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Revised structural assignment of azalomycins based on genomic and chemical analysis

Symbiotic Actinomycetes are known to produce a plethora of natural products of pharmacological importance and global genome sequencing efforts unraveled their unique and still mostly untapped biosynthetic potential. To activate natural product biosynthesis in Actinobacteria and to harvest the wealth of natural products, cultivation conditions mimicking the natural environment turned out to be amongst the most promising approach next to molecular biotechnological tools. We have recently applied ecology-driven interaction studies between bacterial symbionts of fungus-farming termites and their natural antagonists to activate the biosynthetic repertoire of actinomycetous symbionts. In light of these studies, we revisited the bacterial symbiont Streptomyces sp. M56 (from now on named M56), which showed very strong antagonistic effect against parasitic co-isolated fungi and was found to produce, not only the ansamycin-derived natural products natalamycin and geldanamycin, but also elaiophylins and the structurally related efomycins.  

Our group thoroughly investigated culture extracts obtained from strain M56 by liquid chromatography/high resolution tandem mass spectrometry (LC-HRMS2) and Global Natural Product Social Molecular Networking (GNPS) analysis. Indeed, dereplication of the acquired MS2 data based on available databases resulted in the detection of several polyhydroxylated macrolides identified as the antifungal azalomycins (Figure 1). Although the planar structures of azalomycins were reported as early as 1959 and the first skeletal structure assigned already in 1982, reports on their absolute structures remained inconclusive with varying structural assignments across the literature (Figure 2). 

Figure. 1. A) HRMS2-based GNPS analysis depicting molecular ion cluster putatively assigned as an azalomycin cluster with putative structural features assigned to m/z 1096.69, 1082.67 and 1068.66 (diol moiety C-18 and C-19); m/z 1080.69 and 1066.68 (C-19 alcohol); m/z 1062.68 and 1048.67 (enoyl derivatives); m/z 1078.68 (C-19/C-18 epoxy). Data obtained from HRMS2 measurements of EtOAc extract (7 d, ISP2 liquid broth) in positive mode ESI-HRMS. B) Stereochemical assignment of isolated azalomycins (1–4) from Streptomyces sp. M56.

Figure 2. A) Structure of azalomycin (1) with key COSY (bold) and HMBC (pink arrow) and NOE (blue double-headed arrow) correlations and coupling constant analysis. B) Stereochemical assignment of azalomycins substructures isolated from different producer strains based on a) NMR analysis and b) in silico PKS domain predictions. C) Chemical structures of azalomycins reported from Streptomyces sp. 211726,22,29 and Streptomyces malaysiensis DSM 413723 and Streptomyces hygroscopicus. Stereocenters that differ from herein proposed structure or have been newly assigned based on analytical experiments are colour-coded in red.

Due to their strong antimicrobial activity, but inconclusive structural assignments, we re-evaluated the analytical and bioactivity data of azalomycins. Here, we provide a conclusive analysis of their stereochemical assignment based on comparative NMR and gene clusters studies and propose to partially revise the absolute structures and names of azalomycins from previous reports (Figure 3).

Figure 3. A) Graphical comparison of azalomycins biosynthesis gene cluster (azu) from Streptomyces sp. M56 and azalomycin F3a biosynthesis gene cluster (azl) from Streptomyces sp. 211726, and niphimycin C biosynthesis gene cluster (npm) from Streptomyces sp. IMB7-145. B) Schematic representation of important biosynthetic transformations yielding the azalomycin core structure. The ER domain of module 1 is assumed to be non-functional; dash-circulated domain represents the missing module required for chain elongation. Ata (blue): malonyl-CoA selective AT domain (acetate unit); ATp (light red): methylmalonyl-CoA selective AT domain (propionate unit); ACP (dark red): acyl carrier protein; DH (light orange): dehydratase; ER (brown-black): enoylreductase; KR: ketoreductase (A1 or B1); TE (purple): thioesterase.

