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Wennrich JP, Holzenkamp C, Kolařík M, Maier W, Mándi A, Kurtán T, Ashrafi S, Ebada SS, Stadler M. Dactylfungins and Tetralones: Bioactive Metabolites from a Nematode-Associated Laburnicola nematophila. JOURNAL OF NATURAL PRODUCTS 2024; 87:1860-1871. [PMID: 39012621 DOI: 10.1021/acs.jnatprod.4c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
A chemical investigation of Laburnicola nematophila, isolated from cysts of the plant parasitic nematode Heterodera filipjevi, affored three dactylfungin derivatives (1-3) and three tetralone congeners (4-6). Dactylfungin C (1), laburnicolin (4), and laburnicolenone (5) are previously undescribed natural products. Chemical structures of the isolated compounds were determined based on 1D and 2D NMR spectroscopic analyses together with HR-ESI-MS spectrometry and comparison with data reported in the literature. The relative configurations of compounds 1, 2, and 4-6 were determined based on their ROESY data and analysis of their coupling constants (J values). The absolute configurations of 4-6 were determined through the comparison of their measured and calculated TDDFT-ECD spectra. Compounds 1-3 were active against azole-resistant Aspergillus fumigatus.
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Affiliation(s)
- Jan-Peer Wennrich
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Caren Holzenkamp
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Miroslav Kolařík
- Institute of Microbiology, Czech Academy of Science, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Wolfgang Maier
- Institute for Epidemiology and Pathogen Diagonstics, Julius Kühn Institut (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Samad Ashrafi
- Institute for Epidemiology and Pathogen Diagonstics, Julius Kühn Institut (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
- Institute for Crop and Soil Science, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Bundesallee 58, 38116 Braunschweig, Germany
| | - Sherif S Ebada
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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2
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Li T, Jiang S, Li T, Xu H, Zhang X, Yan R, Wu X, Jin Y, Wang Z. Exploring the Potential of Cyclic Peptidyl Antitumor Agents Derived from Natural Macrocyclic Peptide Phakellistatin 13. J Med Chem 2024; 67:11789-11813. [PMID: 38990190 DOI: 10.1021/acs.jmedchem.4c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The exploration of novel anticancer compounds based on natural cyclopeptides has emerged as a pivotal paradigm in the contemporary advancement of macrocyclic pharmaceuticals. Phakellistatin 13 is a cycloheptapeptide derived from the brown snubby sponge and exhibits remarkable antitumor activity. In this study, we have designed and synthesized a series of chiral cyclopeptides incorporating the rigid isoindolinone moiety at various sites within the natural cycloheptapeptide Phakellistatin 13, with the aim of investigating conformationally constrained cyclopeptides as potential antitumor agents. Cyclopeptide 3, comprising alternating l-/d-amino acid residues, exhibited promising antihepatocellular carcinoma effects. Detailed biological experiments have revealed that Phakellistatin 13 analogs effectively inhibit the proliferation of tumor cells and induce apoptosis and autophagy, while also causing cell cycle arrest through the modulation of the p53 and mitogen-activated protein kinase (MAPK) signaling pathway. This study not only provides valuable insights into chemical structural modifications but also contributes to a deeper understanding of the biological mechanisms underlying the development of natural cyclopeptide-based drugs.
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Affiliation(s)
- Tong Li
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Shitian Jiang
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Tingting Li
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Hongyu Xu
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Xiong Zhang
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Rui Yan
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Xiaodan Wu
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Yingxue Jin
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Zhiqiang Wang
- Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry & Chemical Engineering, Harbin Normal University, Harbin 150025, China
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Mándi A, Rimóczi A, Vasas A, Hohmann J, Swamy MMM, Monde K, Barta RA, Kicsák M, Komáromi I, Fehér K, Kurtán T. Testing the Simplified Molecular Dynamics Approach to Improve the Reproduction of ECD Spectra and Monitor Aggregation. Int J Mol Sci 2024; 25:6453. [PMID: 38928181 PMCID: PMC11204327 DOI: 10.3390/ijms25126453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
A simplified molecular-dynamics-based electronic circular dichroism (ECD) approach was tested on three condensed derivatives with limited conformational flexibility and an isochroman-2H-chromene hybrid, the ECD spectra of which could not be precisely reproduced by the conventional ECD calculation protocol. Application of explicit solvent molecules at the molecular mechanics (MD) level in the dynamics simulations and subsequent TDDFT-ECD calculation for the unoptimized MD structures was able to improve the agreements between experimental and computed spectra. Since enhancements were achieved even for molecules with limited conformational flexibility, deformations caused by the solvent molecules and multitudes of conformers produced with unoptimized geometries seem to be key factors for better agreement. The MD approach could confirm that aggregation of the phenanthrene natural product luzulin A had a significant contribution to a specific wavelength range of the experimental ECD. The MD approach has proved that dimer formation occurred in solution and this was responsible for the anomalous ECD spectrum. The scope and limitations of the method have also been discussed.
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Affiliation(s)
- Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.R.); (R.A.B.); (M.K.); (T.K.)
| | - Aliz Rimóczi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.R.); (R.A.B.); (M.K.); (T.K.)
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Andrea Vasas
- Institute of Pharmacognosy, University of Szeged, 6720 Szeged, Hungary; (A.V.); (J.H.)
- HUN-REN-USZ Biologically Active Natural Products Research Group, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Judit Hohmann
- Institute of Pharmacognosy, University of Szeged, 6720 Szeged, Hungary; (A.V.); (J.H.)
- HUN-REN-USZ Biologically Active Natural Products Research Group, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Mahadeva M. M. Swamy
- Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Sapporo 001-0021, Japan; (M.M.M.S.); (K.M.)
| | - Kenji Monde
- Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Sapporo 001-0021, Japan; (M.M.M.S.); (K.M.)
| | - Roland A. Barta
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.R.); (R.A.B.); (M.K.); (T.K.)
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Máté Kicsák
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.R.); (R.A.B.); (M.K.); (T.K.)
| | - István Komáromi
- Vascular Biology, Thrombosis and Hemostasis Research Group, Hungarian Academy of Sciences, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Krisztina Fehér
- HUN-REN–UD Molecular Recognition and Interaction Research Group, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.R.); (R.A.B.); (M.K.); (T.K.)
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Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
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Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
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Osadchuk I, Luts HE, Zahharova A, Tamm T, Borovkov V. Controlling Chirogenic Effects in Porphyrin Based Supramolecular Systems: Theoretical Analysis Versus Experimental Observations. Chemphyschem 2024; 25:e202400104. [PMID: 38693766 DOI: 10.1002/cphc.202400104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/18/2024] [Indexed: 05/03/2024]
Abstract
Electronic circular dichroism (ECD) spectroscopy is a widely employed method for studying chiral analysis, requiring the presence of a chromophore close to a chiral centre. Porphyrinoids are found to be one of the best chromophoric systems serving for this purpose and enabling the application of ECD spectroscopy for chirality determination across diverse classes of organic compounds. Consequently, it is crucial to understand the induction mechanisms of ECD in the porphyrin-based complexes. The present study explores systematically the influence of secondary chromophores, bonded to an achiral zinc porphyrin or to chiral guest molecules, on the B-region of ECD spectra using the time-dependent density functional theory (TD-DFT) calculations. The study analyses the impact of change in both the conformation of achiral porphyrin (host) and change in position and conformation of chiral organic molecule (guest) on the B-band of ECD spectra (energy, intensity, sign of Cotton effect). Finally, conclusions made on model complexes are applied to published experimental data, contributing to a deeper understanding of various factors influencing ECD spectra in chiral systems. In addition, a computer program aimed to help rationalise ECD spectra by visualizing corresponding orbital energies, rotatory strengths, electric and magnetic transition moments, and angles between them, is presented.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Aleksandra Zahharova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Toomas Tamm
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
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Wang Y, Cao F, Zhou L, Liu H, Gao H, Cui G, Niu C, Zhang P, Li D, Liu S, Jiang Y, Wu G. Combining the Elicitor Up-Regulated Production of Unusual Linear Diterpene-Derived Variants for an In-Depth Assessment of the Application Value and Risk of the Medicinal and Edible Basidiomycete Schizophyllum commune. Molecules 2024; 29:2608. [PMID: 38893484 PMCID: PMC11173764 DOI: 10.3390/molecules29112608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
To better assess the practical value and avoid potential risks of the traditionally medicinal and edible basidiomycete Schizophyllum commune, which may arise from undescribed metabolites, a combination of elicitors was introduced for the first time to discover products from cryptic and low-expressed gene clusters under laboratory cultivation. Treating S. commune NJFU21 with the combination of five elicitors led to the upregulated production of a class of unusual linear diterpene-derived variants, including eleven new ones (1-11), along with three known ones (12-14). The structures and stereochemistry were determined by 1D and 2D NMR, HRESIMS, ECD, OR and VCD calculations. Notably, the elongation terminus of all the diterpenes was decorated by an unusual butenedioic acid moiety. Compound 1 was a rare monocyclic diterpene, while 2-6 possessed a tetrahydrofuran moiety. The truncated metabolites 4, 5 and 13 belong to the trinorditerpenes. All the diterpenes displayed approximately 70% scavenging of hydroxyl radicals at 50 μM and null cytotoxic activity at 10 μM. In addition, compound 1 exhibited potent antifungal activity against the plant pathogenic fungi Colletotrichum camelliae, with MIC values of 8 μg/mL. Our findings indicated that this class of diterpenes could provide valuable protectants for cosmetic ingredients and the lead compounds for agricultural fungicide development.
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Affiliation(s)
- Ying Wang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (H.G.); (G.C.); (S.L.)
| | - Fei Cao
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China;
| | - Luning Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (L.Z.); (D.L.)
| | - Hanwei Liu
- Ningbo Customs District Technology Center, Ningbo 315100, China;
| | - Hua Gao
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (H.G.); (G.C.); (S.L.)
| | - Ge Cui
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (H.G.); (G.C.); (S.L.)
| | - Changshan Niu
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA; (C.N.); (P.Z.)
| | - Peng Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA; (C.N.); (P.Z.)
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (L.Z.); (D.L.)
| | - Songqi Liu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (H.G.); (G.C.); (S.L.)
| | - Yan Jiang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (H.G.); (G.C.); (S.L.)
| | - Guangwei Wu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (Y.W.); (H.G.); (G.C.); (S.L.)
