ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202400884
Jiatong Guo, Weiping Li, Cheri X Deng, Zhongwu Guo
{"title":"Mechanoglycobiology: The Roles of Cell Surface Glycans in Mechanosensing and Mechanotransduction.","authors":"Jiatong Guo, Weiping Li, Cheri X Deng, Zhongwu Guo","doi":"10.1002/cbic.202400884","DOIUrl":"https://doi.org/10.1002/cbic.202400884","url":null,"abstract":"<p><p>Mechanoglycobiology has emerged as a rapidly expanding interdisciplinary field that involves chemistry, biology, and engineering. Despite the great advancements in this field, in-depth investigation of mechanoglycobiology remains challenging due to the complex nature of glycans and cell glycocalyx, as well as the difficulty to mechanically target these biomolecules. To address the issues, novel methods and models have been established to facilitate the investigation of glycan-mediated mechanosensing and mechanotransduction. Recently, a new, metabolic glycoengineering-based approach has been developed to selectively label cell surface glycans. This enables the application of molecularly specific acoustic tweezing cytometry to exert targeted mechanical forces to understand how mechanical actuation of glycans influences cellular activities. This approach is applicable to different glycans and cell types and, therefore, can have a broad impact. The current perspective highlights how recent developments in mechanoglycobiology may improve the knowledge and appreciation of the significance of glycans in mechanotransduction as well as the potential applications of mechanoglycobiology in medicine.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2400884"},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032456","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":"AtGH3.10 and JAR1 Produce 12-Hydroxyjasmonoyl-l-isoleucine from 12-Hydroxyjasmonic Acid in Arabidopsis thaliana","authors":"Katsunari Oki, Akane Enoki, Yoshitaka Yokota, Taiki Kurihara, Takafumi Shimizu, Wataru Saburi, Takayuki Tohge, Haruhide Mori, Guido Van den Ackerveken, Naoki Kitaoka, Hideyuki Matsuura","doi":"10.1002/cbic.202500151","DOIUrl":"10.1002/cbic.202500151","url":null,"abstract":"<p>Jasmonates are plant hormones that regulate plant defense and development. 7-<i>iso</i>-Jasmonoyl-<span>l</span>-isoleucine (JA-Ile) is a representative active jasmonate which is biosynthesized from 7-<i>iso</i>-jasmonic acid (JA) by the jasmonoyl-amido synthases JASMONATE RESISTANT 1 (JAR1) and AtGH3.10 in <i>Arabidopsis thaliana</i>. 12-Hydroxy-7-<i>iso</i>-jasmonoyl-<span>l</span>-isoleucine (12-OH-JA-Ile) is another active jasmonate, and 12-hydroxylation of JA-Ile is considered the major biosynthetic pathway toward 12-OH-JA-Ile. Previous report elucidated that recombinant JAR1 showed a weak activity against 12-hydroxy-7-<i>iso</i>-jasmonic acid (12-OH-JA). However, the direct conversion from 12-OH-JA to 12-OH-JA-Ile in planta and the enzyme activity of AtG3.10 against 12-OH-JA have never been reported. Herein, a feeding experiment with deuterated 12-OH-JA confirms the direct conversion of 12-OH-JA to 12-OH-JA-Ile in wild-type <i>Arabidopsis</i> plants. The conversion from 12-OH-JA to 12-OH-JA-Ile is not observed in <i>jar1</i> <i>gh3.10</i> double mutant, suggesting that 12-OH-JA is converted to 12-OH-JA-Ile by JAR1 and AtGH3.10. Notably, enzyme assays show that the catalytic efficiency with 12-OH-JA for AtGH3.10 is higher than those with JA for AtGH3.10 and with 12-OH-JA for JAR1. Comparative analysis of JAR1 and AtGH3.10 structures and site-directed mutation analysis reveals that Ser120 in AtGH3.10 is the key amino acid residue responsible for its high catalytic efficiency against 12-OH-JA.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032483","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}
ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202500405
Antos B. Sachanka, Yaraslau U. Dzichenka, Veronika V. Shchur, Aliaksei V. Yantsevich
