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18 pages, 9053 KB  
Article
Computational and Experimental Analysis of Sophora alopecuroides L. Chloroform Fraction: Active Components and Anti-Breast Cancer Resistance Mechanisms
by Rui Xi, Xiaoying Yin, Chuangchuang Xiao, Haoran Chen, Yang Lu, Qin Zhao, Daming Shi and Fangyun Sun
Molecules 2026, 31(4), 660; https://doi.org/10.3390/molecules31040660 - 14 Feb 2026
Viewed by 123
Abstract
We discovered that the chloroform extracted from Sophora alopecuroides L. exhibited the capacity to counteract multidrug resistance in breast cancer significantly. However, the precise active ingredients and their underlying mechanisms of action remain to be elucidated, necessitating the urgent undertaking of in-depth studies. [...] Read more.
We discovered that the chloroform extracted from Sophora alopecuroides L. exhibited the capacity to counteract multidrug resistance in breast cancer significantly. However, the precise active ingredients and their underlying mechanisms of action remain to be elucidated, necessitating the urgent undertaking of in-depth studies. In this study, an extract of Sophora alopecuroides L. was obtained through ethanol extraction and chloroform solvent extraction. Subsequent isolation and multi-round screening using MCF-7/ADR cells yielded the highly active chloroform derivative SaL-30. The active compound group of Sophora alopecuroides L. (SACG), consisting of 13 compounds, was confirmed by HPLC-QTOF-MS/MS and compositional screening. Network pharmacological analysis and molecular docking technology demonstrated that SACG reversed breast cancer resistance through an intricate multi-component (flavonoids/alkaloids), multi-target (AKT1/TNF/CDK2), and multi-pathway (PI3K-AKT/FoxO/MAPK) synergistic mode of action, with the PI3K-AKT pathway acting as the core regulator. Cell experiments further demonstrate that SaL-30 has strong toxicity against MCF-7/ADR by cellular assay, with an IC50 value of 8.941 ± 0.327 µg/mL and a synergistic index of CI = 0.3258, exhibiting a strong synergistic anti-breast cancer effect when co-administered with Adriamycin. These findings provide a theoretical foundation for elucidating the anti-drug resistance mechanism of Sophora alopecuroides L. Full article
(This article belongs to the Special Issue Advancement in Phytochemistry and Pharmacology of Medicinal Plants)
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24 pages, 2481 KB  
Article
Design and Evaluation of New 6-Trifluoromethoxy-Isatin Derivatives as Potential CDK2 Inhibitors
by Przemysław Czeleń and Beata Szefler
Int. J. Mol. Sci. 2026, 27(4), 1802; https://doi.org/10.3390/ijms27041802 - 13 Feb 2026
Viewed by 115
Abstract
Cyclin-dependent kinase 2 (CDK2) plays a central role in cell cycle regulation and represents an important molecular target in anticancer drug development. In this study, a series of novel isatin derivatives substituted with a trifluoromethoxy group at the C6 position were designed and [...] Read more.
Cyclin-dependent kinase 2 (CDK2) plays a central role in cell cycle regulation and represents an important molecular target in anticancer drug development. In this study, a series of novel isatin derivatives substituted with a trifluoromethoxy group at the C6 position were designed and evaluated as potential CDK2 inhibitors using a comprehensive in silico approach. Density functional theory calculations were applied to analyze the electronic properties of the proposed compounds. Molecular docking and molecular dynamics simulations were used to investigate binding modes, conformational stability, and key interactions within the CDK2 active site. Binding free energies were estimated using the Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) method, while QSAR-based (Quantitative Structure–Activity Relationship) ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses were performed to assess drug-likeness and pharmacokinetic profiles. The results indicate that the investigated derivatives form stable complexes with CDK2, supported by persistent hydrogen bonds in the hinge region and favorable hydrophobic interactions. The trifluoromethoxy substituent significantly affects ligand orientation and promotes deeper insertion into the hydrophobic pocket compared with previously studied isatin analogues. ADMET predictions suggest generally favorable absorption and toxicity profiles, with moderate solubility limitations. Overall, these findings support the potential of 6-trifluoromethoxy-isatin derivatives as promising CDK2 inhibitors and provide a basis for further experimental studies. Full article
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23 pages, 3958 KB  
Article
Discovery of Plant-Derived Natural Compounds as Novel GABA Aminotransferase Inhibitors: Structure-Based Discovery, Experimental Validation, and Molecular Dynamics Analysis
by Jinyoung Park, Muhammad Yasir, Eun-Taek Han, Won Sun Park, Jin-Hee Han, Jongseon Choe and Wanjoo Chun
Pharmaceuticals 2026, 19(2), 307; https://doi.org/10.3390/ph19020307 - 12 Feb 2026
Viewed by 266
Abstract
Background/Objectives: γ-Aminobutyric acid aminotransferase (GABA-AT) is a key enzyme responsible for GABA catabolism and represents a validated therapeutic target for epilepsy. Although existing GABA-AT inhibitors such as vigabatrin are clinically effective, their long-term use is limited by safety concerns, highlighting the need for [...] Read more.
