Organic & Biomolecular Chemistry最新文献

{"title":"Structural analyses of Glycyrrhiza glabra C-glycosyltransferase: a molecular dynamics study to elucidate catalytically active complexes†","authors":"Gonzalo A. Jaña, Fabiola E. Medina, Francisco Barrios, Jorge I. Martínez-Araya and Fernanda Mendoza","doi":"10.1039/D4OB01814A","DOIUrl":"10.1039/D4OB01814A","url":null,"abstract":"<p >C-Glycosides belong to a class of bioactive compounds biosynthesized by C-glycosyltransferases, also known as C-GTs. Despite their practical significance, C-GTs have scarcely been studied due to the limited availability of their crystal structures. In this study, we applied molecular dynamics (MD) simulations and density functional theory (DFT) calculations to investigate <em>Glycyrrhiza glabra</em> C-GT (<em>Gg</em>CGT), focusing on the impact of protonation states of two histidine residues and specific mutations on enzyme–substrate configurations. We explored nine native ternary models, considering all possible combinations of protonation states for the His351/His373 pair, which we proposed as fundamental for catalysis. We also included four different mutants designed to assess the role of residues found to be essential for catalytic activity through mutagenesis experiments: His12Ala, His12Lys, His12Lysn and Asp375Ala. MD simulations revealed that only two models (M1 and M3) satisfied the criteria for catalytic competence, where the protonation states of His351 and His373 significantly influenced the relative position between donor and acceptor substrates, as well as the acceptor substrate conformation, adopting extended and packed states. DFT calculations confirmed that these conformations impact the electron density distribution, influencing substrate reactivity. Mutant simulations further supported the experimental data: His12Ala, His12Lys, and Asp375Ala mutants failed to meet the catalytic distance criteria, leading us to infer that these mutations prevented the formation of a reactive enzyme–substrate complex. Conversely, the His12Lysn mutant partially meets the criteria, which could help to explain the catalytic activity of this mutant. These findings provide the first molecular interpretation of the role of key residues in substrate binding and catalysis, which are essential for understanding catalytic activity. Furthermore, they offer new structural insights into residues such as His351/His373, which are often overlooked in GT modeling despite their potential to modulate the Michaelis complex. We hope that these findings will contribute to the rational engineering of more efficient C-GTs for biotechnological applications.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 16","pages":" 3899-3912"},"PeriodicalIF":2.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visible-light-induced thiol-ene/air oxidation tandem reaction for sulfoxide synthesis: a photocatalyst-free and metal-free approach†","authors":"Ming-Hao Zhao, Xu Liu, Yu-Chen Yang and Lijia Wang","doi":"10.1039/D5OB00136F","DOIUrl":"10.1039/D5OB00136F","url":null,"abstract":"<p >A photocatalyst-free, metal-free visible light-promoted thiol-ene/oxidation tandem reaction for sulfoxide synthesis has been developed under mild conditions with air as oxidant. Broad substrate scope as well as gram-scale synthesis enables this environmentally friendly approach with potential for further synthetic applications.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 16","pages":" 3806-3811"},"PeriodicalIF":2.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The formation reaction of a carbon–carbon bond promoted by Eosin-Y under visible light","authors":"Lirong Han, Hui Zhou, Jinsong Hou, Xiaohao Shi and Qinghan Li","doi":"10.1039/D5OB00141B","DOIUrl":"10.1039/D5OB00141B","url":null,"abstract":"<p >In recent years, photochemical organic conversion promoted by visible light has attracted the interest of many organic chemists. Compared with traditional methods, visible light for the photoredox catalysis of renewable energy has been proved to be a mild and powerful tool that can promote the activation of organic molecules through the single electron transfer (SET) process. Therefore, the formation reaction of a C–C bond can be achieved by activating these molecules with visible light, which can effectively modify the structure of these compounds and obtain compounds with multiple structures and functions. At present, this research has become an important research field in organic synthesis. Eosin-Y, a cheap and widely-used organic dye, has been employed as an economically and environmentally friendly substitute for many transition-metal-based photocatalysts. In recent years, it has gained much more attention due to its ease of handling and eco-friendliness, and it has great potential for applications in visible-light-mediated organic synthesis. This article reviews the research results on the formation of carbon–carbon bonds promoted by the organic photocatalyst Eosin-Y under visible light in recent years, and discusses representative examples and their different mechanistic pathways (such as SET, HAT, and energy transfer).