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Search Results (1,363)

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18 pages, 341 KB  
Article
In Silico Mutational Analysis of Two-Component System Genes Associated with Colistin Resistance in Clinical Pseudomonas aeruginosa Isolates from Peshawar
by Bashir Ahmad, Qaisar Ali, Sadiq Azam, Muhammad Asghar, Noor Rehman, Gul-e-Sehra Mujib, Syed Sohail Shah, Jamila Javed, Ibrar Khan, Taj Ali Khan and Taane G. Clark
Biomolecules 2026, 16(7), 962; https://doi.org/10.3390/biom16070962 (registering DOI) - 29 Jun 2026
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen causing healthcare-associated infections. Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative bacteria. Resistance arises through mutations in two-component systems (TCS) regulating the arn operon. Data on colistin resistance in P. aeruginosa from Pakistan remain limited. A total [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen causing healthcare-associated infections. Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative bacteria. Resistance arises through mutations in two-component systems (TCS) regulating the arn operon. Data on colistin resistance in P. aeruginosa from Pakistan remain limited. A total of 3189 clinical samples (urine, blood, sputum, pus, wound swabs) were cultured. P. aeruginosa was identified by Gram staining, biochemical tests (catalase, oxidase, API 20E), and oprL gene amplification. Antibiotic susceptibility was determined by disk diffusion and MIC strips. Resistance genes (PhoP, PhoQ, PmrA, PmrB, mcr-1, oprD) were detected by PCR and Sanger sequencing. Wild-type protein structures were retrieved from PDB; mutant structures were predicted using AlphaFold3. ANP (phosphoaminophosphonic acid-adenylate ester) was docked using MOE 2019.0102. Of 3189 samples, 384 (12.0%) yielded P. aeruginosa. Wound/pus (38.0%) and surgical wards (30.0%) were the predominant sources. Colistin and polymyxin B showed 99.0% susceptibility (MIC50/MIC90 = 1 µg/mL). High resistance was observed for Piperacillin–Tazobactam (96.4%), Aztreonam (70.6%), and Gentamicin (64.2%). oprD was the most prevalent gene (87.5%), followed by PmrB (54.0%), PhoQ (44.0%), PhoP (36.0%), PmrA (18.0%), and mcr-1 (8.0%). Docking revealed the strongest binding in wild-type PhoQ (1ID0; −12.0 kcal/mol, LYS392), wild-type PmrB (2JSO; −9.8 kcal/mol, ASP37), and wild-type PhoP (2PKX; −9.1 kcal/mol, LYS87/ARG111). Mutant proteins showed reduced binding affinities and dispersed interaction networks. Mutant PhoP formed 16 contacts (strongest −4.3 kcal/mol) versus wild-type PhoP with 13 contacts (−9.1 kcal/mol). Colistin remains highly effective against P. aeruginosa in this setting (99.0% susceptibility). The presence of mcr-1 (8.0%) and high oprD prevalence (87.5%) require continued surveillance. Mutations in TCS proteins reduce ANP binding affinity and alter interaction specificity, suggesting that ATP-competitive inhibitors targeting these kinases merit further investigation and experimental validation. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
23 pages, 3124 KB  
Article
Proteomic Analysis of Tropical Maize Inbred Line QR273 at Different Growth Stages Under Long-Day Conditions
by Wenju Luo, Xiaofen Xie, Xiaoli Wang, Yufeng Li, Xianbin Hou and Zhengjie Zhu
Diversity 2026, 18(7), 390; https://doi.org/10.3390/d18070390 - 25 Jun 2026
Viewed by 92
Abstract
Tropical maize often exhibits photoperiod sensitivity, which limits its adaptation to temperate regions. Understanding its proteomic dynamics under long-day conditions is therefore crucial for germplasm improvement. This study employed a Tandem Mass Tag (TMT)-based proteomic approach to investigate stage-specific protein expression patterns in [...] Read more.
