ChemBioChem最新文献_第8页

Recent Chemical Biology Insights Towards Reversible Stapled Peptides.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-26 DOI: 10.1002/cbic.202500052

Ying Chen, Chuan Dai, Jinyan Han, Yun Xing, Feng Yin, Zigang Li

{"title":"Recent Chemical Biology Insights Towards Reversible Stapled Peptides.","authors":"Ying Chen, Chuan Dai, Jinyan Han, Yun Xing, Feng Yin, Zigang Li","doi":"10.1002/cbic.202500052","DOIUrl":"10.1002/cbic.202500052","url":null,"abstract":"Peptides are increasingly recognized for their advantages over small molecules in the modulation of protein-protein interactions (PPIs), particularly in terms of potency and selectivity. \"Staples\" can be coupled to the amino acid residues of linear peptides to limit their conformation, improving the stability, membrane permeability, and resistance to proteolysis of peptides. However, the addition of staples can sometimes lead to the complete inactivation of the original peptide or result in extensive interactions that complicate biophysical analysis. Reversible stapled peptides provide an excellent solution to these issues. Besides, probes based on reversible stapled peptides are also indispensable tools for thoroughly investigating PPIs. Consequently, the development of diverse reversible stapling techniques for stapled peptides is crucial for broadening the applications of peptide molecules in drug discovery, drug delivery, and as tools in chemical biology research. This review aims to summarize representative chemical design strategies for reversible stapled peptides, focusing on reversible chemical stapling methods involving sulfhydryl, amino, and methylthio groups, as well as reversible modulation of the conformational states of stapled peptides. Additionally, we demonstrate some intriguing biological applications of stapled peptides and, finally, suggest future research directions in the field that will serve as references for related researchers.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202500052"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514109","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}

引用次数: 0

Biosynthesis of Polyhydroxyalkanoates From Sucrose by Recombinant Pseudomonas putida KT2440.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-26 DOI: 10.1002/cbic.202401000

Hye Min Song, Seo Hyun Lim, Eun Seo Lee, Dojin Kim, Sang Yup Lee, Ki Jun Jeong, Si Jae Park

{"title":"Biosynthesis of Polyhydroxyalkanoates From Sucrose by Recombinant Pseudomonas putida KT2440.","authors":"Hye Min Song, Seo Hyun Lim, Eun Seo Lee, Dojin Kim, Sang Yup Lee, Ki Jun Jeong, Si Jae Park","doi":"10.1002/cbic.202401000","DOIUrl":"10.1002/cbic.202401000","url":null,"abstract":"A sucrose-utilization pathway was developed in Pseudomonas putida using sacC from Mannheimia succiniciproducens, which encodes a β-fructofuranosidase that hydrolyzes sucrose into glucose and fructose. Excretion of β-fructofuranosidase into the culture medium was confirmed via western blot analysis. In nitrogen-limited cultivation, P. putida expressing SacC produced 10.52 wt % medium-chain-length polyhydroxyalkanoate (MCL-PHA), while P. putida expressing SacC along with poly(3-hydroxybutyrate) [P(3HB)] biosynthesis genes produced 9.16 wt % P(3HB) from sucrose. Batch and fed-batch cultures of recombinant P. putida suggested that the glucose and fructose derived from sucrose can be completely utilized for cell growth and P(3HB) production. In fed-batch cultures, sucrose supplied into the fermentor to maintain its concentration around 20 g/L was rapidly hydrolyzed into glucose and fructose supporting the production of 30.2 g/L P(3HB) with 38.1 wt %. The engineered P. putida reported herein can facilitate the production of PHAs from sucrose, an abundant and inexpensive carbon source.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202401000"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497479","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}

引用次数: 0

A Silicon Rhodamine-fused Glibenclamide to Label and Detect Malaria-infected Red Blood Cells.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-25 DOI: 10.1002/cbic.202400628

