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Search Results (518)

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Keywords = ADMET properties

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29 pages, 1112 KB  
Article
Integrated In Silico Profiling of Chelidonium majus Alkaloids Identifies Potential Anti-Melanoma Candidates
by Catalina Mares, Andra-Maria Paun, Maria Mernea, Stefania-Nicola Tatarus, Bogdan Mihai Cristea, Ioana Cristina Marinas and Speranta Avram
Processes 2026, 14(7), 1099; https://doi.org/10.3390/pr14071099 (registering DOI) - 28 Mar 2026
Abstract
Melanoma remains a highly aggressive malignancy, particularly in advanced metastatic stages where therapeutic options are limited. Natural compounds provide a structural basis for discovering novel anticancer agents. In this study, we employed an integrated in silico approach to evaluate the pharmacokinetic properties, toxicity [...] Read more.
Melanoma remains a highly aggressive malignancy, particularly in advanced metastatic stages where therapeutic options are limited. Natural compounds provide a structural basis for discovering novel anticancer agents. In this study, we employed an integrated in silico approach to evaluate the pharmacokinetic properties, toxicity profiles, and molecular targets of key alkaloids from Chelidonium majus, including berberine, sanguinarine, chelerythrine, chelidonine, protopine, umbelliferone and coptisine. ADME/T predictions (SwissADME and DeepPK) revealed favorable drug-likeness and oral bioavailability for most compounds, with berberine exhibiting the most balanced safety and absorption profile. All compounds demonstrated high intestinal absorption (>99%) and implicated key melanoma targets, including APE1/Ref-1, CXCR4, CCR2, TLR8, galectin-3, and VEGFR2. These molecules represent valuable templates for the development of melanoma therapies. Among the tested compounds, chelidonine emerged as a potential APE1 inhibitor, exhibiting the highest binding affinity and forming specific interactions within the enzyme’s catalytic site, suggesting its potential as a DNA repair-targeted agent in melanoma. These findings support the further exploration of natural alkaloids, including structural optimization or advanced formulation strategies, to enhance safety, bioavailability, and therapeutic efficacy in melanoma. Full article
(This article belongs to the Section Biological Processes and Systems)
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27 pages, 6817 KB  
Article
Benzyl-Naphthoquinones as Selective Anticancer Agents for Oral Squamous Cell Carcinoma via Apoptosis Induction
by Antonio Mendonça Marconi-Nicolau, Rebeca Gripp de Sá, Caroline Reis Santiago Paschoal, Lethícia Andrade de Almeida, Gabriel Ouverney, Ana Caroline dos Santos-Diniz, Anamel Blaudt Meira, João Pedro da Costa Faria Brunhosa, Luiz Carlos da Silva Pinheiro, Paula Alvarez Abreu, Vinicius Rangel Campos and Bruno Kaufmann Robbs
Biomedicines 2026, 14(4), 757; https://doi.org/10.3390/biomedicines14040757 - 26 Mar 2026
Viewed by 206
Abstract
Background: Oral squamous cell carcinoma (OSCC) is an aggressive cancer closely associated with smoking and alcohol consumption, with a higher incidence in men. Despite changes in treatment strategies, poor survival persists in most patients, highlighting the need for novel and improved therapeutic [...] Read more.
Background: Oral squamous cell carcinoma (OSCC) is an aggressive cancer closely associated with smoking and alcohol consumption, with a higher incidence in men. Despite changes in treatment strategies, poor survival persists in most patients, highlighting the need for novel and improved therapeutic options. Naphthoquinone analogs are being investigated because of their active redox structure and broad pharmacological profile; they demonstrate cytotoxic antitumor activity, making them potential candidates for new drug agents. Objective: This study investigated new benzyl-naphthoquinone compounds as potential anticancer agents for various genotypes of oral squamous cell carcinoma (OSCC) and other cancer cells. Methods: This study reports the synthesis and evaluation of a series of eight benzyl-naphthoquinone compounds against oral squamous cell carcinoma. Results: Four compounds 14 showed the best cytotoxic profiles, with a selectivity index ≥ 3 for all OSCC cell lines tested. Compound 1 was the most selective compound in all OSCC models, showing a higher selectivity index than both carboplatin and shikonin. Furthermore, compound 1 induced DNA fragmentation, cell-cycle arrest, and caspase-3/7 activation, changes consistent with apoptosis, and time-lapse imaging corroborated the apoptotic phenotype. Hemolysis assays showed minimal toxicity in human erythrocytes, and acute in vivo evaluation in mice revealed no evident adverse effects under the conditions tested, indicating low acute toxicity, although more detailed histopathological and biochemical studies will be required to fully establish the safety profile. Molecular modeling suggested that compound 1 may interact with topoisomerase II, RSK2, and PKM2, which could contribute to the activation of apoptotic pathways, although these interactions remain predictive and require biochemical validation. Finally, in silico analysis of physicochemical and ADMET parameters indicated properties compatible with oral absorption and systemic exposure, together with predicted low toxicity; however, these results are model-based and should be confirmed experimentally. Conclusions: Based on these findings, compound 1 emerges as a promising lead candidate for the development of a novel chemotherapeutic agent against OSCC, with potential therapeutic efficacy against other cancer types. Full article
(This article belongs to the Special Issue Drug Resistance and Novel Targets for Cancer Therapy—Third Edition)
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32 pages, 5723 KB  
Article
Comparative Molecular Docking and Pharmacokinetic Profiling of Cinnamic Acid and Oleic Acid from Cinnamomum verum as Potential Inhibitors of Dengue Virus Proteins
by Wafaa Hussien Habeeb, Noor Hameed Hanoush, Meena Thaar Alani, Ali Hazim Abdulkareem, Mohammed Obaid Ibrahim, Mohammed Salih Al-Janaby, Mohammed Mukhles Ahmed, Saja Saadallah Abduljaleel and Zaid Mustafa Khaleel
Infect. Dis. Rep. 2026, 18(2), 26; https://doi.org/10.3390/idr18020026 - 26 Mar 2026
Viewed by 104
Abstract
Background: Dengue virus (DENV) does not have any effective antiviral therapy. The Cinnamomum verum has cinnamic acid and oleic acid that could inhibit important viral proteins. Aim: To compare their inhibitory capacity with the key DENV proteins through molecular docking, molecular dynamics and [...] Read more.