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Simons VE, Mándi A, Frank M, van Geelen L, Tran-Cong N, Albrecht D, Coort A, Gebhard C, Kurtán T, Kalscheuer R. Colletodiol derivatives of the endophytic fungus Trichocladium sp. Fitoterapia 2024; 175:105914. [PMID: 38508500 DOI: 10.1016/j.fitote.2024.105914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/21/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
The OSMAC (one strain many compounds) concept is a cultivation-based approach to increase the diversity of secondary metabolites in microorganisms. In this study, we applied the OSMAC-approach to the endophytic fungus Trichocladium sp. by supplementation of the cultivation medium with 2.5% phenylalanine. This experiment yielded five new compounds, trichocladiol (1), trichocladic acid (2), colletodiolic acid (3), colletolactone (4) and colletolic acid (5), together with five previously described ones (6-10). The structures were elucidated via comprehensive spectroscopic measurements, and the absolute configurations of compound 1 was elucidated by using TDDFT-ECD calculations. For formation of compounds 3-5, a pathway based on colletodiol biosynthesis is proposed. Compound 6 exhibited strong antibacterial activity against methicillin-resistant Staphylococcus aureus with a minimal inhibitory concentration (MIC) of 0.78 μM as well as a strong cytotoxic effect against the human monocytic cell line THP1 with an IC50 of 0.7 μM. Compound 8 showed moderate antibacterial activity against Mycobacterium tuberculosis with a MIC of 25 μM and a weak cytotoxic effect against THP1 cells with an IC50 of 42 μM.
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Affiliation(s)
- Viktor E Simons
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, Debrecen 4002, Hungary
| | - Marian Frank
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Lasse van Geelen
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Nam Tran-Cong
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Dorothea Albrecht
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Annika Coort
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Christina Gebhard
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, Debrecen 4002, Hungary
| | - Rainer Kalscheuer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstrasse 1, Düsseldorf 40225, Germany.
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8
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Just D, Palivec V, Bártová K, Bednárová L, Pazderková M, Císařová I, Martinez-Seara H, Jahn U. Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides. Commun Chem 2024; 7:114. [PMID: 38796536 PMCID: PMC11128005 DOI: 10.1038/s42004-024-01201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024] Open
Abstract
Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.
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Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843, Prague 2, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
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9
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Lin FL, Gao JL, Xu Q, Wang GQ, Xiao LY, Dong L, Tang W, Lv JM, Chen GD, Wang Y, Yin ZN, Lu LG, Hu D, Gao H. Absolute Configuration of Oxabornyl Polyenes Prugosenes A1-A3 and Structural Revision of Prugosene A2. JOURNAL OF NATURAL PRODUCTS 2024; 87:1338-1346. [PMID: 38447084 DOI: 10.1021/acs.jnatprod.3c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Oxabornyl polyenes represent a unique group of polyketides characterized by a central polyene core flanked by a conserved oxabornyl moiety and a structurally diverse oxygen heterocyclic ring. They are widely distributed in fungi and possess a variety of biological activities. Due to the significant spatial separation between the two stereogenic ring systems, it is difficult to establish their overall relative configurations. Here, we isolated three oxabornyl polyenes, prugosenes A1-A3 (1-3), from Talaromyces sp. JNU18266-01. Although these compounds were first reported from Penicillium rugulosum, their overall relative and absolute configurations remained unassigned. By employing ozonolysis in combination with ECD calculations, we were able to establish their absolute configurations, and additionally obtained seven new chemical derivatives (4-10). Notably, through NMR data analysis and quantum chemical calculations, we achieved the structural revision of prugosene A2. Furthermore, prugosenes A1-A3 exhibited potent antiviral activity against the respiratory syncytial virus, with compound 1 displaying an IC50 value of 6.3 μM. Our study thus provides a valuable reference for absolute configuration assignment of oxabornyl polyene compounds.
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Affiliation(s)
- Fu-Long Lin
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, Guangdong China
| | - Jia-Ling Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Qian Xu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Liang-Yan Xiao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Lu Dong
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Wei Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Ying Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Zhi-Nan Yin
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, Guangdong China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, China
| | - Li-Gong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, Guangdong China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
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10
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Feineis D, Bringmann G. Structural variety and pharmacological potential of naphthylisoquinoline alkaloids. THE ALKALOIDS. CHEMISTRY AND BIOLOGY 2024; 91:1-410. [PMID: 38811064 DOI: 10.1016/bs.alkal.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Naphthylisoquinoline alkaloids are a fascinating class of natural biaryl compounds. They show characteristic mono- and dimeric scaffolds, with chiral axes and stereogenic centers. Since the appearance of the last comprehensive overview on these secondary plant metabolites in this series in 1995, the number of discovered representatives has tremendously increased to more than 280 examples known today. Many novel-type compounds have meanwhile been discovered, among them naphthylisoquinoline-related follow-up products like e.g., the first seco-type (i.e., ring-opened) and ring-contracted analogues. As highlighted in this review, the knowledge on the broad structural chemodiversity of naphthylisoquinoline alkaloids has been decisively driven forward by extensive phytochemical studies on the metabolite pattern of Ancistrocladus abbreviatus from Coastal West Africa, which is a particularly "creative" plant. These investigations furnished a considerable number of more than 80-mostly new-natural products from this single species, with promising antiplasmodial activities and with pronounced cytotoxic effects against human leukemia, pancreatic, cervical, and breast cancer cells. Another unique feature of naphthylisoquinoline alkaloids is their unprecedented biosynthetic origin from polyketidic precursors and not, as usual for isoquinoline alkaloids, from aromatic amino acids-a striking example of biosynthetic convergence in nature. Furthermore, remarkable botanical results are presented on the natural producers of naphthylisoquinoline alkaloids, the paleotropical Dioncophyllaceae and Ancistrocladaceae lianas, including first investigations on the chemoecological role of these plant metabolites and their storage and accumulation in particular plant organs.
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Affiliation(s)
- Doris Feineis
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany.
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11
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Hu Y, Zhao X, Song Y, Jiang J, Long T, Cong M, Miao Y, Liu Y, Yang Z, Zhu Y, Wang J. Anti-inflammatory and Neuroprotective α-Pyrones from a Marine-Derived Strain of the Fungus Arthrinium arundinis and Their Heterologous Expression. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38687877 DOI: 10.1021/acs.jnatprod.4c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Fungal linear polyketides, such as α-pyrones with a 6-alkenyl chain, have been a rich source of biologically active compounds. Two new (1 and 2) and four known (3-6) 6-alkenylpyrone polyketides were isolated from a marine-derived strain of the fungus Arthrinium arundinis. Their structures were determined based on extensive spectroscopic analysis. The biosynthetic gene cluster (alt) for alternapyrones was identified from A. arundinis ZSDS-F3 and validated by heterologous expression in Aspergillus nidulans A1145 ΔSTΔEM, which revealed that the cytochrome P450 monooxygenase Alt2' could convert the methyl group 26-CH3 to a carboxyl group to produce 4 from 3. Another cytochrome P450 monooxygenase, Alt3', catalyzed successive hydroxylation, epoxidation, and oxidation steps to produce 1, 2, 5, and 6 from 4. Alternapyrone G (1) not only suppressed M1 polarization in lipopolysaccharide (LPS)-stimulated BV2 microglia but also stimulated dendrite regeneration and neuronal survival after Aβ treatment, suggesting alternapyrone G may be utilized as a privileged scaffold for Alzheimer's disease drug discovery.
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Affiliation(s)
- Yiwei Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaoyang Zhao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yue Song
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jiahui Jiang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ting Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengjing Cong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yuhua Miao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Zhiyou Yang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Junfeng Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
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12
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Rode JE, Wasilczenko J, Górecki M. Differentiation of solvatomorphs of active pharmaceutical ingredients (API) by solid-state vibrational circular dichroism (VCD). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123851. [PMID: 38295593 DOI: 10.1016/j.saa.2024.123851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Here, we present the new application of solid-state Vibrational Circular Dichroism (VCD) spectroscopy to differentiate several dutasteride (DS) solvatomorphs - the model active pharmaceutical ingredient (API). Several crystalline DS hydrochloride hydrates solvated with methanol, ethanol, acetonitrile, acetone, and acetic acid were prepared. In contrast to almost identical IR spectra, the VCD ones were very sensitive to changes in the sample composition. We marked significant differences in the shape of VCD spectra of studied DS solvatomorphs, DS hydrates, and DS polymorphic forms. Our findings, supported by DFT calculations, show that VCD spectroscopy has the pronounced ability to distinguish their crystal arrangements. We believe that this contribution will extend the use of VCD in the pharmaceutical industry for developing and designing new chiral drug products for the identification, description, and in-depth probing of several pharmaceutical solvatomorphs in the future.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, Dorodna 16 St., 03-195 Warsaw, Poland
| | - Justyna Wasilczenko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224 Warsaw, Poland.
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13
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Lv TM, Guo R, Yang BH, Zhao P, Lin B, Huang XX, Song SJ. Structurally diverse 1,2-diarylpropanes from the fruit of Crataegus pinnatifida and the investigation on their mirror-image ECD spectra with the same absolute configurations. PHYTOCHEMISTRY 2024; 222:114067. [PMID: 38583852 DOI: 10.1016/j.phytochem.2024.114067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
1,2-diarylpropanes are a kind of abundant natural products formed by radical coupling. On account of molecular flexibility, it was challenged in the identifications of relative and absolute configurations of the 1,2-diarylpropanes. In this research, fourteen pairs of enantiomeric 1,2-diarylpropanes (1a/1b-14a/14b), comprising twelve previously undescribed pairs (1a/1b-4a/4b, 6a/6b-10a/10b, and 12a/12b-14a/14b), were isolated from the fruit of Crataegus pinnatifida. Their structures were determined through multiple NMR spectral analyses, empirical NMR rules, X-ray crystallography, and the comparison of experimental ECD spectra with calculated data. In addition, the analysis of ECD spectra revealed that substituent effects could generate an inverted chiroptical response, exhibiting in mirror-image ECD signals. This phenomenon was investigated by conformational analysis, molecular orbital analysis, the transition density matrix and hole/electron distributions. Moreover, a potential experimental rule was proposed for the rapid determination of the absolute configurations of the 1,2-diarylpropanes.
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Affiliation(s)
- Tian-Ming Lv
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Rui Guo
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Bo-Han Yang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Peng Zhao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China.