Claudia Bastl, Cindy M Close, Ingo Holtz, Blaise Gatin-Fraudet, Mareike Eis, Michelle Werum, Smilla Konrad, Laura Kneller, Kilian Roßmann, Christiane Huhn, Souvik Ghosh, Julia Ast, Dorien A Roosen, Martin Lehmann, Volker Haucke, Luc Reymond, David J Hodson, Philip Tinnefeld, Kai Johnsson, Viktorija Glembockyte, Nicole Kilian, Johannes Broichhagen

{"title":"A Silicon Rhodamine-fused Glibenclamide to Label and Detect Malaria-infected Red Blood Cells.","authors":"Claudia Bastl, Cindy M Close, Ingo Holtz, Blaise Gatin-Fraudet, Mareike Eis, Michelle Werum, Smilla Konrad, Laura Kneller, Kilian Roßmann, Christiane Huhn, Souvik Ghosh, Julia Ast, Dorien A Roosen, Martin Lehmann, Volker Haucke, Luc Reymond, David J Hodson, Philip Tinnefeld, Kai Johnsson, Viktorija Glembockyte, Nicole Kilian, Johannes Broichhagen","doi":"10.1002/cbic.202400628","DOIUrl":"10.1002/cbic.202400628","url":null,"abstract":"The malaria parasite Plasmodium falciparum affects the lives of millions of people worldwide every year. The detection of replicating parasites within human red blood cells is of paramount importance, requiring appropriate diagnostic tools. Herein, we design and apply a silicon rhodamine-fused glibenclamide (SiR-glib). We first test this far-red fluorescent, fluorogenic and endoplasmic reticulum-targeting sulfonylurea in mammalian cells and pancreatic islets, before characterizing its labeling performance in red blood cells infected with the asexual developmental stages of Plasmodium falciparum. We further combine SiR-glib with a portable smartphone-based microscope to easily and rapidly identify parasitized red blood cells, providing proof of principle for diagnostic use in rural endemic areas without major healthcare facilities.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400628"},"PeriodicalIF":2.6,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490231","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}

引用次数: 0

Harnessing Synthetic Riboswitches for Tunable Gene Regulation in Mammalian Cells.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-24 DOI: 10.1002/cbic.202401015

Rushikesh M Khadake, Vaani Arora, Payal Gupta, Ambadas B Rode

引用次数: 0

Quantification of Propargylated RNA Nucleosides After Metabolic Labeling Via the Methylation Pathway.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-24 DOI: 10.1002/cbic.202400986

Nadine A Kueck, Sabine Hüwel, Arne Hoffmann, Andrea Rentmeister

{"title":"Quantification of Propargylated RNA Nucleosides After Metabolic Labeling Via the Methylation Pathway.","authors":"Nadine A Kueck, Sabine Hüwel, Arne Hoffmann, Andrea Rentmeister","doi":"10.1002/cbic.202400986","DOIUrl":"10.1002/cbic.202400986","url":null,"abstract":"RNA modifications are involved in numerous biological processes and vary in different cell types. Methylation is the most widespread type of RNA modification and occurs via S-adenosyl-L-methionine (SAM). We recently developed a metabolic labeling approach based on intracellular formation of a clickable SAM analog (SeAdoYn) and demonstrated its use in mapping methyltransferase (MTase) target sites in mRNA from HeLa cells. Here we investigate how metabolic labeling via the clickable SAM analog modifies four different nucleosides in RNA of HEK293T in comparison to HeLa cells. We find that HEK293T cells retain higher cell viability upon feeding the clickable metabolic SAM precursor. In poly(A)+ RNA we find high Aprop/A levels (0.04 %) and in total RNA (but not poly(A)+ RNA) we detect prop3C, which had not been detected previously in HeLa cells. We discuss the findings in the context of data from the literature with respect to mRNA half-lives in cancer and non-cancer cell lines and suggest that CMTr2 is most likely responsible for the high Aprop level in poly(A)+ RNA.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400986"},"PeriodicalIF":2.6,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490236","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}