Background: Dengue virus (DENV) does not have any effective antiviral therapy. The Cinnamomum verum has cinnamic acid and oleic acid that could inhibit important viral proteins. Aim: To compare their inhibitory capacity with the key DENV proteins through molecular docking, molecular dynamics and in silico ADMET. Methods: Phytochemical profiling of the ethanolic extract of the bark was done by GCMS. AutoDock Vina (version 1.2.0) was used to dock cinnamic acid and oleic acid to key proteins of DENV (NS5, NS3, and envelope) in the presence of ribavirin as the reference. The best complexes were then subjected to 50 ns of molecular dynamics simulation and stability measured by RMSD, RMSF, Rg, SASA, hydrogen bonding and RDF. Validated in silico tools were used to predict the ADMET properties. Results: Analysis of GC–MS revealed cinnamic acid (85.92%) and oleic acid (5.33%). The outcome of docking was that the cinnamic acid had the greatest affinity with NS5 (−5.970 kcal/mol) and the capsid protein (−5.755 kcal/mol), and oleic acid showed the highest affinity with the capsid (−6.150 kcal/mol) and then with NS5 (−5.209 kcal/mol). Both ligands had a relatively weak interaction with NS3. Simulation of the molecular dynamics showed the stability of the top complexes, especially the cinnamic acid–NS5 complex, that retained low RMSD (1.6–1.9 A), stable Rg and SASA profiles, and continued hydrogen bonding during the 50 ns period. The use of cinnamic acid in ADMET projections was more preferable, as it was more soluble, orally bioavailable (0.91), and drug-like (QED 0.65), but oleic acid revealed higher lipophilicity and lower drug-like properties (QED 0.29). Conclusions: Cinnamic acid showed specificity towards the NS5 proteins with the help of stable dynamics and good predicted pharmacokinetics, which are features that make it a promising multi-target anti-DENV scaffold. Oleic acid exhibited poor affinity and poor pharmacokinetic properties. The findings are predictive and must be validated using biochemical, cellular, and toxicological means to prove the antiviral efficacy and safety. Full article
(This article belongs to the Special Issue Epidemiology, Prevention and Research on Dengue Virus)
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46 pages, 5344 KB  
Article
From Synthesis to Mechanism: Biological Evaluation of a p-Toluidine-Based Thiazolidinone-Quinoline VEGFR-2 Candidate Supported by CADD
by Emad Manni, Modather F. Hussein, Sara Elkady, Adel A.-H. Abdel-Rahman, Mohamed A. Hawata, Wael A. El-Sayed, Ahmed F. El-Sayed and Hagar S. El-Hema
Int. J. Mol. Sci. 2026, 27(7), 3018; https://doi.org/10.3390/ijms27073018 - 26 Mar 2026
Viewed by 130
Abstract
In response to recent advances in computer-aided drug discovery (CADD) enabled by high-performance computing, computational approaches were employed to support and rationalize the investigation of a VEGFR-2-targeted anticancer candidate, combining molecular-level modeling with experimental validation. Initial in silico ADMET profiling and molecular docking [...] Read more.
