Biomolecules最新文献

{"title":"Metabolic Engineering of <i>Yarrowia lipolytica</i> for De Novo Biosynthesis of Umbelliferone.","authors":"Fengliu Lu, Ying Luo, Zhen Lei, Changfu Li, Yansheng Zhang","doi":"10.3390/biom16101450","DOIUrl":"https://doi.org/10.3390/biom16101450","url":null,"abstract":"<p><p>Umbelliferone, a key precursor for the biosynthesis of high-value furanocoumarin derivatives, is produced via the shikimate pathway. The oleaginous yeast <i>Yarrowia lipolytica</i> possesses an inherently robust shikimate pathway; however, de novo biosynthesis of umbelliferone in this microbial chassis has not been realized to date. Low intracellular pools of <i>p</i>-coumaric acid and suboptimal catalytic activity of downstream hydroxylation and cyclization enzymes represent the major bottlenecks limiting efficient umbelliferone production. In this study, we systematically screened five PAL/TAL variants, three 4CL isoforms, and two C2'H enzymes derived from diverse plant and microbial sources. The bifunctional enzyme RtPAL-TAL exhibited the highest productivity of <i>p</i>-coumaric acid, while the combination of At4CL3 and RgC2'H achieved the maximum umbelliferone accumulation. Expression of feedback-insensitive shikimate pathway mutant enzymes effectively relieved intrinsic pathway feedback inhibition, resulting in a 10.2-fold improvement in <i>p</i>-coumaric acid titer. All synthetic biosynthetic gene cassettes were stably integrated into the <i>Y</i>. <i>lipolytica</i> genome to generate the engineered strain YL-PU, which yielded 3.29 mg/L umbelliferone in shake-flask cultures. Further fed-batch fermentation in a 5 L bioreactor increased the umbelliferone titer to 125.52 mg/L at 84 h of cultivation. This work establishes the first de novo umbelliferone biosynthesis pathway in <i>Y. lipolytica and</i> identifies that C2'H represents a major candidate bottleneck under the tested configuration, in agreement with earlier findings. These findings provide a robust foundation for further metabolic engineering of the <i>Y</i>. <i>lipolytica</i> chassis to enable high-titer production of coumarins and other phenylpropanoid natural products.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lack of Association Between <i>CAT</i> rs1001179 and <i>SOD2</i> rs4880 Variants and Risk for Multiple Sclerosis.","authors":"Elena García-Martín, Javier Gómez-Tabales, José A G Agúndez, Julián Benito-León, Jorge Millán-Pascual, María Díaz-Sánchez, Patricia Calleja, Laura Turpín-Fenoll, Hortensia Alonso-Navarro, Esteban García-Albea, Félix Javier Jiménez-Jiménez","doi":"10.3390/biom16101449","DOIUrl":"https://doi.org/10.3390/biom16101449","url":null,"abstract":"<p><p><b>Objectives:</b> Several lines of evidence point to a potential involvement of oxidative stress in the pathophysiology of multiple sclerosis (MS). Superoxide dismutase isoenzymes 1 and 2 (SOD1 and SOD2) and catalase (CAT) are key components of the enzymatic antioxidant defense system. Consequently, genetic variation in the genes encoding these enzymes may influence susceptibility to MS. However, previous studies examining the relationship between <i>SOD1</i>, <i>SOD2</i>, and <i>CAT</i> variants and MS susceptibility have yielded inconsistent findings. The present study aimed to investigate whether two common single-nucleotide variants (SNVs) in <i>CAT</i> and <i>SOD2</i> are associated with MS risk in a Caucasian Spanish population. <b>Methods:</b> We investigated the <i>CAT</i> rs1001179 and <i>SOD2</i> rs4880 variants in 300 patients with MS and 400 healthy controls using allele-specific TaqMan quantitative PCR assays. We further examined whether these variants were related to relevant clinical characteristics, including age at disease onset, disease severity, and clinical course/subtype. <b>Results:</b> Neither the genotype nor allele distributions of <i>CAT</i> rs1001179 and <i>SOD2</i> rs4880 differed significantly between patients with MS and healthy controls. Furthermore, no significant relationships were observed between either variant and sex, age at disease onset, disease severity, or clinical MS subtype. <b>Conclusions:</b> The present study did not detect significant associations between the <i>CAT</i> rs1001179 or <i>SOD2</i> rs4880 variants and MS susceptibility in the Caucasian Spanish population. Similarly, no significant associations were detected between these variants and the clinical characteristics evaluated. However, smaller genetic effects cannot be excluded.