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11 pages, 1758 KiB  
Article
Nonlinear Absorption Properties of Phthalocyanine-like Squaraine Dyes
by Fan Zhang, Wuyang Shi, Xixiao Li, Yigang Wang, Leilei Si, Wentao Gao, Meng Qi, Minjie Zhou, Jiajun Ma, Ao Li, Zhiqiang Li, Hongming Wang and Bing Jin
Photonics 2025, 12(8), 779; https://doi.org/10.3390/photonics12080779 (registering DOI) - 1 Aug 2025
Abstract
This study synthesizes and comparatively investigates two squaric acid-based phthalocyanine-like dyes, SNF and its long-chain alkylated derivative LNF, to systematically elucidate the influence of peripheral hydrophobic groups on their third-order nonlinear optical (NLO) properties. The NLO characteristics were comprehensively characterized using femtosecond Z-scan [...] Read more.
This study synthesizes and comparatively investigates two squaric acid-based phthalocyanine-like dyes, SNF and its long-chain alkylated derivative LNF, to systematically elucidate the influence of peripheral hydrophobic groups on their third-order nonlinear optical (NLO) properties. The NLO characteristics were comprehensively characterized using femtosecond Z-scan and I-scan techniques at both 800 nm and 900 nm. Both dyes exhibited strong saturable absorption (SA), confirming their potential as saturable absorbers. Critically, the comparative analysis revealed that SNF exhibits a significantly greater nonlinear absorption coefficient (β) compared to LNF under identical conditions. For instance, at 800 nm, the β of SNF was approximately 3–5 times larger than that of LNF. This result conclusively demonstrates that the introduction of long hydrophobic alkyl chains attenuates the NLO response. Furthermore, I-scan measurements revealed excellent SA performance, with high modulation depths (e.g., LNF: 43.0% at 900 nm) and low saturation intensities. This work not only clarifies the structure–property relationship in these D-A-D dyes but also presents a clear strategy for modulating the NLO properties of organic chromophores for applications in near-infrared pulsed lasers. Full article
(This article belongs to the Section Optoelectronics and Optical Materials)
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21 pages, 1962 KiB  
Review
From Survival to Parenthood: The Fertility Journey After Childhood Cancer
by Sofia Rahman, Veronica Sesenna, Diana Osorio Arce, Erika Maugeri and Susanna Esposito
Biomedicines 2025, 13(8), 1859; https://doi.org/10.3390/biomedicines13081859 - 30 Jul 2025
Viewed by 133
Abstract
Background: The advances in cancer diagnosis and treatment have significantly improved survival rates in pediatric patients, with five-year survival now exceeding 80% in many high-income countries. However, these life-saving therapies often carry long-term consequences, including impaired fertility. The reproductive health of childhood [...] Read more.
Background: The advances in cancer diagnosis and treatment have significantly improved survival rates in pediatric patients, with five-year survival now exceeding 80% in many high-income countries. However, these life-saving therapies often carry long-term consequences, including impaired fertility. The reproductive health of childhood cancer survivors has emerged as a key issue in survivorship care. Objective: This narrative review aims to examine the gonadotoxic effects of cancer treatments on pediatric patients, evaluate fertility preservation strategies in both males and females, and provide guidance on the long-term monitoring of reproductive function post treatment. Methods: A comprehensive literature review was conducted using PubMed, including randomized trials, cohort studies, and clinical guidelines published up to March 2024. The keywords focused on pediatric oncology, fertility, and reproductive endocrinology. Studies were selected based on relevance to treatment-related gonadotoxicity, fertility preservation options, and follow-up care. Results: Radiotherapy and alkylating agents pose the highest risk to fertility. Postpubertal patients have access to standardized preservation techniques, while prepubertal options remain experimental. Long-term effects include premature ovarian insufficiency, azoospermia, hypogonadism, and uterine dysfunction. The psychosocial impacts, especially in female survivors, are profound and often overlooked. Conclusions: Fertility preservation should be discussed at diagnosis and integrated into treatment planning in pediatric patients with cancer. While options for postpubertal patients are established, more research is needed to validate safe and effective strategies for younger populations. A multidisciplinary approach and long-term surveillance are essential for safeguarding future reproductive potential in childhood cancer survivors. Full article
(This article belongs to the Special Issue Advanced Cancer Diagnosis and Treatment: Third Edition)
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17 pages, 3206 KiB  
Article
Inverse Punicines: Isomers of Punicine and Their Application in LiAlO2, Melilite and CaSiO3 Separation
by Maximilian H. Fischer, Ali Zgheib, Iliass El Hraoui, Alena Schnickmann, Thomas Schirmer, Gunnar Jeschke and Andreas Schmidt
Separations 2025, 12(8), 202; https://doi.org/10.3390/separations12080202 - 30 Jul 2025
Viewed by 86
Abstract
The transition to sustainable energy systems demands efficient recycling methods for critical raw materials like lithium. In this study, we present a new class of pH- and light-switchable flotation collectors based on isomeric derivatives of the natural product Punicine, termed inverse Punicines. [...] Read more.