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14
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Olszewska K, Mizera A, Ławniczak P, Kamińska A, Santillan R, Morales-Chamorro M, Ochoa ME, Farfán N, Łapiński A, Górecki M, Jastrzebska I, Runka T. Molecular Dynamics of Steroidal Rotors Probed by Theoretical, Spectroscopic and Dielectric Methods. Chemistry 2024; 30:e202303933. [PMID: 38311598 DOI: 10.1002/chem.202303933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/06/2024]
Abstract
Our study focuses on molecular rotors with fast-moving rotators and their potential applications in the development of new amphidynamic crystals. Steroidal molecular rotors with a dipolar fluorine-substituted phenyl group as the rotator were synthesized and characterized. Three different rotors were investigated with varying numbers of fluorine atoms. A comprehensive analysis was performed using vibrational spectroscopy (Raman, FT-IR), electronic circular dichroism (ECD), and dielectric response to understand the behavior of the investigated model rotors. The results were supported by theoretical calculations using Density Functional Theory (DFT) methods. The angle-dependent polarized Raman spectra confirmed the crystallinity of the samples. Nearly frequency and temperature-independent permittivity suggest low-frequency librational motion of stators. An in-depth analysis of ECD spectra revealed high conformational flexibility in solution, resulting in low ECD effects, while in the solid-state with restricted rotation, significant ECD effects were observed. These findings shed light on the conformational behavior and potential applications of the studied steroidal molecular rotors.
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Affiliation(s)
- Karolina Olszewska
- Faculty of Materials Engineering and Technical Physics, Institute of Materials Research and Quantum Engineering, Poznan University of Technology Piotrowo, 3, 60-965, Poznań, Poland
| | - Adam Mizera
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179, Poznań, Poland
| | - Paweł Ławniczak
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179, Poznań, Poland
| | - Anna Kamińska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Rosa Santillan
- Departamento de Química Centro de Investigación y de Estudios Avanzados del IPN, México D.F. Apdo. Postal 14-740, 07000, México
| | - Maricela Morales-Chamorro
- Departamento de Química Centro de Investigación y de Estudios Avanzados del IPN, México D.F. Apdo. Postal 14-740, 07000, México
| | - Ma Eugenia Ochoa
- Departamento de Química Centro de Investigación y de Estudios Avanzados del IPN, México D.F. Apdo. Postal 14-740, 07000, México
| | - Norberto Farfán
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Andrzej Łapiński
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179, Poznań, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Izabella Jastrzebska
- Institute of Chemistry, University of Białystok, Ciołkowskiego 1 K, 15-254, Białystok, Poland
| | - Tomasz Runka
- Faculty of Materials Engineering and Technical Physics, Institute of Materials Research and Quantum Engineering, Poznan University of Technology Piotrowo, 3, 60-965, Poznań, Poland
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15
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Quiros-Guerrero LM, Marcourt L, Chaiwangrach N, Koval A, Ferreira Queiroz E, David B, Grondin A, Katanaev VL, Wolfender JL. Integration of Wnt-inhibitory activity and structural novelty scoring results to uncover novel bioactive natural products: new Bicyclo[3.3.1]non-3-ene-2,9-diones from the leaves of Hymenocardia punctata. Front Chem 2024; 12:1371982. [PMID: 38638877 PMCID: PMC11024435 DOI: 10.3389/fchem.2024.1371982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
In natural products (NPs) research, methods for the efficient prioritization of natural extracts (NEs) are key for discovering novel bioactive NPs. In this study a biodiverse collection of 1,600 NEs, previously analyzed by UHPLC-HRMS2 metabolite profiling was screened for Wnt pathway regulation. The results of the biological screening drove the selection of a subset of 30 non-toxic NEs with an inhibitory IC50 ≤ 5 μg/mL. To increase the chance of finding structurally novel bioactive NPs, Inventa, a computational tool for automated scoring of NEs based on structural novelty was used to mine the HRMS2 analysis and dereplication results. After this, four out of the 30 bioactive NEs were shortlisted by this approach. The most promising sample was the ethyl acetate extract of the leaves of Hymenocardia punctata (Phyllanthaceae). Further phytochemical investigations of this species resulted in the isolation of three known prenylated flavones (3, 5, 7) and ten novel bicyclo[3.3.1]non-3-ene-2,9-diones (1, 2, 4, 6, 8-13), named Hymenotamayonins. Assessment of the Wnt inhibitory activity of these compounds revealed that two prenylated flavones and three novel bicyclic compounds showed interesting activity without apparent cytotoxicity. This study highlights the potential of combining Inventa's structural novelty scores with biological screening results to effectively discover novel bioactive NPs in large NE collections.
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Affiliation(s)
- Luis-Manuel Quiros-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Laurence Marcourt
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Nathareen Chaiwangrach
- Centre of Excellence in Cannabis Research, Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand
| | - Alexey Koval
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, Geneva, Switzerland
| | - Emerson Ferreira Queiroz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Bruno David
- Green Mission Department, Herbal Products Laboratory, Pierre Fabre Research Institute, Toulouse, France
| | - Antonio Grondin
- Green Mission Department, Herbal Products Laboratory, Pierre Fabre Research Institute, Toulouse, France
| | - Vladimir L. Katanaev
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, Geneva, Switzerland
- School of Medicine and Life Sciences, Far Eastern Federal University, Vladivostok, Russia
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
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16
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Wennrich JP, Ebada SS, Sepanian E, Holzenkamp C, Khalid SJ, Schrey H, Maier W, Mándi A, Kurtán T, Ashrafi S, Stadler M. Omnipolyphilins A and B: Chlorinated Cyclotetrapeptides and Naphtho-α-pyranones from the Plant Nematode-Derived Fungus Polyphilus sieberi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6998-7009. [PMID: 38507729 PMCID: PMC10995996 DOI: 10.1021/acs.jafc.4c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Chemical exploration for two isolates of the recently described ascomycete species Polyphilus sieberi, derived from the eggs of the plant parasitic nematode Heterodera filipjevi, afforded the identification of many compounds that belong to various metabolite families: two previously undescribed chlorinated cyclotetrapeptides, omnipolyphilins A (1) and B (2), one new pyranonaphthoquinone, ventiloquinone P (3), a 6,6'-binaphto-α-pyranone dimer, talaroderxine D (4) in addition to nine known metabolites (5-13) were isolated from this biocontrol candidate. All isolated compounds were characterized by comprehensive 1D, 2D NMR, and HR-ESI-MS analyses. The absolute configurations of the cyclotetrapeptides were determined by a combination of advanced Marfey's method, ROE correlation aided by conformational analysis, and TDDFT-ECD calculations, while ECD calculations, Mosher's method, and experimental ECD spectra were used for ventiloquinone P (3) and talaroderxine D (4). Among the isolated compounds, talaroderxine D (4) showed potent antimicrobial activities against Bacillus subtilis and Staphylococcus aureus with MIC values of 2.1 and 8.3 μg mL-1, respectively. Additionally, promising inhibitory effects on talaroderxine D (4) against the formation of S. aureus biofilms were observed up to a concentration of 0.25 μg mL-1. Moreover, ophiocordylongiiside A (10) showed activity against the free-living nematode Caenorhabditis elegans.
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Affiliation(s)
- Jan-Peer Wennrich
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
| | - Sherif S. Ebada
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department
of Pharmacognosy, Faculty of Pharmacy, Ain
Shams University, 11566 Cairo, Egypt
| | - Ellen Sepanian
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Caren Holzenkamp
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
| | - Syeda J. Khalid
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
| | - Hedda Schrey
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
| | - Wolfgang Maier
- Institute
for Epidemiology and Pathogen Diagonstics, Julius Kühn Institut (JKI) - Federal Research Center for Cultivated
Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Attila Mándi
- Department
of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department
of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Samad Ashrafi
- Institute
for Epidemiology and Pathogen Diagonstics, Julius Kühn Institut (JKI) - Federal Research Center for Cultivated
Plants, Messeweg 11-12, 38104 Braunschweig, Germany
- Institute
for Crop and Soil Science, Julius Kühn
Institute (JKI) − Federal Research Centre for Cultivated Plants, Bundesallee 58, 38116 Braunschweig, Germany
| | - Marc Stadler
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI) and German Centre for Infection Research
(DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
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17
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Zou J, Qiu ZC, Yu QQ, Wu JM, Wang YH, Shi KD, Li YF, He RR, Qin L, Yao XS, Wang XL, Gao H. Discovery of a Potent Antiosteoporotic Drug Molecular Scaffold Derived from Angelica sinensis and Its Bioinspired Total Synthesis. ACS CENTRAL SCIENCE 2024; 10:628-636. [PMID: 38559293 PMCID: PMC10979506 DOI: 10.1021/acscentsci.3c01414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 04/04/2024]
Abstract
Angelica sinensis, commonly known as Dong Quai in Europe and America and as Dang-gui in China, is a medicinal plant widely utilized for the prevention and treatment of osteoporosis. In this study, we report the discovery of a new category of phthalide from Angelica sinensis, namely falcarinphthalides A and B (1 and 2), which contains two fragments, (3R,8S)-falcarindiol (3) and (Z)-ligustilide (4). Falcarinphthalides A and B (1 and 2) represent two unprecedented carbon skeletons of phthalide in natural products, and their antiosteoporotic activities were evaluated. The structures of 1 and 2, including their absolute configurations, were established using extensive analysis of NMR spectra, chemical derivatization, and ECD/VCD calculations. Based on LC-HR-ESI-MS analysis and DFT calculations, a production mechanism for 1 and 2 involving enzyme-catalyzed Diels-Alder/retro-Diels-Alder reactions was proposed. Falcarinphthalide A (1), the most promising lead compound, exhibits potent in vitro antiosteoporotic activity by inhibiting NF-κB and c-Fos signaling-mediated osteoclastogenesis. Moreover, the bioinspired gram-scale total synthesis of 1, guided by intensive DFT study, has paved the way for further biological investigation. The discovery and gram-scale total synthesis of falcarinphthalide A (1) provide a compelling lead compound and a novel molecular scaffold for treating osteoporosis and other metabolic bone diseases.