Tropical maize often exhibits photoperiod sensitivity, which limits its adaptation to temperate regions. Understanding its proteomic dynamics under long-day conditions is therefore crucial for germplasm improvement. This study employed a Tandem Mass Tag (TMT)-based proteomic approach to investigate stage-specific protein expression patterns in the tropical maize inbred line QR273 under long-day conditions (16 h light/8 h dark). Seeds were cultivated in climate chambers, and leaves were collected at the four-leaf (P4) and nine-leaf (P9) stages. A total of 2881 differentially expressed proteins (DEPs) were quantified between the P4 and P9 stages, among which only 7 were upregulated and 2874 were downregulated at the P9 stage. Gene Ontology (GO) enrichment analysis revealed that these DEPs were significantly enriched in processes related to proteolysis, membrane components, and ATP binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the enrichment of DEPs in amino acid biosynthesis, secondary metabolite biosynthesis, and aminoacyl-tRNA biosynthesis pathways. Protein–protein interaction (PPI) network analysis identified 60S ribosomal protein L12, adenosine 5′-phosphosulfate reductase, and RuvB helicase as core hub proteins. Based on functional annotation of representative DEPs, the DEPs were classified into four categories: 9 proteins related to storage material protection, 14 proteins related to protein modification, 12 proteins related to photosynthesis, and 25 proteins with other biological functions. Comparative analysis demonstrated a decrease in storage material protection, protein modification, and photosynthetic capacity at the P9 stage relative to the P4 stage. These findings provide insights into the proteomic dynamics underlying tropical maize development under long-day conditions and offer a theoretical basis for genetic improvement of tropical maize germplasm. Notably, inferences regarding nutrient reallocation based on DEP downregulation are derived solely from proteomic data and require further experimental validation. Full article
27 pages, 5424 KB  
Article
Dynamic Effects of Vibrio tubiashii Infection on Pathology, Transcriptome, and Immunology in the Hepatopancreas of Ivory Shell (Babylonia areolata)
by Chen Dai, Dapeng Luo, Qingming Liu, Jing Cui, Yongcai Fu, Haohan Mi, Shihao Yan, Zhongzheng Fu, Guangyuan Xia, Zhigang Tu and Minghui Shen
Biology 2026, 15(13), 992; https://doi.org/10.3390/biology15130992 (registering DOI) - 24 Jun 2026
Viewed by 160
Abstract
Vibrio tubiashii infection has led to several Babylonia areolata pandemics on the southeast coast of China, yet the immune response of the ivory shell against V. tubiashii and the specific pathogen–host interaction remain unclear. This dynamic study aimed to characterize the response of [...] Read more.
Vibrio tubiashii infection has led to several Babylonia areolata pandemics on the southeast coast of China, yet the immune response of the ivory shell against V. tubiashii and the specific pathogen–host interaction remain unclear. This dynamic study aimed to characterize the response of B. areolata to V. tubiashii infection with the use of pathology, transcriptomics, an enzymatic assay, and inflammatory cytokines. Hepatopancreatic cells showed marked vacuolar degeneration with intact cell membrane and extensive cytoplasmic vacuolization after infection. The dynamic transcriptome of the hepatopancreatic tissue was analyzed by RNA-seq after V. tubiashii infection, and a total of 2733 (3 h), 5610 (24 h), 3323 (48 h), and 418 (72 h) differentially expressed genes (DEGs) were identified during infection. The GO and KEGG analyses showed that the DEGs were enriched in metabolic regulation, lysosome, and multiple immune-related pathways such as the MAPK signaling pathway. The immune response of B. areolata was distinct, where the early stage of immune response (3 h) showed binding, focal adhesion, and apoptosis, as well as an activated antioxidant system. Here, expression of TNF-α, IL-1, and IL-8 was significantly increased in the hepatopancreas, whereas expression of IL-6 and IL-17 increased afterward. During the middle stage (24 h and 48 h), a large number of DEGs were suppressed, especially those associated with metabolism and lysosomes, although their expression returned to normal during prolonged infection (72 h). The PPI network showed that ppp2, atp6, and sos1 were the top immune-related DEGs during infection. Key infection-related and time-course-related genes were analyzed by WGCNA. This study illustrates that oxidative stress, inflammation, and apoptosis are strategies of the hepatopancreatic immune response in B. areolata against V. tubiashii infection and enlightens conservation and production by furthering our understanding of gastropod immunity. Full article
(This article belongs to the Section Marine and Freshwater Biology)
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21 pages, 14759 KB  
Article
Association of F-53B Nephrotoxicity with Oxidative Stress-Mediated Mitochondrial Dysfunction and Altered Autophagy–Apoptosis Crosstalk
by Bitong Li, Dongling Liu, Zhiying Qiu, Yaojian Zheng, Yue Wu, Lina Zhang, Ran Li, Cuiqing Liu, Qinghua Sun and Xiang Zeng
Biomolecules 2026, 16(7), 938; https://doi.org/10.3390/biom16070938 (registering DOI) - 24 Jun 2026
Viewed by 161
Abstract
6:2 chlorinated polyfluorinated ether sulfonate (F-53B, also known as 6:2 Cl-PFESA) is a major alternative to perfluorooctane sulfonate (PFOS) and a widespread environmental pollutant with potential public health hazards. However, its nephrotoxic effects and underlying molecular mechanisms remain poorly understood. This study investigated [...] Read more.