Biography

Ki Hyun Kim is associate professor in the School of Pharmacy at the Sungkyunkwan University (Republic of Korea). He earned his pharmacist’s license in 2005 and he received his PhD in the School of Pharmacy at the Sungkyunkwan University in 2011. From 2011 to 2012 he did postdoctoral studies at the School of Pharmacy at the Sungkyunkwan University, and from 2012 to 2013 at Harvard University and Harvard Medical School. He started his faculty in the School of Pharmacy at the Sungkyunkwan University in 2014. The main research field of Professor Kim is the discovery of the secondary metabolites from diverse natural resources including wild mushrooms, insect-associated bacteria, marine natural sources and medicinal plants and his group has substantial experience and expertise in natural product isolation and structural elucidation using mainly NMR-based analysis as well as biological activity evaluations. He is the author of 7 patents and more than 300 articles indexed by SCIE and cited more than 1500 times with an index H = 20.

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Systematic structural variation and visualization of chemical shielding tensors (VIST) provide unique insights into the properties of π-conjugated macrocycles

π-Conjugated macrocycles are molecules with unique properties that are increasingly exploited for applications. Their study began in the early 1960s and many π-conjugated macrocycles have been synthesized since. However, only recently the field has moved towards making use of the unique properties of these cyclic molecules for applications. π-Conjugated macrocycles are now being investigated in organic solar cells, photodetectors, field-effect transistors, light-emitting diodes, and battery electrodes. They can also be used in bioimaging, as templates for the growth of carbon nanotubes, and as molecular nanoreactors.

Figure 1. (a) Reversible two-electron reduction of a π-conjugated macrocycle for charge storage in organic battery electrodes. (b) Visualization of chemical shielding tensors (VIST) helping to rationalize the optoelectronic properties.

Despite this recent interest in π-conjugated macrocycles, there are only a small number of experimental studies that investigate how the properties of π-conjugated macrocycles evolve with systematic structural changes. Recently, a team around Florian Glöcklhofer has reported such a systematic experimental study and combined it with an in-depth computational analysis. The study reveals the central role of local and global aromaticity for rationalizing the optoelectronic properties of the macrocycles. A recently developed computational method for the visualization of chemical shielding tensors (VIST) was applied to provide unique insight into local and global ring currents occurring in different planes along the macrocycles.

Figure 2. Functional group introduction and aromatic unit variation in a set of π-conjugated macrocycles.

The study makes a significant contribution to the development of structure–property relationships and molecular design guidelines and will help to understand, rationalize, and predict the properties of other π-conjugated macrocycles. Furthermore, it shows that cyclophanetetraenes, the investigated class of macrocycles, provide versatile scaffolds for applications due to their unusual properties along with their high tunability. Their remarkable optoelectronic properties, in particular their large Stokes shifts and the accessibility of a variety of charged states, were traced back to their formal ground state antiaromaticity along with high structural flexibility.

Rimmele, M.;  Nogala, W.;  Seif-Eddine, M.;  Roessler, M. M.;  Heeney, M.;  Plasser, F.; Glöcklhofer, F., Functional group introduction and aromatic unit variation in a set of π-conjugated macrocycles: revealing the central role of local and global aromaticity, Organic Chemistry Frontiers 2021, Advance Article. https://doi.org/10.1039/D1QO00901J

Author’s Biography

Florian Glöcklhofer is an Erwin Schrödinger Fellow in the Department of Chemistry at Imperial College London. He received his PhD in 2017 at TU Wien (Vienna) for developing a reaction for the conversion of quinones into cyanated aromatic compounds. His research in the field of π-conjugated organic compounds focuses on the design and synthesis of π-conjugated macrocycles for battery electrodes and organic electronics and on the development of new synthetic approaches to aromatic organic compounds.

https://www.gloecklhofer-research.com/

 

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Recent advance in the C-F bond functionalization of trifluoromethyl-containing compounds

Organofluorine compounds play an important role in pharmaceuticals, agrochemicals, and functional materials, due to their special chemical, physical and biological properties, such as increased electronegativity, hydrophobicity, bioavailability and metabolic stability. Therefore, great efforts have recently been devoted to the development of new methods for the synthesis of fluorinated compounds. Conventional strategies mainly focus on the selective introduction of fluorine atom or fluorine-containing moiety into organic molecules. Alternatively, the development of novel synthetic methodologies via the selective activation of C-F bond is of vital importance, which could allow for the synthesis of partially fluorinated synthetic intermediates from readily available polyfluorinated starting materials. The research of C-F bond activation is the most challenging task in organic synthesis, which has recently drawn increasing attention from chemists. In this review, we mainly focus on the C-F bond activation of CF3 groups for the synthesis of fluorinated compounds as well as discussion of their mechanisms(Scheme 1).