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Affiliation(s)
- Jian Zou
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Zuo-Cheng Qiu
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
- Translational
Medicine R&D Center, Institute of Biomedical and Health Engineering/Key
Laboratory of Biomedical Imaging Science and System, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518057, People’s Republic of China
- College
of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Qiang-Qiang Yu
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Jia-Ming Wu
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Yong-Heng Wang
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Ke-Da Shi
- Translational
Medicine R&D Center, Institute of Biomedical and Health Engineering/Key
Laboratory of Biomedical Imaging Science and System, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518057, People’s Republic of China
| | - Yi-Fang Li
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Rong-Rong He
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Ling Qin
- Translational
Medicine R&D Center, Institute of Biomedical and Health Engineering/Key
Laboratory of Biomedical Imaging Science and System, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518057, People’s Republic of China
| | - Xin-Sheng Yao
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Xin-Luan Wang
- Translational
Medicine R&D Center, Institute of Biomedical and Health Engineering/Key
Laboratory of Biomedical Imaging Science and System, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518057, People’s Republic of China
| | - Hao Gao
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy/International
Cooperative Laboratory of Traditional Chinese Medicine Modernization
and Innovative Drug Development of Chinese Ministry of Education of
China/Guangdong Province Key Laboratory of Pharmacodynamic Constituents
of TCM and New Drugs Research, Jinan University, Guangzhou 510632, People’s Republic of China
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18
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Totini Dos Santos CH, Petrica EEA, Nastri de Luca Batista A, Delphino Rodrigues E, Garcez WS, Ferreira de Albuquerque AC, Dos Santos FM, Batista JM, Garcez FR. 7.1',8.3'- and 7.3',8.5'-Connected Bicyclo[3.2.1]octanoids and Oxabicyclo[3.2.2]nonane-Type Neolignans from Ocotea aciphylla: Structures and Absolute Configurations. JOURNAL OF NATURAL PRODUCTS 2024; 87:456-469. [PMID: 38395785 DOI: 10.1021/acs.jnatprod.3c01013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The phytochemical investigation of the leaves and trunk bark of a specimen of Ocotea aciphylla collected in the southern portion of the Amazon forest led to the isolation of an oxabicyclo[3.2.2]nonane-type neolignan and 15 bicyclo[3.2.1]octanoid neolignans, 14 of which are unreported compounds (2-15), including one with an unusual oxidation pattern of the side chain at C-1' and two rare 7.1',8.3'-connected bicyclo[3.2.1]octanoid derivatives. Their structures and relative configurations were determined by extensive spectrometric analysis based on 1D- and 2D-NMR spectroscopy and HRESIMS data, while their absolute configurations were unambiguously assigned using electronic and vibrational circular dichroism data assisted by density functional theory calculations. Additionally, known sesquiterpenes, phenylpropanoids, and phytosterols were also isolated.
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Affiliation(s)
| | | | | | | | - Walmir Silva Garcez
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, MS 79074-460, Brazil
| | | | | | - João Marcos Batista
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP 12231-280, Brazil
| | - Fernanda Rodrigues Garcez
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, MS 79074-460, Brazil
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19
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Das S, Merz KM. Molecular Gas-Phase Conformational Ensembles. J Chem Inf Model 2024; 64:749-760. [PMID: 38206321 DOI: 10.1021/acs.jcim.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.
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Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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20
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Batista ANL, Santos CHT, de Albuquerque ACF, Santos FM, Garcez FR, Batista JM. Absolute configuration reassignment of nectamazin A: Implications to related neolignans. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123283. [PMID: 37633100 DOI: 10.1016/j.saa.2023.123283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
The ability of nature to produce structurally complex molecules makes the determination of the absolute configuration of natural products a challenging task. Although extensive NMR analysis generally allows for the reliable assignment of relative configurations, the assignments of absolute stereochemistry are commonly performed by empirical comparisons of optical rotation (OR) and/or electronic circular dichroism (ECD) data obtained for related molecules. Such an approach, however, may lead to misassignments and consequent error propagations. Herein, we present the case of the bicyclo(3.2.1)octane neolignan named (+)-nectamazin A. This compound was first reported in 2009 from Nectandra amazonum Nees. (Lauraceae) and had its absolute configuration determined as 7R,8S,3'S,4'R,5'S by means of experimental ECD spectroscopy. Our chemical studies on Ocotea aciphylla (Lauraceae) led to the isolation of (+)-nectamazin A. The extensive analysis of OR, ECD, and vibrational CD data aided by quantum chemical calculations, however, indicated (+)-nectamazin A to have the 7S,8R,3'R,4'S,5'R absolute configuration, in conflict with the configuration reported in the literature. The cause of the original incorrect assignment of (+)-nectamazin A derives from the direct comparison of experimental OR and ECD data obtained for structurally related molecules with different chromophoric systems. As an alternative, VCD spectroscopy is presented as a more reliable and sensitive technique to stereochemical investigations of bicyclo(3.2.1)octane neolignans.
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Affiliation(s)
- Andrea N L Batista
- Universidade Federal Fluminense, Instituto de Química, Outeiro de São João Batista s/n, Niterói, RJ 24020-141, Brazil
| | - Carlos Henrique T Santos
- Universidade Federal de Mato Grosso do Sul, Instituto de Química, Av. Senador Filinto Muller 1555, Campo Grande, MS 79074-460, Brazil
| | - Ana Carolina F de Albuquerque
- Universidade Federal Fluminense, Instituto de Química, Outeiro de São João Batista s/n, Niterói, RJ 24020-141, Brazil
| | - Fernando M Santos
- Universidade Federal Fluminense, Instituto de Química, Outeiro de São João Batista s/n, Niterói, RJ 24020-141, Brazil
| | - Fernanda R Garcez
- Universidade Federal de Mato Grosso do Sul, Instituto de Química, Av. Senador Filinto Muller 1555, Campo Grande, MS 79074-460, Brazil.
| | - João M Batista
- Universidade Federal de São Paulo, Instituto de Ciência e Tecnologia, Rua Talim 330, São José dos Campos, SP 12231-280, Brazil.
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21
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Feyzi N, Ebadi A, Dastan D. Chimgin from Ferula haussknechtii as AChE inhibitor and confirmation of the absolute configuration. J Biomol Struct Dyn 2023:1-10. [PMID: 38109132 DOI: 10.1080/07391102.2023.2294176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/25/2023] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide and is classified as a neurodegenerative disorder. From a drug design perspective, natural products (NPs) are more drug-like and are highly compatible with biological systems compared to most synthetic libraries. NPs provide a more efficient and cost-effective approach to new drug discovery. However, the complexity of NPs makes their identification a challenging task. Chimgin, a bicyclic monoterpene with three chiral centers, exhibits a wide range of biological activity. Despite this, the exact structure of chimgin has remained unclear until now. In this study, we quantified the amount of chimgin in Ferula haussknechtii using analytical Reversed-phase high-pressure liquid chromatography equipped with photodiode array detector (RP-HPLC-PDA). Furthermore, we determined the absolute configuration of chimgin through electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TDDFT) calculations. Finally, we evaluated its inhibitory effect on AChE through in vitro and in silico studies. The extraction process yielded an output of 2.82 ± 0.10% with an exact amount of 0.62 ± 0.04 mg of chimgin per 100 g of plant. Based on the results of ECD and TDDFT calculation, the absolute configuration of chimgin was determined to be 1S, 2S, 4S. Chimgin exhibited an inhibitory effect on AChE with an IC50 of 37.43 µM and its mechanism of action was found to be competitive. HighlightsChimgin was isolated from the roots of Ferula haussknechtii.The amount of chimgin in the plant was determined by RP-HPLC-PDA.Its absolute configuration of chimgin was determined using ECD.In vitro acetylcholinesterase activity of the chimgin was evaluated.The docking and molecular dynamic simulation of chimgin was done.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Feyzi
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ahmad Ebadi
- Department of Medicinal Chemistry, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Dara Dastan
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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22
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Sum W, Ebada SS, Kirchenwitz M, Wanga L, Decock C, Stradal TEB, Matasyoh JC, Mándi A, Kurtán T, Stadler M. Neurite Outgrowth-Inducing Drimane-Type Sesquiterpenoids Isolated from Cultures of the Polypore Abundisporus violaceus MUCL 56355. JOURNAL OF NATURAL PRODUCTS 2023; 86:2457-2467. [PMID: 37910033 PMCID: PMC10683085 DOI: 10.1021/acs.jnatprod.3c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 11/03/2023]
Abstract
Abundisporin A (1), together with seven previously undescribed drimane sesquiterpenes named abundisporins B-H (2-8), were isolated from a polypore, Abundisporus violaceus MUCL 56355 (Polyporaceae), collected in Kenya. Chemical structures of the isolated compounds were elucidated based on exhaustive 1D and 2D NMR spectroscopic measurements and supported by HRESIMS data. The absolute configurations of the isolated compounds were determined by using Mosher's method for 1-4 and TDDFT-ECD calculations for 4 and 5-8. None of the isolated compounds exhibited significant activities in either antimicrobial or cytotoxicity assays. Notably, all of the tested compounds demonstrated neurotrophic effects, with 1 and 6 significantly increasing outgrowth of neurites when treated with 5 ng/mL NGF.
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Affiliation(s)
- Winnie
Chemutai Sum
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
| | - Sherif S. Ebada
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department
of Pharmacognosy, Faculty of Pharmacy, Ain
Shams University, 11566 Cairo, Egypt
| | - Marco Kirchenwitz
- Department
of Cell Biology, Helmholtz Centre for Infection
Research, Inhoffenstrasse
7, 38124 Braunschweig, Germany
| | - Lucy Wanga
- Department
of Biochemistry, Egerton University, P.O. Box 536, 20115, Njoro, Kenya
| | - Cony Decock
- Mycothéque
de l’ Universite Catholique de Louvain (BCCM/MUCL), Place Croix du Sud 3, B-1348 Louvain-la-Neuve, Belgium
| | - Theresia E. B. Stradal
- Department
of Cell Biology, Helmholtz Centre for Infection
Research, Inhoffenstrasse
7, 38124 Braunschweig, Germany
| | | | - Attila Mándi
- Department
of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department
of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Marc Stadler
- Department
of Microbial Drugs, Helmholtz Centre for
Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, 38106 Braunschweig, Germany
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23
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Jing SX, Fu R, Li CH, Hugelshofer CL, Shi YM, Luo SH, Liu YC, Liu Y, Li SH. Discovery of Unusual Sesterterpenoids from Colquhounia coccinea var. mollis and Their Metabolic Implications. JOURNAL OF NATURAL PRODUCTS 2023; 86:2468-2473. [PMID: 37939268 DOI: 10.1021/acs.jnatprod.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Three unusual sesterterpenoids featuring unprecedented rearranged colquhounane (C25) and tetranorcolquhounane (C21) frameworks, colquhounoids E (1) and F (3) and norcolquhounoid F (2), were isolated from a Lamiaceae medicinal plant Colquhounia coccinea var. mollis. Their structures were elucidated by spectroscopic analysis and quantum chemical calculations. A biomimetic inspired regioselective cyclopropane cleavage was achieved under acidic conditions. The immunosuppressive activities of these new sesterterpenoids were also evaluated.