6:2 chlorinated polyfluorinated ether sulfonate (F-53B, also known as 6:2 Cl-PFESA) is a major alternative to perfluorooctane sulfonate (PFOS) and a widespread environmental pollutant with potential public health hazards. However, its nephrotoxic effects and underlying molecular mechanisms remain poorly understood. This study investigated renal injury induced by environmentally relevant concentrations of F-53B and delineated the mechanistic cascade using a mouse model combined with quantitative proteomic and molecular biological approaches. Male C57BL/6 mice were exposed to 0, 4, 40, and 400 μg/L F-53B for 4 weeks. F-53B exposure led to significant renal dysfunction, histopathological damage, elevated renal injury biomarkers, and pronounced oxidative stress in a dose-dependent manner. A proteomic comparison of the 0 μg/L versus 400 μg/L groups identified 276 differentially expressed proteins that were strongly enriched in oxidative phosphorylation, autophagy, and apoptosis pathways, with cytochrome c oxidase subunit 7b (Cox7b) serving as a core downregulated hub molecule. Further validation confirmed that F-53B triggered overt mitochondrial structural damage, impaired respiratory chain complex assembly, aberrant ATP production, and disturbed mitochondrial dynamics. Consequently, excessive autophagy activation and mitochondrial-mediated apoptosis were simultaneously stimulated in renal tissues. Notably, although statistically significant, the alterations induced by F-53B were generally mild in magnitude. Collectively, our findings demonstrate that F-53B induces nephrotoxicity through a sequential pathological cascade. This study provides novel mechanistic insights into F-53B-elicited renal injury and highlights the potential health risks of this emerging per- and polyfluoroalkyl substance (PFAS) alternative. Full article
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20 pages, 729 KB  
Review
Molecular Mechanisms of Photobiomodulation in Retinal Diseases: Cytochrome c Oxidase, Mitochondrial Bioenergetics and Cytoprotective Signalling
by Rubens Camargo Siqueira
Int. J. Mol. Sci. 2026, 27(13), 5683; https://doi.org/10.3390/ijms27135683 - 24 Jun 2026
Viewed by 137
Abstract
Photobiomodulation (PBM) is a non-invasive therapeutic strategy that uses red and near-infrared (NIR) light in the 590–950 nm range to modulate the cellular and molecular pathways involved in retinal homeostasis. At the molecular level, PBM acts primarily through photon absorption by cytochrome c [...] Read more.
Photobiomodulation (PBM) is a non-invasive therapeutic strategy that uses red and near-infrared (NIR) light in the 590–950 nm range to modulate the cellular and molecular pathways involved in retinal homeostasis. At the molecular level, PBM acts primarily through photon absorption by cytochrome c oxidase (CcO, complex IV of the mitochondrial electron transport chain), whose four metal centres—two copper (CuA and CuB) and two heme groups (heme a and heme a3)—absorb light across approximately 600–1000 nm. Photon capture promotes photodissociation of inhibitory nitric oxide (NO) from the binuclear CuB–heme a3 centre, accelerates electron transfer, restores the proton-motive force and increases ATP synthesis. These primary events trigger a coordinated molecular programme that includes (i) transient mitochondrial reactive oxygen species (ROS) bursts that activate the Nrf2/Keap1/ARE axis and upregulate phase II antioxidant enzymes (HO-1, NQO1, GCLC, SOD2, catalase, GPx); (ii) calcium- and cAMP-dependent secondary signalling that converges on PI3K/Akt, MAPK/ERK, AMPK and mTOR pathways; (iii) suppression of NF-κB-driven cytokine production (TNF-α, IL-1β, IL-6) and of NLRP3 inflammasome activation; (iv) downregulation of the HIF-1α/VEGF axis, particularly at 590 nm; (v) anti-apoptotic remodelling of the Bcl-2/Bax ratio with reduced cytochrome c release and caspase-3/9 activation; and (vi) PGC-1α/TFAM/NRF1-driven mitochondrial biogenesis, alongside restoration of fission/fusion homeostasis (Drp1, Mfn1/2, Opa1) and PINK1/Parkin-mediated mitophagy. Wavelength specificity has a defined molecular basis: 590 nm modulates VEGF signalling and RPE pump activity, 660 nm interacts with the CuB centre and enhances O2 binding at CcO, and 850 nm is absorbed by CuA and supports electron entry into complex IV. A second molecular axis is the bidirectional crosstalk between PBM and the circadian system: mitochondrial respiration, ATP turnover and CcO activity oscillate over the 24 h cycle under the control of the BMAL1/CLOCK and PER/CRY core machinery, the NAD+/SIRT1–SIRT3 axis and REV-ERBα. Preliminary preclinical and human observations suggest that NIR-induced bioenergetic and functional gains may be coupled to this rhythm, with greater benefit reported when light is delivered in the morning window (≈08:00–11:00); this time dependence should be regarded as an emerging hypothesis rather than an established clinical principle. The clinical evidence is unevenly developed across indications. It is most robust for non-exudative age-related macular degeneration, where multiwavelength PBM (590/660/850 nm; Valeda Light Delivery System) has shown disease-modifying potential in randomized controlled trials (LIGHTSITE I–III and the LIGHTSITE IIIB extension), with sustained BCVA gains and reduced incidence of geographic atrophy over 24 months and beyond. Evidence for retinitis pigmentosa, central serous chorioretinopathy and, with red-light monotherapy, childhood myopia is at present limited to small or short-term studies and remains preliminary. This narrative review synthesizes the molecular machinery engaged by PBM, integrates clinical findings across retinal diseases and discusses how chronotherapeutic delivery of light, aligned with the molecular clock, may further optimize therapeutic efficacy. Full article
(This article belongs to the Special Issue Progress in Photobiomodulation Therapy)
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38 pages, 7038 KB  
Article
Non-Classical Binding Mechanisms of Ferrocene-Modified Imatinib and Nilotinib Analogues in BCR-ABL1 Kinase Revealed by Computational Analysis
by Rostislava Angelova, Georgi Stavrakov, Danislav S. Spassov, Georgi Momekov and Mariyana Atanasova
Molecules 2026, 31(12), 2156; https://doi.org/10.3390/molecules31122156 - 18 Jun 2026
Viewed by 209
Abstract
Background: Ferrocene-containing compounds have gained attention in medicinal chemistry due to their unique redox and structural properties. This study investigates ferrocene-based analogues of imatinib and nilotinib to define their binding determinants within the ABL1 kinase domain using an integrated in silico approach, in [...] Read more.
