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Search Results (1,076)

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33 pages, 1878 KB  
Review
Strategic and Chemical Advances in Antibody–Drug Conjugates
by Ibrahim A. Alradwan, Meshal K. Alnefaie, Nojoud AL Fayez, Alhassan H. Aodah, Majed A. Majrashi, Meshael Alturki, Mohannad M. Fallatah, Fahad A. Almughem, Essam A. Tawfik and Abdullah A. Alshehri
Pharmaceutics 2025, 17(9), 1164; https://doi.org/10.3390/pharmaceutics17091164 - 5 Sep 2025
Abstract
Antibody–drug conjugates (ADCs) are a rapidly advancing class of targeted cancer therapeutics that couple the antigen specificity of monoclonal antibodies (mAbs) with the potent cytotoxicity of small-molecule drugs. In their core design, a tumor-targeting antibody is covalently linked to a cytotoxic payload via [...] Read more.
Antibody–drug conjugates (ADCs) are a rapidly advancing class of targeted cancer therapeutics that couple the antigen specificity of monoclonal antibodies (mAbs) with the potent cytotoxicity of small-molecule drugs. In their core design, a tumor-targeting antibody is covalently linked to a cytotoxic payload via a chemical linker, enabling the selective delivery of highly potent agents to malignant cells while sparing normal tissues, thereby improving the therapeutic index. Humanized and fully human immunoglobulin G1(IgG1) antibodies are the most common ADC backbones due to their stability in systemic circulation, robust Fcγ receptor engagement for immune effector functions, and reduced immunogenicity. Antibody selection requires balancing tumor specificity, internalization rate, and binding affinity to avoid barriers to tissue penetration, such as the binding-site barrier effect, while emerging designs exploit tumor-specific antigen variants or unique post-translational modifications to further enhance selectivity. Advances in antibody engineering, linker chemistry, and payload innovation have reinforced the clinical success of ADCs, with more than a dozen agents FDA approved for hematologic malignancies and solid tumors and over 200 in active clinical trials. This review critically examines established and emerging conjugation strategies, including lysine- and cysteine-based chemistries, enzymatic tagging, glycan remodeling, non-canonical amino acid incorporation, and affinity peptide-mediated methods, and discusses how conjugation site, drug-to-antibody ratio (DAR) control, and linker stability influence pharmacokinetics, efficacy, and safety. Innovations in site-specific conjugation have improved ADC homogeneity, stability, and clinical predictability, though challenges in large-scale manufacturing and regulatory harmonization remain. Furthermore, novel ADC architectures such as bispecific ADCs, conditionally active (probody) ADCs, immune-stimulating ADCs, protein-degrader ADCs, and dual-payload designs are being developed to address tumor heterogeneity, drug resistance, and off-target toxicity. By integrating mechanistic insights, preclinical and clinical data, and recent technological advances, this work highlights current progress and future directions for next-generation ADCs aimed at achieving superior efficacy, safety, and patient outcomes, especially in treating refractory cancers. Full article
(This article belongs to the Section Biologics and Biosimilars)
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36 pages, 6758 KB  
Article
Integrative In Silico and Experimental Characterization of Endolysin LysPALS22: Structural Diversity, Ligand Binding Affinity, and Heterologous Expression
by Nida Nawaz, Shiza Nawaz, Athar Hussain, Maryam Anayat, Sai Wen and Fenghuan Wang
Int. J. Mol. Sci. 2025, 26(17), 8579; https://doi.org/10.3390/ijms26178579 - 3 Sep 2025
Viewed by 184
Abstract
Endolysins, phage-derived enzymes capable of lysing bacterial cell walls, hold significant promise as novel antimicrobials against resistant Gram-positive and Gram-negative pathogens. In this study, we undertook an integrative approach combining extensive in silico analyses and experimental validation to characterize the novel endolysin LysPALS22. [...] Read more.
