (ER+) breast cancer cell lines MCF-7 and T47-D:A18, as well as ER-negative line SKBr3. Cell viability and cytotoxicity [...] Read more.
The effects of a methanol extract of Nymphaea odorata (MeNO) rhizomes, its fractions and the active compound (methyl gallate, MeG) were investigated in estrogen receptor-positive (ER+) breast cancer cell lines MCF-7 and T47-D:A18, as well as ER-negative line SKBr3. Cell viability and cytotoxicity were determined using CellTiter-Glo® 2.0 assays at concentrations ranging from 1 to 100 μg/mL. Caspase activity and apoptosis were determined using Caspase-Glo® 3/7, Caspase-Glo® 8, and ApoTox-Glo™ triplex assays, as well as qPCR. Total RNA was isolated from MCF-7 cells treated with MeG. RNA-seq libraries were prepared using a Universal Plus mRNASeq kit, and sequencing was performed on a NovaSeq 6000. MeNO inhibited the growth of MCF-7 cells with an IC50 of 14.1 μg/mL, as well as T47-D:A18 (IC50 of 25.6 μg/mL) and SKBr3 cells (IC50 of 35.5 μg/mL). Bioassay-guided fractionation of MeNO in MCF-7 cells identified the active fraction containing one compound, namely methyl gallate (MeG). MeG had an IC50 of 8.6 μg/mL in MCF-7 cells. Transcriptomic analysis of MeG-treated MCF-7 cells showed differential expression of 10,634 genes, with 5643 upregulated and 4991 downregulated (FDR < 0.05). Ingenuity pathway analysis revealed the involvement of 43 canonical pathways, with the top upregulated pathways including apoptosis, autophagy, and the unfolded protein response pathways. Full article
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25 pages, 4169 KiB  
Article
In Vitro Effects of Rumex confertus Extracts on Cell Viability and Molecular Pathways in MCF-7 Breast Cancer Cells
by Levent Gülüm, Emrah Güler, Fatma Lale Aktaş, Ayşe Büşranur Çelik, Hilal Yılmaz and Yusuf Tutar
Antioxidants 2025, 14(7), 879; https://doi.org/10.3390/antiox14070879 - 18 Jul 2025
Viewed by 474
Abstract
Rumex confertus (RC), a plant known for its traditional medicinal uses, has shown potential anticancer properties, particularly due to its rich phenolic content. Despite its promising bioactivity, its effects on breast cancer cells remain underexplored. Here, we investigated the cytotoxic effects of RC [...] Read more.
Rumex confertus (RC), a plant known for its traditional medicinal uses, has shown potential anticancer properties, particularly due to its rich phenolic content. Despite its promising bioactivity, its effects on breast cancer cells remain underexplored. Here, we investigated the cytotoxic effects of RC extracts on MCF-7 breast cancer cells, employing various solvents for extraction. This study revealed that the hexane extract significantly reduced the cell viability, with an IC50 of 9.40 µg/mL after 96 h. The gene expression analysis indicated a substantial modulation of transcriptional networks, including the upregulation of pluripotency-related genes and the downregulation of differentiation markers. The findings suggest that the RC extract may induce a shift towards a less differentiated, stem-like state in cancer cells, potentially enhancing malignancy resistance. This study underscores the potential of RC as a candidate for breast cancer treatment, and a further investigation into its therapeutic applications is suggested. Full article
(This article belongs to the Special Issue Anti-Cancer Potential of Plant-Based Antioxidants)
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22 pages, 15949 KiB  
Article
PD-1/PD-L1 Inhibitors and Chemotherapy Synergy: Impact on Drug Resistance and PD-L1 Expression in Breast Cancer-Immune Cell Co-Cultures
by Güneş Özen Eroğlu, Ayşe Erol Bozkurt, İlhan Yaylım and Dürdane Serap Kuruca
Int. J. Mol. Sci. 2025, 26(14), 6876; https://doi.org/10.3390/ijms26146876 - 17 Jul 2025
Viewed by 305
Abstract
Breast cancer is the most frequently diagnosed cancer among women. In recent years, immunotherapy, a key targeted treatment strategy, has gained prominence in the management of this disease. Immune cells within the tumor microenvironment can significantly affect treatment outcomes. Among immunotherapeutic approaches, or [...] Read more.
