Springer最新文献

{"title":"Machine learning-based activity prediction of phenoxy-imine catalysts and its structure-activity relationship study.","authors":"Xiaoke Zhou, Sisi He, Min Xiao, Jing He, Yuan Wang, Yuanqin Zhu, Haixiang He","doi":"10.1007/s11030-025-11147-0","DOIUrl":"10.1007/s11030-025-11147-0","url":null,"abstract":"<p><p>This study systematically investigates the structure-activity relationships of 30 Ti-phenoxy-imine (FI-Ti) catalysts using machine learning (ML) approaches. Among the tested algorithms, XGBoost demonstrated superior predictive performance, achieving R² values of 0.998 (training set) and 0.859 (test set), with a cross-validated Q² of 0.617. Feature importance analysis identified three composite descriptors-ODI_HOMO_1_Neg_Average GGI2, ALIEmax GATS8d, and Mol_Size_L-as critical contributors, collectively accounting for > 63% of the model's predictive power. Polynomial feature expansion effectively captured nonlinear interactions between descriptors, while SHAP and ICE analyses enhanced interpretability, revealing threshold effects and descriptor-specific trends. However, the model's generalizability may be constrained by the limited dataset size (30 samples) and reliance on density functional theory (DFT)-derived descriptors, necessitating experimental validation. Additionally, the study focused solely on ethylene polymerization at 40 °C; broader applicability to diverse catalytic systems or reaction conditions requires further validation. These findings provide a data-driven framework for catalyst design, though future work should integrate experimental validation and expand datasets to refine predictive robustness.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":"3411-3422"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancing antimalarial drug discovery: ensemble machine learning models for predicting PfPK6 inhibitor activity.","authors":"Maryam Gholami, Mohammad Asadollahi-Baboli","doi":"10.1007/s11030-025-11203-9","DOIUrl":"10.1007/s11030-025-11203-9","url":null,"abstract":"<p><p>Malaria is a significant global health challenge, causing high morbidity and mortality. The rise of drug resistance highlights the urgent need for new antimalarial agents. This study focuses on predictive modeling of 104 Plasmodium falciparum protein kinase 6 (PfPK6) inhibitors, employing a range of machine learning techniques to develop ensemble regression and classification models. Molecular descriptors were refined using classification and regression trees (CART) to identify the most relevant features. Six machine learning algorithms (Random Forest (RF), Relevance Vector Machine (RVM), Support Vector Machine (SVM), Cubist, Artificial Neural Networks (ANN), and XGBoost) were utilized to construct regression models. The consensus model demonstrated superior predictive performance, achieving R²_Test = 0.94, SE_Test = 0.20, Q²_CV = 0.90, and SE_CV = 0.25, outperforming individual models. For classification tasks, five algorithms were evaluated and a majority voting approach yielded an accuracy of 91% and a sensitivity of 93%. The robustness of the models was confirmed through applicability domain analysis (96% coverage) and y-randomization tests, ensuring that the predictive outcomes were not due to chance correlations. This study highlights the effectiveness of ensemble machine learning approaches in predictive modeling and provides critical insights for the rational design of novel PfPK6 inhibitors.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":"3575-3586"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting Poly (ADP-ribose) polymerase-1 (PARP-1) for DNA repair mechanism through QSAR-based virtual screening and MD simulation.","authors":"Kun Cao, Ruonan Wang, Siyu Wu, Dong Ou, Ruixue Li, Lianhai Li, Xinguang Liu","doi":"10.1007/s11030-025-11184-9","DOIUrl":"10.1007/s11030-025-11184-9","url":null,"abstract":"<p><p>Poly (ADP-ribose) polymerase-1 (PARP-1) is a key enzyme in the base excision repair pathway, crucial for maintaining genomic stability by repairing DNA breaks. In cancers with mutations in DNA repair genes, such as BRCA1 and BRCA2, PARP-1 activity becomes essential for tumor cell survival, making it a promising target for therapeutic intervention. This study employs QSAR modeling, virtual screening, and molecular dynamics (MD) simulations to identify potential PARP-1 inhibitors. A dataset of inhibitors was analyzed using 12 molecular fingerprint descriptors to develop robust QSAR models, with the optimal model based on the CDK descriptor achieving R² = 0.96, Q²_CV = 0.78, and Q²_Ext = 0.80. The model was applied to virtually screen three chemical libraries-ZINC, FDA, and NPA-identifying promising candidates for PARP-1 inhibition. Molecular docking revealed that compounds ZINC13132446, Z2037280227, and NPC193377 have strong binding affinity for the PARP-1 active site. MD simulations and MM-PBSA confirmed the stability of these complexes, with Z2037280227 and NPC193377 exhibiting the most stable interactions. These results underscore the potential of targeting PARP-1 as a therapeutic strategy for cancers with homologous recombination deficiencies, including prostate, breast, and ovarian cancer, particularly in patients with DNA repair deficiencies.