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Affiliation(s)
- Shu-Xi Jing
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Ran Fu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Chun-Huan Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Cedric L Hugelshofer
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Yi-Ming Shi
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Shi-Hong Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Yan-Chun Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Yan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Sheng-Hong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
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24
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Anwar A, Elnaggar MS, Elissawy AM, Ibrahim N, Mándi A, Kurtán T, Liu Z, El-Ahmady SH, Kalscheuer R. New Meroterpenoid Derivatives from the Pomegranate-Derived Endophytic Fungus Talaromyces purpureogenus. Molecules 2023; 28:7650. [PMID: 38005373 PMCID: PMC10673506 DOI: 10.3390/molecules28227650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
In this study, we report the isolation of two new meroterpenoids, miniolutelide D (1) and miniolutelide E (13-epi-miniolutelide C) (2), along with two meroterpenoidal analogues (3 and 4) and two phenolic compounds (5 and 6) from the endophytic fungus Talaromyces purpureogenus derived from Punica granatum fruits. Their structures were elucidated using extensive MS, 1D, and 2D NMR spectroscopic analyses as well as by comparing with data in the literature. The absolute configurations of 1 and 2 were determined using TDDFT-ECD calculations. Antimicrobial activity was evaluated. Compound 5 displayed significant activity against methicillin-resistant Staphylococcus aureus strain ATCC 700699 and moderate activity against S. aureus strain ATCC 29213.
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Affiliation(s)
- Alaa Anwar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt; (A.A.); (A.M.E.); (N.I.); (S.H.E.-A.)
| | - Mohamed S. Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt; (A.A.); (A.M.E.); (N.I.); (S.H.E.-A.)
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Ahmed M. Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt; (A.A.); (A.M.E.); (N.I.); (S.H.E.-A.)
- Center for Drug Discovery Research and Development, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt
| | - Nehal Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt; (A.A.); (A.M.E.); (N.I.); (S.H.E.-A.)
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.M.); (T.K.)
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary; (A.M.); (T.K.)
| | - Zhen Liu
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China;
| | - Sherweit H. El-Ahmady
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt; (A.A.); (A.M.E.); (N.I.); (S.H.E.-A.)
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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25
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Taniguchi T, Agbo DO. Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region. Phys Chem Chem Phys 2023; 25:28567-28575. [PMID: 37861094 DOI: 10.1039/d3cp04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
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26
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Sikandar A, Popoff A, Jumde RP, Mándi A, Kaur A, Elgaher WAM, Rosenberger L, Hüttel S, Jansen R, Hunter M, Köhnke J, Hirsch AKH, Kurtán T, Müller R. Revision of the Absolute Configurations of Chelocardin and Amidochelocardin. Angew Chem Int Ed Engl 2023; 62:e202306437. [PMID: 37466921 DOI: 10.1002/anie.202306437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/20/2023]
Abstract
Even with the aid of the available methods, the configurational assignment of natural products can be a challenging task that is prone to errors, and it sometimes needs to be corrected after total synthesis or single-crystal X-ray diffraction (XRD) analysis. Herein, the absolute configuration of amidochelocardin is revised using a combination of XRD, NMR spectroscopy, experimental ECD spectra, and time-dependent density-functional theory (TDDFT)-ECD calculations. As amidochelocardin was obtained via biosynthetic engineering of chelocardin, we propose the same absolute configuration for chelocardin based on the similar biosynthetic origins of the two compounds and result of TDDFT-ECD calculations. The evaluation of spectral data of two closely related analogues, 6-desmethyl-chelocardin and its semisynthetic derivative 1, also supports this conclusion.
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Affiliation(s)
- Asfandyar Sikandar
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Alexander Popoff
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Ravindra P Jumde
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Attila Mándi
- Department of Organic Chemistry University of Debrecen, P. O. Box 400, 4002, Debrecen, Hungary
| | - Amninder Kaur
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Walid A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Lara Rosenberger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Stephan Hüttel
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Rolf Jansen
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Maja Hunter
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Jesko Köhnke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Helmholtz International Lab for Anti-infectives, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Tibor Kurtán
- Department of Organic Chemistry University of Debrecen, P. O. Box 400, 4002, Debrecen, Hungary
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Helmholtz International Lab for Anti-infectives, Campus Building E8.1, 66123, Saarbrücken, Germany
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27
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Llanos-López NA, Ebada SS, Vasco-Palacios AM, Sánchez-Giraldo LM, López L, Rojas LF, Mándi A, Kurtán T, Marin-Felix Y. Panapophenanthrin, a Rare Oligocyclic Diterpene from Panus strigellus. Metabolites 2023; 13:848. [PMID: 37512554 PMCID: PMC10385786 DOI: 10.3390/metabo13070848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
During the course of our search for biologically active secondary metabolites from fungal cultures, a new oligocyclic diterpenoidal derivative, panapophenanthrin (1), was isolated from Panus strigellus. In addition, two known metabolites, panepophenanthrin (2) and dihydrohypnophilin (3), were also obtained. The chemical structures of the isolated compounds were elucidated based on extensive 1D and 2D NMR spectral analyses together with high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). The absolute configuration was determined through TDDFT-ECD calculations. All of the compounds were assessed for their antimicrobial and cytotoxic activities. Compounds 1 and 3 showed moderate to weak activities in the performed antimicrobial assays, while compound 1 exhibited potent cytotoxic activity against the mammalian cell lines mouse fibroblast (L929) and human endocervical adenocarcinoma (KB3.1).
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Affiliation(s)
- Natalia A Llanos-López
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), DZIF Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Sherif Saeed Ebada
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), DZIF Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Aída M Vasco-Palacios
- Grupo de Microbiología Ambientaland Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia, Calle 70 No. 52-21, 050010 Medellin, Colombia
| | - Laura M Sánchez-Giraldo
- Grupo de Investigación de Biotecnología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Calle 59A No. 63-20, 050034 Medellin, Colombia
| | - Lina López
- Grupo de Biotransformación, Escuela de Microbiología, Universidad de Antioquia, Calle 70 No. 52-21, 050010 Medellin, Colombia
| | - Luisa F Rojas
- Grupo de Biotransformación, Escuela de Microbiología, Universidad de Antioquia, Calle 70 No. 52-21, 050010 Medellin, Colombia
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
| | - Yasmina Marin-Felix
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) and German Centre for Infection Research (DZIF), DZIF Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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28
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Wang L, Kiffe-Delf AL, Ostermann PN, Simons VE, He D, Gao Y, van Geelen L, Dai HF, Zhao YX, Schaal H, Mándi A, Király SB, Kurtán T, Liu Z, Kalscheuer R. Asperphenalenones Isolated from the Biocontrol Agent Clonostachys rosea and Their Antimicrobial Activities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37436951 DOI: 10.1021/acs.jafc.3c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Clonostachys rosea is a fungus widely distributed on Earth and has a high capacity to adapt to complex environments in soil, plants, or sea. It is an endophyte that can be used as a potential biocontrol agent to protect plants from pathogenic fungi, nematodes, and insects. However, the spectrum of secondary metabolites produced by C. rosea has only scarcely been studied. In the present study, eight new phenalenones, asperphenalenones F-M (1-8), together with two known derivatives, asperphenalenones E and B (9 and 10), were isolated from the axenic rice culture of this fungus. The structures of the new compounds were elucidated by nuclear magnetic resonance, high-resolution electrospray ionization mass spectrometry, electronic circular dichroism, and gas chromatography-mass spectrometry analyses. Asperphenalenones J-M (5-8) are unusual phenalenone adducts that are conjugated to diterpenoid glycosides. Asperphenalenones F and H showed moderate antibacterial activity against methicillin-resistant Staphylococcus aureus, with minimal inhibitory concentrations of 12.5 and 25 μM, respectively. Asperphenalenone B exhibited low antiviral activity against the human immunodeficiency virus replication. Furthermore, asperphenalenones F and H exhibited low cytotoxicity against Jurkat cells, while all other compounds were devoid of cytotoxicity.
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Affiliation(s)
- Lin Wang
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Anna-Lene Kiffe-Delf
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Philipp Niklas Ostermann
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Viktor Emanuel Simons
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Di He
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ying Gao
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Lasse van Geelen
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Hao-Fu Dai
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, People's Republic of China
| | - You-Xing Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, People's Republic of China
| | - Heiner Schaal
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, Post Office Box 400, 4002 Debrecen, Hungary
| | - Sándor Balázs Király
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, Post Office Box 400, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, Post Office Box 400, 4002 Debrecen, Hungary
| | - Zhen Liu
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, Hunan 410013, People's Republic of China
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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29
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Elnaggar MS, Elissawy AM, Youssef FS, Kicsák M, Kurtán T, Singab ANB, Kalscheuer R. Austalide derivative from marine-derived Aspergillus sp. and evaluation of its cytotoxic and ADME/TOPKAT properties. RSC Adv 2023; 13:16480-16487. [PMID: 37274397 PMCID: PMC10233426 DOI: 10.1039/d3ra02632a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023] Open
Abstract
In-depth chemical investigation of an ethyl acetate extract of Aspergillus sp. isolated from the soft coral Sinularia species resulted in the isolation of one new meroterpenoid, austalide Z (1), one known austalide W (2), six known prenylated indole diketopiperazine alkaloids (3-8), and phthalic acid and its ethyl derivative (9-10). The structures were established by means of 1D and 2D NMR (one- and two-dimensional nuclear magnetic resonance) experiments supported by UV analysis and ESI-MS (electrospray ionization mass spectrometry). In vitro cytotoxic evaluation was performed against the Caco-2 cancer cell line using the MTT assay, which showed that the examined compounds had weak to moderate activities, with the new meroterpenoid austalide Z (1) displaying an IC50 value of 51.6 μg mL-1. ADME/TOPKAT (absorption, distribution, metabolism, excretion, and toxicity) predication performed in silico showed that most of the isolated compounds possessed reasonable pharmacokinetic, pharmacodynamic, and toxicity properties. Thus, it can be concluded that Aspergillus sp. could act as a source of drug leads for cancer prevention with promising pharmacokinetic and pharmacodynamic properties and thus could be incorporated in pharmaceutical dosage forms.