The transition to sustainable energy systems demands efficient recycling methods for critical raw materials like lithium. In this study, we present a new class of pH- and light-switchable flotation collectors based on isomeric derivatives of the natural product Punicine, termed inverse Punicines. These amphoteric molecules were synthesized via a straightforward four-step route and structurally tuned for hydrophobization by alkylation. Their performance as collectors was evaluated in microflotation experiments of lithium aluminate (LiAlO2) and silicate matrix minerals such as melilite and calcium silicate. Characterization techniques including ultraviolet-visible (UV-Vis), nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy as well as contact angle, zeta potential (ζ potential) and microflotation experiments revealed strong pH- and structure-dependent interactions with mineral surfaces. Notably, N-alkylated inverse Punicine derivatives showed high flotation yields for LiAlO2 at pH of 11, with a derivative possessing a dodecyl group attached to the nitrogen as collector achieving up to 86% recovery (collector conc. 0.06 mmol/L). Preliminary separation tests showed Li upgrading from 5.27% to 6.95%. Radical formation and light-response behavior were confirmed by ESR and flotation tests under different illumination conditions. These results demonstrate the potential of inverse Punicines as tunable, sustainable flotation reagents for advanced lithium recycling from complex slag systems. Full article
(This article belongs to the Special Issue Application of Green Flotation Technology in Mineral Processing)
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18 pages, 1263 KiB  
Review
Fertility Protection in Female Cancer Patients: From Molecular Mechanisms of Gonadotoxic Therapies to Pharmacotherapeutic Possibilities
by Weronika Zajączkowska, Maria Buda, Witold Kędzia and Karina Kapczuk
Int. J. Mol. Sci. 2025, 26(15), 7314; https://doi.org/10.3390/ijms26157314 - 29 Jul 2025
Viewed by 271
Abstract
Chemotherapeutic agents and radiotherapy are highly effective in treating malignancies. However, they carry a significant risk of harming the gonads and may lead to endocrine dysfunction and reproductive issues. This review outlines the molecular mechanisms of gonadotoxic therapies, focusing on radiation, alkylating agents, [...] Read more.
Chemotherapeutic agents and radiotherapy are highly effective in treating malignancies. However, they carry a significant risk of harming the gonads and may lead to endocrine dysfunction and reproductive issues. This review outlines the molecular mechanisms of gonadotoxic therapies, focusing on radiation, alkylating agents, and platinum compounds. It discusses the loss of PMFs due to gonadotoxic exposure, including DNA double-strand breaks, oxidative stress, and dysregulated signaling pathways like PI3K/PTEN/Akt/mTOR and TAp63-mediated apoptosis. Furthermore, it explores strategies to mitigate gonadal damage, including GnRH agonists, AMH, imatinib, melatonin, sphingolipid metabolites, G-CSF, mTOR inhibitors, AS101, and LH. These therapies, paired with existing fertility preservation methods, could safeguard reproductive and hormonal functions and improve the quality of life for young cancer patients. Despite the progress made in recent years in understanding gonadotoxic mechanisms, gaps remain due to questionable reliance on mouse models and the lack of models replicating human ovarian dynamics. Long-term studies are vital for wider analyses and exploration of protective strategies based on various animal models and clinical trials. It is essential to verify that these substances do not hinder the anti-cancer effectiveness of treatments or cause lasting DNA changes in granulosa cells, raising the risk of miscarriages and infertility. Full article
(This article belongs to the Section Molecular Oncology)
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15 pages, 1043 KiB  
Article
Rational Design, Synthesis and In Vitro Activity of Diastereomeric Cis-/Trans-3-Substituted-3,4-Dihydroisocoumarin-4-Carboxylic Acids as Potential Carnitine Acetyltransferase Inhibitors
by Savina Stoyanova and Milen G. Bogdanov
Molecules 2025, 30(15), 3159; https://doi.org/10.3390/molecules30153159 - 28 Jul 2025
Viewed by 368
Abstract
This study explores a series of 3,4-dihydroisocoumarins as potential inhibitors of fatty acid oxidation through rational design, synthesis and in vitro evaluation. The compounds studied were designed as structural analogs of the natural substrates of carnitine acetyltransferase (CAT) and other enzymes in the [...] Read more.