Background/Objectives: γ-Aminobutyric acid aminotransferase (GABA-AT) is a key enzyme responsible for GABA catabolism and represents a validated therapeutic target for epilepsy. Although existing GABA-AT inhibitors such as vigabatrin are clinically effective, their long-term use is limited by safety concerns, highlighting the need for alternative inhibitors with improved profiles. In this study, we employed an integrated natural product-oriented discovery strategy to identify novel GABA-AT inhibitors from plant-derived compounds. Methods: A library of 1006 plant-derived compounds collected from seven medicinal plants traditionally associated with sedative or anxiolytic effects was subjected to primary virtual screening using GNINA. Top-ranked candidates were further refined through secondary precision docking using aglycone forms to account for biologically relevant metabolic conversion. Detailed interaction analyses and molecular dynamics simulations were performed to assess binding stability and energetic favorability. Results: Based on computational prioritization, quercetin, salvianolic acid A, and scutellarein were selected for experimental validation. Cell-based GABA-AT activity assays in HepG2 cells demonstrated that quercetin and salvianolic acid A significantly inhibited intracellular GABA-AT activity, exhibiting comparable or greater efficacy than vigabatrin, while scutellarein showed moderate inhibition. The observed cellular inhibitory effects were consistent with predicted binding modes and dynamic stability observed in in silico analyses. Conclusions: Collectively, this study highlights the utility of an aglycone-focused, structure-based screening strategy for natural product drug discovery and identifies plant-derived aglycones as promising GABA-AT inhibitor candidates for further pharmacological development. Full article
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40 pages, 3023 KB  
Article
Molecular Informatics, Chemometrics, and Sensory Omics for Constructing an Umami Peptide Cluster Library Across the Entire Lager Beer Brewing Process
by Yashuai Wu, Ruiyang Yin, Wenjing Tian, Wanqiu Zhao, Jiayang Luo, Mingtao Huang and Dongrui Zhao
Foods 2026, 15(4), 641; https://doi.org/10.3390/foods15040641 - 10 Feb 2026
Viewed by 184
Abstract
Umami taste in lager beer not only determined body fullness and the backbone of aftertaste, but also affected the controllability and interpretability of flavor expression across the entire brewing process. Based on stage-wise sampling, peptidomic profiles were established on wort fermentation day 0, [...] Read more.
Umami taste in lager beer not only determined body fullness and the backbone of aftertaste, but also affected the controllability and interpretability of flavor expression across the entire brewing process. Based on stage-wise sampling, peptidomic profiles were established on wort fermentation day 0, day 1, day 3, and day 9. A total of 25,592 peptides were identified by reversed-phase liquid chromatography–quadrupole time-of-flight mass spectrometry (RPLC-QTOF-MS). Molecular informatics screening was performed using UMPred-FRL (a feature representation learning-based meta-predictor for umami peptides) and TastePeptides-Meta (a one-stop platform for taste peptides and prediction models), yielding 7255 potential umami peptides. From these, 145 peptides were further selected for molecular docking. In addition, 6 representative umami peptides were selected for receptor-level validation and structural analysis. Mechanistically, the umami receptor taste receptor type 1 member 1/taste receptor type 1 member 3 (T1R1/T1R3) belonged to class C G protein-coupled receptor (GPCR) and relied on the extracellular Venus flytrap (VFT) domain for ligand capture. Ligand-induced VFT conformational convergence transmitted changes to the transmembrane region and triggered signal transduction. Docking and energy decomposition indicated that the ionic group primarily contributed to orientation and anchoring. Salt-bridge or hydrogen-bond networks were formed around Lys228, Arg240, Glu206, Asp210, Asn141, and Gln138, thereby reducing conformational freedom. Meanwhile, hydrophobic side chains obtained major binding gains within a hydrophobic microenvironment formed by Val135, Ile137, Leu165, Tyr166, Trp78, and His79. These results reflected a synergistic mode in which charge pairing enabled positioning and hydro-phobic complementarity promoted VFT closure. To experimentally confirm sensory relevance, 6 representative peptides were individually spiked into 4 brewing-stage beer samples, which produced a clear stratification pattern across stages. Notably, peptides with favorable docking-derived binding propensity did not necessarily enhance umami perception, and several longer peptides showed persistent negative sensory shifts, supporting that binding affinity alone could not be treated as a proxy for perceived umami in the beer matrix. At the node level, the cumulative abundance of umami peptides showed a significant positive correlation with umami scores, with a Pearson correlation coefficient of r = 0.963 and p = 0.037. This result indicated good linear consistency between umami peptide content and the upward shift in umami taste in lager beer. Umami peptide clusters were further proposed as a more appropriate functional unit, and an umami peptide cluster database spanning the full process was constructed. This database provided a reusable resource for process control and flavor prediction. Full article
(This article belongs to the Section Food Analytical Methods)
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17 pages, 988 KB  
Article
Synthesis of Hydrazidoureidobenzensulfonamides Incorporating a Nicotinoyl Tail and Their Carbonic Anhydrase I, II, IX and XII Inhibitory Activity
by Alberto Deplano, Davide Moi, Serena Vittorio, Andrea Angeli, Claudiu T. Supuran and Valentina Onnis
Pharmaceuticals 2026, 19(2), 290; https://doi.org/10.3390/ph19020290 - 9 Feb 2026
Viewed by 283
Abstract
Background: Carbonic anhydrases (CAs) are known to play important roles in several physiological and pathological processes; among them, CAs IX and XII are of particular relevance in cancer therapy due to their involvement in tumor growth and progression. Methods: In this [...] Read more.
