{"title":"Exploring the Substrate Flexibility of GrsB Thioesterase Leads to the Structural Reassignment of a Gramicidin S Variant.","authors":"Sho Konno, Tomoe Mizuguchi, Atsuko Suzuki, Miyu Tanaka, Fumihiro Ishikawa, Akihiro Taguchi, Atsuhiko Taniguchi, Genzoh Tanabe, Yoshio Hayashi","doi":"10.1002/cbic.202500412","DOIUrl":"https://doi.org/10.1002/cbic.202500412","url":null,"abstract":"<p><p>Gramicidin S (GS) is a cyclic decapeptide derived from two pentapeptides. The C-terminal thioesterase (TE) domain of gramicidin S synthetase B (GrsB) dimerizes precursor pentapeptides and cyclizes the resulting linear decapeptide. Recently, a GS variant (GS-SA), in which a single D-Phe was replaced by L-Ser(Allyl), was reported via precursor-directed biosynthesis in a native GS producer. To understand how GrsB-TE processes such modified precursors, we investigated its substrate specificity using synthetic linear peptides. GrsB-TE cyclized a substrate containing L-Ser(Allyl) at position 6 but not at position 1. However, the enzymatically synthesized GS-SA showed a different HPLC retention time than that of the reported GS variant. Further structural and functional analyses, including 1H NMR, antimicrobial assays, and circular dichroism spectroscopy, revealed that the reported GS-SA contained D-Ser(Allyl) rather than L-Ser(Allyl). These findings reveal a previously unrecognized stereochemical flexibility in GrsB-TE and support the structural revision of the reported GS variant.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202500412"},"PeriodicalIF":2.6,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551504","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 : 2025-07-02DOI: 10.1002/cbic.202500387
Boyu Qiu, Xinlei Wei, Chun You
{"title":"Efficient Biosynthesis of Polyhydroxybutyrate from Xylose via an In Vitro Synthetic Enzymatic Biosystem with Self-Sustained Cofactor Regeneration.","authors":"Boyu Qiu, Xinlei Wei, Chun You","doi":"10.1002/cbic.202500387","DOIUrl":"https://doi.org/10.1002/cbic.202500387","url":null,"abstract":"<p><p>In vitro biotransformation (ivBT) mediated by in vitro synthetic enzymatic biosystems (ivSEBs) represents a highly promising platform for sustainable biomanufacturing, offering enhanced reaction efficiency by circumventing cellular constraints. In this study, we developed an ivSEB comprising 17 enzymes for the cell-free biosynthesis of polyhydroxybutyrate (PHB) from D-xylose via the acetyl-coenzyme A. This ivSEB integrates partial glycolysis and the pentose phosphate pathway, enabling self-sustained balance of several cofactors including coenzyme A (CoA), NADP+/NADPH and ATP/ADP. Stoichiometric analysis demonstrated a theoretical molar yield of PHB from xylose of 111.1%. Through optimizing concentrations of cofactors and enzymes, the one-pot reaction produced 44.0 mM (3.8 g/L) PHB from 44.8 mM (6.7 g/L) xylose, corresponding to a molar yield of 98.2%. Even at a higher substrate concentration (13.5 g/L), the yield remained robust (84.5%). This study demonstrated the potential of ivSEB as a scalable and efficient approach for the large-scale production of PHB and other xylose-based or acetyl-CoA-derived chemicals.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202500387"},"PeriodicalIF":2.6,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537548","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 : 2025-07-02DOI: 10.1002/cbic.202500310
Francesco Palmieri, Marième Gueye, Lucía Vicario Del Rio, Saskia Bunschuh, Pradeep Chopra, Silvia Mihăilă, Tina Vermonden, Riccardo Levato, Geert-Jan Boons
{"title":"Photo-triggered Hyaluronic Acid Hydrogel for 3D Culture and Cell Recovery.","authors":"Francesco Palmieri, Marième Gueye, Lucía Vicario Del Rio, Saskia Bunschuh, Pradeep Chopra, Silvia Mihăilă, Tina Vermonden, Riccardo Levato, Geert-Jan Boons","doi":"10.1002/cbic.202500310","DOIUrl":"https://doi.org/10.1002/cbic.202500310","url":null,"abstract":"<p><p>Properties of semi-synthetic hydrogels can be fine-tuned making these attractive for various applications in regenerative medicine. Here, we describe a hydrogel platform based on hyaluronic acid (HA) modified by (1R,8S,9S)-bicycle[6.1.0]non-4-yn-9-ylmethanol (BCN) and a cross-linker composed of light sensitive o-nitrobenzyl and polyethylene glycol (PEG) chains terminating in azides. The two components can undergo strain-promoted azide-alkyne cycloaddition (SPAAC) resulting in rapid gel formation. First, we incorporated adipose-derived mesenchymal stromal cells (aMSCs) in the hydrogel and demonstrated that the cells can be easily retrieved by UV light mediated degradation maintaining viability and retaining spindle-like