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Affiliation(s)
- Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-Universität Düsseldorf 40225 Germany
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Center of Drug Discovery Research and Development, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Fadia S Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Máté Kicsák
- Department of Organic Chemistry, University of Debrecen Debrecen 4032 Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen Debrecen 4032 Hungary
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Center of Drug Discovery Research and Development, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-Universität Düsseldorf 40225 Germany
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30
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Pandey P, Neal WM, Zulfiqar F, Ali Z, Khan IA, Ferreira D, Chittiboyina AG. A combined experimental and computational chiroptical approach to establish the biosynthesis and absolute configuration of licochalcone L. PHYTOCHEMISTRY 2023:113732. [PMID: 37245686 DOI: 10.1016/j.phytochem.2023.113732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/30/2023]
Abstract
Often, chiral natural products exist as single stereoisomers; however, simultaneous occurrences of both enantiomers can exist in nature, resulting in scalemic or racemic mixtures. Ascertaining natural products' absolute configuration (AC) is pivotal for attributing their specific biological signature. Specific rotation data commonly characterize chiral non-racemic natural products; however, measurement conditions, viz., solvent and concentration, can influence the sign of specific rotation values, especially when characterizing natural products possessing small specific rotation values. For example, licochalcone L, a minor constituent of Glycyrrhiza inflata, was reported with a specific rotation of [α]D22= +13 (c 0.1, CHCl3); however, not establishing the AC and the reported zero specific rotation for an identical compound, licochalcone AF1, resulted in debatable chirality and its biogenesis. In this study, a combined experimental and computational chiroptical approach involving specific rotation and electronic circular dichroism (ECD) data, supported by time-dependent density functional theory (TDDFT), were effectively utilized to establish the AC of licochalcone L as the (E, 2″S)-isomer. Establishing the 2″S absolute configuration permitted the conception of a reasonable biosynthetic pathway involving intramolecular '5-exo-tet' ring opening of a chiral oxirane to form chiral licochalcone L in G. inflata.
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Affiliation(s)
- Pankaj Pandey
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States
| | - William M Neal
- Department of BioMolecular Sciences, Division of Pharmacognosy, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States
| | - Fazila Zulfiqar
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States
| | - Zulfiqar Ali
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States
| | - Ikhlas A Khan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States; Department of BioMolecular Sciences, Division of Pharmacognosy, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States.
| | - Daneel Ferreira
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States; Department of BioMolecular Sciences, Division of Pharmacognosy, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States
| | - Amar G Chittiboyina
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, United States.
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31
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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32
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Vermeyen T, Batista ANL, Valverde AL, Herrebout W, Batista JM. Pushing the boundaries of VCD spectroscopy in natural product chemistry. Phys Chem Chem Phys 2023; 25:13825-13832. [PMID: 37191271 DOI: 10.1039/d3cp00886j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Vibrational circular dichroism (VCD) is one of the most powerful techniques to assess the stereochemistry of chiral molecules in solution state. The need for quantum chemical calculations to interpret experimental data, however, has precluded its widespread use by non-experts. Herein, we propose the search and validation of IR and VCD spectral markers to circumvent the requirement of DFT calculations allowing for absolute configuration assignments even in complex mixtures. To that end, a combination of visual inspection and machine learning based methods is used. Monoterpene mixtures are selected for this proof-of-concept study.
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Affiliation(s)
- Tom Vermeyen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
- Department of Chemistry, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium
| | - Andrea N L Batista
- Institute of Chemistry, Fluminense Federal University, Outeiro de São João Batista s/n, 24020-141 Niterói-RJ, Brazil
| | - Alessandra L Valverde
- Institute of Chemistry, Fluminense Federal University, Outeiro de São João Batista s/n, 24020-141 Niterói-RJ, Brazil
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - João M Batista
- Federal University of São Paulo, Institute of Science and Technology, R. Talim 330, 12231-280, São José dos Campos-SP, Brazil.
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33
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Li YH, Mándi A, Li HL, Li XM, Li X, Meng LH, Yang SQ, Shi XS, Kurtán T, Wang BG. Isolation and characterization of three pairs of verrucosidin epimers from the marine sediment-derived fungus Penicillium cyclopium and configuration revision of penicyrone A and related analogues. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:223-231. [PMID: 37275535 PMCID: PMC10232390 DOI: 10.1007/s42995-023-00173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 01/27/2023] [Indexed: 06/07/2023]
Abstract
Verrucosidins, a methylated α-pyrone class of polyketides rarely reported upon, have been implicated in one or more neurological diseases. Despite the significance of verrucosidins as neurotoxins, the absolute configurations of most of the derivatives have not been accurately characterized yet. In this study, three pairs of C-9 epimeric verrucosidin derivatives, including the known compounds penicyrones A and B (1a/1b) and 9-O-methylpenicyrones A and B (2a/2b), the new compounds 9-O-ethylpenicyrones A and B (3a/3b), together with the related known derivative verrucosidin (4), were isolated and identified from the culture extract of Penicillium cyclopium SD-413, which was obtained from the marine sediment collected from the East China sea. Their structures were established based on an in-depth analysis of nuclear magnetic resonances (NMR) and mass spectroscopic data. Determination of the absolute configurations of these compounds was accomplished by Mosher's method and time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (ECD) and optical rotation (OR). The configurational assignment of penicyrone A demonstrated that the previously reported C-6 absolute configuration of verrucosidin derivatives needs to be revised from (6S) to (6R). The 9R/9S epimers of compounds 1-3 were found to exhibit growth inhibition against some pathogenic bacteria, indicating that they have potential as lead compounds for the creation of antimicrobial agents. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00173-2.
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Affiliation(s)
- Yan-He Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- School of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, Egyetem Tér 1, Debrecen, 4032 Hungary
| | - Hong-Lei Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Xiao-Ming Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Xin Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Ling-Hong Meng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Sui-Qun Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Xiao-Shan Shi
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, Egyetem Tér 1, Debrecen, 4032 Hungary
| | - Bin-Gui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology at the Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- School of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049 China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071 China
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Lee JR, Park KJ, Ham SL, Kim J, Kim CS. Structure Revision of Anti-Inflammatory Indole Alkaloids with a 1,2-Benzisoxazole Ring. ACS OMEGA 2023; 8:13967-13970. [PMID: 37091423 PMCID: PMC10116614 DOI: 10.1021/acsomega.3c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
(R)- and (S)-2-(benzo[d]isoxazol-3-yl)-2-ethylindolin-3-one [(±)-1] were previously isolated from NIRAM, a natural blue dye from Polygonum tinctorium, and their structures were initially proposed to possess a 1,2-benzisoxazole ring. In this study, the structures of (±)-1 were revised to have an indole-anthranilic acid fused tetracyclic ring rather than the 1,2-benzisoxazole ring by reanalysis of one-dimensional (1D) and two-dimensional (2D) NMR followed by density functional theory (DFT) chemical shift calculation, DP4+ technique, and ECD simulation.
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Affiliation(s)
- Ju Ryeong Lee
- Department
of Biopharmaceutical Convergence, Sungkyunkwan
University, Suwon 16419, Republic
of Korea
| | - Kyoung Jin Park
- School
of Pharmacy, Sungkyunkwan Univ ersity, Suwon 16419, Republic of Korea
| | - Song Lim Ham
- Department
of Biopharmaceutical Convergence, Sungkyunkwan
University, Suwon 16419, Republic
of Korea
| | - Jonghwan Kim
- Department
of Biopharmaceutical Convergence, Sungkyunkwan
University, Suwon 16419, Republic
of Korea
| | - Chung Sub Kim
- Department
of Biopharmaceutical Convergence, Sungkyunkwan
University, Suwon 16419, Republic
of Korea
- School
of Pharmacy, Sungkyunkwan Univ ersity, Suwon 16419, Republic of Korea
- Department
of Biohealth Regulatory Science, Sungkyunkwan
University, Suwon 16419, Republic of Korea
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Kovács T, Lajter I, Kúsz N, Schelz Z, Bózsity-Faragó N, Borbás A, Zupkó I, Krupitza G, Frisch R, Hohmann J, Vasas A, Mándi A. Isolation and NMR Scaling Factors for the Structure Determination of Lobatolide H, a Flexible Sesquiterpene from Neurolaena lobata. Int J Mol Sci 2023; 24:ijms24065841. [PMID: 36982924 PMCID: PMC10052924 DOI: 10.3390/ijms24065841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
A new flexible germacranolide (1, lobatolide H) was isolated from the aerial parts of Neurolaena lobata. The structure elucidation was performed by classical NMR experiments and DFT NMR calculations. Altogether, 80 theoretical level combinations with existing 13C NMR scaling factors were tested, and the best performing ones were applied on 1. 1H and 13C NMR scaling factors were also developed for two combinations utilizing known exomethylene containing derivatives, and the results were complemented by homonuclear coupling constant (JHH) and TDDFT-ECD calculations to elucidate the stereochemistry of 1. Lobatolide H possessed remarkable antiproliferative activity against human cervical tumor cell lines with different HPV status (SiHa and C33A), induced cell cycle disturbance and exhibited a substantial antimigratory effect in SiHa cells.
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Affiliation(s)
- Tibor Kovács
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Ildikó Lajter
- Institute of Pharmacognosy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Norbert Kúsz
- Institute of Pharmacognosy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Zsuzsanna Schelz
- Institute of Pharmacodynamics and Biopharmacy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Noémi Bózsity-Faragó
- Institute of Pharmacodynamics and Biopharmacy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - István Zupkó
- Institute of Pharmacodynamics and Biopharmacy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Georg Krupitza
- Department of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Richard Frisch
- Institute for Ethnobiology, Playa Diana, San José GT-170, Guatemala
| | - Judit Hohmann
- Institute of Pharmacognosy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
- ELKH-USZ Biologically Active Natural Products Research Group, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Andrea Vasas
- Institute of Pharmacognosy, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
- ELKH-USZ Biologically Active Natural Products Research Group, University of Szeged, Eötvös u. 6, 6720 Szeged, Hungary
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P.O. Box 400, 4002 Debrecen, Hungary
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Zhang L, Yang M, Chen ZH, Ge ZY, Li SW, Yan XY, Yao LG, Liang LF, Guo YW. Cembrane Diterpenes Possessing Nonaromatic Oxacycles from the Hainan Soft Coral Sarcophyton mililatensis. Int J Mol Sci 2023; 24:ijms24031979. [PMID: 36768306 PMCID: PMC9915928 DOI: 10.3390/ijms24031979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Documents on the chemical composition of the soft coral Sarcophyton mililatensis are sparse. The present investigation of the Hainan soft coral S. mililatensis resulted in the discovery of six new cembrane diterpenes, sarcoxacyclols A-F (1-6) and four known analogs (7-10). Their structures were elucidated by extensive spectroscopic analysis along with a comparison with the data in current literature. The nonaromatic oxacycles in their structures were the rarely found tetrahydrofuran ether across C-1 and C-12 and tetrahydropyran ether across C-1 and C-11, respectively. Moreover, the absolute configuration of compound 4 was established unambiguously by X-ray diffraction analysis using Ga Kα radiation (λ = 1.34139 Å). Based on the biogenetical consideration, the absolute configurations of other five new compounds were tentatively assumed. Assessment of the bioactivity for these secondary metabolites revealed that compound 1 exhibited significant tumor necrosis factor (TNF)-α inhibitory activity (IC50 = 9.5 μmol/L), similar to the positive control dexamethasone (IC50 = 8.7 μmol/L), but no obvious cytotoxicity towards RAW264.7 cells (CC50 > 50 μmol/L). The preliminary molecular docking suggested the crucial roles of the hydroxyl and acetoxyl groups in the computational prediction of the binding mode between the diterpene and the protein.