Background: Carbonic anhydrases (CAs) are known to play important roles in several physiological and pathological processes; among them, CAs IX and XII are of particular relevance in cancer therapy due to their involvement in tumor growth and progression. Methods: In this study, a novel series of benzenesulfonamides incorporating a hydrazinocarbonyl-ureido linker alongside a 6-arylpyridine tail was synthesized and evaluated for inhibitory activity through a stopped-flow CO2 hydrase assay on four hCA isoforms. Results: Some of the new compounds exhibited great activity and selectivity toward the tumor-expressed CA XII isoform over the off-target isoforms CA I and CA II. Based on these results, they were selected for ADME prediction studies, showing favorable drug-like properties. To further investigate their binding mode, these compounds were docked into the four hCA isoforms. Conclusions: Overall, the results underscore the potential of compounds bearing a 6-arylpyridine tail along with a hydrazinocarbonyl-ureido linker as a foundation for further inhibitor development. Full article
(This article belongs to the Section Medicinal Chemistry)
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23 pages, 8670 KB  
Article
Mechanistic Investigation of Astragalus Root in the Management of T2DM-NAFLD Comorbidity: An Integrated Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, and In Vitro Study
by Jie Li, Nanqi Shao, Ying Gao, Baojian Li, Yan Liang, Yinglai Yang and Jianguang Li
Pharmaceuticals 2026, 19(2), 289; https://doi.org/10.3390/ph19020289 - 9 Feb 2026
Viewed by 248
Abstract
Background/Objectives: Astragalus root is a classical qi-tonifying traditional Chinese medicine that has demonstrated potential therapeutic efficacy in type 2 diabetes mellitus (T2DM) and non-alcoholic fatty liver disease (NAFLD). However, the precise mechanisms underlying its effects on the comorbidity of these two disorders [...] Read more.
Background/Objectives: Astragalus root is a classical qi-tonifying traditional Chinese medicine that has demonstrated potential therapeutic efficacy in type 2 diabetes mellitus (T2DM) and non-alcoholic fatty liver disease (NAFLD). However, the precise mechanisms underlying its effects on the comorbidity of these two disorders remain unclear. This study investigated the molecular mechanisms by which Astragalus root ameliorated T2DM-NAFLD comorbidity. Methods: Network pharmacology, molecular docking, molecular dynamics simulation, and in vitro experiments were employed to elucidate the potential roles and mechanisms of Astragalus root in the management of T2DM-NAFLD comorbidity. Results: A total of 25 bioactive constituents and 152 corresponding targets associated with Astragalus root were identified. PPI network analysis revealed the top ten core candidate targets, among which six possessed suitable crystal structures for molecular docking, including interleukin-6 (IL-6), threonine-protein kinase 1(AKT1), transcription factor AP-1(JUN), tumor necrosis factor (TNF), cysteine-dependent aspartate-specific protease 3 (CASP3), and estrogen Receptor 1(ESR1). Kyoto encyclopedia of genes and genomes (KEGG) analysis further identified the phosphatidylinositol 3-kinase (PI3K)-AKT as the most significantly enriched pathway. Molecular docking validated the potential binding modes of formononetin to the six core targets, a finding that was further confirmed by molecular dynamics simulations, which proved the stability of the resulting complexes. In vitro experiments demonstrated that formononetin obviously decreased lipid droplet accumulation, downregulated total cholesterol (TC) and triglyceride (TG) levels, suppressed the expression of TNF-α, IL-6, and interleukin-1β (IL-1β), decreased reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and enhanced glutathione (GSH) content and superoxide dismutase (SOD) activity. These therapeutic effects were achieved through inhibition of protein expression within the PI3K/AKT/mechanistic target of rapamycin (mTOR) signaling pathway. Conclusions: This study determined the potential therapeutic targets and underlying mechanisms of formononetin derived from Astragalus root in the T2DM-NAFLD management, thereby providing a scientific basis for its clinical application. Full article
(This article belongs to the Section Natural Products)
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31 pages, 3208 KB  
Article
Integrative LC-HR-QTOF-MS and Computational Metabolomics Approaches for Compound Annotation, Chemometric Profiling and In Silico Antibacterial Evaluation of Ugandan Propolis
by Ivan Kahwa, Christina Seel, Ronnie Tumwesigye, Patrick Onen, Ramona Oehme, Susan Billig, Rapheal Wangalwa, Jonans Tusiimire, Claudia Wiesner and Leonard Kaysser
Metabolites 2026, 16(2), 109; https://doi.org/10.3390/metabo16020109 - 3 Feb 2026
Viewed by 478
Abstract
Background/Objectives: Propolis is a complex bee product with a composition that varies according to local vegetation, environmental conditions, and bee foraging behaviours. Recently, gas chromatography–mass spectrometry (GC–MS) has been employed in Uganda to analyse its volatile components. This study examined Ugandan propolis [...] Read more.