</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 16","pages":" 3741-3799"},"PeriodicalIF":2.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Swermilactones A and B: racemic xanthone–secoiridoid heterodimers from Swertia mileensis†","authors":"Yao Du, Hao Li, Xiao-Yu Qi, Yuan-Liang Xu, Yan Liu, Xue-Mei Niu, Kai Guo and Sheng-Hong Li","doi":"10.1039/D5OB00326A","DOIUrl":"10.1039/D5OB00326A","url":null,"abstract":"<p >Two pairs of racemic xanthone–secoiridoid heterodimers, (±)-swermilactones A (<strong>1</strong>) and B (<strong>2</strong>), were isolated from the whole plants of <em>Swertia mileensis</em>. Their structures, featuring an unusual C–C bond linkage between the xanthone and secoiridoid moieties, were elucidated by extensive spectroscopic analysis and ECD calculations. Compounds (+)-<strong>1</strong>, (−)-<strong>1</strong>, (+)-<strong>2</strong>, and (−)-<strong>2</strong> moderately inhibited the secretion of cytokines TNF-α and IL-6 in LPS-induced RAW 264.7 macrophages with IC<small>₅₀</small> values ranging from 12.01 to 39.06 μM.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 16","pages":" 3860-3864"},"PeriodicalIF":2.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Base-controlled regioselectivity via distinct mechanisms during C–H thionation of azinium salts with elemental sulfur†","authors":"Olga A. Kositova, Dmitry I. Bugaenko, Victoria E. Goncharenko, Mikhail S. Nechaev and Alexander V. Karchava","doi":"10.1039/D5OB00209E","DOIUrl":"10.1039/D5OB00209E","url":null,"abstract":"<p >Regioselective C–H-thionation of pyridine and quinoline rings can be achieved through the reaction of the corresponding quaternary azinium salts with sulfur and a base <em>via</em> a radical- or carbene-involved reaction pathway. The selectivity of C<img>S group installation is determined by the reaction mechanism and affected by the base used.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 15","pages":" 3547-3552"},"PeriodicalIF":2.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TM-free full utilization of S atoms: synthesis of thioethers from disulfides and quaternary ammonium salts†","authors":"Xiantao Ma, Yingying Zhu, Yuying Chen, Xiaoyu Yan and Mengcheng Zhang","doi":"10.1039/D5OB00011D","DOIUrl":"10.1039/D5OB00011D","url":null,"abstract":"<p >Disulfides are commonly used as alternatives of thiols; however, the full utilization of both S atoms of disulfides under TM-, oxidant/reductant-free conditions is still challenging. In this study, an efficient synthesis of thioethers from disulfides and quaternary ammonium salts under TM-, oxidant/reductant-free conditions has been developed. Both S atoms of disulfides can be transformed into thioether products, thus improving sulfur resource utilization. The method can be easily extended to the synthesis of valuable alkyl dithiocarbamates and can be readily scaled up to the gram scale, showing good practicality value.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 15","pages":" 3590-3594"},"PeriodicalIF":2.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meyer–Schuster rearrangement/allylic alkenylation of propynolaldehydes with olefins to synthesize skipped 1,4-dienes†","authors":"Cheng-Ping Shen, Hai-Tao Zhu, Guo-Hua Li, Xin Chang, Jia-Jun Xi, Ni-Ni Zhou and An-Xi Zhou","doi":"10.1039/D5OB00173K","DOIUrl":"10.1039/D5OB00173K","url":null,"abstract":"<p >A highly efficient method for the straightforward synthesis of skipped 1,4-dienes is presented <em>via p</em>-TsOH·H<small>₂</small>O-catalyzed intramolecular intercepted Meyer–Schuster rearrangement/allylic alkenylation of propynolaldehydes with olefins in a one-pot manner. This cascade transformation is characterized by metal-free and mild conditions, extensive substrate applicability, atom economy, gram-scale production, and water as the sole by-product. Furthermore, the resulting functionalized 1,4-dienes could be derivatized by Fe(<small>III</small>)-promoted radical cyclization, allylic methoxylation under reductive conditions, and Pd(<small>II</small>)-catalyzed Sonogashira coupling.