Background: Ferrocene-containing compounds have gained attention in medicinal chemistry due to their unique redox and structural properties. This study investigates ferrocene-based analogues of imatinib and nilotinib to define their binding determinants within the ABL1 kinase domain using an integrated in silico approach, in relation to their previously reported cytotoxic activity. Methods: Ligand geometries were optimized at the B3LYP/def2-TZVP level with D3(BJ) dispersion and SMD solvation. Molecular docking against ABL1 (PDB ID: 2HYY) was performed using Glide SP, validated by re-docking and enrichment screening. Docked poses were refined using MM-GBSA (Prime, VSGB 2.1/OPLS4). The most active compounds (9 and 15a), together with the inactive control 15e, were subjected to three independent 500 ns molecular dynamics simulations (Desmond, OPLS4), followed by trajectory analysis including RMSD, RMSF, radius of gyration, SASA, and polar surface area. Results: Compounds 9 and 15a maintained stable binding within the ATP-binding pocket despite lacking the canonical hinge interaction with Met318, indicating hinge-independent binding. Their binding was mainly driven by interactions with Asp381 (DFG motif) and cation–π contacts with Lys271. In contrast, the compound 15e showed unstable binding, increased conformational flexibility, reduced pocket burial, and loss of key stabilizing interactions. Active compounds also preserved stable P-loop dynamics, with Tyr253 engagement suggesting a role in loop stabilization. Compound 9 exhibited the most constrained and reproducible binding mode among all analogues. Conclusions: Ferrocene-based analogues can sustain stable ABL1 binding via non-classical interaction networks independent of hinge recognition. The clear distinction between active compounds and the inactive analogue 15e supports the robustness of the proposed binding mode and provides a structural basis for their reported cytotoxic activity. These findings support further experimental evaluation of ferrocene-containing scaffolds as potential BCR-ABL1 inhibitors. Full article
(This article belongs to the Special Issue Computational Approaches for Drug and Protein Design)
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14 pages, 1454 KB  
Article
Longitudinal Transcriptomic Analysis Reveals Systemic Effects of Risdiplam in Adults with Spinal Muscular Atrophy
by Maria Liguori, Arianna Consiglio, Eustachio D’Errico, Ylenia Antonacci, Martina Coffa, Alessandro Introna and Isabella Laura Simone
Brain Sci. 2026, 16(6), 643; https://doi.org/10.3390/brainsci16060643 - 17 Jun 2026
Viewed by 317
Abstract
Background: Spinal Muscular Atrophy (SMA) is a neurodegenerative disease caused by reduced survival motor neuron (SMN) protein levels due to SMN1 gene mutations. The natural history of SMA has dramatically changed since innovative therapies were approved; among them, Risdiplam (an oral molecule) increases [...] Read more.
Background: Spinal Muscular Atrophy (SMA) is a neurodegenerative disease caused by reduced survival motor neuron (SMN) protein levels due to SMN1 gene mutations. The natural history of SMA has dramatically changed since innovative therapies were approved; among them, Risdiplam (an oral molecule) increases the peripheral levels of SMN by modifying the pre-mRNA slicing of the paralogous SMN2 that also codes for the protein. Methods: We performed longitudinal RNA sequencing on peripheral blood samples from 16 adult SMA patients (types II and III) before and after 12 months of Risdiplam treatment to assess transcriptomic changes. Results: During Risdiplam treatment, increased SMN2 transcript levels were observed, which was coherent with the clinical condition of the investigated SMA cohort. Upregulated mitochondria genes or pseudogenes (i.e., MT-ATP8 and MTND1P11) and downregulated autophagy-related pathways were also found. Baseline differences in gene expression between SMA type II and type III involved neurodegenerative (i.e., MS4A3, C4BPA, and NEILS3) and immune-related (B2M) genes. Conclusions: These findings support Risdiplam’s systemic impact in adult SMA subjects and reveal molecular distinctions between SMA phenotypes (types II and III), which may be of some relevance for future clinical and therapeutic strategies. Full article
(This article belongs to the Special Issue Molecular and Cellular Research in Neurodegenerative Diseases)
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45 pages, 4752 KB  
Review
Protein Kinase Inhibitors as Regulators of ABC Transporters in Overcoming Cancer Multidrug Resistance: A Comprehensive Review of Recent Advances
by Fatemeh Moosavi, Bahareh Hassani, Motahareh Mortazavi, Godefridus J. Peters and Omidreza Firuzi
Cancers 2026, 18(12), 1957; https://doi.org/10.3390/cancers18121957 - 16 Jun 2026
Viewed by 412
Abstract
Multidrug resistance (MDR) is defined as resistance to apparently unrelated drugs with different mechanisms of action, a phenomenon that seriously decreases the efficacy of many anticancer therapeutic regimens. MDR is mainly associated with a high expression of ATP-binding cassette (ABC) transporters, including ABCB1, [...] Read more.