Endolysins, phage-derived enzymes capable of lysing bacterial cell walls, hold significant promise as novel antimicrobials against resistant Gram-positive and Gram-negative pathogens. In this study, we undertook an integrative approach combining extensive in silico analyses and experimental validation to characterize the novel endolysin LysPALS22. Initially, sixteen endolysin sequences were selected based on documented lytic activity and enzymatic diversity, and subjected to multiple sequence alignment and phylogenetic analysis, which revealed highly conserved catalytic and binding domains, particularly localized to the N-terminal region, underscoring their functional importance. Building upon these sequence insights, we generated three-dimensional structural models using Swiss-Model, EBI-EMBL, and AlphaFold Colab, where comparative evaluation via Ramachandran plots and ERRAT scores identified the Swiss-Model prediction as the highest quality structure, featuring over 90% residues in favored conformations and superior atomic interaction profiles. Leveraging this validated model, molecular docking studies were conducted in PyRx with AutoDock Vina, performing blind docking of key peptidoglycan-derived ligands such as N-Acetylmuramic Acid-L-Alanine, which exhibited the strongest binding affinity (−7.3 kcal/mol), with stable hydrogen bonding to catalytic residues ASP46 and TYR61, indicating precise substrate recognition. Visualization of docking poses using Discovery Studio further confirmed critical hydrophobic and polar interactions stabilizing ligand binding. Subsequent molecular dynamics simulations validated the stability of the LysPALS22–NAM-LA complex, showing minimal structural fluctuations, persistent hydrogen bonding, and favorable interaction energies throughout the 100 ns trajectory. Parallel to computational analyses, LysPALS22 was heterologously expressed in Escherichia coli (E. coli) and Pichia pastoris (P. pastoris), where SDS-PAGE and bicinchoninic acid assays validated successful protein production; notably, the P. pastoris-expressed enzyme displayed an increased molecular weight (~45 kDa) consistent with glycosylation, and achieved higher volumetric yields (1.56 ± 0.31 mg/mL) compared to E. coli (1.31 ± 0.16 mg/mL), reflecting advantages of yeast expression for large-scale production. Collectively, these findings provide a robust structural and functional foundation for LysPALS22, highlighting its conserved enzymatic features, specific ligand interactions, and successful recombinant expression, thereby setting the stage for future in vivo antimicrobial efficacy studies and rational engineering efforts aimed at combating multidrug-resistant Gram-negative infections. Full article
(This article belongs to the Special Issue Antimicrobial Agents: Synthesis and Design)
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20 pages, 1185 KB  
Communication
Anti-Aging Potential of Bioactive Peptides Derived from Casein Hydrolyzed with Kiwi Actinidin: Integration of In Silico and In Vitro Study
by Nicolas Caicedo, Lady L. Gamboa, Yhors Ciro, Constain H. Salamanca and Jose Oñate-Garzón
Cosmetics 2025, 12(5), 189; https://doi.org/10.3390/cosmetics12050189 - 1 Sep 2025
Viewed by 337
Abstract
Background: Skin aging is mainly associated with oxidative stress and enzymatic degradation of collagen and elastin by protease activity. Peptides have antioxidant capacity and inhibitory effects on protease enzymes. Objective: The purpose of this study was to obtain peptides with in vitro anti-aging [...] Read more.
Background: Skin aging is mainly associated with oxidative stress and enzymatic degradation of collagen and elastin by protease activity. Peptides have antioxidant capacity and inhibitory effects on protease enzymes. Objective: The purpose of this study was to obtain peptides with in vitro anti-aging activity from the enzymatic hydrolysis of bovine casein with actinidin, a protease extracted from the green kiwi fruit (Actinidia deliciosa) Methodology: The enzyme actinidin was extracted from the pulp of the kiwi fruit, purified by ion exchange chromatography and characterized by polyacrylamide electrophoresis (SDS-PAGE). Subsequently, the extracted enzyme was used to hydrolyze commercial bovine casein at 37 °C for 30 min, precipitating the peptide fraction with trichloroacetic acid (TCA), and centrifuged. To determine the anti-aging potential of the peptides in vitro, antioxidant activity was evaluated using the ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) radical. Additionally, the inhibitory capacity of the peptides against collagenase and elastase enzymes was also studied. To complement the in vitro results, the enzymatic hydrolysis of casein with actinidin was simulated. The binding energy (ΔG) of each of the hydrolysates with the collagenase and elastase enzymes was calculated using molecular docking to predict the peptide sequences with the highest probability of interaction. Results: Actinidin was extracted and purified exhibiting a molecular weight close to 27 kDa. The enzyme hydrolyzed the substrate by 91.6%, and the resulting hydrolysates showed moderate in vitro anti-aging activity: antioxidant (17.5%), anticollagenase (18.55%), and antielastase (28.6%). In silico results revealed 66 peptide sequences of which 30.3% consisted of 4–8 amino acids, a suitable size to facilitate interaction with structural targets. The sequences with the highest affinity were FALPQYLK and VIPYVRYL for collagenase and elastase, respectively. Conclusions: Despite the modest inhibition values, the use of a fruit-derived enzyme and a food-grade substrate is in line with current trends in sustainable and natural cosmetics. These findings highlight the great potential for laying the groundwork for future research into actinidin-derived peptides as multifunctional and eco-conscious ingredients for the development of next-generation anti-aging formulations. Full article
(This article belongs to the Special Issue Functional Molecules as Novel Cosmetic Ingredients)
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24 pages, 20800 KB  
Article
Excavating Precursors from Herb Pairs Polygala tenuifolia and Acori tatarinowii: Synthesis and Anticonvulsant Activity Evaluation of 3,4,5-Trimethoxycinnamic Acid (TMCA) Piperazine Amide Derivatives
by Zefeng Zhao, Mengchen Lei, Yongqi Wang, Yujun Bai and Haifa Qiao
Pharmaceuticals 2025, 18(9), 1312; https://doi.org/10.3390/ph18091312 - 1 Sep 2025
Viewed by 213
Abstract
Background: Epilepsy is a cluster of central nervous system (CNS) disorders identified by recurrent seizures, which affects about 60 million people around the world. In this research, a total of 40 types of 3,4,5-trimethoxycinnamic acid (TMCA) piperazine amide derivatives were designed and [...] Read more.