In response to recent advances in computer-aided drug discovery (CADD) enabled by high-performance computing, computational approaches were employed to support and rationalize the investigation of a VEGFR-2-targeted anticancer candidate, combining molecular-level modeling with experimental validation. Initial in silico ADMET profiling and molecular docking were conducted to support the evaluation of drug-like properties and target engagement within a series of para-toluidine-based derivatives (114). The most biologically active compound was further evaluated through 100 ns molecular dynamics simulations and comprehensive DFT calculations to investigate binding stability and electronic characteristics. Based on a rational design strategy and supported by computational analyses, the compounds were synthesized and fully characterized using IR, MS, 1H/13C NMR, and elemental analysis. Biological evaluation was performed against HepG-2, MCF-7, HCT-116, and normal WI-38 cells. Mechanistic studies included VEGFR-2 inhibition, wound-healing migration assays, cell-cycle distribution analysis, apoptosis assessment, and caspase-3 activation. Several derivatives exhibited micromolar cytotoxic activity, with compound 14 emerging as the most active against HepG-2 cells (IC50 = 7.84 ± 0.5 µM), showing cytotoxic activity comparable to that of sorafenib (IC50 = 9.18 ± 0.6 µM) and demonstrating favorable selectivity toward normal WI-38 cells (IC50 = 67.75 ± 3.6 µM). Compound 14 showed moderate VEGFR-2 inhibitory activity (IC50 = 0.55 µM), significant suppression of cell migration, pronounced G0/G1 cell-cycle arrest, and robust apoptosis induction supported by caspase-3 activation. Molecular docking and MD simulations supported a stable binding mode within the VEGFR-2 active site. This integrated framework highlights compound 14 as a selectively active VEGFR-2-oriented anticancer candidate scaffold with a favorable selectivity profile, supported by experimental and computational analyses, warranting further lead optimization. Full article
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20 pages, 3116 KB  
Article
Exploring the Prognostic, Mutational and Therapeutic Potential of ANXA2 in Ovarian Cancer via Multi-Omics and In Silico Approach
by Prithvi Singh, Joyeeta Talukdar, Hajed Obaid A. Alharbi, Wanian M. Alwanian, Indrakant Kumar Singh and Arshad Husain Rahmani
Biology 2026, 15(7), 523; https://doi.org/10.3390/biology15070523 - 25 Mar 2026
Viewed by 216
Abstract
Background: Among gynecological malignancies, ovarian cancer (OC) remains a leading cause of mortality worldwide, often characterized by the highest fatality-to-case ratio due to its asymptomatic progression and late-stage detection. Despite substantial investigation, the root cause of disease development and pathology remains unknown. Early [...] Read more.
Background: Among gynecological malignancies, ovarian cancer (OC) remains a leading cause of mortality worldwide, often characterized by the highest fatality-to-case ratio due to its asymptomatic progression and late-stage detection. Despite substantial investigation, the root cause of disease development and pathology remains unknown. Early detection is critical for improving OC prognosis. Unfortunately, because of the lack of identifiable symptoms in the early stages, the disease is frequently detected late. As a result, regular check-ups, being aware of risk factors, and paying attention to unusual symptoms can all help discover OC early. Apolipoproteins (APOs) and Annexins (ANXs) have recently been linked to OC. Aim: We conducted a cutting-edge bioinformatics investigation to find novel therapeutic targets and precise biomarkers linked to OC against APO and ANX. Methods: We started by compiling the ANX and APO families via HUGO Gene Nomenclature Committee (HGNC) homepage. Next, we accessed GEPIA2 to compare the relative messenger RNA (mRNA) expression levels of all ANX and APO family members across the cancer genome atlas (TCGA)-OC cohort and matched normal and GTEx data. Prognostic analysis of all significantly expressed ANXs and APOs was performed via Kaplan–Meier (KM) plotter. cBioPortal was used for mutational analysis of prognostic ANXs and APOs. Finally, we ran functional enrichment, molecular docking, and molecular dynamics (MD) simulation analyses. Results: Overall, the results suggest that ANXA2 and its related genetic changes represent potential focal points for precision oncology, offering a computational rationale for the development of target-driven therapeutic interventions in OC. Conclusions: Molecular docking and MD simulation analyses identified curcumin as a potential inhibitor of ANXA2, demonstrating stable binding affinity and structural conservation throughout the simulation period. These computational findings characterize curcumin as a promising candidate for targeting ANXA2 in OC, warranting further experimental validation to confirm its therapeutic efficacy. Full article
(This article belongs to the Special Issue Multi-Omics Data Integration in Complex Diseases (2nd Edition))
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30 pages, 5639 KB  
Article
Antioxidant and Anticancer Potentials of Apple Peel and Fruit Extracts: A Combined Docking and Chemical Composition Study
by Ayla Hançer, Gülşen Güçlü, Ömer Kayır, Serkan Kapancık, Esra Uçar and Burak Tüzün
Curr. Issues Mol. Biol. 2026, 48(4), 343; https://doi.org/10.3390/cimb48040343 - 25 Mar 2026
Viewed by 127
Abstract
The apple (Malus domestica Borkh.) is one of the most widely consumed fruits worldwide due to its pleasant sensory properties and rich phytochemical composition. Therefore, the present study aimed to comprehensively investigate the chemical composition, antioxidant activity, anticancer effects, and molecular interactions [...] Read more.
