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Marinho AMDR, de Oliveira CMSC, Silva-Silva JV, de Jesus SCA, Siqueira JES, de Oliveira LC, Auzier JF, Soares LN, Pinheiro MLB, Silva SC, Medeiros LS, Costa EV, Marinho PSB. Antimicrobial Activity and Molecular Docking Studies of the Biotransformation of Diterpene Acanthoic Acid Using the Fungus Xylaria sp. Antibiotics (Basel) 2023; 12:1331. [PMID: 37627751 PMCID: PMC10451833 DOI: 10.3390/antibiotics12081331] [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: 06/30/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Biotransformations are reactions mediated by microorganisms, such as fungi. These bioreactions have high chemo- and stereoselectivity on organic substrates and can be applied in the search for new bioactive compounds. In this study, acanthoic acid (AA) was biotransformed using the fungus Xylaria sp., giving the novel compound 3β,7β-dihydroxyacanthoic acid (S1). Both the AA and the product S1 were tested against Gram-positive and Gram-negative bacteria. To identify and validate possible biological targets as enzymes or proteins involved in the activity observed in vitro, we used the molecular docking method. Hydroxylation at the C-3 and C-7 positions of the biotransformation product enhanced its activity against Escherichia coli as well as its binding affinity and interactions with superoxide dismutase 1 (SOD1; PDB ID 4A7G). Based on our results, the SOD1 enzyme was suggested to be a possible target for the antioxidant activity of product S1.
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Affiliation(s)
- Andrey Moacir do Rosario Marinho
- Post-Graduation in Chemistry, Federal University of Pará, Belém 66075-110, PA, Brazil; (S.C.A.d.J.); (J.E.S.S.); (L.C.d.O.); (P.S.B.M.)
| | - Claudia Maria S. C. de Oliveira
- Post-Graduation in Chemistry, Federal University of South and Southeast of Pará, Marabá 68507-590, PA, Brazil; (C.M.S.C.d.O.); (S.C.S.)
| | - João Victor Silva-Silva
- Laboratory of Medicinal and Computational Chemistry, Institute of Physics of São Carlos, University of São Paulo, São Carlos 13418-900, SP, Brazil
| | - Samara C. Anchieta de Jesus
- Post-Graduation in Chemistry, Federal University of Pará, Belém 66075-110, PA, Brazil; (S.C.A.d.J.); (J.E.S.S.); (L.C.d.O.); (P.S.B.M.)
| | - José Edson S. Siqueira
- Post-Graduation in Chemistry, Federal University of Pará, Belém 66075-110, PA, Brazil; (S.C.A.d.J.); (J.E.S.S.); (L.C.d.O.); (P.S.B.M.)
| | - Luana C. de Oliveira
- Post-Graduation in Chemistry, Federal University of Pará, Belém 66075-110, PA, Brazil; (S.C.A.d.J.); (J.E.S.S.); (L.C.d.O.); (P.S.B.M.)
| | - Jéssica Fernandes Auzier
- Post-Graduation in Chemistry, Federal University of Amazonas, Manaus 69077-000, AM, Brazil; (J.F.A.); (L.N.S.); (M.L.B.P.); (E.V.C.)
| | - Liviane N. Soares
- Post-Graduation in Chemistry, Federal University of Amazonas, Manaus 69077-000, AM, Brazil; (J.F.A.); (L.N.S.); (M.L.B.P.); (E.V.C.)
| | - Maria Lúcia Belém Pinheiro
- Post-Graduation in Chemistry, Federal University of Amazonas, Manaus 69077-000, AM, Brazil; (J.F.A.); (L.N.S.); (M.L.B.P.); (E.V.C.)
| | - Sebastião C. Silva
- Post-Graduation in Chemistry, Federal University of South and Southeast of Pará, Marabá 68507-590, PA, Brazil; (C.M.S.C.d.O.); (S.C.S.)
| | - Lívia S. Medeiros
- Post-Graduation in Chemistry, Federal University of São Paulo, Diadema 09920-000, SP, Brazil;
| | - Emmanoel V. Costa
- Post-Graduation in Chemistry, Federal University of Amazonas, Manaus 69077-000, AM, Brazil; (J.F.A.); (L.N.S.); (M.L.B.P.); (E.V.C.)
| | - Patrícia S. Barbosa Marinho
- Post-Graduation in Chemistry, Federal University of Pará, Belém 66075-110, PA, Brazil; (S.C.A.d.J.); (J.E.S.S.); (L.C.d.O.); (P.S.B.M.)