Background: Epilepsy is a cluster of central nervous system (CNS) disorders identified by recurrent seizures, which affects about 60 million people around the world. In this research, a total of 40 types of 3,4,5-trimethoxycinnamic acid (TMCA) piperazine amide derivatives were designed and synthesized, inspired by the traditional Chinese medicine (TCM) herb pair drugs Polygala tenuifolia and Acori tatarinowii, followed by determination of their anticonvulsant potency. Methods: All the TMCA analogues were tested for their anticonvulsant potential through two acute models of seizures induced in mice: the maximal electroshock (MES) and sc-pentylenetetrazole (PTZ) models. In addition, the lactate dehydrogenase (LDH) inhibitory activity was determined in vitro. Results: The results showed that compounds A3, A9, A12, A14, B9, and B12 exhibited preferable anticonvulsant activity in the primary evaluation. In addition, the molecular docking results predicted good interactions of screened analogues with the LDH. Molecular dynamic simulation was used to reveal the consensual binding affinity between the most promising compound (B9) and active site interactions with LDH. Electroencephalogram (EEG) analysis and silver and immunofluorescence staining were performed to illustrate the anti-epilepsy potential of compound B9. Conclusions: Novel derivatives in this study provide new cores for the further design and optimization inspired by TCM herb pair drugs P. tenuifolia and A. tatarinowii, with the aim to explore new anticonvulsant agents. Full article
(This article belongs to the Section Medicinal Chemistry)
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16 pages, 2125 KB  
Article
Granzyme B PET Imaging Enables Early Assessment of Immunotherapy Response in a Humanized Melanoma Mouse Model
by Priska Summer, Naomi Gallon, Niklas Bulmer, Umar Mahmood and Pedram Heidari
Pharmaceuticals 2025, 18(9), 1309; https://doi.org/10.3390/ph18091309 - 31 Aug 2025
Viewed by 404
Abstract
Background/Objectives: This study evaluated a novel PET tracer, 68Ga-NOTA-CYT-200, which targets human granzyme B (GZB) as a biomarker for cytotoxic T-cell activation in a clinically relevant model of melanoma-bearing mice with a humanized immune system treated with immune checkpoint inhibitor (ICI) [...] Read more.
Background/Objectives: This study evaluated a novel PET tracer, 68Ga-NOTA-CYT-200, which targets human granzyme B (GZB) as a biomarker for cytotoxic T-cell activation in a clinically relevant model of melanoma-bearing mice with a humanized immune system treated with immune checkpoint inhibitor (ICI) therapy. Methods: The binding affinity of the tracer was determined using an enzymatic colorimetric assay. Tumor-bearing humanized NSG mice underwent PET imaging before and during ICI monotherapy or combination therapy to assess 68Ga-NOTA-CYT-200 uptake within tumors and other organs. The tumor growth was carefully monitored. The treatment response was evaluated based on the percentage change in tumor size at days 5 and 15 after the treatment started. A tracer biodistribution study and immunohistochemical staining of the tumors and organs were also performed. Results: The inhibition constant (Ki) of 68Ga-NOTA-CYT-200 was estimated at 4.2 nM. PET imaging showed a significantly higher 68Ga-NOTA-CYT-200 uptake in mice receiving the combination therapy compared to those receiving monotherapy or a vehicle (p < 0.0001 or p = 0.0005, respectively), which correlated with the greatest reduction in tumor size in the combination ICI group. Regardless of treatment, the responders presented with a significantly higher 68Ga-NOTA-CYT-200 uptake at days 4 or 7 after the treatment began (p = 0.0002 and p = 0.0109, respectively). An increased uptake of 68Ga-NOTA-CYT-200, especially in the intestines and liver within the combination ICI group, suggested immune-related adverse events (IrAEs). Conclusions: Our study demonstrates that 68Ga-NOTA-CYT-200 PET imaging can predict the early treatment response in melanoma models treated with ICI and may also help in detecting IrAEs. Full article
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17 pages, 13754 KB  
Article
Identifying Key Genes of Proanthocyanidin Intervention in Fluoride-Induced Liver Injury: Integrated Molecular Docking and Experimental Validation
by Zhiyu Wu, Menghuan Xiao, Zelin Gong, Benjie Wang, Wenxin Zhao, Yiyuan Guo and Lu Yang
Genes 2025, 16(9), 1037; https://doi.org/10.3390/genes16091037 - 31 Aug 2025
Viewed by 285
Abstract
Objectives: The objectives of this study are to investigate the therapeutic targets and mechanisms of proanthocyanidins in alleviating fluoride-induced liver injury through network pharmacology and animal experimental validation and to explore the medicinal value of grape seed proanthocyanidins. Methods: Potential targets [...] Read more.