shape when the cells were replated. Next, we provided a proof-of-concept of inducing light-mediated softening of the hydrogel to modulate the morphology of the encapsulated cells. A co-culture of endothelial cells (cord blood-derived endothelial colony forming cells (ECFCs) and bone marrow derived mesenchymal stromal cells (bmMSCs), which are commonly studied for their ability to form capillary-like vascular networks, were cultured in the regular and light induced softened hydrogels. Non-photoexposed hydrogels showed cells with a prevalently rounded morphology, whereas stretched cells connecting into a primitive capillary network were observed in the light-softened hydrogels. Photo-induced softening offers potential to locally control cell shape and self-organization capacity.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202500310"},"PeriodicalIF":2.6,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537550","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 : 2025-07-01DOI: 10.1002/cbic.202500059
Long Sun, Yuefei Zhou, Jie Wang, Lili Yao, Hao Qu, Yu Mao, Lei Zheng
{"title":"Matrix-Assisted Efficient Selection of a High-Affinity Circular Aptamer for Sensitive Detection of Low-Density Lipoprotein in Human Serum.","authors":"Long Sun, Yuefei Zhou, Jie Wang, Lili Yao, Hao Qu, Yu Mao, Lei Zheng","doi":"10.1002/cbic.202500059","DOIUrl":"https://doi.org/10.1002/cbic.202500059","url":null,"abstract":"<p><p>The accurate and rapid detection of human serum biomakers is crucial for the early diagnosis of related diseases. Circular aptamers emerge as promising candidates for the precise recognition of these biomakers due to their remarkable biological and structural stability. In this study, we successfully identified a high-affinity circular DNA aptamer for Low-density lipoprotein (LDL), a key biomarker for cardiovascular diseases, through matrix-assisted efficient selection strategy conducted directly in human serum. This circular aptamer demonstrated a dissociation constant (Kd) as low as 18 nM and exhibited exceptional specificity for LDL, showing negligible responses to closely related analogs such as high-density lipoprotein and other abunzaidant human serum substances. We subsequently developed a sensitive aptasensor that utilizes the superior recognition capability of the circular DNA aptamer, which performed well even in human serum (with a limit of detection down to 0.4 μM and a wide linear concentration range of three orders of magnitude). This work underscores the feasibility of rapidly isolating highly functional circular DNA aptamers in one selection round, thereby accelerating the discovery of various circular DNA aptamers that are well-suited for molecular recognition of a wide array of emerging human serum biomarkers.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202500059"},"PeriodicalIF":2.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537549","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 : 2025-06-30DOI: 10.1002/cbic.202500286
Madiha Saqlain, Hafiz Muhammad Zohaib, Dilawar Akram, Samina Qamar, Iqra Tabassum, Muhammad Irfan, Hui Li
{"title":"Coordination Polymer Carrying Antimicrobial Peptide for Enhanced Anti-Infective Therapy.","authors":"Madiha Saqlain, Hafiz Muhammad Zohaib, Dilawar Akram, Samina Qamar, Iqra Tabassum, Muhammad Irfan, Hui Li","doi":"10.1002/cbic.202500286","DOIUrl":"https://doi.org/10.1002/cbic.202500286","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) offer a promising avenue for combating drug-resistant bacterial infections, but their clinical utility is often limited by poor bioavailability and stability. This study presents the design and synthesis of a novel, enantiomerically pure 2D-coordination polymer, {[Cu(dUMP)(dpp)<sub>2</sub>]·3(H<sub>2</sub>O)·(NO<sub>3</sub>)]}<sub>n</sub> (CP-1), derived from Cu(II) ions, deoxy-uridine monophosphate, and 1,3-di(4-pyridyl)propane (dpp), as a potential delivery system for AMPs. Single-crystal X-ray diffraction reveals a 2D double helical structure with square pyramidal Cu(II) coordination. Spectroscopic characterization (IR, UV-vis, thermogravimetric analysis, X-ray diffraction, circular dichroism) confirms the successful synthesis and reveals chirality transfer to the achiral dpp ligand. Molecular docking studies identify DGL 13K as the AMP exhibiting the strongest binding affinity to CP-1 (ΔG = -13.03 kcal mol<sup>-1</sup>). Critically, molecular dynamics simulations provide detailed insights into the mechanism of action of the CP-1-DGL 13K complex against a Gram-negative bacterial membrane. The simulations demonstrate that DGL 13K, stabilized by CP-1, undergoes conformational changes, penetrating the membrane and disrupting its integrity through pore formation. These findings highlight the potential of CP-1 as an effective carrier for AMPs, enhancing their stability and facilitating membrane disruption, offering a promising strategy for developing novel antimicrobial therapies to combat drug resistance.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500286"},"PeriodicalIF":2.6,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525682","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 : 2025-06-30DOI: 10.1002/cbic.202500184