{"title":"Design and Characterization of the Fusion Enzyme of Bovine Terminal Deoxynucleotidyl Transferase and DNA Binding Protein Sso7d from Sulfolobus solfataricus","authors":"Antos B. Sachanka, Yaraslau U. Dzichenka, Veronika V. Shchur, Aliaksei V. Yantsevich","doi":"10.1002/cbic.202500405","DOIUrl":"10.1002/cbic.202500405","url":null,"abstract":"<p>The terminal deoxynucleotidyl transferase is a unique polymerase that incorporates nucleotides at the 3′-terminus of single-stranded DNA primers in a template-independent manner. This biological function propels the development of numerous biomedical and bioengineering applications. However, the extensive use of TdT is constrained by its low expression levels in <i>E. coli</i> and low optimal operating temperature. To address these limitations, a fusion enzyme combining TdT and the DNA-binding protein Sso7d from <i>Sulfolobus solfataricus</i> is designed and isolated. This fusion protein exhibits a threefold increase in DNA-binding affinity to double-stranded DNA and demonstrates improved thermostability, denaturing at temperatures up to 48 °C, along with an enhancement in the expression yield of the target protein. The fusion of Sso7d to the C-terminus of TdT enhances catalytic activity for nucleotide removal from the coding end, while completely abolishing nucleotide addition activity. Conversely, the presence of Sso7d at the N-terminus of TdT decreases nucleotide incorporation and enhances nucleotide removal activity, with this effect significantly influenced by substrate length and the presence of metal ions in the reaction mixture. Overall, the obtained fusion enzymes could serve as promising candidates for novel specific applications, such as gene editing, mutagenesis studies, and aptamer engineering.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032518","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}
ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202500618
Luca Nespoli, Silvia Donzella, Martina Bigliardi, Martina Letizia Contente, Ricardo Pinheiro de Souza Oliveira, Diego Romano, Francesco Molinari
{"title":"Cooperative Enhancement of Aldoxime Dehydratase Stability through Whole-Cell Immobilization and Flow Reactor Integration","authors":"Luca Nespoli, Silvia Donzella, Martina Bigliardi, Martina Letizia Contente, Ricardo Pinheiro de Souza Oliveira, Diego Romano, Francesco Molinari","doi":"10.1002/cbic.202500618","DOIUrl":"10.1002/cbic.202500618","url":null,"abstract":"<p>This study investigates the synthesis of aromatic nitriles using an evolved variant of OxdF1 (L318F/F306Y), an aldoxime dehydratase from <i>Pseudomonas putida</i> F1, engineered for improved catalytic efficiency toward benzaldehyde oxime. The double OxdF1 (L318F/F306Y) mutant effectively catalyzes the conversion of various benzaldoxime derivatives to the corresponding nitriles. Due to the enzyme's inherent instability, immobilized whole-cell systems are employed in a flow reactor to improve its stability and broaden its applicability, with the biotransformation of benzaldehyde oxime and 2,6-difluorobenzaldehyde oxime serving as case studies. The enzyme's stability is markedly improved, maintaining 87% yield even after 8 h of processing in the preparation of benzonitrile. Preparation of 2,6-difluorobenzontirile poses additional challenges due to the low water solubility of both the substrate, and even more so, the product, an important intermediate in various chemical applications. To overcome solubility limitations, a segmented liquid–liquid flow system (water/cyclohexane) was implemented, significantly improving the enzyme stability. The process was run continuously for 12 h, with a conversion of ≈70% by the end of the operation. Furthermore, 2,6-difluorobenzonitrile is selectively extracted in-line using a liquid–liquid extractor, thus, facilitating its efficient recovery and purification.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032439","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}
ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202500563
Thomas Benning, Hannah R. Zwiefelhofer, Cadence F. Cordova, Grace C. Rooney, Tyler J. Doyon
{"title":"Characterization of an Extradiol Dioxygenase Using Integrating Cavity Spectrophotometry","authors":"Thomas Benning, Hannah R. Zwiefelhofer, Cadence F. Cordova, Grace C. Rooney, Tyler J. Doyon","doi":"10.1002/cbic.202500563","DOIUrl":"10.1002/cbic.202500563","url":null,"abstract":"<p>The development of synthetically-useful biocatalysts requires characterizing the behavior of an enzyme under conditions amenable to preparative-scale reactions. Whole cells harboring the catalyst of interest are often used in such reactions, as protein purification is laborious and expensive. However, monitoring reaction rates when using whole cells is challenging, as cellular debris precludes the use of a continuous assay. Herein, we describe an approach to continuous monitoring of whole cell reactions that is enabled by the use of an integrating cavity spectrophotometer. This approach was used to directly profile the kinetic behavior of a previously uncharacterized extradiol dioxygenase DfdB from <i>Rhodococcus</i> sp. YK2. Data obtained from these experiments were compared with traditional in vitro assays. In both whole cell and purified enzyme kinetic assays, similar enzymatic behaviors were observed, including substrate inhibition. Measured K<sub>M</sub> values and observed trends in catalytic efficiency were comparable for both types of enzyme preparation. Information provided by this analysis was leveraged to optimize preparative-scale whole cell reactions with DfdB, enabling the synthesis of two DfdB products in high yield. Importantly, this work showcases the potential for ICS-based methods to rapidly evaluate kinetic trends on analytical scale and thereby enables efficient reaction optimization for preparative-scale synthesis.