The apple (Malus domestica Borkh.) is one of the most widely consumed fruits worldwide due to its pleasant sensory properties and rich phytochemical composition. Therefore, the present study aimed to comprehensively investigate the chemical composition, antioxidant activity, anticancer effects, and molecular interactions of peel and pulp extracts of the Hünkar apple cultivar collected from different locations, using a combined experimental and computational strategy. These factors had a big effect on the extracts’ phenolic composition and biological activity. Moreover, the anticancer results were corroborated by molecular docking analyses, which offered further understanding of the interactions between bioactive compounds and cancer-associated target proteins. This integrative approach underscores the impact of both biological and methodological variables on the antioxidant and anticancer properties of apple-derived extracts, reinforcing their potential as natural sources of bioactive compounds. Cytotoxic activity against HT-22 and C6 cell lines was evaluated using the MTT assay, showing dose- and time-dependent antiproliferative effects. Apple extracts exhibited anticancer effects that were dependent on dosage and duration. The activities of chemicals found in extracts of Hünkar apple samples collected from four different locations against brain cancer proteins (PDB ID: 2DME, 6YPE, 1RV1) were examined. ADME/T analysis was then performed on the three molecules with the highest activity. The quantum chemical properties of these three molecules were also examined using the Gaussian package program with B3LYP, HF, M062X level in 6–31g, 6–31++g, and 6–31++g(d,p) basis sets. Full article
(This article belongs to the Special Issue Advances in Phytochemicals: Biological Activities and Applications)
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29 pages, 5236 KB  
Article
QSAR-Guided and Fragment-Based Drug Design of Monoterpenoid Inhibitors Targeting Ebola Virus Glycoprotein
by Nouhaila Ait Lahcen, Wissal Liman, Saad Zekri, Adnane Ait Lahcen, Ashwag S. Alanazi, Mohammed M. Alanazi, Christelle Delaite, Mohamed Maatallah and Driss Cherqaoui
Int. J. Mol. Sci. 2026, 27(7), 2987; https://doi.org/10.3390/ijms27072987 - 25 Mar 2026
Viewed by 136
Abstract
Ebola virus disease remains one of the most serious viral infections with no approved small-molecule treatments. The Ebola virus glycoprotein (EBOV-GP), which enables the virus’s entry to host cells, is a promising target for drug discovery. In this study, a multistage computer-aided drug [...] Read more.
Ebola virus disease remains one of the most serious viral infections with no approved small-molecule treatments. The Ebola virus glycoprotein (EBOV-GP), which enables the virus’s entry to host cells, is a promising target for drug discovery. In this study, a multistage computer-aided drug discovery approach was used to identify new specific EBOV-GP inhibitors. A reliable QSAR model was built using 55 terpenoid derivatives. This model was able to predict the activity of newly designed compounds with good accuracy and validated statistical metrics (Rtr2 = 0.70; Rext2 = 0.73). It was subsequently applied to screen over 15,500 newly generated compounds from three lead molecules by fragment-based design tools. Predicted activity, binding affinity toward EBOV-GP, and good ADMET drug-like properties prioritized the eleven most promising hits. Through 150 ns molecular dynamics simulations, these compounds remained stable in the EBOV-GP binding site. Further binding free energy analysis (MM/PBSA) showed strong binding affinities, especially for the compounds L-60, L-832, M-1618, and L-1366. This study showed how combining QSAR, fragment-based design, docking, ADMET, and molecular dynamics could help in identifying potent and safe small molecules against the EBOV-GP. The top compounds are ready for further experimental and in vitro biological testing. Full article
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12 pages, 918 KB  
Proceeding Paper
Computational Evaluation of Philippine Vitex negundo Phytochemicals as Potential Inhibitors of Rhinovirus 3C Protease: Molecular Docking, Pharmacokinetic Analysis, and ADMET Studies
by Francis Ceniza, Harll Fawwenn Hayes Paderanga, Sheena Alexa Yacapin and Nesteve John Agosto
Eng. Proc. 2026, 124(1), 90; https://doi.org/10.3390/engproc2026124090 - 25 Mar 2026
Viewed by 308
Abstract
Human rhinoviruses (HRVs) are the primary cause of the common cold, a highly contagious upper respiratory tract infection characterized by nasal congestion, sneezing, and sore throat. HRV replication depends on its 3C protease (HRV-3Cpro), a key enzyme that cleaves the viral polyprotein into [...] Read more.