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":"3517-3535"},"PeriodicalIF":3.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The emerging institutionalisation of knowledge co-production in sustainability research.","authors":"Janina Käyhkö, Mikael Hildén, Ia Hyttinen, Kaisa Korhonen-Kurki","doi":"10.1007/s13280-025-02161-5","DOIUrl":"10.1007/s13280-025-02161-5","url":null,"abstract":"<p><p>Co-production of knowledge in science-policy interfaces has received increased attention as a way of addressing grand societal challenges with the hope that it will create a base for enacting transformative change. We explore the development and outputs of projects funded by the Strategic Research Council of Finland, which has had the aim of generating strategic knowledge through interactions with stakeholders. We examine how producers and users of knowledge understand co-production as revealed by a researcher survey and stakeholder interviews in relation to different domains in the institutionalisation process. Our results show advanced, emerging and explorative levels of institutionalisation of knowledge co-production practices and highlight the differences between needs-based and transformative approaches to co-production. We conclude that to succeed, efforts to institutionalise knowledge co-production should recognise several societal domains from governance to resources and culture. Advanced institutionalisation for the co-production of transformative knowledge can significantly strengthen the potential of sustainability research.</p>","PeriodicalId":461,"journal":{"name":"Ambio","volume":" ","pages":"1372-1385"},"PeriodicalIF":5.8,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12214086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small but Mighty: Genetic Diversity of the Thai Ridgeback Dog Population.","authors":"Chadaphon Thatukan, Chananya Patta, Worapong Singchat, Wattanawan Jaito, Nichakorn Kumnan, Piangjai Chalermwong, Thitipong Panthum, Wongsathit Wongloet, Pish Wattanadilokchatkun, Thanyapat Thong, Syed Farhan Ahmad, Narongrit Muangmai, Kyudong Han, Akihiko Koga, Prateep Duengkae, Ratthanin Patcharakulvorawat, Kornsorn Srikulnath","doi":"10.1007/s10528-024-10858-7","DOIUrl":"10.1007/s10528-024-10858-7","url":null,"abstract":"<p><p>Originating in Thailand, the Thai Ridgeback dog is known for its unique fur ridge that grows in the opposite direction along its back. Selective breeding and a limited populations in Thailand have led to significant close inbreeding among related individuals. The current Thai Ridgeback population is assumed to have experienced a loss of genetic diversity and bottleneck events. Furthermore, studies on the genetic diversity and structure of Thai Ridgeback dogs are limited. Therefore, the aim of this study was to assess the genetic diversity in Thai Ridgeback dogs. Microsatellite genotyping and mitochondrial DNA D-loop sequences were used to assess genetic diversity in 105 Thai Ridgeback dogs from various farms throughout Thailand. Significant genetic diversity and minimal inbreeding were observed in the current Thai Ridgeback population. Signs of bottlenecks were not observed because the exchange of genetic material among Thai Ridgeback owners effectively preserved the genetic diversity. Moreover, the genetic parameters in this study supported owner-to-owner exchanges animals for mating programs. To sustain the genetic diversity of Thai Ridgeback dogs, the use of genetic parameters to manage genetic closeness while preserving breed characteristics is essential. These data are crucial for ensuring demographic stability, which is pivotal for long-term conservation and effective population management.