Objectives: The objectives of this study are to investigate the therapeutic targets and mechanisms of proanthocyanidins in alleviating fluoride-induced liver injury through network pharmacology and animal experimental validation and to explore the medicinal value of grape seed proanthocyanidins. Methods: Potential targets of proanthocyanidins were predicted using databases such as PubChem, SwissTargetPrediction, and GeneCards, and disease-related targets of fluoride-induced liver injury were retrieved to identify common targets between proanthocyanidins and fluoride-induced liver injury. The STRING database was utilized to construct a protein–protein interaction network, and key targets were analyzed for network topology using Cytoscape software. GO and KEGG enrichment analyses were performed on core target genes to explore the potential molecular mechanisms by which proanthocyanidins alleviate fluoride-induced liver injury. The Genes-miRNA interaction network was generated using Networkanalyst, and the molecular docking results between active components and key targets were validated using the CB-Dock2 visualization tool. In the academic context, a rat model of chronic fluoride poisoning was successfully established by means of intragastric administration of sodium fluoride. The protein expression levels of p-mTOR, p-p70s6, p62, LC3-II, and PARP1 in rat liver tissues were detected via Western blot analysis. Results: Network pharmacological analysis successfully identified 96 key genes, through which proanthocyanidins mitigate fluoride-induced liver injury. KEGG enrichment analysis predicted that proanthocyanidins mainly exert their therapeutic effects through the mTOR signaling pathway. The molecular docking results further demonstrated strong binding affinities between proanthocyanidins and key targets, including mTOR and PARP1. The in vivo experimental results indicate that, compared with the control group, the protein expression levels of p-mTOR, p-p70s6k, and p62 in the liver tissues of rats exposed to sodium fluoride significantly increase. Conversely, the protein expression levels of LC3-II and PARP1 significantly decrease (p < 0.05). The outcome of liver intervention with proanthocyanidins is exactly the opposite. Conclusions: Proanthocyanidins can effectively alleviate fluoride-induced liver injury, potentially by regulating the mTOR signaling pathway, autophagy, and apoptosis mechanisms. This study provides valuable insights into the protective effects of proanthocyanidins against fluoride-induced hepatic damage and offers a theoretical basis for further research in this field. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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23 pages, 4402 KB  
Article
Elucidating Key Components and Mechanisms Underlying the Synergistic Anti-Type 2 Diabetes Effect of Morus alba L. and Siraitia grosvenorii Combination: An Integrated In Vitro Enzymology, Untargeted Metabolomics, and Network Pharmacology Approach
by Fang He, Shenglan Su, Ruihan Song, Yan Li, Luyan Zou, Zongjun Li, Yu Xiao, Aixiang Hou, Ke Li and Yuanliang Wang
Antioxidants 2025, 14(9), 1065; https://doi.org/10.3390/antiox14091065 - 29 Aug 2025
Viewed by 295
Abstract
Although mulberry leaf (Morus alba L., ML) and Siraitia grosvenorii (SG) individually demonstrate anti-diabetic properties, their combined efficacy against type 2 diabetes mellitus (T2DM) remains unexplored. This study systematically explored the multi-target mechanisms and synergistic potential of the MLSG combination (MLSG) for [...] Read more.