This study explores a series of 3,4-dihydroisocoumarins as potential inhibitors of fatty acid oxidation through rational design, synthesis and in vitro evaluation. The compounds studied were designed as structural analogs of the natural substrates of carnitine acetyltransferase (CAT) and other enzymes in the carnitine transferase family, which play a crucial role in fatty acid metabolism. Comparative in vitro analyses revealed that the presence of an alkyl substituent at position 3 of the heterocyclic core, along with its chain length, significantly influences inhibitory activity, yielding IC50 values in the micromolar range. Kinetic studies of one of the most potent compounds—cis- and trans-3-decyl-6,7-dimethoxy-3,4-dihydroisocoumarin-4-carboxylic acids—demonstrated mixed inhibition of CAT, with Ki values of 130 μM and 380 μM, respectively. These findings underscore the therapeutic potential of the compounds under investigation in modulating fatty acid catabolism, with possible applications in treating metabolic disorders. Full article
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13 pages, 25732 KiB  
Article
Simple Cobalt Nanoparticle-Catalyzed Reductive Amination for Selective Synthesis of a Broad Range of Primary Amines
by Bingxiao Zheng, Liqin Yang, Yashuang Hei, Ling Yu, Sisi Wen, Lisi Ba, Long Ao and Zhiju Zhao
Molecules 2025, 30(15), 3089; https://doi.org/10.3390/molecules30153089 - 23 Jul 2025
Viewed by 189
Abstract
In the field of green chemistry, the development of more sustainable and cost-efficient methods for synthesizing primary amines is of paramount importance, with catalyst research being central to this effort. This work presents a facile, aqueous-phase synthesis of highly active cobalt catalysts (Co-Ph@SiO [...] Read more.
In the field of green chemistry, the development of more sustainable and cost-efficient methods for synthesizing primary amines is of paramount importance, with catalyst research being central to this effort. This work presents a facile, aqueous-phase synthesis of highly active cobalt catalysts (Co-Ph@SiO2(x)) via pyrolysis of silica-supported cobalt–phenanthroline complexes. The optimized Co-Ph@SiO2(900) catalyst achieved exceptional performance (>99% conversion, >98% selectivity) in the reductive amination of acetophenone to 1-phenylethanamine using NH3/H2. Systematic studies revealed that its exceptional performance originates from the in situ pyrolysis of the cobalt–phyllosilicate complex. This process promotes the uniform distribution of metal cobalt nanoparticles, simultaneously enhancing porosity and imparting bifunctional (acidic and basic) properties to the catalyst, resulting in outstanding catalytic activity and selectivity. The catalyst demonstrated broad applicability, efficiently converting diverse ketones (aryl-alkyl, dialkyl, bioactive) and aldehydes (halogenated, heterocyclic, biomass-derived) into primary amines with high yields (up to 99%) and chemoselectivity (>40 examples). This sustainable, non-noble metal-based catalyst system offers significant potential for industrial primary amine synthesis and provides a versatile tool for developing highly selective and active heterogeneous catalysts. Full article
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12 pages, 5740 KiB  
Article
Effect of pH on the Efficiency of Pyrogallol, Gallic Acid, and Alkyl Gallates in Trapping Methylglyoxal
by Haria Hadjipakkou and Eftychia Pinakoulaki
Molecules 2025, 30(15), 3086; https://doi.org/10.3390/molecules30153086 - 23 Jul 2025
Viewed by 163
Abstract
Methylglyoxal (MGO) is a highly reactive a-dicarbonyl compound produced in foods and endogenously in humans and constitutes a predominant precursor of advanced glycation end products that contribute to the pathology of several diseases, including diabetes and neurodegenerative diseases. In this study, the [...] Read more.