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellulase and Xylanase from <i>Phanerochaete chrysosporium</i> ATCC24725: Production, Regulation of Synthesis, and Properties.","authors":"Eva Kachlishvili, Mikheil Asatiani, Aza Kobakhidze, Mariam Rusitashvili, Vladimir Elisashvili","doi":"10.3390/biom16101446","DOIUrl":"https://doi.org/10.3390/biom16101446","url":null,"abstract":"<p><p>In this study, nine wood-rotting basidiomycete species were screened for cellulase and xylanase production in submerged fermentation of crystalline cellulose. <i>Phanerochaete chrysosporium</i> ATCC 24725 was the best producer of CMCase and xylanase, with enzymatic activity of 71.7 U/mL and 75.9 U/mL, respectively. The total cellulase, endoglucanase, and xylanase activities of <i>P. chrysosporium</i> ATCC24725 in the presence of lignocellulosic substrates were 3-7 times lower than the activity of these enzymes in the medium with crystalline cellulose. However, the endoglucanase activity of <i>Trametes ochracea</i> BCC76 in the medium containing tangerine pomace was the same as in the medium containing Avicel, whereas the xylanase activity was 3 times higher. Cellulase and xylanase synthesis in <i>P. chrysosporium</i> ATCC24725 occurs through induction mechanisms. Cellulose and cellulose-containing materials are the most suitable substrates for cellulase and xylanase production in <i>P. chrysosporium</i> ATCC24725, whereas CMC and xylan proved to be poor substrates for stimulating the secretion of these enzymes. In <i>P. chrysosporium</i> ATCC24725, cellulase and xylanase synthesis do not occur in the presence of easily metabolizable carbon sources due to catabolite repression, even if cellulose is present in the nutrient medium. Induction of enzyme synthesis resumes only after the easily metabolizable carbon source is depleted. The enzyme preparation isolated after culturing the fungus in a fermenter was partially purified and characterized. A crude cellulase preparation from <i>P. chrysosporium</i> ATCC24725 showed similar efficiency as Accellerase 1500 in the hydrolysis of alkali-pretreated wheat straw. The obtained results highlight the potential of <i>P. chrysosporium</i> ATCC 24725 as a reliable fungal cellulase producer for biorefinery applications.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Artificial Intelligence for Therapeutic Peptide Discovery and Development.","authors":"Salvador Ventura","doi":"10.3390/biom16101445","DOIUrl":"https://doi.org/10.3390/biom16101445","url":null,"abstract":"<p><p>Therapeutic peptides combine biological specificity with chemical versatility, and artificial intelligence (AI) now contributes to their identification, design, and optimisation. Peptide discovery, however, cannot be reduced to generating amino-acid sequences: therapeutic performance also depends on chemistry, conformation, assay context, stability, delivery, safety, manufacturability, and in vivo exposure. This critical review examines AI use across the major peptide classes: receptor agonists, protein-protein interaction inhibitors, oncology and tumour-targeting peptides, antimicrobial and phenotype-driven peptides, delivery peptides, vaccine epitopes, self-assembling materials, and chemically constrained macrocycles. It compares sequence-based, chemical, graph, structure-aware, and multimodal representations across predictive, generative, and experimentally integrated workflows. Coverage spans recent general protein foundation, prediction, and design systems (ProtGPT2, ESM-2/ESM3, ProGen/ProGen2, ProteinMPNN, RFdiffusion, and AlphaFold 3) and peptide-focused methods (RFpeptides, PepFlow, and PepGLAD). Particular attention is given to benchmark integrity, the limits of structure prediction for short and non-canonical molecules, and the gap between retrospective and prospective evidence. To make claims comparable, the review adapts established reporting, validation, and readiness concepts into a peptide-specific, two-dimensional Peptide-AI Evidence Grid that separates methodological rigour (M0-M3) from translational depth (T0-T3), applies it to representative studies, and provides a checklist extending DOME, TRIPOD + AI, and FAIR guidance with the chemistry- and assay-specific items peptide work requires.