Human rhinoviruses (HRVs) are the primary cause of the common cold, a highly contagious upper respiratory tract infection characterized by nasal congestion, sneezing, and sore throat. HRV replication depends on its 3C protease (HRV-3Cpro), a key enzyme that cleaves the viral polyprotein into functional proteins essential for viral maturation. Currently, no FDA-approved inhibitors specifically target HRV-3Cpro. While rupintrivir, a synthetic inhibitor, advanced to clinical trials, it ultimately failed due to limited efficacy. This study investigated the potential of Vitex negundo (or lagundi)—a medicinal plant traditionally used in the Philippines for treating colds and respiratory ailments—as a source of natural HRV-3Cpro inhibitors through in silico molecular docking and pharmacokinetic (ADMET) evaluation. Fifteen phytochemicals were screened, with five compounds exhibiting strong binding affinities exceeding that of the reference inhibitor rupintrivir (−6.1 kcal/mol): agnuside (−6.9 kcal/mol), luteolin 7-O-glucoside (−6.7 kcal/mol), 2′-p-hydroxybenzoyl mussaenosidic acid (−6.5 kcal/mol), 6′-(p-hydroxybenzoyl) mussaenosidic acid (−6.5 kcal/mol), and luteolin (−6.2 kcal/mol). Among these, luteolin emerged as a particularly promising lead compound, forming stable hydrogen bonding and hydrophobic interactions with HRV-3Cpro. Luteolin also demonstrates a favorable ADMET and safety profile, predicted to be non-mutagenic and non-hepatotoxic. These findings position luteolin as a potential plant-based HRV-3Cpro inhibitor, warranting further in vitro and in vivo studies to validate its antiviral efficacy and pharmacokinetic properties. Full article
(This article belongs to the Proceedings of The 6th International Electronic Conference on Applied Sciences)
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25 pages, 4718 KB  
Article
Design and Biological Profiling of a Drug-like Chloropyridine Diamine as a Dual Antioxidant–Antimicrobial Lead: In Vitro Evaluation and In Silico Multi-Target Studies
by Oussama Merzouki, Elhachmia Ech-chihbi, Nadia Arrousse, El Houssine Mabrouk, Mohamed Hefnawy, Yasmine Fernine, Manal El-Gendy and Mustapha Taleb
Int. J. Mol. Sci. 2026, 27(6), 2777; https://doi.org/10.3390/ijms27062777 - 19 Mar 2026
Viewed by 190
Abstract
Bacterial and fungal infections, together with oxidative stress-mediated damage, remain major challenges in human health and in the protection of materials, highlighting the need for new multifunctional molecules that combine antioxidant and antimicrobial properties. In this context, a new chloropyridine-based derivative, N4,N4-bis((6-chloropyridin-3-yl)methyl)-N1,N1-diethylpentane-1,4-diamine (AMZ), [...] Read more.
Bacterial and fungal infections, together with oxidative stress-mediated damage, remain major challenges in human health and in the protection of materials, highlighting the need for new multifunctional molecules that combine antioxidant and antimicrobial properties. In this context, a new chloropyridine-based derivative, N4,N4-bis((6-chloropyridin-3-yl)methyl)-N1,N1-diethylpentane-1,4-diamine (AMZ), was synthesized via a simple, catalyst-free N-alkylation of N1,N1-diethylpentane-1,4-diamine with 2-chloro-4-(chloromethyl)pyridine in acetonitrile at 55 °C, affording a 62% yield. The structure of AMZ was confirmed by melting point determination, 1H and 13C NMR spectroscopy, and EI–MS analysis. Its antioxidant activity was evaluated using DPPH and FRAP assays with BHT as a reference standard, while antibacterial and antifungal activities were assessed via disk diffusion and microdilution methods to determine inhibition zones and MIC/MBC values. In silico investigations included drug-likeness and ADMET predictions, as well as molecular docking on catalase (PDB: 2CAG) and fungal CYP51 (PDB: 1EA1). AMZ exhibited dose-dependent radical scavenging in the DPPH assay, reaching 76.88 ± 3.20% inhibition at 1000 µg/mL, with an EC50 of 26.03 ± 0.21 µg/mL, close to that of BHT (23.65 ± 0.22 µg/mL). In the FRAP assay, AMZ showed a higher reducing power than BHT at a low concentration (OD50 µg/mL 0.177 ± 0.023 vs. 0.134 ± 0.017), although its FRAP EC50 was higher (700.48 ± 22.54 vs. 400.16 ± 8.67 µg/mL). AMZ displayed broad-spectrum antimicrobial activity against Gram-positive and Gram-negative bacteria and fungi, with particularly strong effects on Bacillus subtilis (44.5 ± 0.5 mm; MIC/MBC 0.008 mg/mL) and Aspergillus niger (30 mm; MIC/MBC 0.030 mg/mL), in some cases comparable or superior to streptomycin and fluconazole. In silico analysis indicated that AMZ fulfilled major drug-likeness rules, showed high predicted intestinal absorption (91.14%), and was classified as non-AMES toxic, while docking predicted favorable binding to catalase and CYP51, in agreement with the experimental antioxidant and antifungal activities. These findings highlight the potential of AMZ as a multi-target pyridine-based lead compound that warrants further structural optimization and in vivo evaluation for applications in oxidative-stress-related and infectious conditions. Full article
(This article belongs to the Section Molecular Pharmacology)
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28 pages, 12236 KB  
Article
The Effect of Viniferin on Liver Cancer: Research Based on Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation
by Saowanee Maungchanburi, Onwara Wongmek, Poolsak Baitahay, Asron Saweak, Maroof Wangkaranae, Wanmai Kongwattananon, Suphasarang Sirirattanakul, Moragot Chatatikun, Atthaphong Phongphithakchai, Jason C. Huang, Aman Tedasen and Chutima Jansakun
Med. Sci. 2026, 14(1), 130; https://doi.org/10.3390/medsci14010130 - 11 Mar 2026
Viewed by 244
Abstract
Background/Objectives: Hepatocellular carcinoma (HCC) is a primary malignancy often driven by metabolic syndrome, fatty liver disease, and chronic hepatitis. These conditions foster a pro-inflammatory microenvironment that promotes tumor progression. Viniferin, a natural oligostilbene, has gained attention for its potential bioactivity. This study utilized [...] Read more.