Multidrug resistance (MDR) is defined as resistance to apparently unrelated drugs with different mechanisms of action, a phenomenon that seriously decreases the efficacy of many anticancer therapeutic regimens. MDR is mainly associated with a high expression of ATP-binding cassette (ABC) transporters, including ABCB1, ABCG2, and members of the ABCC subfamily, which actively extrude many anticancer drugs of various classes out of the cells. Protein kinase inhibitors (PKIs) were developed as therapies targeting oncogenic kinases but later appeared to be both substrates and inhibitors of ABC transporters and thus can potentially reverse MDR. This comprehensive review evaluates how PKIs regulate ABC transporters through three key mechanisms: altering expression, modifying subcellular localization, and inhibiting the efflux function. We evaluated the effect of PKIs that target tyrosine and serine/threonine kinases, such as EGFR/ErbB, JAK, VEGFR, BCR-Abl, ALK, FGFR, MEK1/2, B-RAF, BTK, CDK4/6, MET, RET, PDGFR and SYK. We have collected both computational studies and experimental reports, including functional assays, mechanistic studies of inhibition, and structural approaches that have evaluated PKIs’ effects on ABC transporters. We conclude that although PKIs can be ABC substrates, they mainly inhibit drug efflux, with minimal and context-dependent effects on transporter expression or localization. Full article
(This article belongs to the Special Issue Cancer Drug Resistance: Mechanisms and Overcoming Strategies)
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24 pages, 16704 KB  
Article
Immunometabolic Stratification of Autism Spectrum Disorder by CD4+ T-Cell Phenotype Reveals Subtype-Specific Energetic Deficit and Coordinated Suppression of Micronutrient Acquisition Pathways
by Albion Dervishi
Metabolites 2026, 16(6), 416; https://doi.org/10.3390/metabo16060416 - 15 Jun 2026
Viewed by 766
Abstract
Background: Autism spectrum disorder (ASD) is associated with immune dysregulation in a subset of individuals, though findings remain heterogeneous and poorly defined, particularly regarding immune subtypes and metabolic context. Methods: We analyzed whole-blood microarray data from GSE18123 (GPL570: ASD n = 46, controls [...] Read more.
Background: Autism spectrum disorder (ASD) is associated with immune dysregulation in a subset of individuals, though findings remain heterogeneous and poorly defined, particularly regarding immune subtypes and metabolic context. Methods: We analyzed whole-blood microarray data from GSE18123 (GPL570: ASD n = 46, controls n = 19; GPL6244: ASD n = 68, controls n = 21) using an integrated immunometabolic framework. CD4+ T-cell transcriptional programs were used to assign dominant immune phenotypes (TH1, TH2, TH17, Tfh, FOXP3+ Treg, Tr1-like). Metabolic demand was quantified via the τ-axis; execution capacity was assessed using cytosolic and mitochondrial energy compensation ratios (CECR, MECR). Induction–execution mismatch was captured by three Gap metrics (Cytosolic, Warburg, Global). Functional validation correlated these metrics with transcriptional signatures of folate transport, one-carbon metabolism, receptor-mediated micronutrient uptake (LRP2–CUBN–AMN), cobalamin processing, and vitamin D activation across both platforms. Results: Six immunometabolic CD4+ subtypes were identified within ASD. τ-axis discrimination was strongest for Tr1-like (AUC = 0.811) and Tfh (AUC = 0.825) states, while TH17 profiles were indistinguishable from controls. Despite variation in metabolic demand, CECR and MECR remained relatively preserved, indicating decoupling between induction and execution capacity. Global Gap values were most negative in Tfh and TH1 states and positive in TH17 and controls. Negative Gap states showed coordinated suppression of ATP-intensive micronutrient acquisition pathways, including folate transport (FOLR1/2, SLC19A1), megalin–cubilin-mediated uptake (r ≈ 0.77–0.79), and vitamin D activation (CYP27B1). Intracellular cobalamin processing was upregulated in proportion to metabolic demand (r > 0.9). Findings were directionally replicated across both datasets. Conclusions: These data demonstrate that ASD exhibits structured immunometabolic heterogeneity characterized by subtype-specific demand–capacity imbalance. The Global Gap framework provides transcriptomic evidence of energetic deficit in Tfh- and Tr1-like-dominant states. Future clinical studies should incorporate subtype-stratified assessment of micronutrient status and metabolic execution capacity. Full article
(This article belongs to the Special Issue Computational Modeling of Metabolite-Modulated Cellular Processes)
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19 pages, 9536 KB  
Article
Membrane Access and Orbital Localization Govern ABC Transporter Substrate Recognition
by Saad Harrizi, Imane Nait Irahal, Kaouthar El Birgui and Mostafa Kabine
Molecules 2026, 31(12), 2084; https://doi.org/10.3390/molecules31122084 - 13 Jun 2026
Viewed by 275
Abstract
The ATP-binding cassette transport protein Pdr5p is known to play a role in multidrug resistance in Saccharomyces cerevisiae by effluxing structurally diverse xenobiotics; yet the physicochemical determinants of substrate recognition remain poorly defined. To address this, density functional theory (DFT) calculations at the [...] Read more.