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Long-Acting Farnesoid X Receptor (FXR) Agonist Prevents Fibrosis.","authors":"Ashrafi Sultana, Grace Bybee, Anup S Pathania, Weimin Wang, Nam Thai Hoang Le, Brandon W Hanson, Christopher D Bauer, Deanna D Mosley, Howard E Gendelman, Samuel M Cohen, Todd A Wyatt, Larisa Y Poluektova, Benson J Edagwa, Natalia A Osna","doi":"10.3390/biom16101443","DOIUrl":"https://doi.org/10.3390/biom16101443","url":null,"abstract":"<p><p>Despite effective vaccines and antiviral therapies, patients with chronic hepatitis B (CHB) remain at risk of developing progressive liver fibrosis and cirrhosis. Vonafexor (VON), a second-generation synthetic non-steroidal, non-bile acid farnesoid X receptor agonist, has been shown to prevent liver fibrosis and target the HBV cccDNA reservoir. However, adherence to daily oral therapy is an established barrier to successful treatment of chronic infections. To overcome this barrier, VON was transformed into a long-acting (LA) prodrug nanosuspension. The LA prodrug formulation suppressed αSMA, TGFβ, and Col1A1 gene expression in the LX2 hepatic stellate cell line. The formulation was well tolerated and prevented liver and lung damage in a carbon tetrachloride-induced chronic liver injury model. The promising preclinical data support further development of LA VON prodrugs as potential treatments for liver and lung fibrosis.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hyaluronan Synthase Isoforms Direct Distinct Patterns of Fibroblast Activation Linked to Fibrosis Progression Versus Resolution Following Renal Ischaemia.","authors":"Irina V Grigorieva, Adam C Midgley, Charlotte V M Brown, Gilda Pino Chavez, Barbara Szomolay, Aled Williams, Rachel DePaul, Richard J Stanton, John M Hancock, Timothy Bowen, Deva Chan, Anna Plaas, Rafael Chavez, Robert Steadman, Usman Khalid, Soma Meran","doi":"10.3390/biom16101442","DOIUrl":"https://doi.org/10.3390/biom16101442","url":null,"abstract":"<p><p>The stroma plays key roles in development and tissue regeneration after injury, but its expansion following injury can drive fibrosis and chronic disease. In the kidney, hyaluronan (HA) is largely absent from the healthy stroma but becomes abundant during disease. To investigate HA regulation in stromal responses, we compared HA and hyaluronan synthase (HAS) expression during kidney development, homeostasis, injury, and recovery. A rat model of ischaemia-reperfusion injury (IRI) with or without ischaemic pre-conditioning (IPC) was studied alongside embryonic and <i>Has1/3</i>^-/- mouse kidneys, with mechanistic studies performed in primary human fibroblasts. In healthy kidneys, stromal HA was absent, HAS1 showed limited epithelial expression, and HAS2 was undetectable. Following IRI, stromal HA accumulation and increased HAS2 expression were associated with chronic fibrosis. In contrast, during development, prominent stromal HA matrices were evident in areas of tubular generation, with strong HAS1 (not HAS2) expression. During recovery, stromal HA and HAS2 were attenuated, whereas HAS1+ stromal cells expanded but were distinct from α-SMA+ myofibroblasts. Functionally, HAS1+ fibroblasts displayed enhanced migration, fibroblast activation protein (FAP) expression and reduced profibrotic marker expression, whereas HAS2+ fibroblasts exhibited a contractile myofibroblast phenotype with high extra domain A fibronectin (EDA-FN) and type I collagen, alpha-1 subunit (COL1A1). Together, these findings identify HA as a regulator of stromal fibroblast phenotype and associate HAS1 and HAS2 in divergent fibrotic outcomes following kidney injury.