Although mulberry leaf (Morus alba L., ML) and Siraitia grosvenorii (SG) individually demonstrate anti-diabetic properties, their combined efficacy against type 2 diabetes mellitus (T2DM) remains unexplored. This study systematically explored the multi-target mechanisms and synergistic potential of the MLSG combination (MLSG) for T2DM intervention. We evaluated the in vitro inhibitory activities of MLSG, ML, and SG on α-amylase and α-glucosidase, alongside antioxidant capacity assessments through DPPH/ABTS radical scavenging, reducing power, and FRAP assays. Bioactive metabolites were identified using non-targeted metabolomics, while core targets and pathways were predicted using network pharmacology and validated through molecular docking. The results reveal MLSG’s significantly enhanced inhibition of α-amylase (IC50 = 14.06 mg/mL) and α-glucosidase (IC50 = 0.02 mg/mL) compared to individual extracts, exhibiting 1.3–15.5-fold higher potency with synergistic effects (combination index < 1). MLSG also showed improved antioxidant capacity, outperforming SG in DPPH/ABTS+ scavenging and reducing power (p < 0.05), and surpassing ML in ABTS+ scavenging, reducing power, and FRAP values (p < 0.05). Metabolomics identified 26 MLSG-derived metabolites with anti-T2DM potential, and network analysis pinpointed 26 active components primarily targeting STAT3, AKT1, PIK3CA, EGFR, and MAPK1 to regulate T2DM pathways. Molecular docking confirmed strong binding affinities between these components and core targets. Collectively, MLSG exerts potent synergistic anti-T2DM effects through dual-enzyme inhibition, elevated antioxidant activity, and multi-target pathway regulation, providing a solid foundation for developing MLSG as functional food ingredients. Full article
(This article belongs to the Special Issue Potential Health Benefits of Dietary Antioxidants)
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25 pages, 2652 KB  
Article
Establishment of Callus Cultures from Dalbergia sissoo Leaf Explants for Production of Skin Therapeutics: An In Vitro and In Silico Study
by Jyotsana and Promila Gupta
Molecules 2025, 30(17), 3531; https://doi.org/10.3390/molecules30173531 - 29 Aug 2025
Viewed by 381
Abstract
Dalbergia sissoo is a commercially exploited timber tree also known for its varied phytochemical constituents holding significant importance in folk medicines with documented biological properties. The present study reports the establishment of callus cultures from its leaf explants for the in vitro production [...] Read more.
Dalbergia sissoo is a commercially exploited timber tree also known for its varied phytochemical constituents holding significant importance in folk medicines with documented biological properties. The present study reports the establishment of callus cultures from its leaf explants for the in vitro production of skin therapeutics. The growth parameters of the callus cultures were calculated. The antioxidant potential of the methanolic extracts of leaf and its callus cultures was evaluated through DPPH assay. Calli at third subculture stage showed the highest antioxidant potential (IC50 273 ± 14.14 µg/mL). A comparative analysis of phytochemical composition was performed using Gas Chromatography–Mass Spectrometry (GC-MS) which revealed the presence of potential skin therapeutic compounds. Out of 146 compounds, only 15 are unique to leaf explants, with the rest being produced in callus cultures. ADME predictions of potential compounds showed their drug likeness properties. The molecular docking of selected phytochemicals such as Chondrillasterol, Stearic acid, and n-Hexadecanoic acid against the tyrosinase enzyme showed better binding affinities than the reference drug (Kojic acid). Molecular dynamics simulation also showed stable conformations of the docked complexes with the target protein. Overall, these investigations unveil for the first time the successful in vitro production of skin therapeutics from D. sissoo, ensuring the sustainable and conservation-friendly utilization of its biomass for medicinal purposes. Full article
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23 pages, 8552 KB  
Article
Integrating Transcriptomics, Network Pharmacology, and Machine Learning to Reveal Transglutaminase 2 (TGM2) as a Key Target Mediating Taurocholate Efficacy in Colitis
by Junhong Zhu, Huijin Jia, Lanlan Yi, Guangyao Song, Pengfei Fu, Wenjie Cheng, Yuxiao Xie, Wenzhe Shi and Sumei Zhao
Genes 2025, 16(9), 1024; https://doi.org/10.3390/genes16091024 - 29 Aug 2025
Viewed by 381
Abstract
Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with a rising global incidence. Natural conjugated taurocholic acid (TCA) possesses anti-inflammatory properties and shows potential therapeutic effects against UC, although the underlying mechanisms remain unclear. Methods: This study employed an [...] Read more.
Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with a rising global incidence. Natural conjugated taurocholic acid (TCA) possesses anti-inflammatory properties and shows potential therapeutic effects against UC, although the underlying mechanisms remain unclear. Methods: This study employed an integrative approach—combining network pharmacology, bioinformatics, machine learning, immune infiltration analysis, and molecular docking—to investigate the therapeutic mechanisms of TCA in UC. UC-related gene expression datasets were obtained from the Gene Expression Omnibus (GEO) database, and potential TCA targets were predicted using the Comparative Toxicogenomics Database (CTD) and TargetNet platforms. Differentially expressed genes (DEGs) were identified and analyzed via GO and KEGG enrichment analyses. Results: Four machine learning algorithms (XGBoost, RF, SVM, and NNet) were used to identify six hub genes (TGM2, MMP9, ABCB1, NOS2, ABCG2, CASP1), which were further validated using an artificial neural network. Immune infiltration analysis with CIBERSORT revealed significant alterations in immune cell populations in UC tissues. Further validation through an artificial neural network model confirmed their predictive ability. The enrichment analysis of the hub genes highlighted their roles in immune-related pathways, while the immune infiltration analysis indicated significant differences in immune cell populations between ulcerative colitis tissues and control tissues. The molecular docking results showed that the binding energies of these six proteins to TCA were lower than −5 kcal/mol, with TGM2 having the strongest binding affinity (−10 kcal/mol). The intervention of TCA on colitis mice could improve the inflammatory response by regulating the expression of the TGM2 gene. Conclusions: In conclusion, this study suggests that taurocholate alleviates ulcerative colitis by targeting key genes such as TGM2 and modulating immune-related pathways, providing a novel basis for future therapeutic exploration. Full article
(This article belongs to the Section Pharmacogenetics)
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15 pages, 1384 KB  
Article
Metabolism of Cannabidiol in Respiratory-Associated Cells and HepG2-Derived Cells and Molecular Docking of Cannabidiol and Its Metabolites with CYP Enzymes and Cannabinoid Receptors
by Krittawan Tongkanarak, Pijush Kumar Paul, Muhammad A. Khumaini Mudhar Bintang, Roongnapa Suedee, Somchai Sawatdee and Teerapol Srichana
Int. J. Mol. Sci. 2025, 26(17), 8384; https://doi.org/10.3390/ijms26178384 - 28 Aug 2025
Viewed by 394
Abstract
Cannabidiol (CBD) has been reported in medical applications for various indications. The enzymatic metabolism of CBD is not fully understood in the different routes of administration. This research aimed to identify the CBD metabolites after incubation of CBD with derived hepatocyte cells (HepG2), [...] Read more.
Cannabidiol (CBD) has been reported in medical applications for various indications. The enzymatic metabolism of CBD is not fully understood in the different routes of administration. This research aimed to identify the CBD metabolites after incubation of CBD with derived hepatocyte cells (HepG2), bronchial epithelial cells (NCI-H358), alveolar cells (A549), and alveolar macrophage cells (NR8383). A liquid chromatography–mass spectrometry technique was developed to quantify the CBD and its metabolites. Molecular docking was employed to evaluate the binding affinity of CBD with different cytochrome P-450 (CYP-450) enzymes and further predict the implication of drug–drug interactions. CBD and major metabolites of CBD were also docked with cannabinoid receptors. The results revealed that only HepG2 cells metabolized CBD to 7-hydroxy-CBD (7-OH-CBD) and 7-carboxy-CBD (7-COOH-CBD), whereas other respiratory cell lines and alveolar macrophages were found to have mainly CBD in the incubated samples without any metabolites. The CYP2C19 and CYP3A4 enzymes were responsible for CBD conversion to hydroxylated CBD metabolites. The 7-OH-CBD and 7-COOH-CBD metabolites were found to bind to cannabinoid receptors with different affinities. The relative abundance of CBD and major metabolites may indicate the potential route of CBD administration. Full article
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21 pages, 2215 KB  
Article
Computational Prediction of Single-Domain Immunoglobulin Aggregation Propensities Facilitates Discovery and Humanization of Recombinant Nanobodies
by Felix Klaus Geyer, Julian Borbeck, Wiktoria Palka, Xueyuan Zhou, Jeffrey Takimoto, Brian Rabinovich, Bernd Reifenhäuser, Karlheinz Friedrich and Harald Kolmar
Antibodies 2025, 14(3), 73; https://doi.org/10.3390/antib14030073 - 28 Aug 2025
Viewed by 715
Abstract
Background/Objectives: Single-domain immunoglobulins are small protein modules with specific affinities. Among them, the variable domains of heavy chains of heavy-chain-only antibodies (VHH) as the antigen-binding fragment of heavy-chain-only antibodies (also termed nanobodies) have been widely investigated for their applicability, e.g., therapeutics and immunodiagnostics. [...] Read more.
Background/Objectives: Single-domain immunoglobulins are small protein modules with specific affinities. Among them, the variable domains of heavy chains of heavy-chain-only antibodies (VHH) as the antigen-binding fragment of heavy-chain-only antibodies (also termed nanobodies) have been widely investigated for their applicability, e.g., therapeutics and immunodiagnostics. However, despite their advantageous biochemical and biophysical characteristics, protein aggregation throughout recombinant synthesis is a serious drawback in the development of nanobodies with application perspectives. Therefore, we aimed to develop a computational method to predict the aggregation propensity of VHH antibodies for the selection of promising candidates in early discovery. Methods: We employed a deep learning-based structure prediction for VHHs and derived from it likely biophysical and biochemical properties of the framework region 2 with relevance for aggregation. A total of 106 nanobody variants were produced by recombinant expression and characterized for their aggregation behavior using size exclusion chromatography (SEC). Results: Quantitative characteristics of framework region 2 patches were combined into a function that defines an aggregation score (AS) predicting the aggregation propensities of VHH variants. AS was evaluated for its capability to forecast recombinant VHH aggregation by experimentally studying VHH Fc-fusion proteins for their aggregation. We observed a clear correlation between the calculated aggregation score and the actual aggregation propensities of biochemically characterized VHHs Fc-fusion proteins. Moreover, we implemented an easily accessible pipeline of software modules to design nanobodies with desired solubility properties. Conclusions: AI-based prediction of VHH structures, followed by analysis of framework region 2 properties, can be used to predict the aggregation propensities of VHHs, providing a convenient and efficient tool for selecting stable recombinant nanobodies. Full article
(This article belongs to the Collection Computational Antibody and Antigen Design)
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24 pages, 2706 KB  
Article
Functionalized Indolizines as Potential Anticancer Agents: Synthetic, Biological and In Silico Investigations
by Roxana Ciorteanu, Catalina Ionica Ciobanu, Narcis Cibotariu, Sergiu Shova, Vasilichia Antoci, Ionel I. Mangalagiu and Ramona Danac
Int. J. Mol. Sci. 2025, 26(17), 8368; https://doi.org/10.3390/ijms26178368 - 28 Aug 2025
Viewed by 251
Abstract
Three new series of indolizines (5af, 6af and 7ag), functionalized with bromine or ethyl ester substituents on the pyridine ring, were designed and synthesized as promising anticancer agents. The synthesis of indolizine derivatives was [...] Read more.
