Ferran Nieto-Fabregat, Maria Pia Lenza, Angela Marseglia, Cristina Di Carluccio, Antonio Molinaro, Alba Silipo, Roberta Marchetti
{"title":"Computational toolbox for the analysis of protein-glycan interactions.","authors":"Ferran Nieto-Fabregat, Maria Pia Lenza, Angela Marseglia, Cristina Di Carluccio, Antonio Molinaro, Alba Silipo, Roberta Marchetti","doi":"10.3762/bjoc.20.180","DOIUrl":"10.3762/bjoc.20.180","url":null,"abstract":"<p><p>Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"2084-2107"},"PeriodicalIF":2.2,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ignaz Betcke, Alissa C Götzinger, Maryna M Kornet, Thomas J J Müller
{"title":"Multicomponent syntheses of pyrazoles via (3 + 2)-cyclocondensation and (3 + 2)-cycloaddition key steps.","authors":"Ignaz Betcke, Alissa C Götzinger, Maryna M Kornet, Thomas J J Müller","doi":"10.3762/bjoc.20.178","DOIUrl":"10.3762/bjoc.20.178","url":null,"abstract":"<p><p>Pyrazoles are rarely found in nature but are traditionally used in the agrochemical and pharmaceutical industries, while other areas of use are also actively developing. However, they have also found numerous other applications. The search for new and efficient syntheses of these heterocycles is therefore highly relevant. The modular concept of multicomponent reactions (MCR) has paved a broad alley to heteroaromatics. The advantages over traditional methods are the broader scope and increased efficiency of these reactions. In particular, traditional multistep syntheses of pyrazoles have considerably been extended by MCR. Progress has been made in the cyclocondensation of 1,3-dielectrophiles that are generated in situ. Limitations in the regioselectivity of cyclocondensation with 1,3-dicarbonyls were overcome by the addition-cyclocondensation of α,β-unsaturated ketones. Embedding 1,3-dipolar cycloadditions into a one-pot process has additionally been developed for concise syntheses of pyrazoles. The MCR strategy also allows for concatenating classical condensation-based methodology with modern cross-coupling and radical chemistry, as well as providing versatile synthetic approaches to pyrazoles. This overview summarizes the most important MCR syntheses of pyrazoles based on ring-forming sequences in a flashlight fashion.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"2024-2077"},"PeriodicalIF":2.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Deepa Nair, Abhishek Tiwari, Banamali Laha, Irishi N N Namboothiri
{"title":"Diastereoselective synthesis of highly substituted cyclohexanones and tetrahydrochromene-4-ones via conjugate addition of curcumins to arylidenemalonates.","authors":"Deepa Nair, Abhishek Tiwari, Banamali Laha, Irishi N N Namboothiri","doi":"10.3762/bjoc.20.177","DOIUrl":"10.3762/bjoc.20.177","url":null,"abstract":"<p><p>A cascade inter-intramolecular double Michael strategy for the synthesis of highly functionalized cyclohexanones from curcumins and arylidenemalonates is reported. This strategy works in the presence of aqueous KOH using TBAB as a suitable phase transfer catalyst at room temperature. The functionalized cyclohexanones are formed as major products in moderate to excellent yields with complete diastereoselectivity in most cases. A triple Michael adduct, tetrahydrochromen-4-one, is also formed as a side product in a few cases with excellent diastereoselectivity.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"2016-2023"},"PeriodicalIF":2.2,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Harnessing the versatility of hydrazones through electrosynthetic oxidative transformations.","authors":"Aurélie Claraz","doi":"10.3762/bjoc.20.175","DOIUrl":"10.3762/bjoc.20.175","url":null,"abstract":"<p><p>Hydrazones are important structural motifs in organic synthesis, providing a useful molecular platform for the construction of valuable compounds. Electrooxidative transformations of hydrazones constitute an attractive opportunity to take advantage of the versatility of these reagents. By directly harnessing the electrical current to perform the oxidative process, a large panel of organic molecules can be accessed from readily available hydrazones under mild, safe and oxidant-free reaction conditions. This review presents a comprehensive overview of oxidative electrosynthetic transformations of hydrazones. It includes the construction of azacycles, the C(sp<sup>2</sup>)-H functionalization of aldehyde-derived hydrazones and the access to diazo compounds as either synthetic intermediates or products. A special attention is paid to the reaction mechanism with the aim to encourage further development in this field.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"1988-2004"},"PeriodicalIF":2.2,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Beatrice E Jones, Camille Blayo, Jake L Greenfield, Matthew J Fuchter, Nathan Cowieson, Rachel C Evans