The ATP-binding cassette transport protein Pdr5p is known to play a role in multidrug resistance in Saccharomyces cerevisiae by effluxing structurally diverse xenobiotics; yet the physicochemical determinants of substrate recognition remain poorly defined. To address this, density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-SVP level were combined with machine learning to derive a predictive model of substrate recognition using a curated dataset of 66 compounds spanning 9 functional categories. A hybrid support vector machine (SVM) classifier achieved 96.3% accuracy (95% CI: 81.0–99.9%, Clopper–Pearson exact) in discriminating substrates from non-substrates under leave-one-out cross-validation. Feature importance analysis identified lipophilicity (LogP, F-score = 37.5) as the dominant descriptor, suggesting that membrane partitioning constitutes the initial recognition step. The HOMO–LUMO gap contributed secondarily (F-score = 12.4). Substrates were further distinguished by high frontier orbital focalization, with frontier orbital spread of 1.8–2.6%, compared to 4.18–7.22% for non-substrates. Notably, a model trained exclusively on Pdr5p data achieved 87% prediction accuracy when applied without retraining to the human P-glycoprotein (ABCB1) dataset, suggesting conserved physicochemical principles of substrate recognition across evolutionarily distant ABC transporters. These findings provide a quantum chemical framework for understanding and potentially predicting MDR transporter substrate specificity. Full article
(This article belongs to the Section Computational and Theoretical Chemistry)
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20 pages, 5367 KB  
Article
Small-Molecule Targeting of VDAC Disrupts Mitochondrial Bioenergetics and Suppresses Melanoma Cell Survival and Migration
by Zhi-Wei Ye, Leilei Zhang, Xuhong Zhang, John Culpepper, Eduardo N. Maldonado, Kenneth D. Tew, Jie Zhang and Danyelle M. Townsend
Cells 2026, 15(12), 1066; https://doi.org/10.3390/cells15121066 - 11 Jun 2026
Viewed by 283
Abstract
Melanoma is a highly aggressive and metabolically adaptable cancer that often resists conventional therapies. Targeting core bioenergetic pathways may, therefore, represent an effective strategy to improve therapeutic responses, particularly in tumors dependent on mitochondrial function. SC18 is an imidazolidine-2,4-dione compound that binds the [...] Read more.
Melanoma is a highly aggressive and metabolically adaptable cancer that often resists conventional therapies. Targeting core bioenergetic pathways may, therefore, represent an effective strategy to improve therapeutic responses, particularly in tumors dependent on mitochondrial function. SC18 is an imidazolidine-2,4-dione compound that binds the NADH-binding pocket of voltage-dependent anion channels (VDACs), inducing mitochondrial dysfunction. VDAC expression is increased in melanoma and strongly associated with advanced disease stage and poor prognosis. In this study, we evaluated the effects of SC18 in melanoma cell lines with distinct pigmentation states, including melanin-rich melanotic human MNT-1 and mouse B16-F1, as well as low/amelanotic human SKMel28 and mouse YUMM cells. VDAC1, VDAC2 and VDAC3 were highly expressed across these melanoma lines, all of which relied on both glycolysis and mitochondrial oxidative phosphorylation for ATP production. SC18 reduced mitochondrial membrane potential and oxygen consumption rates, accompanied by declines in intracellular ATP levels and TCA cycle substrate utilization. SC18 also increased reactive oxygen species, mitochondrial superoxide, and lipid peroxidation, indicating enhanced oxidative stress. These metabolic and redox disturbances were associated with reduced cell viability and significantly impaired migration in multiple melanoma cell lines, supporting a potential anti-metastatic effect. In addition, SC18 showed synergistic cytotoxicity when combined with other chemotherapeutic agents. Overall, SC18 disrupted mitochondrial metabolism, induced oxidative stress, and impaired survival and motility pathways, with more pronounced effects in low/amelanotic than in melanotic melanoma cells. Together, these findings support the further development of SC18 as a mitochondrial metabolic disruptor that targets redox vulnerabilities in melanoma. Full article
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21 pages, 2345 KB  
Article
Targeting ABL Tyrosine Kinase in Chronic Myeloid Leukemia: Design, Synthesis, Biological Evaluation, and Computational Studies of Novel Thiazolone Derivatives
by Belgin Sever and Halilibrahim Ciftci
Pharmaceutics 2026, 18(6), 709; https://doi.org/10.3390/pharmaceutics18060709 - 9 Jun 2026
Viewed by 390
Abstract
Background/Objectives: Chronic myeloid leukemia (CML) is primarily associated with the BCR:ABL1 fusion protein. Although tyrosine kinase inhibitors (TKIs) have markedly enhanced treatment outcomes, the development of agents with improved therapeutic characteristics remains necessary. The present work focused on the synthesis of a new [...] Read more.