Background/Objectives: Hepatocellular carcinoma (HCC) is a primary malignancy often driven by metabolic syndrome, fatty liver disease, and chronic hepatitis. These conditions foster a pro-inflammatory microenvironment that promotes tumor progression. Viniferin, a natural oligostilbene, has gained attention for its potential bioactivity. This study utilized an in silico network pharmacology approach to elucidate the pharmacokinetic properties and molecular mechanisms of ε- and δ-viniferin against HCC within the context of metabolic and inflammatory liver pathologies. Methods: ADMET profiles were characterized using SwissADME and pkCSM. Therapeutic targets were identified by intersecting viniferin-associated molecules with disease genes from GeneCards. A protein–protein interaction (PPI) network was constructed, supplemented by GO and KEGG enrichment analyses. Molecular docking and 200 ns of molecular dynamics (MD) simulations evaluated the binding affinity and structural stability between viniferin isomers and identified hub proteins. Results: Both ε- and δ-viniferin showed favorable drug-like properties, including high gastrointestinal absorption and low hepatotoxicity. We identified 247 overlapping targets, with network analysis highlighting ten essential hub genes, including AKT1, HSP90AA1, ESR1, HIF1A, NFKB1, GSK3B, PTGS2, APP, MTOR, and PIK3CA. Enrichment analysis confirmed their involvement in critical oncogenic pathways. Molecular docking showed strong interactions with APP, HSP90AA1, and AKT1, while MD simulations validated the long-term stability of ε-viniferin within the APP binding pocket. Conclusions: These findings provide mechanistic insights into viniferin as a multi-target agent for HCC, justifying further experimental validation in pre-clinical models. Full article
(This article belongs to the Special Issue Feature Papers in Section “Cancer and Cancer-Related Research”)
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32 pages, 2609 KB  
Article
QSAR-Guided Design of Serotonin Transporter Inhibitors Supported by Molecular Docking and Biased Molecular Dynamics
by Aleksandar M. Veselinović, Giulia Culletta, Jelena V. Živković, Slavica Sunarić, Žarko Mitić, Muhammad Sohaib Roomi and Marco Tutone
Pharmaceuticals 2026, 19(3), 444; https://doi.org/10.3390/ph19030444 - 10 Mar 2026
Viewed by 400
Abstract
Background/Objectives: Serotonin transporter (SERT) inhibition represents a central pharmacological strategy in the treatment of major depressive disorder. In this study, an integrated computational framework combining quantitative structure–activity relationship (QSAR) modeling, molecular docking analysis, and in silico ADMET profiling was applied to identify [...] Read more.
Background/Objectives: Serotonin transporter (SERT) inhibition represents a central pharmacological strategy in the treatment of major depressive disorder. In this study, an integrated computational framework combining quantitative structure–activity relationship (QSAR) modeling, molecular docking analysis, and in silico ADMET profiling was applied to identify and prioritize novel candidate structures. Methods: Conformation-independent QSAR models were developed using local molecular graph invariants and SMILES-based descriptors optimized through a Monte Carlo learning procedure, while a genetic algorithm–multiple linear regression (GA–MLR) was employed to derive statistically robust predictive models from a large descriptor pool. Model quality, robustness, and external predictivity were rigorously evaluated using multiple statistical validation criteria. In parallel, a field-based contribution analysis was applied to construct a three-dimensional QSAR model, enabling spatial interpretation of structure–activity relationships. Fragment-level contributions associated with activity enhancement or attenuation were subsequently identified and used to design new candidate inhibitor structures. Results: The designed compounds were further evaluated by molecular docking, InducedFit Docking and Binding Pose MetaDynamics (BPMD) into the SERT binding site, providing a structure-based assessment consistent with the trends observed in QSAR modeling. In addition, in silico ADMET analysis was performed to assess key pharmacokinetic and safety-related properties relevant to central nervous system drug development. Conclusions: The proposed workflow demonstrates the utility of combining data-driven QSAR modeling with structure-based and pharmacokinetic considerations to rationalize and prioritize novel serotonin transporter-focused scaffold optimization, offering a transferable strategy for early-stage antidepressant drug discovery. Full article
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26 pages, 7234 KB  
Article
Discovery of a Novel Coumarin/Thiazole Chalcone Hybrid as a Potent Dual Inhibitor of Tubulin and Carbonic Anhydrases IX & XII with Promising Anti-Proliferative Activity
by Basima A. A. Saleem, Ashraf A. Qurtam, Mohamed Ahmed, Raed Fanoukh Aboqader Al-Aouadi, Ali Abdulrazzaq Abdulhussein Alrikabi, Helal F. Hetta, Stefan Bräse, Ghallab Alotaibi, Abdullah Alkhammash and Sara Mahmoud Farhan
Molecules 2026, 31(6), 917; https://doi.org/10.3390/molecules31060917 - 10 Mar 2026
Viewed by 394
Abstract
Multitarget-directed ligands offer a promising strategy for overcoming tumor complexity through simultaneous modulation of complementary oncogenic pathways. In this work, a novel (E)-6-(3-(4-methyl-2-thioxo-2,3-dihydrothiazol-5-yl)-3-oxoprop-1-en-1-yl)-2H-chromen-2-one (compound 6) was synthesized and evaluated as a dual inhibitor of tubulin polymerization and tumor-associated carbonic anhydrases [...] Read more.