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Affiliation(s)
- Ling Zhang
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Min Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Zi-Hui Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Zeng-Yue Ge
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Song-Wei Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Xian-Yun Yan
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Li-Gong Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Lin-Fu Liang
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
- Correspondence: (L.-F.L.); (Y.-W.G.)
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals and College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Correspondence: (L.-F.L.); (Y.-W.G.)
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Taniguchi T, Mutmainah, Takimoto S, Suzuki T, Watanabe S, Matsuda F, Umezawa T, Monde K. Scope and limitations of absolute configuration determination of allenic natural products using the CCC stretching VCD signal. Org Biomol Chem 2023; 21:569-574. [PMID: 36541676 DOI: 10.1039/d2ob01520j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The allene functional group in natural products isolated so far exists in a non-racemic form, but its axial chirality is difficult to elucidate. Allenes exhibit a characteristic antisymmetric CCC stretching mode at around 1950 cm-1, and their VCD properties have not been studied in detail. This work, for the first time, applied VCD spectroscopy to allenic natural products and allenic molecules with other asymmetric centers focusing on the antisymmetric CCC stretching mode. This vibrational mode yielded a negligibly weak VCD signal for several molecules, but in the presence of electron-withdrawing and/or conjugating substituents, it generated a stronger one. Its sign was found to be influenced by the nature of substituents. These findings should deepen the understanding of the VCD properties of the allene functional group and should be useful for future studies of chiral allenes.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Mutmainah
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
| | - Shu Takimoto
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
| | - Takahiro Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, North 10 West 8, Sapporo 060-0810, Japan
| | - Soichiro Watanabe
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Sapporo 060-8628, Japan
| | - Fuyuhiko Matsuda
- Division of Environmental Materials Science, Graduate School of Environmental Science, Hokkaido University, North 10 West 5, Sapporo 060-0810, Japan
| | - Taiki Umezawa
- Division of Environmental Materials Science, Graduate School of Environmental Science, Hokkaido University, North 10 West 5, Sapporo 060-0810, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
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Shen SM, Li SW, Su MZ, Yao LG, Appendino G, Guo YW. Structurally Diverse Diterpenoids from the Sanya Bay Nudibranch Hexabranchus sanguineus and Its Sponge-Prey Chelonaplysilla sp. Chemistry 2023; 29:e202203858. [PMID: 36617497 DOI: 10.1002/chem.202203858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/10/2023]
Abstract
Investigation of the South China Sea nudibranch Hexabranchus sanguineus from Sanya Bay afforded, in addition to three known compounds, nine new diterpenoids of the 5,19-cycloclerodane- (sanyanolides A-D), clerodane- (sanyanolide E) and subersin- (sanyanolides F-I) type. Remarkably, six diterpenoids aforementioned from H. sanguineus were also isolated from the sponge Chelonaplysilla sp. from the same water region, suggesting a trophic relationship between H. sanguineus and Chelonaplysilla sp. The structure and absolute configuration of new compounds were established by a combination of spectroscopic data, X-ray diffraction analysis and/or time-dependent density functional theory/electronic circular dichroism calculations. A plausible biogenetic relationship between these diterpenoids, along with the chemo-ecological implications of their co-occurrence in the two organisms investigated, was proposed and discussed. In in vitro bioassays, echinoclerodane A exhibited a potent inhibitory effect (IC50 =2.81 μM) on LPS-induced inflammatory response in RAW 264.7 macrophage cells. In addition, echinoclerodane A and oculatolide showed considerable antibacterial activities with MIC values ranging from 1.0 to 8.0 μg/mL.
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Affiliation(s)
- Shou-Mao Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, P. R. China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, P. R. China
| | - Song-Wei Li
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 310014, Hangzhou, P. R. China
| | - Ming-Zhi Su
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, 264117, Yantai, Shandong, P. R. China
| | - Li-Gong Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, P. R. China
| | - Giovanni Appendino
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, P. R. China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, P. R. China.,Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, 264117, Yantai, Shandong, P. R. China
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39
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Stereochemistry of Chiral 2-Substituted Chromanes: Twist of the Dihydropyran Ring and Specific Optical Rotation. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010439. [PMID: 36615631 PMCID: PMC9823451 DOI: 10.3390/molecules28010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
Chiral 2-substituted chromanes are important substructures in organic synthesis and appear in numerous natural products. Herein, the correlation between specific optical rotations (SORs) and the stereochemistry at C2 of chiral 2-substituted chromanes was investigated through data mining, quantum-chemical calculations using density functional theory (DFT), and mechanistic analyses. For 2-aliphatic (including acyloxy and alkenyl) chromanes, the P-helicity of the dihydropyran ring usually corresponds to a positive SOR; however, 2-aryl chromanes with P-helicity tend to exhibit negative SORs. 2-Carboxyl (including alkoxycarbonyl and carbonyl) chromanes often display small experimental SORs, and theoretical calculations for them are prone to error because of the fluctuating conformational distribution with computational parameters. Several typical compounds were discussed, including detailed descriptions of the asymmetric synthesis, absolute configuration (AC) assignment methods, and systematic conformational analysis. We hope this work will enrich the knowledge of the stereochemistry of chiral 2-substituted chromanes.
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Identification of Small-Molecule Bioactive Constituents from the Leaves of Vaccinium bracteatum Confirms It as a Potential Functional Food with Health Benefits. Foods 2023; 12:foods12010177. [PMID: 36613392 PMCID: PMC9818789 DOI: 10.3390/foods12010177] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
The health benefits of Vaccinium bracteatum are well recorded in ancient Chinese medical books and were also demonstrated by modern researches. However, the relationship between its beneficial functions and specific chemical constituents has not been fully characterized. This study investigated the bioactive small-molecule constituents in the leaves of V. bracteatum, which afforded 32 compounds including ten new ones (1-9) and ten pairs of enantiomers (9-18). Their structures with absolute configurations were elucidated by spectroscopic methods, especially nuclear magnetic resonance (NMR) and electronic circular dichroism (ECD) analyses, with 1-4 bearing a novel revolving-door shaped scaffold. While half-compounds exhibited decent antioxidant activity by scavenging 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals, all except 19 and 20 exerted significant capturing activity against diammonium 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) radicals. In addition, the new iridoids 1, 5, 6, and 7 exerted apparent neuroprotective activity toward PC12 cells, with 1 being comparable to the positive control, and selective compounds also displayed anti-diabetic and anti-inflammatory properties by inhibiting α-glucosidase and NO production, respectively. The current work revealed that the bioactive small-molecule constituents could be closely related to the functional food property of the title species.
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Choi WJ, Lee SH, Park BC, Kotov NA. Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures. J Am Chem Soc 2022; 144:22789-22804. [DOI: 10.1021/jacs.2c04817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Won Jin Choi
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sang Hyun Lee
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bum Chul Park
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas A. Kotov
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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42
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Fu XZ, Zhang SM, Wang GF, Yang QL, Guo L, Pescitelli G, Xie ZP. Atypical Angucyclinones with Ring Expansion and Cleavage from a Marine Streptomyces sp. J Org Chem 2022; 87:15998-16010. [PMID: 36395479 DOI: 10.1021/acs.joc.2c02134] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A unique ring C-expanded angucyclinone, oxemycin A (1), and seven new ring-cleavage derivatives (2-5 and 9-11) were isolated from the marine actinomycete Streptomyces pratensis KCB-132, together with eight known analogues (6-8 and 12-16). Their structures were elucidated by spectroscopic analyses, single-crystal X-ray diffractions, and NMR and ECD calculations. Among these atypical angucyclinones, compound 1 represented the first seven-membered ketoester in the angucyclinone family, which sheds light on the origin of fragmented angucyclinones with C-ring cleavage at C-12/C-12a in the Baeyer-Villiger hypothesis, such as 2-4, while the related "nonoxidized" analogues 5-8 seem to originate from a diverse pathway within the Grob fragmentation hypothesis. Additionally, we have succeeded in the challenging separation of elmenols E and F (12) into their four stereoisomers, which remained stable in aprotic solvents but rapidly racemized under protic conditions. Furthermore, the absolute configurations of LS1924 and its isomers (14 and 15) were assigned by ECD calculations for the first time. Surprisingly, these two bicyclic acetals are susceptible to hydrolysis in solution, resulting in fragmented derivatives 17 and 18 with C-ring cleavage between C-6a and C-7. Compared with ring C-modified angucyclinones, ring A-cleaved 11 was more active to multiple resistant "ESKAPE" pathogens with MIC values ranging from 4.7 to 37.5 μg/mL.
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Affiliation(s)
- Xin-Zhen Fu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Shu-Min Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Guang-Fei Wang
- College of Life Sciences, Yantai University, Yantai 264003, China
| | - Qiao-Li Yang
- College of Life Sciences, Yantai University, Yantai 264003, China
| | - Lin Guo
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy
| | - Ze-Ping Xie
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
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Quiros-Guerrero LM, Nothias LF, Gaudry A, Marcourt L, Allard PM, Rutz A, David B, Queiroz EF, Wolfender JL. Inventa: A computational tool to discover structural novelty in natural extracts libraries. Front Mol Biosci 2022; 9:1028334. [PMID: 36438653 PMCID: PMC9692083 DOI: 10.3389/fmolb.2022.1028334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 09/05/2023] Open
Abstract
Collections of natural extracts hold potential for the discovery of novel natural products with original modes of action. The prioritization of extracts from collections remains challenging due to the lack of a workflow that combines multiple-source information to facilitate the data interpretation. Results from different analytical techniques and literature reports need to be organized, processed, and interpreted to enable optimal decision-making for extracts prioritization. Here, we introduce Inventa, a computational tool that highlights the structural novelty potential within extracts, considering untargeted mass spectrometry data, spectral annotation, and literature reports. Based on this information, Inventa calculates multiple scores that inform their structural potential. Thus, Inventa has the potential to accelerate new natural products discovery. Inventa was applied to a set of plants from the Celastraceae family as a proof of concept. The Pristimera indica (Willd.) A.C.Sm roots extract was highlighted as a promising source of potentially novel compounds. Its phytochemical investigation resulted in the isolation and de novo characterization of thirteen new dihydro-β-agarofuran sesquiterpenes, five of them presenting a new 9-oxodihydro-β-agarofuran base scaffold.