Methylglyoxal (MGO) is a highly reactive a-dicarbonyl compound produced in foods and endogenously in humans and constitutes a predominant precursor of advanced glycation end products that contribute to the pathology of several diseases, including diabetes and neurodegenerative diseases. In this study, the efficiency of pyrogallol, gallic acid, ethyl, and propyl gallate in trapping MGO was investigated at pH 6.5 to 8.0. Pyrogallol was the most efficient MGO-trapping agent, followed by gallic acid, whereas the alkyl gallates were notably less efficient, particularly at slightly acidic and neutral pH. The increase of pH from slightly acidic to alkaline enhanced the MGO-trapping efficiency of all compounds, albeit to a different extent that correlated inversely to the pKa of the most acidic -OH phenolic group, demonstrating the contribution of the deprotonated forms of the phenolic compounds in the enhanced reactivity towards MGO. The reaction products of pyrogallol, identified as the most efficient compound in MGO-trapping, were analyzed and characterized by liquid chromatography-mass spectrometry (LC-MS). Both mono-MGO and di-MGO conjugated adducts of pyrogallol were detected, with the mono-MGO adduct being dominant solely at acidic pH and the di-MGO pyrogallol adducts becoming prevalent at neutral and alkaline pH. Therefore, the pH was determined as a main factor that controls the reaction pathways of the phenolic compounds with MGO. Full article
(This article belongs to the Section Food Chemistry)
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18 pages, 1829 KiB  
Article
The Red Shift in Estrogen Research: An Estrogen-Receptor Targeted aza-BODIPY–Estradiol Fluorescent Conjugate
by Tamás Hlogyik, Noémi Bózsity, Rita Börzsei, Benjámin Kovács, Péter Labos, Csaba Hetényi, Mónika Kiricsi, Ildikó Huliák, Zoltán Kele, Miklós Poór, János Erostyák, Attila Hunyadi, István Zupkó and Erzsébet Mernyák
Int. J. Mol. Sci. 2025, 26(15), 7075; https://doi.org/10.3390/ijms26157075 - 23 Jul 2025
Viewed by 183
Abstract
Estradiol (E2) plays an important role in cell proliferation and certain brain functions. To reveal its mechanism of action, its detectability is essential. Only a few fluorescent-labeled hormonally active E2s exist in the literature, and their mechanism of action usually remains unclear. It [...] Read more.
Estradiol (E2) plays an important role in cell proliferation and certain brain functions. To reveal its mechanism of action, its detectability is essential. Only a few fluorescent-labeled hormonally active E2s exist in the literature, and their mechanism of action usually remains unclear. It would be of particular interest to develop novel labeled estradiol derivatives with retained biological activity and improved optical properties. Due to their superior optical characteristics, aza-BODIPY dyes are frequently used labeling agents in biomedical applications. E2 was labeled with the aza-BODIPY dye at its phenolic hydroxy function via an alkyl linker and a triazole coupling moiety. The estrogenic activity of the newly synthesized fluorescent conjugate was evaluated via transcriptional luciferase assay. Docking calculations were performed for the classical and alternative binding sites (CBS and ABS) of human estrogen receptor α. The terminal alkyne function was introduced into the tetraphenyl aza-BODIPY core via selective formylation, oxidation, and subsequent amidation with propargyl amine. The conjugation was achieved via Cu(I)-catalyzed azide–alkyne click reaction of the aza-BODIPY-alkyne with the 3-O-(4-azidobut-1-yl) derivative of E2. The labeled estrogen induced a dose-dependent transcriptional activity of human estrogen receptor α with a submicromolar EC50 value. Docking calculations revealed that the steroid part has a perfect overlap with E2 in ABS. In CBS, however, a head-tail binding deviation was observed. A facile, fluorescent labeling methodology has been elaborated for the development of a novel red-emitting E2 conjugate with substantial estrogenic activity. Docking experiments uncovered the binding mode of the conjugate in both ABS and CBS. Full article
(This article belongs to the Section Biochemistry)
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14 pages, 901 KiB  
Article
Structural Modifications at the C3 and C30 Positions of the Lupane Skeleton with Carbon-Centered Nucleophiles
by Davide Castiglione, Gianfranco Fontana, Laura Castoldi and Vittorio Pace
Molecules 2025, 30(15), 3064; https://doi.org/10.3390/molecules30153064 - 22 Jul 2025
Viewed by 283
Abstract
Lupeol, a naturally occurring pentacyclic triterpenoid widely distributed in various medicinal plants, has attracted significant attention due to its diverse pharmacological properties. In this study, we report the synthesis and structural modification of 14 lupeol derivatives through selective functionalizations at C3 and C30 [...] Read more.