Multitarget-directed ligands offer a promising strategy for overcoming tumor complexity through simultaneous modulation of complementary oncogenic pathways. In this work, a novel (E)-6-(3-(4-methyl-2-thioxo-2,3-dihydrothiazol-5-yl)-3-oxoprop-1-en-1-yl)-2H-chromen-2-one (compound 6) was synthesized and evaluated as a dual inhibitor of tubulin polymerization and tumor-associated carbonic anhydrases (CAs) IX and XII. Compound 6 displayed potent antiproliferative activity, particularly against MDA-MB-231 triple-negative breast cancer cells (IC50 = 0.37 µM), with excellent selectivity toward non-tumorigenic cells. Mechanistic studies demonstrated strong tubulin polymerization inhibition (IC50 = 3.40 ± 0.09 µM) and submicromolar inhibition of CA IX (IC50 = 0.102 ± 0.005 µM) and CA XII (IC50 = 0.213 ± 0.004 µM), accompanied by downregulation of CA-IX and CA-XII protein expression. Cellular investigations revealed pronounced G2/M phase arrest and apoptosis induction via mitochondrial signaling and caspase activation. Anti-angiogenic activity was supported by inhibition of endothelial migration and concentration-dependent suppression of VEGFR-2 (Tyr1175) phosphorylation in HUVEC cells. Human liver microsomal assays indicated measurable metabolic stability, while molecular docking and in silico ADMET predictions supported target engagement and drug-like properties. Collectively, these findings identify compound 6 as a promising multitarget anticancer lead integrating antimitotic, metabolic, and anti-angiogenic mechanisms. Full article
(This article belongs to the Section Medicinal Chemistry)
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30 pages, 8490 KB  
Article
Repurposing Clotrimazole for Pancreatic Ductal Adenocarcinoma: Comparative In Vitro Evaluation and In Silico ADMET Context
by Inês Mendes, Lara Marques, Eduarda Ribeiro and Nuno Vale
Physchem 2026, 6(1), 17; https://doi.org/10.3390/physchem6010017 - 10 Mar 2026
Viewed by 295
Abstract
Background: Clotrimazole (CLZ) is an approved antifungal with reported pleiotropic effects. Beyond its antifungal use, CLZ can perturb glycolytic flux and ionic homeostasis, motivating its evaluation as a repurposing candidate in oncology. Objective: We aimed to evaluate CLZ and nitazoxanide (NTZ) [...] Read more.
Background: Clotrimazole (CLZ) is an approved antifungal with reported pleiotropic effects. Beyond its antifungal use, CLZ can perturb glycolytic flux and ionic homeostasis, motivating its evaluation as a repurposing candidate in oncology. Objective: We aimed to evaluate CLZ and nitazoxanide (NTZ) as drug repurposing candidates for pancreatic ductal adenocarcinoma (PDAC) in comparison with standard chemotherapeutics gemcitabine (GEM) and 5-fluorouracil (5-FU). Methods: T3M4 PDAC cells were treated (0.1–100 µM; 48–72 h) with 5-FU, GEM, CLZ, and NTZ. Cell viability (MTT) and morphology were assessed, and CLZ-based combinations were analyzed by the Chou–Talalay method. In silico studies provided physicochemical descriptors and ADMET profiles, along with predicted interactions with relevant bioorganic targets (e.g., KCa3.1/KCNN4 ion channels). Results: CLZ produced marked cytotoxicity at 72 h (IC50 ≈ 9 µM) and achieved a greater reduction in cell viability at higher concentrations compared to 5-FU and GEM under identical conditions, whereas NTZ showed modest and inconsistent effects. CLZ combinations with 5-FU or GEM were mainly antagonistic. In silico analyses indicated high membrane permeability and suggested potential interactions with KCa3.1, supporting a hypothesis-generating interpretation of the observed in vitro effects. Conclusions: Within a drug repurposing framework, CLZ exhibited consistent cytotoxic activity as a single agent in a PDAC cell model, whereas NTZ revealed limited effects and CLZ-based combinations were not beneficial under the tested conditions. These findings position CLZ as a monotherapy-oriented repurposing candidate for PDAC and motivate further mechanistic and translational studies to clarify the biological basis of its in vitro activity. Full article
(This article belongs to the Section Biophysical Chemistry)
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23 pages, 1864 KB  
Article
Harnessing Substituted 4-Chlorothieno[2,3-b]pyridine as a New Cap for Potent and Selective Antiproliferative HDAC Inhibitors
by Mostafa M. Badran, Berkay Beyri, Hiroshi Tateishi, Kazunori Shimagaki, Akiko Nakata, Akihiro Ito, Nao Nishimura, Samar H. Abbas, Mohamed Abdel-Aziz, Masami Otsuka, Minoru Yoshida, Mikako Fujita, Stefan Bräse and Mohamed O. Radwan
Pharmaceuticals 2026, 19(3), 442; https://doi.org/10.3390/ph19030442 - 9 Mar 2026
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Abstract
Background: Inhibition of histone deacetylase is a highly sought-after objective in the fight against cancer. Thus, the development of innovative HDAC inhibitors with significantly higher potency than SAHA against specific cancer cell types represents complex and demanding work. Method: The utilization of the [...] Read more.