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 16","pages":" 3870-3874"},"PeriodicalIF":2.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and synthesis of 4′-ortho-aminobenzoyl ascarosides as sex pheromones of gonochoristic Caenorhabditis nigoni†","authors":"Célia P. Bergame, Chuanfu Dong, Siva Bandi, Marie-Désirée Schlemper-Scheidt, Sylvain Sutour and Stephan H. von Reuß","doi":"10.1039/D5OB00271K","DOIUrl":"10.1039/D5OB00271K","url":null,"abstract":"<p >Using a combination of RP-C18 chromatography, MS and NMR techniques, a new class of homologous modular ascarosides carrying a 4′-<em>ortho</em>-aminobenzoyl moiety was identified from <em>Caenorhabditis nigoni</em> and <em>Caenorhabditis tropicalis</em>. These compounds could not be detected using targeted ascaroside screens based on precursor ion screening for <em>m</em>/<em>z</em> 73.0294 [C<small>₃</small>H<small>₅</small>O<small>₂</small>]<small>⁻</small>, which highlighted a limitation of the current protocols. Their structure assignment was established by total synthesis of AB-asc-C5 (SMID: abas#9) as a representative example in about 1% yield over 14 steps. To achieve this aim, a new method for the synthesis of orthogonally protected ascarosides has been developed which provides methyl 2-benzoyl-ascaroside as a highly versatile building block for regioselective ascaroside synthesis. Furthermore, a new synthesis for short chain C5 ascarosides was developed that employs selective reduction and Grubbs cross metathesis. The identity of synthetic AB-asc-C5 and the natural product isolated from <em>C. nigoni</em> was established by an NMR mixing experiment. Retention of <em>C. nigoni</em> males by the exclusively female produced AB-asc-C5 suggests a function as a sex pheromone component. Along with the indole ascarosides (icas), the new class of 4′-<em>ortho</em>-aminobenzoyl ascarosides (abas) represents a mechanism to translate bacterial food dependent <small>L</small>-tryptophan availability into species-specific signaling molecules.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 15","pages":" 3654-3670"},"PeriodicalIF":2.9,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in the selective functionalization of B(3,6)–H of o-carboranes","authors":"Ji Wu and Ke Cao","doi":"10.1039/D4OB01778A","DOIUrl":"10.1039/D4OB01778A","url":null,"abstract":"<p >This review summarizes the methodologies for the selective functionalization of the B(3,6) vertices of <em>o</em>-carboranes, including the deboration-capitation reaction, the coupling reaction of B–X (X = I, Br) bonds, reactions of 1,3-dehydro-<em>o</em>-carborane and [3-N<small>₂</small>-<em>o</em>-C<small>₂</small>B<small>₁₀</small>H<small>₁₁</small>][BF<small>₄</small>] as well as transition-metal-catalyzed B–H activation. These works offer a versatile toolbox for synthesizing B(3,6)-substituted <em>o</em>-carborane derivatives and will promote their applications in material science, pharmaceutical chemistry, and related disciplines.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 16","pages":" 3701-3711"},"PeriodicalIF":2.9,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Concise practical avenues toward 5,5-spiro-α-prolines†","authors":"Ievgenii A. Iermolenko, Artem A. Artemenko, Dmytro O. Vasko, Alina O. Shcherbyna, Oleksandr P. Datsenko, Eugeniy N. Ostapchuk, Dmytro O. Leha, Alexandr B. Rozhenko, Dmytro M. Volochnyuk and Serhiy V. Ryabukhin","doi":"10.1039/D4OB01669F","DOIUrl":"10.1039/D4OB01669F","url":null,"abstract":"<p >This article describes concise and practical synthetic approaches toward the multigram-scale preparation of value-added conformationally constrained 5-spirocyclic α-prolines from readily accessible starting materials. Direct carboxylation of 2-spiropyrrolidines is a novel and promising approach to achieve this goal, particularly for substrates with no acidic centers within the spiro-linked portion of the pyrrolidine core. The method allows for quick, one-step preparation of the target chemicals in good yields. An alternative synthetic avenue was designed for substrates unsuitable for direct carboxylation. This 4-step protocol involves common laboratory practice transformations and is comparable in its efficiency to the carboxylation method. This study concludes a series of our investigations on the elaboration of efficient methods for the construction of spiro-proline frameworks.</p>","PeriodicalId":96,"journal":{"name":"Organic & Biomolecular Chemistry","volume":" 15","pages":" 3601-3611"},"PeriodicalIF":2.9,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}