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Affiliation(s)
- Luis-Manuel Quiros-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Louis-Félix Nothias
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Arnaud Gaudry
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Laurence Marcourt
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Adriano Rutz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Emerson Ferreira Queiroz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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Ma X. Recent Advances in Mass Spectrometry-Based Structural Elucidation Techniques. Molecules 2022; 27:molecules27196466. [PMID: 36235003 PMCID: PMC9572214 DOI: 10.3390/molecules27196466] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Mass spectrometry (MS) has become the central technique that is extensively used for the analysis of molecular structures of unknown compounds in the gas phase. It manipulates the molecules by converting them into ions using various ionization sources. With high-resolution MS, accurate molecular weights (MW) of the intact molecular ions can be measured so that they can be assigned a molecular formula with high confidence. Furthermore, the application of tandem MS has enabled detailed structural characterization by breaking the intact molecular ions and protonated or deprotonated molecules into key fragment ions. This approach is not only used for the structural elucidation of small molecules (MW < 2000 Da), but also crucial biopolymers such as proteins and polypeptides; therefore, MS has been extensively used in multiomics studies for revealing the structures and functions of important biomolecules and their interactions with each other. The high sensitivity of MS has enabled the analysis of low-level analytes in complex matrices. It is also a versatile technique that can be coupled with separation techniques, including chromatography and ion mobility, and many other analytical instruments such as NMR. In this review, we aim to focus on the technical advances of MS-based structural elucidation methods over the past five years, and provide an overview of their applications in complex mixture analysis. We hope this review can be of interest for a wide range of audiences who may not have extensive experience in MS-based techniques.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr NW, Atlanta, GA 30332, USA
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Bu Q, Yang M, Yan XY, Yao LG, Guo YW, Liang LF. New flexible cembrane-type macrocyclic diterpenes as TNF-α inhibitors from the South China Sea soft coral Sarcophyton mililatensis. Int J Biol Macromol 2022; 222:880-886. [PMID: 36179867 DOI: 10.1016/j.ijbiomac.2022.09.210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
A further study on the rarely reported soft coral Sarcophyton mililatensis disclosed five new flexible cembrane-type macrocyclic diterpenes sarcomililatols C-G (1-5) and two known analogues 6 and 7. The structures and absolute configurations of natural macrocyclic compounds 1-6 were established by the extensive spectroscopic analysis, X-ray diffraction analysis, time-dependent density functional theory/electronic circular dichroism (TDDFT ECD) calculations, chemical reaction, and modified Mosher's method. In the bioassays, the macrocyclic diterpene 2 exhibited potent TNF-α inhibition (IC50 = 6.1 μmol/L), which was better than the positive control dexamethasone (IC50 = 8.7 μmol/L), and no obvious cytotoxicity against RAW264.7 cells with CC50 values over 50 μmol/L, indicating natural macrocyclic compound 2 could be served as a model compound to develop a new and prospective chemotype of an anti-inflammatory lead compound or drug candidate.
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Affiliation(s)
- Qing Bu
- College of Materials Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, China
| | - Min Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Xian-Yun Yan
- College of Materials Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, China
| | - Li-Gong Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China; Shandong Laboratory of Yantai Drug Discovery, Bohai rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China; Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals and College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Lin-Fu Liang
- College of Materials Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, China.
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Mazzone F, Simons VE, van Geelen L, Frank M, Mándi A, Kurtán T, Pfeffer K, Kalscheuer R. In Vitro Biological Activity of Natural Products from the Endophytic Fungus Paraboeremia selaginellae against Toxoplasma gondii. Antibiotics (Basel) 2022; 11:antibiotics11091176. [PMID: 36139955 PMCID: PMC9495004 DOI: 10.3390/antibiotics11091176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Toxoplasma gondii is an apicomplexan pathogen able to infect a wide range of warm-blooded animals, including humans, leading to toxoplasmosis. Current treatments for toxoplasmosis are associated with severe side-effects and a lack efficacy to eradicate chronic infection. Thus, there is an urgent need for developing novel, highly efficient agents against toxoplasmosis with low toxicity. For decades, natural products have been a useful source of novel bioactive compounds for the treatment of infectious pathogens. In the present study, we isolated eight natural products from the crude extract of the endophytic fungus Paraboeremia selaginellae obtained from the leaves of the plant Philodendron monstera. The natural products were tested for inhibiting Toxoplasma gondii proliferation, and their cytotoxicity was evaluated in different human cell lines. Six natural products showed antitoxoplasma activity with low or no cytotoxicity in human cell lines. Together, these findings indicate that biphenyl ethers, bioxanthracenes, and 5S,6S-phomalactone from P. selaginellae are potential candidates for novel anti-toxoplasma drugs.
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Affiliation(s)
- Flaminia Mazzone
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Viktor E. Simons
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Lasse van Geelen
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Marian Frank
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, 4002 Debrecen, Hungary
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, 40225 Duesseldorf, Germany
- Correspondence: (K.P.); (R.K.); Tel.: +49-211-8112459 (K.P.); +49-211-8114180 (R.K.)
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Duesseldorf, Germany
- Correspondence: (K.P.); (R.K.); Tel.: +49-211-8112459 (K.P.); +49-211-8114180 (R.K.)
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Huang MJ, Wang JC, Shen SM, Si JY, Guo YW. Stereochemical insights into neuroprotective alkaloids from the aerial parts of Emilia sonchifolia. Fitoterapia 2022; 162:105267. [PMID: 35961597 DOI: 10.1016/j.fitote.2022.105267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/18/2022]
Abstract
A new alkaloid featured with a dibenz[c,e]azepin-5-one scaffold, namely emililactam A (3), together with a known pyrrolidine alkaloid (emilisonchine, 1) and a known flavonoid alkaloid [8-(2″-pyrrolidinone-5″-yl)-quercetin, 2] were isolated from the aerial parts of Emilia sonchifolia. Compounds 1 and 2 were isolated as racemic forms which were further separated, for the first time, to their corresponding enantiomers [(+)-1/(-)-1 and (+)-2/(-)-2], respectively, by using chiral-phase HPLC. The structure of new compound 3 was elucidated by extensive spectroscopic analysis. In addition, the absolute configurations of optically pure (+)-1/(-)-1 and (+)-2/(-)-2 were determined by the time-dependent density functional theory electronic circular dichroism (TDDFT-ECD) calculations. In an in vitro bioassay, compounds (+)-1, (-)-1, (±)-1, and 3 exhibited moderate neuroprotective effects against corticosterone-induced injuries of PC12 cells.
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Affiliation(s)
- Ming-Jin Huang
- College of Agriculture, Guizhou University, Guiyang 550025, China; Dendrobium Research Laboratory, Guizhou University, Guiyang 550025, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jun-Chi Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Shou-Mao Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, Yancheng Teachers University, Yancheng 224007, China
| | - Jian-Yong Si
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Yang YD, Yang BB, Li L. A nonneglectable stereochemical factor in drug development: Atropisomerism. Chirality 2022; 34:1355-1370. [PMID: 35904531 DOI: 10.1002/chir.23497] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 11/07/2022]
Abstract
Chirality is one of the key factors affecting the medicinal efficacy of compounds. In addition to central chirality, sterically hindered chiral axes commonly appear in drugs and the resulting chirality is known as atropisomerism. With developments in medicinal chemistry, atropisomerism has attracted increasing attention. This review discusses the classification, biological activity, pharmacokinetics, toxicity and side effects of atropisomers, and can serve as a reference in the research and development of potential chiral drugs.
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Affiliation(s)
- Ya-Dong Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bei-Bei Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Li
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Anti-inflammatory Polyketides from the Marine-Derived Fungus Eutypella scoparia. Mar Drugs 2022; 20:md20080486. [PMID: 36005490 PMCID: PMC9410037 DOI: 10.3390/md20080486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
Three new polyketides, eutyketides A and B (1 and 2) and cytosporin X (3), along with four known compounds (4–7), were obtained from the marine-derived fungus Eutypella scoparia. The planar structures of 1 and 2 were elucidated by extensive HRMS and 1D and 2D NMR analyses. Their relative configurations of C-13 and C-14 were determined with chemical conversions by introducing an acetonylidene group. The absolute configurations of 1–3 were determined by comparing their experimental electronic circular dichroism (ECD) data with their computed ECD results. All of the isolated compounds were tested for their anti-inflammatory activities on lipopolysaccharide-induced nitric oxide production in RAW 264.7 macrophages. Compounds 5 and 6 showed stronger anti-inflammatory activities than the other compounds, with the inhibition of 49.0% and 54.9% at a concentration of 50.0 µg/mL, respectively.
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50
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Shen SM, Yang Q, Zang Y, Li J, Liu X, Guo YW. Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa. Beilstein J Org Chem 2022; 18:916-925. [PMID: 35957756 PMCID: PMC9344550 DOI: 10.3762/bjoc.18.91] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
One new aromadendrane-type sesquiterpenoid, namely ximaocavernosin P [(+)-1], and three new cadinane-type sesquiterpenoids, namely (+)-maninsigin D [(+)-4], (+)- and (−)-ximaocavernosin Q [(+)- and (−)-5], together with five related known ones [2, 3, (−)-4, 6, and 7], were isolated from the Hainan sponge Acanthella cavernosa. Compounds 4 and 5 were isolated as racemic forms, which were further separated to the corresponding enantiomers [(+)-4/(−)-4 and (+)-5/(−)-5], respectively, by using chiral-phase HPLC. The structures of new compounds were elucidated by extensive spectroscopic analysis and comparison with the reported data. In addition, the absolute configuration of optically pure (+)-1 and 2 were determined by time-dependent density functional theory/electronic circular dichroism (TDDFT-ECD) calculations or X-ray diffraction analysis. A plausible biosynthetic pathway of these sesquiterpenoids and their internal correlation were proposed and discussed. In an in vitro bioassay, (+)-aristolone (3) exhibited promising anti-inflammatory activity by the inhibition of LPS-induced TNF-α and CCL2 release in RAW 264.7 macrophages.
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Affiliation(s)
- Shou-Mao Shen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qing Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science, Nanchang University, Nanchang 330006, China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yue-Wei Guo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
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