Background/Objectives: Propolis is a complex bee product with a composition that varies according to local vegetation, environmental conditions, and bee foraging behaviours. Recently, gas chromatography–mass spectrometry (GC–MS) has been employed in Uganda to analyse its volatile components. This study examined Ugandan propolis non-volatile metabolites to determine chemotypes and identify antibacterial compounds. Methods: Ethanolic extracts were analysed using liquid chromatography–high-resolution quadrupole time-of-flight mass spectrometry (LC-HR-QTOF-MS) in an untargeted MS/MS mode. Data processing was carried out using MZmine, then annotated with Global Natural Products Social Molecular Networking (GNPS) and SIRIUS. Chemometric methods assisted in identifying regional chemical signatures. Metabolites highlighted by the heatmap were evaluated for antibacterial activity using molecular docking against bacterial targets, followed by ADMET (absorption, distribution, metabolism, excretion, and toxicity) assessments. Results: Out of 3252 features, 234 and 52 putative compounds were annotated in GNPS and SIRIUS, respectively, as indicated by molecular networking, suggesting high chemical complexity. The chemical space mainly comprises flavonoids (including glycosides, aglycones, methylated, and prenylated derivatives), phenolic acids, amides, hydroxycinnamate derivatives, lignans, megastigmanes, and various diterpenoid skeletons. Multivariate analyses clearly distinguish geographical chemotypes, separating flavonoid-rich regions from diterpenoid-rich regions. Docking studies revealed flavonoids, diterpenoids, and lignans with strong predicted antibacterial activities and favourable ADMET profiles. Conclusions: This study provides the first LC–MS characterisation of the non-volatile metabolome of Ugandan propolis, thereby expanding its chemical diversity. Metabolomics and computational approaches lay a foundation for future ecological, chemotaxonomic, and pharmacological research. Full article
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26 pages, 3171 KB  
Article
Design and Synthesis of 4-Arylazo Pyrazole Carboxamides as Dual AChE/BChE Inhibitors: Kinetic and In Silico Evaluation
by Suleyman Akocak, Nebih Lolak, Hatice Esra Duran, Büşra Demir Çetinkaya, Hamada Hashem, Stefan Bräse and Cüneyt Türkeş
Pharmaceuticals 2026, 19(2), 239; https://doi.org/10.3390/ph19020239 - 29 Jan 2026
Viewed by 713
Abstract
Background/Objectives: Pyrazole carboxamides are widely used as adaptable medicinal-chemistry scaffolds and have been explored as cholinesterase (ChE) inhibitor chemotypes. In this work, we prepared a new series of 4-arylazo-3,5-diamino-N-tosyl-1H-pyrazole-1-carboxamides 5(am) and evaluated their [...] Read more.