Background: Inhibition of histone deacetylase is a highly sought-after objective in the fight against cancer. Thus, the development of innovative HDAC inhibitors with significantly higher potency than SAHA against specific cancer cell types represents complex and demanding work. Method: The utilization of the underexplored and privileged scaffold 4-chlorothieno[2,3-b]pyridine as a cap tethering diverse aliphatic and aromatic linkers, followed by the screening of both cellular and enzymatic activities, is undertaken in this study. Results: Compounds 7a and 9a demonstrated impressive mean GI50 values of 2.15 µM and 1.89 µM, respectively. Both compounds reduced caspase-3 levels in RPMI-8226 cells, suggesting induction of apoptosis. Compound 7a showed remarkable IC50 values of 0.37 µM, 0.58 µM, and 0.70 µM against HDACs 1, 4, and 6, respectively, consistent with the cellular assay. Additionally, compound 7a exhibited a selectivity index of 11 for RPMI-8226 cells over PBMCs, reflecting its high selectivity and potential safety. Moreover, ADMET prediction tools indicated that compounds 7a and 9b may have more favorable pharmacokinetic properties than the gold-standard HDAC inhibitor, SAHA. Conclusions: Further study and exploration of the derivatives of compounds 7a and 9a can lead to further advancement in the development of potent HDAC inhibitor anticancer drugs. Full article
(This article belongs to the Special Issue Targeting Enzymes in Drug Design and Discovery)
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32 pages, 6515 KB  
Article
Metabolomic Study of 7-Ethyl-9-(N-methyl)aminomethyl-10-hydroxycamptothecin Derivative (NMe)—The Chemotherapeutic Drug Candidate Versus Irinotecan (IR) on a Mouse Model
by Piotr Surynt, Beata Naumczuk, Magdalena Popławska, Magdalena Urbanowicz, Katarzyna Unrug-Bielawska, Magdalena Cybulska-Lubak, Zuzanna Sadowska-Markiewicz, Jerzy Sitkowski, Elżbieta Bednarek, Natalia Zeber-Lubecka, Lech Kozerski, Michał Mikula and Jerzy Ostrowski
Metabolites 2026, 16(3), 172; https://doi.org/10.3390/metabo16030172 - 5 Mar 2026
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Abstract
Background: In this study, we aimed to compare metabolomic profiles, biodistribution, and detoxification patterns of the novel SN-38 derivative NMe with irinotecan (IR), and to identify NMe-specific metabolites to evaluate its preclinical pharmacokinetic advantages. Methods: In vivo ADME studies were conducted for NMe, [...] Read more.
Background: In this study, we aimed to compare metabolomic profiles, biodistribution, and detoxification patterns of the novel SN-38 derivative NMe with irinotecan (IR), and to identify NMe-specific metabolites to evaluate its preclinical pharmacokinetic advantages. Methods: In vivo ADME studies were conducted for NMe, a 9-aminomethyl SN-38 derivative, and IR following a single intraperitoneal dose of 40 mg/kg in mice. Additionally, ADMET properties were predicted using ADMETlab and SwissADME tools for comparison. Levels of NMe and irinotecan absorbed into plasma, distributed to tissues, and metabolized were monitored in liver, lung, spleen, kidney, and stool samples at 15, 30, and 60 min post-administration. Tissue extracts were analysed using high-performance liquid chromatography (HPLC), liquid chromatography–electrospray ionization quadrupole time-of-flight-tandem mass spectrometry (LC-ESI-QTOF-MS), and nuclear magnetic resonance (NMR) techniques after lyophilization and reconstitution. We compared the metabolomic profiles of irinotecan and NMe. Results: We identified and confirmed NMe-specific metabolites, including 9-CH2-S-cysteine conjugate, 9-CH2OH, and NMe-formyl. Notably, novel irinotecan metabolites (IR-OH and IR-ΔE) were detected in small amounts in kidney samples. In some cases, two literature-known photodegradation products of irinotecan were present. NMe was found to quickly metabolize with different distribution to tissues, significantly greater to kidney and liver. Two SN-38 glucuronides, SN-38G(α) and SN-38G(β), were detected corresponding to α- and β-anomers. Where it was possible, NMe, IR and SN-38 were quantified using external calibration curves. In IR group, controlled and prolonged release of SN-38 was confirmed in all samples, yet SN-38G was observed in minority only in plasma, kidney, or lungs. In NMe groups, great relative amounts of SN-38 and SN-38G were detected. Greater content of SN-38G in NMe group than in irinotecan is expected to contribute to modulation and alleviation of some side effects in irinotecan-involved therapies, such as gastrointestinal toxicities (GIT). Conclusions: NMe shows a distinct metabolic profile characterized by rapid biotransformation, higher systemic glucuronidation of SN-38, and formation of unique metabolites, suggesting a potentially wider therapeutic window and reduced toxicity compared with IR. Full article
(This article belongs to the Section Pharmacology and Drug Metabolism)
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