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032500","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":"Recent Advances in P450 Enzyme Engineering for the Production of Natural Products","authors":"Liping Wang, Chixiang Sun, Baodong Hu, Xinrui Zhao","doi":"10.1002/cbic.202500585","DOIUrl":"10.1002/cbic.202500585","url":null,"abstract":"<p>Natural products exhibit a wide range of biological activities and are the crucial resources for drug development and compound modification. Cytochrome P450 enzymes (P450s, CYP) are a class of multifunctional and stereoselective biocatalysts that utilize heme as a cofactor and can be employed in the biosynthesis of natural products. With the development of biotechnology, P450s have been widely applied in the synthesis of natural products. However, several challenges still exist during the catalytic process, including the difficulties in the soluble expression of P450s, the insufficient supply of cofactor heme, the limited substrate selectivity, and the low efficiency of electron transfer. This concept systematically summarizes recent advances in P450 enzyme engineering for the synthesis of natural products. It covers the engineering strategies to improve heme supply and enhance the catalytic efficiency for various P450 enzymes and their applications in synthesizing steroids, flavonoids, alkaloids, and terpenoids. This concept provides a foundation for overcoming catalytic bottlenecks and promoting the green biomanufacturing of high-value natural products.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032488","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}
ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202500500
Laurence K. Jennings, Filippo Spriano, Maggie M. Reddy, Luciano Cascione, Elisa Civanelli, Andrea Rinaldi, Francesco Bertoni, Olivier P. Thomas
{"title":"Screening the Irish Marine Biorepository Identifies a New Bryostatin Analog as Potent Inhibitor of Activated B-Cells Diffuse Large B-Cell Lymphoma","authors":"Laurence K. Jennings, Filippo Spriano, Maggie M. Reddy, Luciano Cascione, Elisa Civanelli, Andrea Rinaldi, Francesco Bertoni, Olivier P. Thomas","doi":"10.1002/cbic.202500500","DOIUrl":"10.1002/cbic.202500500","url":null,"abstract":"<p>Activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL) is an aggressive cancer with poor response to standard chemotherapy. In search of new therapeutic leads, a library of 435 fractions prepared from the Irish marine biorepository was screened against 2 ABC-DLBCL cell lines (TMD8 and OCI<b>-</b>Ly10) and a non-cancerous control cell line (CB33). Active fractions are prioritized based on potency and selectivity. Among them, fractions from the nudibranch <i>Antiopella cristata</i> and the ascidian <i>Diplosoma listerianum</i> exhibit the most potent and selective cytotoxicity. Bioassay-guided fractionation of <i>D. listerianum</i> led to the identification of the known loliolide and epiloliolide. On the other hand, <i>A. cristata</i> yielded several bryostatin analogs, including bryostatin 13 and a new natural product, its 18-demethylated analog. Both compounds demonstrated nanomolar cytotoxicity against ABC-DLBCL cell lines with minimal activity in CB33. Transcriptomic profiling showed significant gene expression changes, particularly for the 18-demethylated analog, implicating modulation of key signaling pathways. This study identifies <i>A. cristata</i> as a novel and highly enriched source of bioactive bryostatins and supports the dietary sequestration hypothesis in nudibranchs, highlighting the value of marine invertebrates as reservoirs of selective anticancer agents for drug discovery.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202500500","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202500551
Pengyu Wang, Ranran Zhang, Yihui Pan, Wei Wu, Tao Zhang, Cai-Guang Yang