Scheme 1 The C-F bond functionalization of trifluoromethyl-containing compounds.

Due to the electron-deficient property, α-trifluoromethylstyrenes exhibit unique reactivities in their C-F bonds activation, mainly including three kinds of reactions (SN2′-type, SNV and ipso-substitution reactions, Scheme 2).

Scheme 2 Allylic and vinylic C-F bond activation in SN2’-type, SNV and ipso-sunstitution reactions

The cleavage of C-F bond in trifluoromethylated aromatic (Scheme 3) and alkyl compounds (Scheme 4) could be achieved through using transition metal complexes, main-group Lewis acids and base-conditions. An alternative strategy mainly relied on the single-electron transfer (SET) via Low-valent metals, irradiation with visible light.

Scheme 3 Photoredox-catalyzed defluoroalkylation of ArCF3 with unactivated alkenes.

Scheme 4 Pd-catalyzed defluorination/arylation reaction of α-trifluoromethyl ketones with aryl boronic acids.

Trifluoromethyl ketones (Scheme 5) and their corresponding diazo compounds (Scheme 6) , N‑tosylhydrazones (Scheme 7) have been utilized as the coupling partners in modern synthetic organic chemistry. Recently, the C-F bond cleavage of these compounds has also been reported through transition-metal catalysts.

Scheme 5 Cu-catalyzed reaction of trifluoromethylketones with aldehydes.

Scheme 6 Cu-catalyzed gem-difluoroolefination of diazo compounds.

Scheme 7 Cu-catalyzed cross-coupling of N-tosylhydrazones with terminal alkynes.

Although great progress has been made in this rapidly developing area, these reactions still suffer from some issues of the limitation of substrates and poor regioselectivity. To overcome these central challenges, it is more important to extend the substrate scope of the existing methodologies, especial trifluoromethylated alkyl compounds. Furthermore, the robust catalytic systems will be developed for the selective activation of a single C-F bond in CF3 groups.

 Guobing Yan

Zhejiang A&F University

Guobing Yan is a Professor in college of Jiyang at Zhejiang A&F University. He obtained B.Sc. degree from Jinggangshan Normal University, his M.Sc. degree from Suzhou University, and his Ph.D. degree from Tongji University in 2010. He spent two years in 2008 and 2009 as visiting student in professor Jianbo Wang’s laboratory at Peking University. In 2013, He joined Dr. Dong’s group at the University of Texas at Austin as a visiting professor. His current research interests focus on the transition-metal-catalyzed activation of inert chemical bonds and green synthetic chemistry. He is the author of 6 patents and more than 70 articles indexed by SCI.

 

Recent Advance in the C-F bond functionalization of trifluoromethyl-containing compounds

Guobing Yan, Kaiying Qiu and Ming Guo

https://doi.org/10.1039/D1QO00037C

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C(sp3)–H functionalization with isocyanides

Isocyanides have proven to be versatile building blocks in organic synthesis and medicinal chemistry due to their synthetic possibilities capable of reacting with electrophiles, nucleophiles and radicals. Multi-component reactions involving isocyanides have been well developed with the advantages of diverse skeletons of products, functional group compatibility, high chemo-, regio and stereoselectivities, and atom economy. With the continuous research on isocyanides, C(sp3)–H functionalization with isocyanides has made significant progresses with the advancement of mechanistic studies, new techniques and novel strategies in recent years. In this review, the group of Xu and coworkers of Shanghai University of China highlights the most recent advances of isocyanide chemistry in the C(sp3)–H functionalization since 2015 by elaborating the strategies of state-of-the-art synthetic routes. The synergistic combination of the isocyanide insertion and the C(sp3)–H bond activation offers a novel and efficient route to establish complicated reactions and provides an effective strategy for the synthesis of various nitrogen- and oxygen-containing compounds.