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"2967-2986"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Characterization of LBD Gene Family in Pseudoroegneria libanotica Reveals Functions of PseLBD1 and PseLBD12 in Response to Abiotic Stress.","authors":"Xunzhe Yang, Xiang Li, Xia Wang, Chen Chen, Dandan Wu, Yiran Cheng, Yi Wang, Lina Sha, Houyang Kang, Songqing Liu, Xing Fan, Yinglong Chen, Yonghong Zhou, Haiqin Zhang","doi":"10.1007/s10528-024-10859-6","DOIUrl":"10.1007/s10528-024-10859-6","url":null,"abstract":"<p><p>The lateral organ boundaries domain (LBD) plays a vital role as a transcriptional coactivator within plants, serving as an indispensable function in growth, development, and stress response. In a previous study, we found that the LBD genes of Pseudoroegneria libanotica (a maternal donor for three-quarter of perennial Triticeae species with good stress resistance, holds great significance in exploring its response mechanisms to abiotic stress for the Triticeae tribe) might be involved in responding to drought stress. Therefore, we further identified the LBD gene family in this study. A total of 29 PseLBDs were identified. Among them, 24 were categorized into subclass I, while 5 fell into subclass II. The identification of cis-acting elements reveals the extensive involvement of PseLBDs in various biological processes in P. libanotica. Collinearity analysis indicates that 86% of PseLBDs were single-copy genes and have undergone a single whole-genome duplication event. Transcriptomic differential expression analysis of PseLBDs under drought stress reveals that the most likely candidates for responding to abiotic stress were PseLBD1 and PseLBD12. They have been demonstrated to respond to drought, salt, heavy metal, and heat stress in yeast. Furthermore, it is plausible that functional divergence might have occurred among their orthologous genes in wheat. This study not only establishes a foundation for a deeper understanding of the biological roles of PseLBDs in P. libanotica but also unveils novel potential genes for enhancing the genetic background of crops within Triticeae crops, such as wheat.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"2857-2878"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolome and Genome Analysis of a Novel Endophytic Fungus Aureobasidium pullulans KB3: Discovery of Polyketones and Polyketone Biosynthesis Pathway.","authors":"Shuai Wang, Jia-Nuo He, Ying-Jie Wang, Wen-Ya Zhao, Qing-Xia Yang, Ya-Na Wang, Yang Zhang, Li-Ping Zhang, Hong-Wei Liu","doi":"10.1007/s10528-024-10866-7","DOIUrl":"10.1007/s10528-024-10866-7","url":null,"abstract":"<p><p>Endophytic fungi associated with plants may contain undiscovered bioactive compounds. Under standard laboratory conditions, most undiscovered compounds are inactive, whereas their production could be stimulated under different cultivation conditions. In this study, six endophytic fungi were isolated from the bark of Koelreuteria paniculata in Quancheng Park, Jinan City, Shandong Province, one of which was identified as a new subspecies of Aureobasidium pullulans, named A. pullulans KB3. Additionally, metabolomic tools were used to screen suitable media for A. pullulans KB3 fermentation, and the results showed that peptone dextrose medium (PDM) was more beneficial to culture A. pullulans KB3 for isolation of novel compounds. Sphaerolone, a polyketone compound, was initially isolated from A. pullulans KB3 via scaled up fermentation utilizing PDM. Additionally, the whole-genome DNA of A. pullulans KB3 was sequenced to facilitate compound isolation and identify the biosynthesis gene clusters (BGCs). This study reports the multi-omics (metabolome and genome) analysis of A. pullulans KB3, laying the foundation for discovering novel compounds of silent BGCs and identifying their biosynthesis pathway.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3047-3064"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141320375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNA-204-5p Attenuates Oxidative Stress, Apoptosis and Inflammation by Targeting TXNIP in Diabetic Cataract.","authors":"Xiang Cao, Zhixin Jiang, Xiaofei Bu, Qingyu Li, Ye Tian, Zijiao Xu, Boyang Zhang, Xiaoyong Yuan","doi":"10.1007/s10528-024-10863-w","DOIUrl":"10.1007/s10528-024-10863-w","url":null,"abstract":"<p><p>Diabetic cataract (DC) is a major cause of blindness in diabetic patients and it is characterized by early onset and rapid progression. MiR-204-5p was previously identified as one of the top five down-regulated miRNAs in human DC lens tissues. We aimed to determine the expression of miR-204-5p in human lens epithelial cells (HLECs) and explore its effects and mechanisms in regulating the progression of DC. The expression of miR-204-5p in the anterior capsules of DC patients and HLECs was examined by RT-qPCR. Bioinformatics tools were then used to identify the potential target of miR-204-5p. The relationship between miR-204-5p and the target gene was confirmed through a dual luciferase reporter assay. Additionally, the regulatory mechanism of oxidative stress, apoptosis, and inflammation in DC was investigated by overexpressing miR-204-5p using miR-204-5p agomir. The expression of miR-204-5p was downregulated in the anterior capsules of DC patients and HLECs. Overexpression of miR-204-5p reduced ROS levels, pro-apoptosis genes (Bid, Bax, caspase-3), and IL-1β production in HG-treated HLECs. TXNIP was the direct target of miR-204-5p