Lupeol, a naturally occurring pentacyclic triterpenoid widely distributed in various medicinal plants, has attracted significant attention due to its diverse pharmacological properties. In this study, we report the synthesis and structural modification of 14 lupeol derivatives through selective functionalizations at C3 and C30 positions of the lupane skeleton, via the sequential chemoselective introduction of carbonyl moieties and the addition of organometallics. Emphasis has been given to the stereoselective alkylation at C3 using a range of carbanions, including organolithiums, organomagnesiums and organoindiums. The C30 position was modified through oxidative pathways to introduce several functionalities. Full article
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16 pages, 1696 KiB  
Communication
Synthesis and Characterization of Amide-Based Cyclotriphosphazene Derivatives with Alkoxy Terminal Groups
by Khairunnisa Abdul Rahim and Zuhair Jamain
Molbank 2025, 2025(3), M2039; https://doi.org/10.3390/M2039 - 21 Jul 2025
Viewed by 211
Abstract
A series of new amide-based cyclotriphosphazene molecules consisting of different terminal groups (heptyl, decyl, and tetradecyl) at the periphery was successfully synthesized and characterized. The reaction began with the alkylation of methyl-4-hydroxybenzoate with 1-bromoheptane, 1-bromodecane, and 1-bromotetradecane, which was followed by reduction with [...] Read more.
A series of new amide-based cyclotriphosphazene molecules consisting of different terminal groups (heptyl, decyl, and tetradecyl) at the periphery was successfully synthesized and characterized. The reaction began with the alkylation of methyl-4-hydroxybenzoate with 1-bromoheptane, 1-bromodecane, and 1-bromotetradecane, which was followed by reduction with potassium hydroxide to form a series of benzoic acid intermediates (1a–c). These intermediates underwent a reaction with thionyl chloride, followed by a reaction with 4-nitroaniline and triethylamine, to form para-substituted amides (2a–c). Further reduction of intermediates 2a–c with sodium sulfide hydrate produced the anilines 3a–c. Another reaction of hexachlorocyclotriphosphazene (HCCP) with methyl-4-hydroxybenzoate yielded intermediate 4, which was then reduced with sodium hydroxide to form intermediate 5. Finally, chlorination of intermediate 5 with thionyl chloride, followed by a reaction with the aniline derivatives (3a–c), formed the hexasubstituted cyclotriphosphazene compounds 6a–c, with two amide linkages. The structures of these compounds were confirmed using Fourier transform infrared (FTIR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy and CHN elemental analysis. Full article
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22 pages, 1532 KiB  
Article
Novel Alkyl-Polyglucoside-Based Topical Creams Containing Basil Essential Oil (Ocimum basilicum L. Lamiaceae): Assessment of Physical, Mechanical, and Sensory Characteristics
by Ana Barjaktarević, Georgeta Coneac, Snežana Cupara, Olivera Kostić, Marina Kostić, Ioana Olariu, Vicenţiu Vlaia, Ana-Maria Cotan, Ştefania Neamu and Lavinia Vlaia
Pharmaceutics 2025, 17(7), 934; https://doi.org/10.3390/pharmaceutics17070934 - 19 Jul 2025
Viewed by 395
Abstract
Background/Objectives: Basil essential oil exhibits a wide range of biological activities, including strong antimicrobial and anti-inflammatory effects. Considering the health benefits of basil essential oil (BEO) and the favorable properties of alkyl polyglucoside emulsifiers, novel Montanov™-68-based O/W creams containing BEO were developed and [...] Read more.