Background/Objectives: Pyrazole carboxamides are widely used as adaptable medicinal-chemistry scaffolds and have been explored as cholinesterase (ChE) inhibitor chemotypes. In this work, we prepared a new series of 4-arylazo-3,5-diamino-N-tosyl-1H-pyrazole-1-carboxamides 5(am) and evaluated their inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), supported by structure-based computational analyses. Methods: Thirteen derivatives 5(am) were synthesized, fully characterized with analytical techniques (FT-IR, H NMR, and C NMR), and tested in vitro against AChE and BChE, with tacrine (THA) used as the reference inhibitor. Docking calculations were used to examine plausible binding modes. The top-ranked complexes (7XN1–5e and 4BDS–5i) were further examined by 100 ns explicit-solvent molecular dynamics (MD) simulations in Cresset Flare, followed by RMSD/RMSF analysis and contact-persistence profiling. Predicted ADME/Tox. properties were also assessed to identify potential developability issues. Results: The series showed strong ChE inhibition, and several compounds were more potent than THA. Compound 5e (4-nitro) was the most active AChE inhibitor (KI = 20.86 ± 1.61 nM) compared with THA (KI = 164.40 ± 20.84 nM). For BChE, the KI values ranged from 31.21 to 87.07 nM and exceeded the reference compound’s activity. MD trajectories supported stable binding in both systems (10–100 ns mean backbone RMSD: 2.21 ± 0.17 Å for 7XN1–5e; 1.89 ± 0.11 Å for 4BDS–5i). Most fluctuations were confined to flexible regions, while key contacts remained in place, consistent with the docking models. ADME/Tox. predictions suggested moderate lipophilicity but generally low aqueous solubility; all compounds were predicted as non-BBB permeant, and selected liabilities were flagged (e.g., carcinogenicity for 5e/5g/5h/5i; nephrotoxicity for 5f/5g). Conclusions: The 4-arylazo-3,5-diamino-N-tosyl-1H-pyrazole-1-carboxamide scaffold delivers low-nanomolar ChE inhibition, with docking and MD supporting stable binding modes. Future optimization should prioritize solubility improvement and mitigation of predicted toxicities and metabolic liabilities, especially given the predicted lack of BBB permeability for CNS-directed applications. Full article
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16 pages, 4627 KB  
Article
Evaluation of AI-Predicted GH11 Xylanase Models Against a Previously Unreported Experimental Structure: Implications for Conformational Accuracy and Ligand Binding
by Ki Hyun Nam
Int. J. Mol. Sci. 2026, 27(3), 1370; https://doi.org/10.3390/ijms27031370 - 29 Jan 2026
Viewed by 259
Abstract
Artificial intelligence (AI)-based structure prediction tools have emerged as powerful methods for understanding previously unsolved structures. AI-predicted models are widely used for protein function identification, drug development, and protein engineering. Although AI-predicted structures offer significant opportunities to advance research, their inaccuracies can lead [...] Read more.
Artificial intelligence (AI)-based structure prediction tools have emerged as powerful methods for understanding previously unsolved structures. AI-predicted models are widely used for protein function identification, drug development, and protein engineering. Although AI-predicted structures offer significant opportunities to advance research, their inaccuracies can lead to misinterpretations of molecular mechanisms. Thus, evaluating the structural differences between AI-predicted and experimental structures is crucial for accurately understanding molecular mechanisms and guiding the design of subsequent experiments. In this study, the previously unreported crystal structure of xylanase from Hypocrea virens (HviGH11) was compared with the structures predicted by ESMFold, AlphaFold2, AlphaFold3, and RoseTTAFold. The overall fold of HviGH11 was highly similar between the experimental and AI-predicted models; however, the conformation of the thumb domain of the protein varied across the models. The substrate-binding cleft of experimental HviGH11 was similar to that in the model structures generated by ESMFold, AlphaFold2, and AlphaFold3, but significantly different from those in the model structures generated by RoseTTAFold. The substrate docking study illustrated that the binding mode of xylohexaose in the substrate-binding cleft differed between the experimental and AI-predicted HviGH11 structures. These findings provide insights into the applications of AI-predicted models and offer guidance for appropriate application in structural and functional studies and biotechnology. Full article
(This article belongs to the Special Issue Computer Simulation Insight into Ligand–Receptor Interaction)
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27 pages, 4785 KB  
Article
Rational Design, Synthesis, and Molecular Docking of Novel Terpene Analogues of Imatinib, and Their Inhibition on Downstream BCR-ABL Signaling
by Rositsa Mihaylova, Asine Dailova-Barzeva, Irena Philipova, Georgi Momekov, Irini Doytchinova, Mariyana Atanasova and Georgi Stavrakov
Pharmaceuticals 2026, 19(2), 198; https://doi.org/10.3390/ph19020198 - 23 Jan 2026
Viewed by 328
Abstract
Background/Objectives: Imatinib, the first tyrosine kinase inhibitor, marks the beginning of a revolution in clinical oncology. Disrupting oncogenic kinase-dependent signaling pathways represents a key strategy for advancing targeted cancer therapies. Terpene analogues of imatinib were developed to probe the influence of terminal [...] Read more.