Three new series of indolizines (5af, 6af and 7ag), functionalized with bromine or ethyl ester substituents on the pyridine ring, were designed and synthesized as promising anticancer agents. The synthesis of indolizine derivatives was carried out using the 1,3-dipolar cycloaddition of pyridinium N-ylides to ethyl propiolate as a key step. Spectral characterization (using NMR, FT-IR, HRMS and X-ray diffraction) showed that two types of cycloadducts 5af and 6af were obtained when the ylides generated by the 3-bromopyridinium salts were used as 1,3-dipoles in Huisgen cycloaddition reactions to ethyl propiolate. The anticancer effect of selected compounds was in vitro assessed against the National Cancer Institute (NCI) panel of 60 human tumor cells, at 10 μM concentration, with three compounds (5c, 6c and 7g) showing promising inhibitory activity on the growth of several cell lines including lung, brain, renal cancer and melanoma, as well as a cytotoxic effect against HOP-62 non-small cell lung cells (34% for compound 5c and 15% for compound 7g) and SNB-75 glioblastoma cells (15% for compound 5c and 14% for derivative 7c). Molecular docking revealed favorable binding affinities for 5c, 6c and 7g (–9.22 to –9.88 kcal/mol) at the colchicine-binding site of tubulin with key interactions involving βASN-258, βALA-317, and βLYS-352 residues for 5c, βASN-258 in case of 6c, and αVAL-181 and βLYS-254 for derivative 7g. According to the in silico ADMET analysis, the active compounds are predicted to exhibit good oral bioavailability, promising drug-like qualities and low toxicity risks. Full article
(This article belongs to the Section Molecular Pharmacology)
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24 pages, 3364 KB  
Article
In Silico Analysis of Curcumin and Its Analogs MS13 and MS17 Against HSF1 and HSP Family Proteins
by Kha Wai Hon, Shafi Ullah Khan, Thet Thet Htar and Rakesh Naidu
Chemistry 2025, 7(5), 139; https://doi.org/10.3390/chemistry7050139 - 28 Aug 2025
Viewed by 294
Abstract
Heat shock proteins (HSPs), a family of proteins including HSP27, HSP40, HSP60, HSP70, and HSP90, play critical roles in cellular processes and are often dysregulated in cancer. Heat Shock Factor 1 (HSF1) protein, the master regulator of HSP expression, is also a promising [...] Read more.