Breast cancer is the most frequently diagnosed cancer among women. In recent years, immunotherapy, a key targeted treatment strategy, has gained prominence in the management of this disease. Immune cells within the tumor microenvironment can significantly affect treatment outcomes. Among immunotherapeutic approaches, or programmed death protein 1(PD-1) and programmed death-ligand 1(PD-L1)-targeted therapies are increasingly recognized for their role in modulating cancer–immune system interactions. This study investigated the impact of PD-1/PD-L1 pathway inhibition on the expression of drug resistance-related proteins in an in vitro breast cancer model incorporating immune cells. MDA-MB-231 and MCF-7 cell lines were used as breast cancer cells, while THP-1 and Jurkat cells represented monocytes and lymphocytes, respectively. The effects of paclitaxel (PTX), doxorubicin (Dox), and PD-1/PD-L1 inhibitors (BMS-1166 and Human PD-L1 Inhibitor IV (PI4)) on cell viability were evaluated using an MTT assay, and the IC50 values were determined. Flow cytometry was used to analyze PD-1/PD-L1 expression and the drug resistance proteins ABCG2 (ATP-binding cassette sub-family G member 2, breast cancer resistance protein), MDR-1 (multidrug resistance protein 1), and MRP-1 (multidrug resistance-associated protein 1) across co-culture models. Based on the results, Dox reduced PD-L1 expression in all groups except for MDA-MB-231:THP-1, while generally lowering drug resistance protein levels, except in MDA-MB-231:Jurkat. BMS-1166 significantly decreased cell viability and enhanced chemotherapy-induced cytotoxicity. Interestingly, in the MDA-MB-231:Jurkat co-culture, both inhibitors reduced PD-L1 but increased drug resistance protein expression. Paclitaxel’s effect on PD-L1 varied depending on the immune context. These findings highlight that PD-1/PD-L1 inhibitors and chemotherapeutic agents differentially affect PD-L1 and drug resistance-related protein expression depending on the immune cell composition within the tumor microenvironment. Full article
(This article belongs to the Section Molecular Oncology)
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21 pages, 2524 KiB  
Article
The Relevance of G-Quadruplexes in Gene Promoters and the First Introns Associated with Transcriptional Regulation in Breast Cancer
by Huiling Shu, Ke Xiao, Wenyong Zhu, Rongxin Zhang, Tiantong Tao and Xiao Sun
Int. J. Mol. Sci. 2025, 26(14), 6874; https://doi.org/10.3390/ijms26146874 - 17 Jul 2025
Viewed by 244
Abstract
The role of G-quadruplexes (G4s) in gene regulation has been widely documented, especially in gene promoters. However, the transcriptional mechanisms involving G4s in other regulatory regions remain largely unexplored. In this study, we integrated the G4-DNA data derived from 22 breast cancer patient-derived [...] Read more.
The role of G-quadruplexes (G4s) in gene regulation has been widely documented, especially in gene promoters. However, the transcriptional mechanisms involving G4s in other regulatory regions remain largely unexplored. In this study, we integrated the G4-DNA data derived from 22 breast cancer patient-derived tumor xenograft (PDTX) models and MCF7 cell line as potential breast cancer-associated G4s (BC-G4s). Genome-wide analysis showed that BC-G4s are more prevalent in gene promoters and the first introns. The genes accommodating promoter or intronic BC-G4s show significantly higher transcriptional output than their non-G4 counterparts. The biased distribution of BC-G4s in close proximity to the transcription start site (TSS) is associated with an enrichment of transcription factor (TF) interactions. A significant negative correlation was detected between the G4–TF interactions within the first introns and their cognate promoters. These different interactions are complementary rather than redundant. Furthermore, the differentially expressed genes (DEGs) harboring promoter and first intron BC-G4s are significantly enriched in the cell cycle pathway. Notably, promoter BC-G4s of DEGs could be a central hub for TF–TF co-occurrence. Our analysis also revealed that G4-related single nucleotide variants (SNVs) affect the stability of G4 structures and the transcription of disease-related genes. Collectively, our results shed light on how BC-G4s within promoters and first introns regulate gene expression and reinforce the critical role of G4s and G4-related genes in breast cancer-associated processes. Full article
(This article belongs to the Special Issue Molecular Research of Multi-omics in Cancer)
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21 pages, 6281 KiB  
Article
Novel Compounds Featuring a Thiophene Carboxamide Scaffold: Synthesis, Characterization and Antiproliferative Evaluation
by Bogdan-Ionuț Mara, Alexandra Mioc, Livia-Nicoleta Deveseleanu-Corici, Codruța Șoica and Liliana Cseh
Int. J. Mol. Sci. 2025, 26(14), 6823; https://doi.org/10.3390/ijms26146823 - 16 Jul 2025
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Abstract
Thiophene derivatives are particularly attractive for application in drug development for their versatile pharmacological properties. We synthesized a series of four compounds with thiophene carboxamide as a scaffold. The structures were established based on HR-MS and 1D- and 2D-NMR. The purity of the [...] Read more.
Thiophene derivatives are particularly attractive for application in drug development for their versatile pharmacological properties. We synthesized a series of four compounds with thiophene carboxamide as a scaffold. The structures were established based on HR-MS and 1D- and 2D-NMR. The purity of the compounds was established to be greater than 92% by thin-layer chromatography and NMR. The cytotoxic effects of the newly synthesized compounds were evaluated against the normal HaCaT cell line and A375, HT-29, and MCF-7 cancer cell lines. The cytotoxic assessment revealed that two compounds exhibit a significant cytotoxic effect on all cancer cell lines. To investigate their potential underlying mechanisms of action, several tests were performed: immunofluorescence imaging, caspase-3/7 assay, mitochondrial membrane potential (JC-1) assay, and 2′,7′–dichlorofluorescein diacetate (DCFDA) assay. MB-D2 proved to be the most cytotoxic and effective in terms of caspase 3/7 activation, mitochondrial depolarization and decrease in ROS production; these effects did not occur in normal HaCaT cells, revealing that MB-D2 has a high selectivity against A375 cancer cells. Full article
(This article belongs to the Section Biochemistry)
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