Figure 1.C(sp3)–H functionalization with isocyanides

Bin Xu received his bachelor’s degree from Shanghai University of Science and Technology in 1992. He conducted his PhD research with Professor Shengming Ma at Shanghai Institute of Organic Chemistry and completed his degree in 2000. After a two-year postdoctoral training at National Institutes of Health (NIH) as a Visiting Fellow (Mentor: Dr Kenneth A. Jacobson), he joined VivoQuest as a staff scientist (2002–2005). He began his independent academic career at Shanghai University in the end of 2005 as a Full Professor. His current research interests span the development of new methodology for nitrogen-containing heterocycles and their biological applications.

C(sp3)–H Functionalization with Isocyanides

Org. Chem. Front., 2021, Accepted Manuscript

https://pubs.rsc.org/en/content/articlelanding/2021/qo/d1qo00153a#!divAbstract

 

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Outstanding Reviewers for Organic Chemistry Frontiers in 2019

We would like to highlight the Outstanding Reviewers for Organic Chemistry Frontiers in 2019, as selected by the editorial team, for their significant contribution to the journal. The reviewers have been chosen based on the number, timeliness and quality of the reports completed over the last 12 months.

We would like to say a big thank you to those individuals listed here as well as to all of the reviewers that have supported the journal. Each Outstanding Reviewer will receive a certificate to give recognition for their significant contribution.

Dr Pablo Ballester, Institute of Chemical Research of Catalonia (ICIQ), ORCID: 0000-0001-8377-6610

Dr Ying-Chun Chen, Sichuan University, ORCID: 0000-0003-1902-0979

Prof Xuefeng Jiang East China Normal University, ORCID: 0000-0002-1849-6572

Dr Shukkoor Muhammed Kondengaden, Georgia State University

Prof Zhan Lu, Zhejiang Universitry, ORCID: 0000-0002-3069-079X

Dr Feng Shi, Jiangsu Normal University, ORCID: 0000-0003-3922-0708

Dr Qiuling Song, Huaqiao Univeristy, ORCID: 0000-0002-9836-8860

Dr Jie Wu, Fudan University, ORCID: 0000-0002-0967-6360

Dr Da-Gang Yu, Sichuan University, ORCID: 0000-0001-5888-1494

Dr Yonghui Zhang, Huazhong University of Science and Technology, ORCID: 0000-0002-7222-2142

We would also like to thank the Organic Chemistry Frontiers board and the organic chemistry community for their continued support of the journal, as authors, reviewers and readers.

 

If you would like to become a reviewer for our journal, just email us with details of your research interests and an up-to-date CV or résumé.  You can find more details in our author and reviewer resource centre

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Welcome to Issue 13 of Organic Chemistry Frontiers in 2019

Welcome to issue 13 of Organic Chemistry Frontiers for 2019 ! The latest OrgChemFront issue is published online now.

 

The front cover story, Palladiumcatalyzed regioselective C–H alkynylation of indoles with bromoalkynes in water by Wanqing Wu and co-authors. The inside cover features a story on Trifluoromethyl-substituted selenium ylide: a broadly applicable electrophilic trifluoromethylating reagent by Hangming Ge and Qilong Shen .

 

 

 

 

 

 

 

Follow review type articles are included in current issue:

Developments towards synthesis of N-heterocycles from amidines via C–N/C–C bond formation
Wei Guo, Mingming Zhao, Wen Tan, Lvyin Zheng, Kailiang Tao and Xiaolin Fan

Org. Chem. Front., 2019,6, 2120-2141
https://doi.org/10.1039/C9QO00283A

 

Recent synthetic applications of α-amido sulfones as precursors of N-acylimino derivatives
Enrico Marcantoni, Alessandro Palmieri and Marino Petrini

Org. Chem. Front., 2019,6, 2142-2182
https://doi.org/10.1039/C9QO00196D

 

Metal-catalyzed radical-type transformation of unactivated alkyl halides with C–C bond formation
under photoinduced conditions
Shengqing Ye, Tianyi Xiang, Xiaofang Li and Jie Wu

Org. Chem. Front., 2019,6, 2183-2199
https://doi.org/10.1039/C9QO00272C

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Welcome to Issue 7 of Organic Chemistry Frontiers in 2019

Welcome to issue 7 of Organic Chemistry Frontiers for 2019 ! The latest OrgChemFront issue is published online now.