Heat shock proteins (HSPs), a family of proteins including HSP27, HSP40, HSP60, HSP70, and HSP90, play critical roles in cellular processes and are often dysregulated in cancer. Heat Shock Factor 1 (HSF1) protein, the master regulator of HSP expression, is also a promising target for cancer therapy due to its involvement in tumorigenesis. This study is the first to investigate the potential of two novel curcumin analogs, MS13 (1,2-bis(4-hydroxy-3-methoxyphenyl)-1,4-pentadiene-3-one) and MS17 (1,5-bis(2-hydroxyphenyl)-1,4-pentadiene-3-one), as modulators of these key targets. Employing molecular docking and molecular dynamics (MD) simulations, we investigated the interactions of MS13 and MS17 with HSF1 and the panel of HSPs. Both compounds demonstrated strong binding affinity for all the proteins, particularly for HSP70, exhibiting greater affinity compared to curcumin. Molecular docking revealed specific binding sites for both compounds on each target protein, which were further investigated using MD simulations. MS17 generally formed more stable complexes with HSP27, HSP40, HSP60, and HSP70, suggesting it might be a more potent modulator of these specific proteins. In contrast, MS13 displayed greater stability when bound to HSF1 and HSP90. These different variations could be attributed to variations in the chemical structures of MS13 and MS17, leading to distinct interactions with each protein’s binding site. MS13 and MS17 exhibit more advantageous ADMET profiles compared to curcumin, particularly in their predicted Blood–Brain Barrier (BBB) permeability and MS17’s superior passive membrane permeability and absorption. These findings highlight the potential of both MS13 and MS17 as promising leads for developing HSP modulators for cancer treatment. Full article
(This article belongs to the Section Biological and Natural Products)
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19 pages, 8897 KB  
Article
Chemical Composition of Clove and Fennel Seed Essential Oils and a Comparison of Their In Silico and In Vitro Antibacterial Activity with That of Their Main Compounds
by Achraf Abdou, Fatima Ezzahra Maaghloud, Fatima Zahra Kamal, Said Rammali, Alin Ciobica, Vasile Burlui, Cristina Albert, Abdelhakim Elmakssoudi, Bogdan Novac and Mohamed Dakir
Curr. Issues Mol. Biol. 2025, 47(9), 694; https://doi.org/10.3390/cimb47090694 - 27 Aug 2025
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Abstract
This study aimed to assess the chemical composition and antibacterial potential of essential oils (EOs) from two plants: clove buds (Syzygium aromaticum) and fennel seeds (Foeniculum vulgare) EOs. The major compounds, eugenol and estragole, were isolated from these oils [...] Read more.
This study aimed to assess the chemical composition and antibacterial potential of essential oils (EOs) from two plants: clove buds (Syzygium aromaticum) and fennel seeds (Foeniculum vulgare) EOs. The major compounds, eugenol and estragole, were isolated from these oils and tested against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. The EOs were obtained via hydrodistillation and analyzed using Gas Chromatography–Mass Spectrometry (GC-MS). Clove oil was found to be rich in eugenol (68.51%), while fennel seed oil was dominated by estragole (93.30%). Antibacterial activity, assessed by the agar disc diffusion method and supported by MIC/MBC testing, revealed that eugenol exhibited the highest efficacy, with MIC values ranging from 0.58 to 1.15 mg/mL and MBC values from 1.15 to 2.30 mg/mL, particularly against S. aureus and P. aeruginosa. In silico analysis was conducted to evaluate pharmacokinetics, toxicity, and molecular docking interactions. ADME predictions indicated good oral bioavailability and high membrane permeability for both compounds, with eugenol displaying superior solubility and better compliance with Lipinski’s Rule of Five. Molecular docking simulations confirmed the antibacterial potential, with eugenol showing stronger binding affinities to bacterial targets (−7.8 kcal/mol), forming more stable and diverse interactions compared to estragole. However, toxicity predictions indicated potential mutagenic, carcinogenic, and cardiotoxic (hERG inhibition) risks for both compounds. Full article
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21 pages, 4387 KB  
Article
Comparative Analysis of Aggregation of β- and γ-Synucleins in Vertebrates
by Maria Carmela Bonaccorsi di Patti, Martina Meoni and Mattia Toni
Biomolecules 2025, 15(9), 1231; https://doi.org/10.3390/biom15091231 - 26 Aug 2025
Viewed by 404
Abstract
This study explores the structural transitions and aggregation behaviour of recombinant β- and γ-synucleins from five vertebrate species—Cyprinus carpio, Danio rerio, Xenopus laevis, Anolis carolinensis, and Homo sapiens—using thioflavin T fluorescence and circular dichroism spectroscopy, with and without [...] Read more.
This study explores the structural transitions and aggregation behaviour of recombinant β- and γ-synucleins from five vertebrate species—Cyprinus carpio, Danio rerio, Xenopus laevis, Anolis carolinensis, and Homo sapiens—using thioflavin T fluorescence and circular dichroism spectroscopy, with and without copper ions. Although synucleins are well-conserved proteins among vertebrates, species-specific differences in amino acid composition and predicted secondary structures were observed, particularly within β-strand-forming regions. During a six-day incubation, human β-synuclein exhibited a time-dependent increase in β-sheet-rich structures, while non-mammalian β-synucleins showed limited variation. In contrast, γ-synucleins from all species displayed greater aggregation propensity, with variations in kinetics and magnitude. The presence of copper reduced the rate of aggregation in human β-synuclein, likely due to high-affinity metal-binding sites, whereas γ-synuclein aggregation was only mildly affected. Notably, copper enhanced late-phase aggregation in A. carolinensis β-synuclein. These findings suggest that sequence divergence among synuclein isoforms may underlie species-specific aggregation mechanisms and metal sensitivity. The differential aggregation behaviour observed across taxa may reflect evolutionary adaptations in synuclein function and folding propensity, with implications for understanding the molecular basis of synucleinopathies and their potential modulation by metal ions. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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