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Nazarski RB. Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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3
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Martínez-Fructuoso L, Pereda-Miranda R, Fragoso-Serrano M, da Silva AS, Leitão SG. Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments. PHYTOCHEMISTRY 2020; 179:112481. [PMID: 33017733 DOI: 10.1016/j.phytochem.2020.112481] [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: 05/18/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Dihydro-furanones are bioactive compounds isolated from various plants, marine fungi, and sponges. The present investigation describes the isolation by recycling HPLC and structural characterization by NMR of four previously undescribed 2(5H)-furanones, monticofuranolide A and pectinolides N-P, one phenylpropanoid, rosmarinic acid, and five known flavonoids, in addition to the undescribed natural flavonoid, 2R,3R-dihydrogossipetin or 5,7,8,3',4'-pentahydroxy flavanonol, from collections of H. monticola Mart. ex Benth and Hyptis pectinata (L.) Poit. Chemical correlations, resembling the biogenetic relationship of the isolated 2(5H)-furanones with their 5,6-dihydro-2H-pyran-2-one precursors, were accomplished to confirm their absolute configuration. Density functional theory-NMR/ECD calculations have been used to solve the absolute configuration for this type of compounds.
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Affiliation(s)
- Lucero Martínez-Fructuoso
- Departamento de Farmacia, Facultad de Química and Programa de Maestría y Doctorado en Ciencias Químicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Rogelio Pereda-Miranda
- Departamento de Farmacia, Facultad de Química and Programa de Maestría y Doctorado en Ciencias Químicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, 04510, Mexico.
| | - Mabel Fragoso-Serrano
- Departamento de Farmacia, Facultad de Química and Programa de Maestría y Doctorado en Ciencias Químicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Aline Soares da Silva
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, CCS, Bloco A, Ilha do Fundão, 21941-902, Rio de Janeiro, Brazil
| | - Suzana Guimarães Leitão
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, CCS, Bloco A, Ilha do Fundão, 21941-902, Rio de Janeiro, Brazil
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4
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Martins GR, da Fonseca TS, Martínez-Fructuoso L, Simas RC, Silva FT, Salimena FRG, Alviano DS, Alviano CS, Leitão GG, Pereda-Miranda R, Leitão SG. Antifungal Phenylpropanoid Glycosides from Lippia rubella. JOURNAL OF NATURAL PRODUCTS 2019; 82:566-572. [PMID: 30817148 DOI: 10.1021/acs.jnatprod.8b00975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lippia species share various pharmacological activities and are used in traditional cooking and medicine worldwide. Combined chromatographic techniques such as column chromatography, high-performance liquid chromatography, and countercurrent chromatography led to the purification of two new antifungal phenylpropanoid glycosides, lippiarubelloside A (1) and lippiarubelloside B (2), by bioactivity-directed fractionation of an ethanol-soluble extract from Lippia rubella, in addition to the known active related compounds forsythoside A (3), verbascoside (4), isoverbascoside (5), and poliumoside (6). The structures of compounds 1 and 2 were determined by comparison of their NMR spectroscopic data with the prototype active compound 4. Cryptococcus neoformans, which causes opportunistic lung infections, was sensitive to compounds 1-6 in the concentration range of 15-125 μg/mL. A synergistic effect (FICindex = 0.5) between 3 and amphotericin B was demonstrated. The glycosylated flavonoids pectolinarin (7), linarin (8), and siparunoside (9) were also isolated.