Background/Objectives: Basil essential oil exhibits a wide range of biological activities, including strong antimicrobial and anti-inflammatory effects. Considering the health benefits of basil essential oil (BEO) and the favorable properties of alkyl polyglucoside emulsifiers, novel Montanov™-68-based O/W creams containing BEO were developed and characterized. Additionally, the influence of the emulsifier content on the cream’s properties was evaluated. Methods: The physicochemical properties were evaluated by organoleptic examination, physical stability test, and pH and electrical conductivity measurement. The mechanical properties were investigated by rheological, textural, and consistency analyses. In addition, a sensory evaluation protocol was applied. Results: The cream formulations containing 5% and 7% Montanov™ 68 demonstrated physical stability, with no evidence of phase separation during the observation period or following accelerated aging. The pH values remained within the acceptable range for topical use, and a gradual decrease in electrical conductivity over time was observed. The rheological analyses confirmed the non-Newtonian pseudoplastic behavior with thixotropic flow characteristics. The textural analyses demonstrated that the higher emulsifier content led to increased firmness, consistency, cohesiveness, and index of viscosity. The sensory analysis revealed differences between the alkyl polyglucoside (APG)-based cream formulations only in terms of the elasticity and stickiness. Conclusions: Although the rheological analyses suggested the better spreadability of the formulation with 5% emulsifier, this was not confirmed by the sensory analysis. However, the APG-based formulations performed significantly better than the synthetic surfactant-based formulation in terms of the absorption, stickiness, and greasiness (during and after application). These results are encouraging for the further evaluation of APG-based creams containing basil essential oil for topical application. Full article
(This article belongs to the Special Issue Novel Drug Delivery Systems for the Treatment of Skin Disorders)
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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 435
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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23 pages, 4866 KiB  
Article
Role of Individual Amino Acid Residues Directly Involved in Damage Recognition in Active Demethylation by ABH2 Dioxygenase
by Anastasiia T. Davletgildeeva, Timofey E. Tyugashev, Mingxing Zhao, Alexander A. Ishchenko, Murat Saparbaev and Nikita A. Kuznetsov
Int. J. Mol. Sci. 2025, 26(14), 6912; https://doi.org/10.3390/ijms26146912 - 18 Jul 2025
Viewed by 183
Abstract
The enzyme ABH2, one of nine human DNA dioxygenases of the AlkB family, belongs to the superfamily of Fe(II)/α-ketoglutarate-dependent dioxygenases and plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases. ABH2 has broad substrate specificity, directly [...] Read more.
The enzyme ABH2, one of nine human DNA dioxygenases of the AlkB family, belongs to the superfamily of Fe(II)/α-ketoglutarate-dependent dioxygenases and plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases. ABH2 has broad substrate specificity, directly oxidizing DNA damages such as N1-methyladenine, N3-methylcytosine, 1,N6-ethenoadenine, 3,N4-ethenocytosine, and a number of others. In our investigation, we sought to uncover the subtleties of the mechanisms governing substrate specificity in ABH2 by focusing on several critical amino acid residues situated in its active site. To gain insight into the function of this enzyme, we performed a functional mapping of its active site region, concentrating on pivotal residues, participating in forming a damaged binding pocket of the enzyme (Val99 and Ser125), as well as the residues directly involved in interactions with damaged bases, namely Arg110, Phe124, Arg172, and Glu175. To support our experimental data, we conducted a series of molecular dynamics simulations, exploring the interactions between the ABH2 mutant forms, bearing corresponding substitutions and DNA substrates, and harboring various types of methylated bases, specifically N1-methyladenine or N3-methylcytosine. The comparative studies revealed compelling data indicating that alterations in most of the studied amino acid residues significantly influence both the binding affinity of the enzyme for DNA and its catalytic efficiency. Intriguingly, the findings suggest that the mutations impact the catalytic activity of ABH2 to a greater extent than its ability to associate with DNA strands. Collectively, these results show how changes to the active site affect molecular dynamics and reaction kinetics, improving our understanding of the substrate recognition process in this pivotal enzyme. Full article
(This article belongs to the Special Issue Molecular Mechanism in DNA Replication and Repair)
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26 pages, 2712 KiB  
Article
[1,3]Thiazolo[3,2-b][1,2,4]triazolium Salts as Effective Antimicrobial Agents: Synthesis, Biological Activity Evaluation, and Molecular Docking Studies
by Mykhailo Slivka, Boris Sharga, Daryna Pylypiv, Hanna Aleksyk, Nataliya Korol, Maksym Fizer, Olena I. Fedurcya, Oleksandr G. Pshenychnyi and Ruslan Mariychuk
Int. J. Mol. Sci. 2025, 26(14), 6845; https://doi.org/10.3390/ijms26146845 - 16 Jul 2025
Viewed by 397
Abstract
This study focuses on the search for new effective synthetic antimicrobial compounds as a tool against the widespread presence of microorganisms resistant to existing drugs. Five derivatives of [1,3]thiazolo[3,2-b][1,2,4]triazoles were synthesized using an accessible protocol based on electrophilic heterocyclization and were characterized using [...] Read more.