by dual luciferase reporter assay. Therefore, this study demonstrated that miR-204-5p effectively reduced oxidative damage, apoptosis, and inflammation in HLECs under HG conditions by targeting TXNIP. Targeting miR-204-5p could be a promising therapeutic strategy for the potential treatment of DC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3139-3156"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides.","authors":"Yangying Gan, Jingyao Ping, Xiaojing Liu, Caixia Peng","doi":"10.1007/s10528-024-10874-7","DOIUrl":"10.1007/s10528-024-10874-7","url":null,"abstract":"<p><p>Annonaceae is the largest family in Magnoliales, exhibiting the greatest diversity among and within genera. In this study, we conducted an analysis of repetitive sequences and codon usage bias in the previously acquired plastome of Miliusa glochidioides. Using a concatenated dataset of shared genes, we constructed the phylogenetic relationships among 27 Annonaceae species. The results showed that the size of the plastomes in the Annonaceae ranged from 159 to 202 kb, with the size of the inverted repeat region ranging from 40 to 65 kb. Within the plastome of M. glochidioides, we identified 42 SSRs, 36 tandem repeats, and 9 dispersed repeats. These SSRs consist of three nucleotide types and eight motif types, with a preference for A/T bases, primarily located in the large single-copy regions and intergenic spacers. Tandem and dispersed repeat sequences were predominantly detected in the IR region. Through codon usage bias analysis, we identified 30 high-frequency codons and 11 optimal codons. The plastome of M. glochidioides demonstrated relatively weak codon usage bias, favoring codons with A/T endings, primarily influenced by natural selection. Phylogenetic analysis revealed that all four subfamilies formed monophyletic groups, with Cananga odorata (Ambavioideae) and Anaxagorea javanica (Anaxagoreoideae) successively nested outside Annonoideae + Malmeoideae. These findings improve our understanding of the plastome of M. glochidioides and provide additional insights for studying plastome evolution in Annonaceae.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3329-3346"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exosomal miR-17-92 Cluster from BMSCs Alleviates Apoptosis and Inflammation in Spinal Cord Injury.","authors":"Wei Wang, Fei Yao, Haiyuan Xing, Fan Yang, Li Yan","doi":"10.1007/s10528-024-10876-5","DOIUrl":"10.1007/s10528-024-10876-5","url":null,"abstract":"<p><p>Spinal cord injury (SCI) involves neuronal apoptosis and axonal disruption, leading to severe motor dysfunction. Studies indicate that exosomes transport microRNAs (miRNAs) and play a crucial role in intercellular communication. This study aimed to explore whether the bone marrow mesenchymal stem cell (BMSCs)-exosomal miR-17-92 cluster can protect against SCI and to explain the underlying mechanisms. In vivo and in vitro SCI models were established and treated with control exosomes (con-exo) or exosomes derived from BMSCs transfected with miR-17-92 cluster plasmid (miR-17-92-exo). Rat BMSCs were isolated and positive markers were identified by flow cytometry. BMSC-derived exosomes were extracted and verified using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and western blotting. The expression of the miR-17-92 cluster was validated by quantitative reverse transcription PCR (qRT-PCR). Spinal cord function, histopathological changes, apoptotic cells, and inflammatory cytokines release in spinal cord tissues were assessed using the Basso-Beattie-Bresnahan (BBB) score, hematoxylin and eosin (HE) staining, terminal deoxynucleotide transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) staining, enzyme-linked immunosorbent assay (ELISA), and qRT-PCR. In PC12 cells, cell proliferation, apoptosis, apoptosis-related proteins cleaved-Caspase3 expression, and inflammatory factors secretion were analyzed using a cell counting kit-8 (CCK8) assay, flow cytometry, western blotting, and ELISA. Our data revealed that the exosomes were successfully isolated from rat BMSCs. The BMSC-exosomal miR-17-92 cluster improved neural functional recovery after SCI, as evidenced by an increased BBB score, improved pathological damage, reduced neuronal apoptosis, and decreased inflammatory factors release. Additionally, miR-17-92-exo treatment significantly inhibited lipopolysaccharide (LPS)-induced reduction in cell viability, increase in cell apoptosis, and upregulation of inflammatory factors in PC12 cells. The exosomal miR-17-92 cluster derived from BMSCs improved functional recovery and exhibited neuroprotective effects in SCI by alleviating apoptosis and inflammation.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"3363-3377"},"PeriodicalIF":2.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}