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Affiliation(s)
- Gabriel R Martins
- Faculdade de Farmácia, Centro de Ciências da Saúde (CCS) , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Thamirys Silva da Fonseca
- Faculdade de Farmácia, Centro de Ciências da Saúde (CCS) , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Lucero Martínez-Fructuoso
- Departamento de Farmacia, Facultad de Química , Universidad Nacional Autónoma de México , Mexico City , 04510 DF , Mexico
| | - Rosineide Costa Simas
- Faculdade de Farmácia, Centro de Ciências da Saúde (CCS) , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Fabio T Silva
- Faculdade de Farmácia, Centro de Ciências da Saúde (CCS) , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Fatima Regina G Salimena
- ICB, Depto de Botânica , Universidade Federal de Juiz de Fora , 84030-900 , Juiz de Fora , MG , Brazil
| | - Daniela S Alviano
- Instituto de Microbiologia Paulo de Góes , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Celuta Sales Alviano
- Instituto de Microbiologia Paulo de Góes , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
| | - Rogelio Pereda-Miranda
- Departamento de Farmacia, Facultad de Química , Universidad Nacional Autónoma de México , Mexico City , 04510 DF , Mexico
| | - Suzana G Leitão
- Faculdade de Farmácia, Centro de Ciências da Saúde (CCS) , Universidade Federal do Rio de Janeiro , 21941-902 , Rio de Janeiro , Brazil
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5
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Martínez-Fructuoso L, Pereda-Miranda R, Rosas-Ramírez D, Fragoso-Serrano M, Cerda-García-Rojas CM, da Silva AS, Leitão GG, Leitão SG. Structure Elucidation, Conformation, and Configuration of Cytotoxic 6-Heptyl-5,6-dihydro-2 H-pyran-2-ones from Hyptis Species and Their Molecular Docking to α-Tubulin. JOURNAL OF NATURAL PRODUCTS 2019; 82:520-531. [PMID: 30601004 DOI: 10.1021/acs.jnatprod.8b00908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cytotoxic 6-heptyl-5,6-dihydro-2 H-pyran-2-ones are chemical markers of Hyptis (Lamiaceae) and are responsible for some of the therapeutic properties of species with relevance to traditional medicine. The present investigation describes the isolation of known pectinolides A-C (1-3), in addition to the new pectinolides I-M (4-8), from two Mexican collections of H. pectinata by HPLC. The novel biosynthetically related monticolides A (9) and B (10) were also isolated by high-speed countercurrent chromatography from H. monticola, an endemic species of the Brazilian southeastern high-altitude regions. A combination of chemical correlations, chiroptical measurements, and Mosher ester NMR analysis was used to confirm their absolute configuration. The utility of DFT-NMR chemical shifts and JH-H calculations was assessed for epimer differentiation. Molecular docking studies indicated that 6-heptyl-5,6-dihydro-2 H-pyran-2-ones have a high affinity for the pironetin-binding site of α-tubulin, which may be a possible mechanism contributing to the cytotoxic potential of these small and flexible molecules.
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Affiliation(s)
- Lucero Martínez-Fructuoso
- Departamento de Farmacia, Facultad de Química , Universidad Nacional Autónoma de México , Ciudad Universitaria, Mexico City 04510 , Mexico
| | - Rogelio Pereda-Miranda
- Departamento de Farmacia, Facultad de Química , Universidad Nacional Autónoma de México , Ciudad Universitaria, Mexico City 04510 , Mexico
| | - Daniel Rosas-Ramírez
- Departamento de Farmacia, Facultad de Química , Universidad Nacional Autónoma de México , Ciudad Universitaria, Mexico City 04510 , Mexico
| | - Mabel Fragoso-Serrano
- Departamento de Farmacia, Facultad de Química , Universidad Nacional Autónoma de México , Ciudad Universitaria, Mexico City 04510 , Mexico
| | - Carlos M Cerda-García-Rojas
- Departamento de Química , Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , A. P. 14-740, Mexico City 07000 , Mexico
| | - Aline Soares da Silva
- Faculdade de Farmacia , Universidade Federal do Rio de Janeiro , CCS, Bloco A, Ilha do Fundão, 21941-902 , Rio de Janeiro , Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais , Universidade Federal do Rio de Janeiro , CCS, Bloco H, Ilha do Fundão, 21941-590 , Rio de Janeiro , Brazil
| | - Suzana Guimarães Leitão
- Faculdade de Farmacia , Universidade Federal do Rio de Janeiro , CCS, Bloco A, Ilha do Fundão, 21941-902 , Rio de Janeiro , Brazil
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6
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Kikuchi J, Ito K, Date Y. Environmental metabolomics with data science for investigating ecosystem homeostasis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:56-88. [PMID: 29405981 DOI: 10.1016/j.pnmrs.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 05/08/2023]
Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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7
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Suárez-Ortiz GA, Cerda-García-Rojas CM, Fragoso-Serrano M, Pereda-Miranda R. Complementarity of DFT Calculations, NMR Anisotropy, and ECD for the Configurational Analysis of Brevipolides K-O from Hyptis brevipes. JOURNAL OF NATURAL PRODUCTS 2017; 80:181-189. [PMID: 28099005 DOI: 10.1021/acs.jnatprod.6b00953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Brevipolides K-O (1-5), five new cytotoxic 6-(6'-cinnamoyloxy-2',5'-epoxy-1'-hydroxyheptyl)-5,6-dihydro-2H-pyran-2-ones (IC50 values against six cancer cell lines, 1.7-10 μM), were purified by recycling HPLC from Hyptis brevipes. The structures, containing a distinctive tetrahydrofuran ring, were established by comprehensive quantum mechanical calculations and experimental spectroscopic analysis of their NMR and ECD data. Detailed analysis of the experimental NMR 1H-1H vicinal coupling constants in comparison with the corresponding DFT-calculated values at the B3LYP/DGDZVP level confirmed the absolute configuration of 3 and revealed its conformational preferences, which were further strengthened by NOESY correlations. NMR anisotropy experiments by the application of Mosher's ester methodology and chemical correlations were also used to conclude that this novel brevipolide series (1-5) share the same absolute configuration corresponding to C-6(R), C-1'(S), C-2'(R), C-5'(S), and C-6'(S).
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Affiliation(s)
- G Alejandra Suárez-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria , Mexico City 04510, Mexico
| | - Carlos M Cerda-García-Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , A. P. 14-740, Mexico City 07000, Mexico
| | - Mabel Fragoso-Serrano
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria , Mexico City 04510, Mexico
| | - Rogelio Pereda-Miranda
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria , Mexico City 04510, Mexico
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8
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Wang J, Tong R. A NMR method for relative stereochemical assignments of the tricyclic core of cephalosporolides, penisporolides and related synthetic analogues. Org Chem Front 2017. [DOI: 10.1039/c6qo00556j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new NMR method is developed to discriminate the four possible diastereomeric SAFLs, leading to revisions of 11 synthetic compounds.
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Affiliation(s)
- Jian Wang
- Department of Chemistry
- Hong Kong University of Science and Technology
- Kowloon
- China
| | - Rongbiao Tong
- Department of Chemistry
- Hong Kong University of Science and Technology
- Kowloon
- China
- HKUST Shenzhen Research Institute
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9
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Rivera-Chávez J, Figueroa M, González MDC, Glenn AE, Mata R. α-Glucosidase Inhibitors from a Xylaria feejeensis Associated with Hintonia latiflora. JOURNAL OF NATURAL PRODUCTS 2015; 78:730-735. [PMID: 25706243 DOI: 10.1021/np500897y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two new compounds, pestalotin 4'-O-methyl-β-mannopyranoside (1) and 3S,4R-(+)-4-hydroxymellein (2), were isolated from an organic extract of a Xylaria feejeensis, which was isolated as an endophytic fungus from Hintonia latiflora. In addition, the known compounds 3S,4S-(+)-4-hydroxymellein (3), 3S-(+)-8-methoxymellein (4), and the quinone derivatives 2-hydroxy-5-methoxy-3-methylcyclohexa-2,5-diene-1,4-dione (5), 4S,5S,6S-4-hydroxy-3-methoxy-5-methyl-5,6-epoxycyclohex-2-en-1-one (6), and 4R,5R-dihydroxy-3-methoxy-5-methylcyclohexen-2-en-1-one (7) were obtained. The structures of 1 and 2 were elucidated using a set of spectroscopic and spectrometric techniques. The absolute configuration of the stereogenic centers of 1 and 2 was determined using ECD spectroscopy combined with time-dependent density functional theory calculations. In the case of 1, comparison of the experimental and theoretical (3)J6-7 coupling constants provided further evidence for the stereochemical assignments. Compounds 2 and 3 inhibited Saccharomyces cerevisiae α-glucosidase (αGHY), with IC50 values of 441 ± 23 and 549 ± 2.5 μM, respectively. Their activity was comparable to that of acarbose (IC50 = 545 ± 19 μM), used as positive control. Molecular docking predicted that both compounds bind to αGHY in a site different from the catalytic domain, which could imply an allosteric type of inhibition.