Background/Objectives: Imatinib, the first tyrosine kinase inhibitor, marks the beginning of a revolution in clinical oncology. Disrupting oncogenic kinase-dependent signaling pathways represents a key strategy for advancing targeted cancer therapies. Terpene analogues of imatinib were developed to probe the influence of terminal ring modifications on BCR-ABL inhibition and downstream oncogenic signaling. Methods: Nine novel imatinib analogues bearing bulky aliphatic moieties were designed, synthesised, and structurally characterized by 1H/13C NMR spectroscopy and high-resolution mass spectrometry (HRMS). Molecular docking calculations were performed to assess the binding modes and intermolecular interactions. The cytotoxicity of the newly synthesized imatinib derivatives was evaluated across a panel of BCR-ABL+ leukemia cell lines. Results: Molecular docking analyses demonstrated conserved interactions within the ATP-binding site of BCR-ABL for all derivatives, with calculated docking scores ranging between 123 and 128, while modifications at the terminal ring introduced subtle changes in electrostatic and steric profiles. Biological evaluation using MTT-based cytotoxicity assays in BCR-ABL+ leukemic cell lines revealed enhanced antiproliferative activity compared with imatinib, with compounds 6a (flexible cyclohexyl) and 6d (rigid camphane-type (+)-isopinocampheyl) exhibiting the lowest micromolar activity in the AR-230 model (IC50 values of 1.1 and 1.2 μM, respectively). Proteome-wide phosphokinase profiling demonstrated shared suppression of STAT5/3/6, RSK1/2, S6K1/p70, and Pyk2, confirming effective disruption of canonical BCR-ABL pathways. Critically, the terpene moiety dictated downstream pathway bias: 6a preferentially attenuated CREB activation, whereas 6d more effectively suppressed the PI3K/Akt oncogenic axis and strongly activated proapoptotic p53-mediated stress responses. Conclusions: Our findings establish terpene-engineered imatinib analogues as tunable modulators and promising candidates for targeting downstream BCR-ABL signaling pathways in leukemia treatment. Full article
(This article belongs to the Special Issue Targeting Enzymes in Drug Design and Discovery)
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36 pages, 4550 KB  
Article
Probabilistic Load Forecasting for Green Marine Shore Power Systems: Enabling Efficient Port Energy Utilization Through Monte Carlo Analysis
by Bingchu Zhao, Fenghui Han, Yu Luo, Shuhang Lu, Yulong Ji and Zhe Wang
J. Mar. Sci. Eng. 2026, 14(2), 213; https://doi.org/10.3390/jmse14020213 - 20 Jan 2026
Viewed by 257
Abstract
The global shipping industry is surging ahead, and with it, a quiet revolution is taking place on the water: marine lithium-ion batteries have emerged as a crucial clean energy carrier, powering everything from ferries to container ships. When these vessels dock, they increasingly [...] Read more.
The global shipping industry is surging ahead, and with it, a quiet revolution is taking place on the water: marine lithium-ion batteries have emerged as a crucial clean energy carrier, powering everything from ferries to container ships. When these vessels dock, they increasingly rely on shore power charging systems to refuel—essentially, plugging in instead of idling on diesel. But predicting how much power they will need is not straightforward. Think about it: different ships, varying battery sizes, mixed charging technologies, and unpredictable port stays all come into play, creating a load profile that is random, uneven, and often concentrated—a real headache for grid planners. So how do you forecast something so inherently variable? This study turned to the Monte Carlo method, a probabilistic technique that thrives on uncertainty. Instead of seeking a single fixed answer, the model embraces randomness, feeding in real-world data on supply modes, vessel types, battery capacity, and operational hours. Through repeated random sampling and load simulation, it builds up a realistic picture of potential charging demand. We ran the numbers for a simulated fleet of 400 vessels, and the results speak for themselves: load factors landed at 0.35 for conventional AC shore power, 0.39 for high-voltage DC, 0.33 for renewable-based systems, 0.64 for smart microgrids, and 0.76 when energy storage joined the mix. Notice how storage and microgrids really smooth things out? What does this mean in practice? Well, it turns out that Monte Carlo is not just academically elegant, it is practically useful. By quantifying uncertainty and delivering load factors within confidence intervals, the method offers port operators something precious: a data-backed foundation for decision-making. Whether it is sizing infrastructure, designing tariff incentives, or weighing the grid impact of different shore power setups, this approach adds clarity. In the bigger picture, that kind of insight matters. As ports worldwide strive to support cleaner shipping and align with climate goals—China’s “dual carbon” ambition being a case in point—achieving a reliable handle on charging demand is not just technical; it is strategic. Here, probabilistic modeling shifts from a simulation exercise to a tangible tool for greener, more resilient port energy management. Full article
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32 pages, 2940 KB  
Article
Integrated In Vitro and In Silico Profiling of Piperazinyl Thiosemicarbazone Derivatives Against Trypanosoma cruzi: Stage-Specific Activity and Enzyme Inhibition
by Héctor A. Baldoni, María L. Sbaraglini, Darío E. Balcazar, Diego G. Arias, Sergio A. Guerrero, Catalina D. Alba Soto, Wioleta Cieslik, Marta Rogalska, Jaroslaw Polański, Ricardo D. Enriz, Josef Jampilek and Robert Musiol
Pharmaceuticals 2026, 19(1), 182; https://doi.org/10.3390/ph19010182 - 20 Jan 2026
Viewed by 475
Abstract
Background: Trypanosoma cruzi, the causative agent of Chagas disease, remains a major public health concern, and there is a continued need for new antitrypanosomal agents. Thiosemicarbazone (TSC) derivatives have emerged as a promising class of compounds with potential antiparasitic activity. Objectives: [...] Read more.