{"title":"Understanding X-ray-induced isomerisation in photoswitchable surfactant assemblies.","authors":"Beatrice E Jones, Camille Blayo, Jake L Greenfield, Matthew J Fuchter, Nathan Cowieson, Rachel C Evans","doi":"10.3762/bjoc.20.176","DOIUrl":"10.3762/bjoc.20.176","url":null,"abstract":"<p><p>Dynamic, responsive materials can be built using photosurfactants (PS) that self-assemble into ordered nanostructures, such as micelles or liquid crystals. These PS contain photoswitchable groups, such as azobenzene (Azo) or, more recently, arylazopyrazoles (AAPs), which change shape and polarity on photoisomerisation between the <i>E</i> and <i>Z</i> states, thus changing the self-assembled structure. Small-angle X-ray scattering (SAXS) is a powerful technique to probe the morphology of PS and can be used to measure the mechanisms of structural changes using in-situ light irradiation with rapid, time-resolved data collection. However, X-ray irradiation has been shown previously to induce <i>Z-</i>to<i>-E</i> isomerisation of Azo-PS, which can lead to inaccuracies in the measured photostationary state. Here, we investigate the effect of light and X-ray irradiation on micelles formed from two different PS, containing either an Azo or AAP photoswitch using SAXS with in-situ light irradiation. The effect of X-ray irradiation on the <i>Z</i> isomer is shown to depend on the photoswitch, solvent, concentration and morphology. We use this to create guidelines for future X-ray experiments using photoswitchable molecules, which can aid more accurate understanding of these materials for application in solar energy storage, catalysis or controlled drug delivery.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"2005-2015"},"PeriodicalIF":2.2,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Masahiro Terada, Zen Iwasaki, Ryohei Yazaki, Shigenobu Umemiya, Jun Kikuchi
{"title":"Development of a flow photochemical process for a π-Lewis acidic metal-catalyzed cyclization/radical addition sequence: in situ-generated 2-benzopyrylium as photoredox catalyst and reactive intermediate.","authors":"Masahiro Terada, Zen Iwasaki, Ryohei Yazaki, Shigenobu Umemiya, Jun Kikuchi","doi":"10.3762/bjoc.20.173","DOIUrl":"10.3762/bjoc.20.173","url":null,"abstract":"<p><p>A flow photochemical reaction system for a π-Lewis acidic metal-catalyzed cyclization/radical addition sequence was developed, which utilizes in situ-generated 2-benzopyrylium intermediates as the photoredox catalyst and electrophilic substrates. The key 2-benzopyrylium intermediates were generated in the flow reaction system through the intramolecular cyclization of <i>ortho</i>-carbonyl alkynylbenzene derivatives by the π-Lewis acidic metal catalyst AgNTf<sub>2</sub> and the subsequent proto-demetalation with trifluoroacetic acid. The 2-benzopyrylium intermediates underwent further photoreactions with benzyltrimethylsilane derivatives as the donor molecule in the flow photoreactor to provide 1<i>H</i>-isochromene derivatives in higher yields in most cases than the batch reaction system.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"1973-1980"},"PeriodicalIF":2.2,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marwa Elsbaey, Naoya Oku, Mohamed S A Abdel-Mottaleb, Yasuhiro Igarashi