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic Metabolomic Landscape of the Murine Brain Across Acute to Chronic Stages of <i>Borrelia garinii</i> Infection.","authors":"Bintao Zhai, Qingli Niu, Hui Yang, Kai-Fei Guo, Yang Liu, Bibo Bao, Yaxin Zhou, Bing Li, Hong Yin, Jiyu Zhang","doi":"10.3390/biom16101441","DOIUrl":"https://doi.org/10.3390/biom16101441","url":null,"abstract":"<p><p>Lyme neuroborreliosis (LNB), caused by <i>Borrelia garinii</i>, often leads to persistent neurological deficits, yet early diagnosis remains insensitive and the temporal metabolic changes in the infected brain are largely unexplored. In this study, a murine model of <i>B. garinii</i> infection was established using 80 female BALB/c mice, and brain tissues were collected at acute 7 (days post-infection, DPI), mid- (15 and 21 DPI), and chronic (30 DPI) stages for untargeted gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS) metabolomics. Thirty-one differential metabolites were identified, with downregulated metabolites predominating acutely and upregulated metabolites prevailing chronically. Twelve common metabolites, including creatine, lysine, and galactose derivatives, were consistently altered. KEGG analysis revealed disrupted amino acid metabolism, particularly valine, leucine, and isoleucine biosynthesis (ko00290), arginine and proline metabolism (ko00330), and aminoacyl-tRNA biosynthesis (ko00970). ROC analysis identified five candidate biomarkers, hydroxylamine, 2,3-dihydroxypyridine, galactose 1, galactose 2, and monostearin, with high diagnostic accuracy. This study provides a comprehensive temporal metabolomic landscape of the brain during <i>B. garinii</i> infection, revealing time-dependent metabolic reprogramming with sustained disruptions in amino acid and energy metabolism, and offering candidate biomarkers for improved diagnosis of central nervous system involvement in Lyme disease.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Periodontal Regeneration Using a Mineralizing Hydrogel Loaded with a Synthetic CEMP1-Derived Peptide.","authors":"Yu Wang, Guangzhao Guan, Li Mei, Huiwen Zheng, Xianghui Xing, Weibin Sun","doi":"10.3390/biom16101444","DOIUrl":"https://doi.org/10.3390/biom16101444","url":null,"abstract":"<p><p><b>Background</b>: Periodontal regeneration requires the coordinated reconstruction of mineralized and non-mineralized tissues. P35 polypeptide derived from Cementum protein-1(CEMP1) has been demonstrated to induce bio-mineralization in vitro, although in vivo applications still need to be further validated. In this study, we developed a novel mineralizing hydrogel system (P35/ACP@PEG Hy) to facilitate periodontal regeneration by encapsulating P35-loaded amorphous calcium phosphate nanoparticles (P35/ACP-NPs) within a four-arm polyethylene glycol (PEG) hydrogel. <b>Methods</b>: In vitro assays were performed to characterize the physicochemical properties, sustained-release behavior, osteogenic/cementogenic effects of P35/ACP-NPs on hPDLCs, together with the mechanical performance and biocompatibility of the PEG hydrogel. The regenerative capacity of the hydrogel was further assessed in a rat periodontal defect model using micro-CT and histological staining. The regenerative efficacy was evaluated in a rat periodontal defect model via micro-CT and histological staining, while transcriptome sequencing (RNA-seq) and immune-blotting were further performed to confirm the molecular mechanisms. <b>Results</b>: P35/ACP@PEG exhibited favorable physicochemical properties, featuring an initial burst release followed by a sustained gradual release profile, along with the excellent biocompatibility. In vitro, P35/ACP-NPs markedly promoted osteogenic and cementogenic differentiation of hPDLCs. Correspondingly, the P35/ACP@PEG hydrogel significantly accelerated periodontal tissue regeneration in the rat model with periodontal defect. And RNA-seq analysis and immune-blotting further revealed that these effects are highly linked to activation of the TGF-β/Smad2/3/LOX signaling pathway. <b>Conclusions</b>: P35/ACP@PEG Hy platform can promote periodontal regeneration via activation of TGF-β/Smad2/3/LOX signaling pathway in vivo. Its sustained bioactivity, favorable biocompatibility and robust regenerative efficacy highlight a potential of P35 polypeptide for periodontal tissue repair.