Background: Trypanosoma cruzi, the causative agent of Chagas disease, remains a major public health concern, and there is a continued need for new antitrypanosomal agents. Thiosemicarbazone (TSC) derivatives have emerged as a promising class of compounds with potential antiparasitic activity. Objectives: This study aimed to report the synthesis, characterization, and biological profiling of a novel series of thiosemicarbazone derivatives as antitrypanosomal agents against Trypanosoma cruzi. Methods: Fourteen new compounds and six previously described analogues were prepared and characterized by 1H/13C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). As a preliminary in vitro screen, activity was assessed by direct parasite counting in epimastigote and bloodstream trypomastigote forms, as tractable models of replicative and infective stages sharing core metabolic targets with intracellular amastigotes. Epimastigote potency was quantified as half-maximal effective concentrations (EC50) derived from dose–response curves, whereas trypomastigote response was evaluated as percent viability after treatment at a fixed concentration of 20 µM. Mechanistic profiling included inhibition assays against the cysteine protease cruzipain (CZP) and selected redox defense enzymes, complemented by in silico similarity clustering and binding-pose affinity scoring. Results: A nitro-methoxy-substituted TSC showed potent CZP inhibition but limited trypomastigote efficacy, whereas brominated analogues displayed dual-stage activity independent of CZP inhibition. Tanimoto similarity analysis identified distinct structure–activity clusters, linking nitro-methoxy substitution to epimastigote selectivity and brominated scaffolds to broader antiparasitic profiles, with hydrophobicity and steric complementarity as key determinants. Enzymatic assays revealed no significant inhibition of cytosolic tryparedoxin peroxidase (cTXNPx) or glutathione peroxidase type I (TcGPx-I), suggesting redox disruption is not a primary mode of action. In vitro and in silico analyses showed low or no non-specific cytotoxicity under the tested conditions, supporting further optimization of these derivatives as antitrypanosomal preliminary hits. Key hits included derivative 3e (epimastigote EC50 = 0.36 ± 0.02 µM) and brominated analogues 2c and 2e (epimastigote EC50 = 3.92 ± 0.13 and 4.36 ± 0.10 µM, respectively), while docking supported favorable binding-pose affinity (e.g., ΔGS-pose = −20.78 ± 2.47 kcal/mol for 3e). Conclusions: These results support further optimization of the identified thiosemicarbazone derivatives as preliminary antitrypanosomal hits and provide insight into structure–activity relationships and potential mechanisms of action. Full article
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35 pages, 8701 KB  
Article
Design, Synthesis, and Biological Evaluation of Novel Acetylcholinesterase and β-Secretase 1 Inhibitors
by Danuta Drozdowska, Damian Pawelski, Agnieszka Wróbel-Tałałaj, Marta Plonska-Brzezinska, Beata Kolesinska, Ryszard Lazny, Barbara Seroka, Cezary Parzych and Artur Ratkiewicz
Int. J. Mol. Sci. 2026, 27(2), 1008; https://doi.org/10.3390/ijms27021008 - 20 Jan 2026
Viewed by 347
Abstract
A series of novel granatane–triazole hybrid molecules was designed, synthesized, and evaluated as dual acetylcholinesterase (AChE) and β-secretase 1 (BACE1) inhibitors. The compounds were obtained through a convergent synthetic route involving azide formation, triazole construction via dipolar cycloaddition, and final coupling with a [...] Read more.
A series of novel granatane–triazole hybrid molecules was designed, synthesized, and evaluated as dual acetylcholinesterase (AChE) and β-secretase 1 (BACE1) inhibitors. The compounds were obtained through a convergent synthetic route involving azide formation, triazole construction via dipolar cycloaddition, and final coupling with a granatane scaffold to give a pseudopelletierine (3-granatanone) analogue. In vitro assays demonstrated that all target compounds inhibited both AChE and BACE1. Molecular docking and molecular dynamics simulations revealed stable interactions with key catalytic residues, suggesting distinct binding modes compared to reference ligands. QSAR-based pharmacokinetic predictions indicated favorable blood–brain barrier permeability and compliance with key drug-likeness filters. These findings identify granatane–triazole hybrids as promising multi-target directed ligand (MTDL) candidates with potential for further optimization in the search for new anti-Alzheimer therapeutics. Full article
(This article belongs to the Special Issue Proteases and Their Inhibitors)
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21 pages, 8293 KB  
Article
In Silico Investigation Reveals IL-6 as a Key Target of Asiatic Acid in Osteoporosis: Insights from Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation
by Wanatsanan Chulrik, Aman Tedasen, Nateelak Kooltheat, Rungruedee Kimseng and Thitinat Duangchan
Med. Sci. 2026, 14(1), 41; https://doi.org/10.3390/medsci14010041 - 15 Jan 2026
Viewed by 325
Abstract
Background/Objectives: Osteoporosis is a multifactorial skeletal disorder in which chronic inflammation, dysregulated cytokine signaling, and metabolic imbalance contribute to excessive bone resorption and impaired bone formation. Asiatic acid has demonstrated bone-protective effects, but its molecular mechanisms in osteoporosis remain incompletely understood. This study [...] Read more.