Background/Objectives: Chronic myeloid leukemia (CML) is primarily associated with the BCR:ABL1 fusion protein. Although tyrosine kinase inhibitors (TKIs) have markedly enhanced treatment outcomes, the development of agents with improved therapeutic characteristics remains necessary. The present work focused on the synthesis of a new series of thiazolone derivatives (F1-11) and the assessment of their anti-CML activity through inhibition of ABL tyrosine kinase (TK). Methods: The designed compounds were prepared through a multistep synthetic pathway involving the formation of a new chalcone intermediate (A), synthesis of a new pyrazoline carbothioamide intermediate (B), and cyclization with different aldehydes to produce the target new thiazolone derivatives (F1-11). Cytotoxic effects were investigated against K562 CML cells using the MTT assay. The lead compound was additionally evaluated in HL-60 AML cells and normal PBMCs. Apoptotic induction was analyzed using Annexin V/ethidium homodimer staining, whereas ABL TK inhibitory activity was measured through the ADP-Glo assay. Molecular docking studies were conducted to explore ligand interactions within the ATP-binding domain of ABL TK. Results: Among the synthesized molecules, F-4 demonstrated the strongest activity against K562 cells with an IC50 value of 6.85 µM, close to that observed for imatinib (IC50 = 5.20 µM). The compound showed reduced cytotoxicity toward HL-60 cells (IC50 = 33.44 µM) and exhibited favorable selectivity toward PBMCs (SI = 13). Apoptosis studies revealed 51% early apoptotic cells and 43% late apoptotic cells following treatment. In the kinase assay, F-4 inhibited ABL TK activity by 39% at 10 µM and by 70% at 100 µM. Docking simulations suggested interactions with residues His361 and Asp381 in addition to nearby hydrophobic amino acids, although the interaction network was less extensive than that of imatinib. Conclusions: The findings identify F-4 as a promising new thiazolone-derived scaffold with selective anti-CML activity and notable ABL TK inhibitory potential. Additional structural optimization may further enhance its binding characteristics and therapeutic efficacy. Full article
(This article belongs to the Special Issue Recent Advances in Inhibitors for Targeted Therapies)
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12 pages, 2076 KB  
Article
The Effects of CB2R Activation on Inflammatory Pathways in Dermatomyositis
by Rohan Dhiman, Ahmed Eldaboush, Navin Vijayarangan, Darae Kang, Nilesh Kodali, DeAnna Diaz, Caroline Stone, Rui Feng and Victoria P. Werth
Biomedicines 2026, 14(6), 1296; https://doi.org/10.3390/biomedicines14061296 - 7 Jun 2026
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Abstract
Background/Objectives: Dermatomyositis is an autoimmune disease with heterogeneous symptoms and many potential drivers. Nonpsychoactive cannabinoids have shown promise in treating some subtypes of DM; however, the reasons behind this were unclear. In this project, we tested the effects of CB2R activation on PBMCs [...] Read more.