The front cover story, A concise approach for determining the relative configuration of H-7 and H-8 in 8,4′-oxyneolignans by 1H NMR spectroscopy, is contributed by  Pei-Cheng Zhang and co-authors.

The inside cover features a story on Guest-mediated chirality transfer in the host–guest complexes of an atropisomeric perylene bisimide cyclophane host by Frank Würthner and co-authors.

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9th Pacific Symposium on Radical Chemistry

OCF is very pleased to be sponsoring the “9th Pacific Symposium on Radical Chemistry (PSRC-9)” to be held at the Asilomar Conference Grounds in Pacific Grove, California, USA. The Symposium will be held from the 16th to the 21st of June 2019.

Register early for reduced fee by 1st April 2019!

The symposium will cover all aspects of free radical chemistry and will bring together industrial and academic chemists from all over the world to report their latest discoveries in the fields of synthetic radical reactions, radical polymerizations, mechanistic insights into important radical reactions, new radical-based functional molecules and materials, as well as all aspects of radicals impacting in biology and medicine. The scientific program of PSRC-9 will include plenary lectures and invited lectures as well as poster sessions.

Find out more about this conference from the official website!

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Hot Articles in November 2018

Organic Chemistry Frontiers is delighted to share with you the HOT article of November 2018!

You can access this publication for free till 31st  January 2019 by logging into your free Royal Society of Chemistry publishing personal account (http://pubs.rsc.org)

Cross-dehydrogenative alkynylation of sulfonamides and amides with terminal alkynes via Ir(III) catalysis
Guocai Wu, Wensen Ouyang, Qian Chen, Yanping Huo and Xianwei Li
Org. Chem. Front., 2018, Advance Article
http://dx.doi.org/10.1039/C8QO01105B

Direct conjugate additions using aryl and alkyl organic halides in air and water
Feng Zhou, Xiaoyun Hu, Wanying Zhang and Chao-Jun Li
Org. Chem. Front., 2018, Advance Article
http://dx.doi.org/10.1039/C8QO01141A

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Outstanding Reviewers for Organic Chemistry Frontiers in 2016

Following the success of Peer Review Week in September 2016 (dedicated to reviewer recognition) during which we published a list of our top reviewers, we are delighted to announce that we will continue to recognise the contribution that our reviewers make to the journal by announcing our Outstanding Reviewers each year.

We would like to highlight the Outstanding Reviewers for Organic Chemistry Frontiers in 2016, as selected by the editorial team, for their significant contribution to the journal. The reviewers have been chosen based on the number, timeliness and quality of the reports completed over the last 12 months.

We would like to say a big thank you to those individuals listed here as well as to all of the reviewers that have supported the journal. Each Outstanding Reviewer will receive a certificate to give recognition for their significant contribution.

Professor Jie Wu, Fudan University

Professor Zhang-jie Shi, Fudan University

Professor Jin-Heng Li,  Hunan University

Professor Yuhong Zhang, Zhejiang University

Professor Shuanhu Gao, East China Normal University

Professor Itaru Nakamura, Tohoku University

Professor Xingwei Li, Dalian Institute of Chemical Physics

Professor Jianbo Wang, Peking University

Professor Qiuling Song, Huaqiao University

Professor Louis Fensterbank, Université Pierre et Marie Curie

We would also like to thank the Organic Chemistry Frontiers board and the Organic Chemistry community for their continued support of the journal, as authors, reviewers and readers.

If you would like to become a reviewer for our journal, just email us with details of your research interests and an up-to-date CV or résumé.  You can find more details in our author and reviewer resource centre

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