Background/Objectives: Osteoporosis is a multifactorial skeletal disorder in which chronic inflammation, dysregulated cytokine signaling, and metabolic imbalance contribute to excessive bone resorption and impaired bone formation. Asiatic acid has demonstrated bone-protective effects, but its molecular mechanisms in osteoporosis remain incompletely understood. This study aimed to investigate the anti-osteoporotic mechanisms of asiatic acid using an integrative in silico strategy. Methods: Network pharmacology analysis was performed to identify osteoporosis-related molecular targets of asiatic acid. Molecular docking was used to predict the binding modes and affinities between asiatic acid and its target proteins. Molecular dynamics simulation was used to assess the structural stability and interaction persistence of the asiatic acid–protein complex. Results: Network pharmacology identified 135 overlapping targets between asiatic acid and osteoporosis, with IL-6, STAT3, PPARG, and NFKB1 emerging as key hubs. KEGG analysis indicated the PPAR signaling pathway as a potential mechanism underlying the anti-osteoporotic effect. Molecular docking showed strong binding energies of asiatic acid with all predicted target proteins, with the highest affinity observed for IL-6, involving key residues ASN61, LEU62, GLU172, LYS66, and ARG168. Consistently, molecular dynamics simulation confirmed stable binding of asiatic acid to IL-6, with persistent interactions with ASN61, LYS66, LEU62, LEU64, and GLN154 mediated by hydrogen bonds, water bridges, and hydrophobic interactions. Conclusions: This integrative in silico study provides mechanistic insight into the potential anti-osteoporotic actions of asiatic acid, implicating IL-6 as a plausible upstream molecular target. These results establish a robust mechanistic framework for future translational studies exploring asiatic acid as a natural therapeutic candidate for osteoporosis. Full article
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17 pages, 2010 KB  
Article
Molecular Mimicry Between Trypanosoma cruzi and Human TUBB as a Potential Autoimmune Mechanism in Chagas
by Ana Valentina Centeno-Iglesias, Celeste Abigail Quille-Juarez, Paul Galvez-Murillo, Anggie Stefany Revilla-Zeballos, Gustavo Alberto Obando-Pereda and Luis Alberto Ponce-Soto
Immuno 2026, 6(1), 8; https://doi.org/10.3390/immuno6010008 - 14 Jan 2026
Viewed by 556
Abstract
Chagas disease, caused by Trypanosoma cruzi, affects a significant proportion of patients who develop digestive and cardiac complications, including megaviscera. This pathogenesis has been associated with autoimmune mechanisms mediated by molecular mimicry. In this study, an in silico evaluation of the potential [...] Read more.
Chagas disease, caused by Trypanosoma cruzi, affects a significant proportion of patients who develop digestive and cardiac complications, including megaviscera. This pathogenesis has been associated with autoimmune mechanisms mediated by molecular mimicry. In this study, an in silico evaluation of the potential structural basis of cross-reactivity of β-tubulin 1.9 of T. cruzi and the human β-4A tubulin isoform 3 was conducted. Using bioinformatics tools, homologous regions were identified and potentially immunogenic epitopes were predicted, considering their structural modeling and molecular docking. The proteins shared 87% sequence identity and 95% similarity, with an almost identical structural overlap, RMSD 0.291 Å. Three epitopes, VPFPRLHFF, NDLVSEYQQYQDATI, and GQSGAGNNWAKGHYTEGAELIDS, exhibited high predicted antigenicity, with the 9-mer and 16-mer peptides displaying structurally compatible docking poses within the binding grooves of MHC class I and class II molecules, respectively, while B-cell epitope potential was inferred from sequence-based property predictions. Normal mode analysis, used as an exploratory approach, suggested comparable flexibility profiles for the parasitic- and human-derived peptide–MHC complexes. These findings provide an exploratory structural framework supporting a potential role of β-tubulin epitopes in molecular mimicry processes implicated in the development of chagasic megaviscera. Full article
(This article belongs to the Section Autoimmunity and Immunoregulation)
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