引用次数: 0

Glyoxalase 2 Coordinates de Novo Serine Metabolism. 乙二醛酶 2 协调新丝氨酸的生物合成。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-23 DOI: 10.1002/cbic.202401086

Marissa N Trujillo, Erin Q Jennings, Dominique O Farrera, Naoya Kitamura, Colin C Anderson, Sarah Gehrke, Julie A Reisz, Mogens Johannsen, James R Roede, Angelo D'Alessandro, James J Galligan

{"title":"Glyoxalase 2 Coordinates de Novo Serine Metabolism.","authors":"Marissa N Trujillo, Erin Q Jennings, Dominique O Farrera, Naoya Kitamura, Colin C Anderson, Sarah Gehrke, Julie A Reisz, Mogens Johannsen, James R Roede, Angelo D'Alessandro, James J Galligan","doi":"10.1002/cbic.202401086","DOIUrl":"10.1002/cbic.202401086","url":null,"abstract":"Phosphoglycerate dehydrogenase (PHGDH) is the first enzyme in de novo Ser biosynthesis. Numerous metabolic pathways rely on Ser as a precursor, most notably one-carbon metabolism, glutathione biosynthesis, and de novo nucleotide biosynthesis. To facilitate proliferation, many cancer cells shunt glycolytic flux through this pathway, placing PHGDH as a metabolic liability and feasible therapeutic target for the treatment of cancer. Herein, we demonstrate the post-translational modification (PTM) of PHGDH by lactoylLys. These PTMs are generated through a non-enzymatic acyl transfer from the glyoxalase cycle intermediate, lactoylglutathione (LGSH). Knockout of the primary LGSH regulatory enzyme, glyoxalase 2 (GLO2), results in increased LGSH and resulting lactoylLys modification of PHGDH. These PTMs reduce enzymatic activity, resulting in a marked reduction in intracellular Ser. Using stable isotope tracing, we demonstrate reduced flux through the de novo Ser biosynthetic pathway. Collectively, these data identify PHGDH as a target for modification by lactoylLys, resulting in reduced enzymatic activity and reduced intracellular Ser.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202401086"},"PeriodicalIF":2.6,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481816","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}

引用次数: 0

Unveiling the Architecture of Human Fibrinogen: A Full-Length Structural Model.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-22 DOI: 10.1002/cbic.202400425

Romina Medeiros, Jorge Cantero, Graciela Borthagaray, Margot Paulino

{"title":"Unveiling the Architecture of Human Fibrinogen: A Full-Length Structural Model.","authors":"Romina Medeiros, Jorge Cantero, Graciela Borthagaray, Margot Paulino","doi":"10.1002/cbic.202400425","DOIUrl":"10.1002/cbic.202400425","url":null,"abstract":"Fibrinogen is a protein involved in the haemostasis process playing a central role by forming the fibrin clot. An understanding of protein structure is vital to determining biological function. Despite many studies on the fibrin polymerization process, its molecular mechanism remains elusive mainly due to the absence of a full-length three-dimensional model of human fibrinogen. Amino- and carboxyl-terminal regions of the three pairs of chains that form this molecule are missing in the crystallographic structure, being the carboxyl-terminal of the Aα chain the most affected with a section of more than 400 amino acids missing. To have a full structure of the fibrinogen molecule would allow the creation of a model of protofibril, shedding light into the fibrin formation process through computational techniques such as molecular dynamics simulations. Absent regions were explored using homology modelling and coarse-grained molecular dynamics simulations. Later on, the model was refined and stabilized with atomistic molecular dynamic simulations. In the present study, we obtained the first realistic full-length structure of fibrinogen, with features in accordance with previous results obtained by experimental techniques.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400425"},"PeriodicalIF":2.6,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476171","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}

引用次数: 0

Biomimetic Recognition of SARS-CoV-2 Receptor-Binding Domain N-Glycans by an Antiviral Synthetic Receptor.