Background/Objectives: Dermatomyositis is an autoimmune disease with heterogeneous symptoms and many potential drivers. Nonpsychoactive cannabinoids have shown promise in treating some subtypes of DM; however, the reasons behind this were unclear. In this project, we tested the effects of CB2R activation on PBMCs from amyopathic and classic DM patients to determine its anti-inflammatory effects on pathways biologically relevant to DM. Methods: We determined the % CB2R positivity and intracellular cytokines in PBMCs from amyopathic DM and classic DM patients. CB2R positivity was determined by analyzing patient PBMCs via flow cytometry. PBMCs were stimulated by dsRNA for RIG1, dsDNA for cGAS, LPS for TLR4, and LPS/ATP for NLRP3, with and without CB2R pretreatment, and IFNβ, IFNγ, p65 NFkB, and pSTING levels were used as markers of pathway activation. The CB2R agonist JWH133 was used to pretreat PBMCs before stimulation. Results: Amyopathic DM PBMCS were found to be 101.3% more positive for CB2R compared to classic DM PBMCS (p < 0.05). In amyopathic DM PBMCs stimulated by LPS/ATP to target the NLRP3 inflammasome, CB2R activation resulted in a significant reduction in IFNβ MFI for MoDCs (p < 0.05) and Macs (p < 0.05), with a similar trend observed in cDCs relative to classic DM PBMCS. On the other hand, no difference in IFNβ response to CB2R activation was observed across all cell types investigated between classic and amyopathic DM PBMCs stimulated with LPS only to target TLR4. Conclusions: Amyopathic DM PBMCs were significantly more positive for CB2R and had better anti-inflammatory responses to CB2R activation for many inflammatory pathways implicated in DM. Full article
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14 pages, 2710 KB  
Article
ATP and Liv-52 Ameliorate Linezolid-Induced Liver Injury via Modulation of NF-κB/NLRP3 Pathways
by Serkan Cerrah, Ahmed Ramiz Baykan, Esra Tuba Sezgin, Gulbaniz Huseynova, Elif Karabacak, Serdar Tanas, Emine Kartal Baykan, Murat Gunay, Ali Gungor and Halis Suleyman
Biomedicines 2026, 14(6), 1286; https://doi.org/10.3390/biomedicines14061286 - 4 Jun 2026
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Abstract
Objective: Linezolid (LZD), an oxazolidinone antibiotic widely used against Gram-positive infections, has been associated with mitochondrial dysfunction and hepatotoxicity, particularly during prolonged use. This study aimed to investigate the protective effects of adenosine triphosphate (ATP) and Liv-52 against LZD-induced liver injury, with [...] Read more.
Objective: Linezolid (LZD), an oxazolidinone antibiotic widely used against Gram-positive infections, has been associated with mitochondrial dysfunction and hepatotoxicity, particularly during prolonged use. This study aimed to investigate the protective effects of adenosine triphosphate (ATP) and Liv-52 against LZD-induced liver injury, with a focus on oxidative stress, inflammation, and necroptosis pathways. Methods: Twenty-four male Wistar rats were randomly assigned to four groups: healthy control (HG), LZD-treated (LZDG), Liv-52 + LZD (LVLZ), and ATP + LZD (ATLZ). Liv-52 (50 mg/kg, orally) and ATP (5 mg/kg, intraperitoneally) were administered prior to LZD (125 mg/kg, orally) for 14 days. Results: Following LZD administration, malondialdehyde (MDA) levels markedly increased, indicating oxidative stress, while total glutathione (tGSH), superoxide dismutase (SOD), and catalase (CAT) activities significantly decreased. Histopathological examination revealed pronounced hepatocellular damage accompanied by increased NF-κB, NLRP3, RIPK3, and MLKL expression, indicating activation of inflammatory and necroptotic pathways. Treatment with ATP and Liv-52 significantly ameliorated these biochemical, histopathological, and molecular alterations. Conclusions: Treatment with ATP and Liv-52 significantly attenuated oxidative stress, improved histopathological alterations, and suppressed the expression of inflammatory and necroptotic markers. Notably, ATP exhibited a more pronounced protective effect compared to Liv-52. In conclusion, LZD induces hepatotoxicity through oxidative stress-mediated inflammatory and necroptotic mechanisms, while ATP and Liv-52 confer hepatoprotection, with ATP showing superior efficacy. Full article
(This article belongs to the Special Issue Advanced Research in Liver Diseases)
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15 pages, 3638 KB  
Article
Changes in the Metabolism of GD2-Specific Murine CAR-T Cells After Co-Culturing with Melanoma
by Aleksey Bulygin, Julia Philippova, Nikita Basov, Ekaterina Butikova, Maria Sotnikova, Yulia Sotnikova, Yuriy Patrushev, Artem Rogachev, Evgeniy Gaisler, Andrey Pokrovsky, Hiroshi Shiku and Sergey Sennikov
Int. J. Mol. Sci. 2026, 27(11), 5093; https://doi.org/10.3390/ijms27115093 - 4 Jun 2026
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Abstract
Immunotherapy with the use of induced CAR-T cells is an effective method of cancer suppression in close to in vivo conditions. The question of the nature of metabolism of CAR-T cells in the conditions of fighting not against single cancer cells, but against [...] Read more.
Immunotherapy with the use of induced CAR-T cells is an effective method of cancer suppression in close to in vivo conditions. The question of the nature of metabolism of CAR-T cells in the conditions of fighting not against single cancer cells, but against tumor cells, remains relevant. Our studies have shown the metabolomic profile of mouse GD2-specific CAR-T cells upon contact with B78-21 melanoma tumor cells and upon exposure to B-21 melanoma 3D spheroid structures. Full article
(This article belongs to the Collection Advances in Cell and Molecular Biology)
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