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stromal Vascular Cell-Mediated Inflammatory and Remodeling Pathways in Alcohol-Induced Visceral Adipose Tissue Dysfunction: A Pilot Study.","authors":"Weilun Ai, Arul Daniel John Kathiravan, Carol A Casey, Sundararajan Mahalingam, Karuna Rasineni, Viswanathan Saraswathi","doi":"10.3390/biom16101440","DOIUrl":"https://doi.org/10.3390/biom16101440","url":null,"abstract":"<p><p>Chronic alcohol use induces adipocyte lipolysis and production of inflammatory mediators from adipose tissue (AT). Stromal vascular cells (SVCs) are a heterogeneous group of AT cells and contribute to AT inflammation and remodeling in metabolic syndrome. However, the role of SVCs in promoting AT dysfunction upon alcohol exposure remains unclear. Male rats were fed a Lieber-DeCarli diet containing 6.7% (<i>v</i>/<i>v</i>) ethanol (ET) or an isocaloric control diet (CON) for six weeks. Primary rat SVCs were isolated from visceral AT (VAT) of CON and ET rats. RNA sequencing analysis was performed to determine the overall changes in the gene-expression profile. Real-time PCR, Western blotting, and histological analyses were performed to validate the transcriptomics results. Chronic alcohol feeding decreased the adipocyte size and increased the formation of crown-like structures in the rat VAT. RNA-seq analysis revealed that signaling pathways related to cellular response to interleukin 1 (IL1) and collagen-containing extracellular matrix were significantly altered upon ethanol exposure in SVCs. Along these lines, ethanol exposure increased the protein levels of purinergic receptor P2Y2 (P2RY2) and IL1β in the SVCs of rat VAT. Furthermore, ethanol increased collagen deposition in both interstitial and perivascular regions, which was associated with an increase in the level of phosphorylated SMAD2/3 and collagen type VIII alpha 1 chain expression. These findings suggest that chronic ethanol exposure is associated with inflammatory and remodeling-related alterations in VAT and the total VAT-derived SVC fraction. This exploratory pilot study identifies P2RY2-associated inflammatory markers and TGFβ-related remodeling markers as candidates for future mechanistic investigation.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparation, Structural Elucidation, and In Silico Prebiotic Evaluation of Pectin Oligosaccharides from Apple Pectin.","authors":"Guoxiang Chi, Shuyu Zu, Yousi Fu, Huipeng Liu","doi":"10.3390/biom16101436","DOIUrl":"https://doi.org/10.3390/biom16101436","url":null,"abstract":"<p><p>Pectin oligosaccharides (POS) recovered from agro-industrial by-products are attracting attention as candidate prebiotics, yet obtaining structurally defined neutral POS and screening their activity remains challenging. This study prepared neutral POS from commercial apple pectin by controlled acid hydrolysis (0.05 M TFA, 80 °C, 1 h), ethanol precipitation, ultrafiltration (<3 kDa), and DEAE-Sepharose CL-6B chromatography, yielding a neutral P-1 fraction (3.6% <i>w</i>/<i>w</i>). The fraction was characterized by PMP-HPLC, HPSEC-RID, and UPLC-HILIC-MS/MS, revealing a bulk composition dominated by galactose, glucose, and arabinose, with five selected neutral oligosaccharides (DP 2-5). The prebiotic potential of these five selected, tentatively assigned oligosaccharides was evaluated in silico by simulation against 13 microbial glycosidases and by simulating colonic fermentation with CompuGUT using kinetic parameters derived from binding energies. The docking matrix showed favorable and enzyme-selective binding (-10.3 to -4.6 kcal/mol), with the strongest complexes involving component D-A7LXS9 (-8.9 kcal/mol) and component E-Q93GI5 (-10.3 kcal/mol). CompuGUT predicted complete hydrolysis of all five components within 48 h and increased mucosal biomass, indicating that these five selected compounds are predicted to be fermentable and to support microbial growth at the mucosal surface. These findings provide an integrated strategy for the preparation, structural characterization, and rapid functional screening of neutral POS, facilitating the identification of structurally defined pectin-derived prebiotic candidates.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"16 10","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}