{"title":"Mitochondrial ClpX Inhibition Induces Ferroptosis and Blocks Pancreatic Cancer Cell Proliferation","authors":"Pengyu Wang, Ranran Zhang, Yihui Pan, Wei Wu, Tao Zhang, Cai-Guang Yang","doi":"10.1002/cbic.202500551","DOIUrl":"10.1002/cbic.202500551","url":null,"abstract":"<p>The ATPase caseinolytic protease X (ClpX), forming the ClpXP complex with caseinolytic protease P (ClpP), is essential for mitochondrial protein homeostasis. While ClpP targeting is a recognized anticancer strategy, the role of ClpX in cancer remains underexplored. In pancreatic ductal adenocarcinoma (PDAC), elevated <i>CLPX</i> expression correlates with poor prognosis, suggesting its oncogenic function. <i>CLPX</i> knockdown disrupts mitochondrial homeostasis, and reduces oxidative phosphorylation, thus leading to mitochondrial dysfunction and impaired PDAC cell proliferation. The ClpX-mediated mitochondrial dysfunction induces oxidative stress, unfolded protein response (UPR), and ferroptosis, which is evidenced by increased reactive oxygen species, ferrous iron, lipid peroxidation, and malondialdehyde levels. Screening ATPase inhibitors identifies MSC1094308 as a hit compound for ClpX inhibition, which suppresses ClpXP activity and induces UPR and ferroptosis in PDAC cells. These findings highlight ClpX inhibition as a promising therapeutic strategy for PDAC.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032424","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}
ChemBioChemPub Date : 2025-09-11DOI: 10.1002/cbic.202500479
Mario K. C. Krespach, Maira Rosin, Kirstin Scherlach, Maria C. Stroe, Christian Hertweck, Axel Brakhage
{"title":"The Linear Arginoketides Neotetrafibricin A, B, and C have Algicidal and Signal Function in Microbial Interactions","authors":"Mario K. C. Krespach, Maira Rosin, Kirstin Scherlach, Maria C. Stroe, Christian Hertweck, Axel Brakhage","doi":"10.1002/cbic.202500479","DOIUrl":"10.1002/cbic.202500479","url":null,"abstract":"<p>Soils harbor some of the most diverse microbiomes on Earth. Interactions within these microbial communities are often mediated by natural products, many functioning as chemical signals. Specialized metabolites known as arginoketides, or arginine-derived polyketides, have been linked to mediate these interactions. However, the effect of linear arginoketides on soil microalgae has not yet been investigated. Here, we report that <i>Streptomyces mashuensis</i> DSM40221 produces the linear arginoketide neotetrafibricin A, and show that it exhibits algicidal activity against the green alga <i>Chlamydomonas reinhardtii</i> and induces production of orsellinic acid and derivatives encoded by the silent <i>ors</i> biosynthetic gene cluster (BGC) in the fungus <i>Aspergillus nidulans</i>. Thus, neotetrafibricin serves as an inter-kingdom signaling molecule. Genome mining identified the neotetrafibricin BGC in <i>S. mashuensis</i>. Disrupting the first polyketide synthase gene abolished neotetrafibricin production. Further mutational studies identified two neotetrafibricin congeners, including the novel neotetrafibricin C, which contains a terminal guanidino group. Structure–activity relationship analyses revealed that neither the terminal amino group nor the sugar moiety is essential for its algicidal activity or the induction of the <i>ors</i> BGC in the fungus. These findings expand the understanding of linear arginoketides in microbial ecology and highlight their potential as multifunctional signaling compounds in soil environments.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032480","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}
ChemBioChemPub Date : 2025-09-02DOI: 10.1002/cbic.202500432
Yuhai Cai, Ling Qiu, Boyu Zhang, Guanya Yang, Jin Cui
{"title":"Artificial Peptides as Autophagy Modulators","authors":"Yuhai Cai, Ling Qiu, Boyu Zhang, Guanya Yang, Jin Cui","doi":"10.1002/cbic.202500432","DOIUrl":"10.1002/cbic.202500432","url":null,"abstract":"<p>Autophagy is a highly conserved lysosomal degradation pathway for maintaining cellular homeostasis. Its dysregulation is implicated in various diseases, including cancer, neurodegeneration, and infections, making precise modulation of autophagy a potentially promising therapeutic strategy. Artificial peptide-based autophagy modulators have emerged as a promising alternative to conventional small molecules, offering several advantages in terms of specificity, biocompatibility, and functional versatility. This review summarizes recent advances in artificial peptide-based autophagy monitoring tools, autophagy inducers, and autophagy inhibitors.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 19","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937136","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}