Xiaoqing Cai, Huanhuan Sun, Na Li
{"title":"Development of Antibody-Based Strategies for Targeted Degradation of Membrane and Extracellular Proteins.","authors":"Xiaoqing Cai, Huanhuan Sun, Na Li","doi":"10.1002/cbic.202500184","DOIUrl":"https://doi.org/10.1002/cbic.202500184","url":null,"abstract":"<p><p>Membrane and extracellular proteins are essential components in various biological processes that ensure cellular function and homeostasis. Their dysregulation is linked to a wide range of diseases, making them pivotal therapeutic targets. Recent innovations in therapeutic strategies have concentrated on targeted protein degradation, particularly via the endocytosis-lysosome pathway, offering a novel approach to restoring balance within cellular systems. This review elucidates recent advancements in antibody-based therapeutics designed for the targeted degradation of membrane and extracellular proteins, specifically emphasizing three key mechanisms: lysosomal targeting receptors, transmembrane E3 ligases, and lysosome-sorting signals that facilitate the degradation of disease-relevant proteins. We focus on various construction strategies for these antibody-based therapeutics, highlighting the potential of antibody-ligand conjugates, bispecific antibodies, and antibody fusion proteins. By leveraging the natural endocytic pathway for efficient protein internalization and subsequent lysosomal degradation, these antibody-based platforms hold significant promise for developing targeted therapies for a variety of diseases. Through this review, we aim to provide insights into the exciting field of antibody-enabled lysosomal degradation and its implications for future therapeutic interventions.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202500184"},"PeriodicalIF":2.6,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525683","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":"Chemically Synthesized LRAD3-D1 Interacts with N-Terminal Domain of SARS-CoV-2 Spike Protein.","authors":"Mrinmoy Jana, Rathina Delipan, Arighna Sarkar, Sreejith Raran-Kurussi, Rajesh P Ringe, Kalyaneswar Mandal","doi":"10.1002/cbic.202500403","DOIUrl":"10.1002/cbic.202500403","url":null,"abstract":"<p><p>Growing evidence of post-COVID neurological complications, such as encephalopathy, neurodegeneration, and cognitive impairment, suggests severe acute respiratory syndrome-related corona virus 2 (SARS-CoV-2) viral infection into the central nervous system (CNS). Therefore, understanding the mechanisms of viral entry into the CNS, where human angiotensin-converting enzyme 2 (ACE2) is barely expressed, is critical for addressing the neurological consequences of COVID-19. Importantly, the low-density lipoprotein receptor class A domain containing 3 (LRAD3) is overexpressed in brain cells, suggesting a possible ACE2-independent alternate pathway of viral entry into brain cells. Herein, the interaction of the chemically synthesized LRAD3 domains with SARS-CoV-2 spike protein is reported. It is observed that the extracellular domains of LRAD3 depend on calcium for proper folding and maintaining their structural integrity. The results reveal that domain 1 of LRAD3, which is most accessible from the cell surface, engages with the N-terminal domain of the viral spike protein. These findings open up possibilities to develop new therapeutic strategies targeting ACE2 independent viral entry pathways.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500403"},"PeriodicalIF":2.6,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525681","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 : 2025-06-26DOI: 10.1002/cbic.202400439
Cangsong Liao, David Lim, Gladwin Suryatin Alim, Florian P Seebeck