{"title":"Allostreptopyrroles A-E, β-alkylpyrrole derivatives from an actinomycete <i>Allostreptomyces</i> sp. RD068384.","authors":"Marwa Elsbaey, Naoya Oku, Mohamed S A Abdel-Mottaleb, Yasuhiro Igarashi","doi":"10.3762/bjoc.20.174","DOIUrl":"10.3762/bjoc.20.174","url":null,"abstract":"<p><p>Five new β-alkylpyrrole derivatives, allostreptopyrroles A-E (<b>1</b>-<b>5</b>), were isolated from the culture broth of <i>Allostreptomyces</i> RD068384. Their structures were elucidated by 1D and 2D NMR spectroscopic analyses, HRESIMS, and chemical derivatization. The absolute configurations of compounds <b>2</b> and <b>3</b> were predicted by comparison of experimental and calculated specific rotation data. Compounds <b>1</b>-<b>5</b> are the first examples of natural pyrroles substituted by formyl and carboxyl functionalities. Compounds <b>1</b>, <b>4</b>, and <b>5</b> showed cytotoxicity against Kasumi-1 human acute myeloblastic leukemia cells with IC<sub>50</sub> values of 103, 105, and 105 μM, respectively, which are less active than the anticancer agent cisplatin, with an IC<sub>50</sub> value of 70 μM.</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"20 ","pages":"1981-1987"},"PeriodicalIF":2.2,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Liubov V. Sokolenko, Taras M. Sokolenko, Yurii L. Yagupolskii
{"title":"1,2-Difluoroethylene (HFO-1132): synthesis and chemistry","authors":"Liubov V. Sokolenko, Taras M. Sokolenko, Yurii L. Yagupolskii","doi":"10.3762/bjoc.20.171","DOIUrl":"https://doi.org/10.3762/bjoc.20.171","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>This article provides a comprehensive overview of the synthesis and chemistry of 1,2-difluoroethylene (HFO-1132). The major routes for the preparation of the <i>E</i>- and <i>Z</i>-isomer of HFO-1132 are reviewed, along with the chemistry in radical, nucleophilic, and electrophilic reactions.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-171-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1955–1966. doi:10.3762/bjoc.20.171</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"5 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141947835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Radical reactivity of antiaromatic Ni(II) norcorroles with azo radical initiators","authors":"Siham Asyiqin Shafie, Ryo Nozawa, Hideaki Takano, Hiroshi Shinokubo","doi":"10.3762/bjoc.20.172","DOIUrl":"https://doi.org/10.3762/bjoc.20.172","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>Norcorrole is a stable 16π-antiaromatic porphyrinoid that exhibits characteristic reactivities and physical properties. Here, we disclose the reaction of Ni(II) norcorroles with alkyl radicals derived from azo radical initiators. The radical selectively attacked the distal α-position relative to the <i>meso</i>-position to construct a nonaromatic bowl-shaped structure. The photophysical and electrochemical properties of the obtained radical adducts were compared to those of the parent Ni(II) norcorrole. The radical reactivity of Ni(II) norcorroles was investigated by density functional theory (DFT) calculations.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-172-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1967–1972. doi:10.3762/bjoc.20.172</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"47 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141947836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ze-Nan Hu, Yan-Hui Wang, Jia-Bing Wu, Ze Chen, Dou Hong, Chi Zhang
{"title":"Solvent-dependent chemoselective synthesis of different isoquinolinones mediated by the hypervalent iodine(III) reagent PISA","authors":"Ze-Nan Hu, Yan-Hui Wang, Jia-Bing Wu, Ze Chen, Dou Hong, Chi Zhang","doi":"10.3762/bjoc.20.167","DOIUrl":"https://doi.org/10.3762/bjoc.20.167","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>Isoquinolinone is an important heterocyclic framework in natural products and biologically active molecules, and the efficient synthesis of this structural motif has received much attention in recent years. Herein, we report a (phenyliodonio)sulfamate (PISA)-mediated, solvent-dependent synthesis of different isoquinolinone derivatives. The method provides highly chemoselective access to 3- or 4-substituted isoquinolinone derivatives by reacting <i>o</i>-alkenylbenzamide derivatives with PISA in either acetonitrile or wet hexafluoro-2-isopropanol.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-167-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1914–1921. doi:10.3762/bjoc.20.167</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":"44 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141947838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}