This study focuses on the search for new effective synthetic antimicrobial compounds as a tool against the widespread presence of microorganisms resistant to existing drugs. Five derivatives of [1,3]thiazolo[3,2-b][1,2,4]triazoles were synthesized using an accessible protocol based on electrophilic heterocyclization and were characterized using infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopies, and their in vitro antimicrobial and antifungal activities were evaluated using the agar plate diffusion method and the microdilution plate procedure. Both antibacterial (Gram-positive and Gram-negative) and antifungal activities were found for the examined samples. The minimum inhibitory concentration (MIC) varied from 0.97 to 250 µg/mL, and the minimum bactericidal concentration (MBC) from 1.95 to 500 µg/mL. Compound 2a showed good antifungal action against Candida albicans and Saccharomyces cerevisiae with minimum fungicidal concentration (MFC) 125 and MIC 31.25 µg/mL. The molecular docking revealed that the 2-heptyl-3-phenyl-6,6-trimethyl-5,6-dihydro-3H-[1,3]thiazolo[3,2-b][1,2,4]triazol-7-ium cation stands out as a highly promising candidate for further investigation due to a wide range of interactions, including conventional hydrogen bonds, π–σ, π–π T-shaped, and hydrophobic alkyl interactions. The synthesis and preliminary evaluation of [1,3]thiazolo[3,2-b][1,2,4]triazoles yielded promising antimicrobial and antifungal candidates. The diverse interaction profile of the 2-heptyl derivative salt allows this compound’s selection for further biological studies. Full article
(This article belongs to the Section Materials Science)
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22 pages, 3439 KiB  
Article
Metabolomics Analysis Reveals the Influence Mechanism of Different Growth Years on the Growth, Metabolism and Accumulation of Medicinal Components of Bupleurum scorzonerifolium Willd. (Apiaceae)
by Jialin Sun, Jianhao Wu, Weinan Li, Xiubo Liu and Wei Ma
Biology 2025, 14(7), 864; https://doi.org/10.3390/biology14070864 - 16 Jul 2025
Viewed by 208
Abstract
Bupleurum scorzonerifolium Willd. is a perennial herbaceous plant of the genus Bupleurum in the Apiaceae family. Also known as red Bupleurum, it is mainly distributed in Northeast China, North China and other regions and is a commonly used medicinal plant. It is [...] Read more.
Bupleurum scorzonerifolium Willd. is a perennial herbaceous plant of the genus Bupleurum in the Apiaceae family. Also known as red Bupleurum, it is mainly distributed in Northeast China, North China and other regions and is a commonly used medicinal plant. It is difficult for the wild plant resources of Bupleurum scorzonerifolium Willd. to meet the market demand. In artificial cultivation, there are problems such as a low yield per plant, low quality, weakened stress resistance and variety degradation. The contents of bioactive components and metabolites in traditional Chinese medicinal materials vary significantly across different growth years. The growth duration directly impacts their quality and clinical efficacy. Therefore, determining the optimal growth period is one of the crucial factors in ensuring the quality of traditional Chinese medicinal materials. In this study, Gas Chromatography–Mass Spectrometry (GC-MS) and High-performance liquid chromatography (HPLC) were comprehensively applied to analyze the metabolically differential substances in different parts of Bupleurum scorzonerifolium Willd. By comparing the compositions and content differences of chemical components in different growth years and different parts, the chemical components with significant differences were accurately screened out. In order to further explore the dynamic change characteristics and internal laws of metabolites, a metabolic network was constructed for a visual analysis and, finally, to see the optimal growth years of Bupleurum scorzonerifolium Willd. This result showed that with the accumulation of the growth cycle, the height, root width, fresh mass and saikosaponins content of Bupleurum scorzonerifolium Willd. increased year by year. Except for sodium and calcium elements in the main shoot, the other elements were significantly reduced. In addition, 59 primary metabolites were identified by GC-MS, with the accumulation of the growth cycle, the contents of organic acids, sugars, alcohols and amino acids gradually decreased, while the contents of alkyl, glycosides and other substances gradually increased. There were 53 positive correlations and 18 negative correlations in the triennial Bupleurum scorzonerifolium Willd. grid, all of which were positively correlated with saikosaponins. Therefore, the triennial Bupleurum scorzonerifolium Willd. was considered to be the suitable growth year. It not only provided a new idea and method for the quality evaluation of Bupleurum scorzonerifolium Willd., but also provided a scientific basis for the quality control of Chinese herbs. Full article
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