{"title":"5-thiohistidine N-acetyltransferase from Proteiniphilum saccharofermentans.","authors":"Cangsong Liao, David Lim, Gladwin Suryatin Alim, Florian P Seebeck","doi":"10.1002/cbic.202400439","DOIUrl":"https://doi.org/10.1002/cbic.202400439","url":null,"abstract":"<p><p>Ovothiol A is a 5-thiohistidine derivative biosynthesized by a broad range of prokaryotic and eukaryotic organisms. Its redox-active mercaptoimidazole side chain is believed to protect cells from oxidative stress. The three enzymes that produce ovothiol A from histidine, cysteine, and S-adenosyl methionine have been identified and characterized. In contrast, no enzymes are known that produce other 5-thiohistidine derivatives. Here, we describe a small family of acetyl-coenzyme A-dependent transferases that produce N-acetyl-5-thiohistidine. The discovery of these enzymes from Proteiniphilum saccharofermentans and related Bacteroidota provides evidence that the 5-thiohistidine class may be structurally and functionally more diverse than previously thought.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400439"},"PeriodicalIF":2.6,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493261","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":"Fucose-Based Glycopolymeric Nanomicelles for Activated Platelet-Targeted Photothermal Thrombolysis.","authors":"Minzhi Song, Wenxi Yang, Lingxin Peng, Changan Ren, Jinghua Chen, Yan Zhang","doi":"10.1002/cbic.202500253","DOIUrl":"10.1002/cbic.202500253","url":null,"abstract":"<p><p>Thrombotic disorders represent a significant global health burden, with conventional thrombolytic therapies often limited by systemic bleeding risks and inadequate thrombus specificity. To address these challenges, a biomimetic glycopolymer-based nanomicelle system is developed for precision thrombosis management. Utilizing reversible addition-fragmentation chain-transfer polymerization, a type of cationic glycopolymer is synthesized from dimethylaminoethyl methacrylate and fucose monomers, which self-assembles into core-shell nanomicelles. The hydrophilic corona features multivalent fucose clusters that selectively bind to P-selectin on activated platelets within the thrombi, enabling targeted accumulation, while the hydrophobic core encapsulates the photothermal agent indocyanine green (ICG), enhancing its aqueous solubility and photostability. Upon near-infrared (NIR) laser irradiation, the ICG-loaded glycopolymeric nanomicelle, ICG@D<sub>20</sub>F<sub>20</sub> exhibits efficient photothermal conversion, generating localized hyperthermia to disrupt fibrin networks. This platform offers several advantages, including precise targeting, synergistic thrombolysis, and enhanced biocompatibility, thereby overcoming the limitations of traditional thrombolytics and providing a novel approach for minimally invasive, image-guided cardiovascular interventions.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500253"},"PeriodicalIF":2.6,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504318","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 of a l-Threonine-Utilizing Hydrazine Synthetase for Thrazarine Biosynthesis in Streptomyces coerulescens MH802-fF5.","authors":"Yusuke Shikai, Hideyuki Muramatsu, Masayuki Igarashi, Yohei Katsuyama, Yasuo Ohnishi","doi":"10.1002/cbic.202500298","DOIUrl":"10.1002/cbic.202500298","url":null,"abstract":"<p><p>Hydrazine synthetases (HSs), consisting of cupin and methionyl-tRNA synthetase (MetRS)-like domains, catalyze hydrazine formation in the biosynthesis of various nitrogennitrogen (NN) bond-containing secondary metabolites. The structural diversity of the NN bond-containing secondary metabolites synthesized using this system is attributed to the diversity of amino acids (e.g., l-Glu, d-Glu, l-Ala, l-Tyr, l-Ser, and Gly) that are recognized by the MetRS domain. However, there are still many HS genes in the genome database whose substrates are unknown. This study identifies a putative biosynthetic gene cluster (BGC) for thrazarine, a diazo group-containing secondary metabolite with antitumor activity, by whole-genome sequencing of the thrazarine producer Streptomyces coerulescens MH802-fF5. In vivo and in vitro analyses showed that ThzN, an HS encoded by this BGC, synthesizes N-((5-carboxy-5-(amino)pentyl)amino)threonine from l-Thr and N<sup>6</sup>-hydroxylysine. This is the first example of l-Thr-utilizing HS. Sequence alignment analysis and structure prediction using Boltz-1 indicated that the space near Gly417 is important for the accommodation of the threonine side chain. The comparison of thrazarine BGC with azaserine BGC indicated that the biosynthetic mechanism of the diazo group of thrazarine is different from that of azaserine. This study expands the diversity of HSs and provides new insights into the biosynthesis of diazo groups.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e2500298"},"PeriodicalIF":2.6,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493262","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}