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-21 DOI: 10.1002/cbic.202500106

Carlo Santambrogio, Mirco Toccafondi, Lorena Donnici, Elisa Pesce, Raffaele De Francesco, Renata Grifantini, Erika Ponzini, Francesco Milanesi, Marco Fragai, Cristina Nativi, Stefano Roelens, Rita Grandori, Oscar Francesconi

引用次数: 0

From Genes to Molecules: The Fusarium PKS16 Gene Cluster Facilitates the Biosynthesis of Proliferapyrones. 从基因到分子：镰刀菌 PKS16 基因簇促进了丙磺舒的生物合成。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-21 DOI: 10.1002/cbic.202401039

Anna K Atanasoff-Kardjalieff, Katharina Steinert, Klaus Bergander, Svetlana Kalinina, Lena Studt-Reinhold

{"title":"From Genes to Molecules: The Fusarium PKS16 Gene Cluster Facilitates the Biosynthesis of Proliferapyrones.","authors":"Anna K Atanasoff-Kardjalieff, Katharina Steinert, Klaus Bergander, Svetlana Kalinina, Lena Studt-Reinhold","doi":"10.1002/cbic.202401039","DOIUrl":"10.1002/cbic.202401039","url":null,"abstract":"Ascomycete fungi of the genus Fusarium are found in manifold ecological niches and thus pursue several lifestyles. On average, individual Fusarium species have the genetic capability to produce 50 natural products (NPs), which are in general thought to improve the fungus's fitness in defined environments. This also includes NPs with toxic potential (mycotoxins) contaminating food and feed sources. Recent research has shown that the production of NPs is tightly regulated on the transcriptional level and depends on the delicate balance between the deposition and removal of histone marks. Within this study, we show that the expression of the prior cryptic Fusarium PKS16 biosynthetic gene cluster (BGC) greatly depends on modifications at histone H3 lysine 27 (H3K27). By combining molecular-, chemical-, and bioinformatic analyses we show that the PKS16 BGC from F. fujikuroi B14 (FfB14) consists of nine genes, including a positively acting pathway-specific transcription factor, which although absent in some fusaria, functions in activating other PKS16 cluster genes. Moreover, we linked the PKS16 BGC to the biosynthesis of proliferapyrone (PRO) E, an isomer of the recently isolated PRO A.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202401039"},"PeriodicalIF":2.6,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472002","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}

引用次数: 0

Interactive 3D Objects Enhance Scientific Communication of Structural Data

IF 2.6 4区生物学

ChemBioChem Pub Date : 2025-02-20 DOI: 10.1002/cbic.202500036

Daniel Mokos, Bastian Daniel

{"title":"Interactive 3D Objects Enhance Scientific Communication of Structural Data","authors":"Daniel Mokos, Bastian Daniel","doi":"10.1002/cbic.202500036","DOIUrl":"10.1002/cbic.202500036","url":null,"abstract":"In scientific communication about three-dimensional structures, creating two-dimensional representations is standard practice. These representations often suffer from the drawback of losing potential information due to dimensionality reduction. Several options exist to present, share and publish 3D figures, however based on recent publications they are not widely utilized. Here we present simple ways to preserve the three-dimensionality of the structure by the creation of a custom-made model in GLTF format that is generated in the same workflow as the conventional figures. They can be published alongside a given manuscript with minimal additional effort to the authors, but a huge impact on the communicative power of the manuscript concerning the three-dimensional features of the reported structures. The scripts we adapted and published for this purpose open up new possibilities for the illustrator and allow the viewer to access the full three-dimensionality of the published structure. In future, this can simplify the publication process of protein structures or other models and be a valuable tool for scientific communication in digital or printed form.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":"26 6","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202500036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456449","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}

引用次数: 0