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Affiliation(s)
- José Rivera-Chávez
- †Facultad de Química, Universidad Nacional Autónoma de México, México DF 04510, Mexico
| | - Mario Figueroa
- †Facultad de Química, Universidad Nacional Autónoma de México, México DF 04510, Mexico
| | | | | | - Rachel Mata
- †Facultad de Química, Universidad Nacional Autónoma de México, México DF 04510, Mexico
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10
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Vinţeler E, Stan NF, Luchian R, Căinap C, Ramalho JPP, Chiş V. Conformational landscape and low lying excited states of imatinib. J Mol Model 2015; 21:84. [DOI: 10.1007/s00894-015-2639-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/22/2015] [Indexed: 11/28/2022]
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11
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Juárez-González F, Suárez-Ortiz GA, Fragoso-Serrano M, Cerda-García-Rojas CM, Pereda-Miranda R. DFT 1H-1H coupling constants in the conformational analysis and stereoisomeric differentiation of 6-heptenyl-2H-pyran-2-ones: configurational reassignment of synargentolide A. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:203-212. [PMID: 25353378 DOI: 10.1002/mrc.4178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/05/2014] [Accepted: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Density functional theory (DFT) (1) H-(1) H NMR coupling constant calculations, including solvation parameters with the polarizable continuum model B3LYP/DGDZVP basis set together with the experimental values measured by spectral simulation, were used to predict the configuration of hydroxylated 6-heptenyl-5,6-dihydro-2H-pyran-2-ones 1, 2, 4, and 7, allowing epimer differentiation. Modeling of these flexible compounds requires the inclusion of solvation models that account for stabilizing interactions derived from intramolecular and intermolecular hydrogen bonds, in contrast with peracetylated derivatives (3, 5, and 6) in which the solvation consideration can be omitted. Using this DFT NMR integrated approach as well as spectral simulation, the configurational reassignment of synargentolide A (8) was accomplished by calculations in the gas phase among four possible diastereoisomers (8-11). Calculated (3) JH,H values established its configuration as 6R-[4'S,5'S,6'S-(triacetyloxy)-2E-heptenyl]-5,6-dihydro-2H-pyran-2-one (8), in contrast with the incorrect 6R,4'R,5'R,6'R-diastereoisomer previously proposed by synthesis (12). Application of this approach increases the probability for successful enantiospecific total syntheses of flexible compounds with multiple chiral centers.
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Affiliation(s)
- Francisco Juárez-González
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, 04510, DF, Mexico
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12
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Li Y. Structural revision of glabramycins B and C, antibiotics from the fungus Neosartorya glabra by DFT calculations of NMR chemical shifts and coupling constants. RSC Adv 2015. [DOI: 10.1039/c5ra01753j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The 13C NMR spectra and vicinal proton–proton coupling constants of two tricyclic macrolactone natural products were analyzed using computational methods, which resulted in their structural revisions.
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Affiliation(s)
- Yang Li
- Department of Chemistry
- Yale University
- New Haven
- USA
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13
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Kutateladze AG, Mukhina OA. Relativistic Force Field: Parametric Computations of Proton–Proton Coupling Constants in 1H NMR Spectra. J Org Chem 2014; 79:8397-406. [DOI: 10.1021/jo501781b] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Andrei G. Kutateladze
- Department
of Chemistry and
Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Olga A. Mukhina
- Department
of Chemistry and
Biochemistry, University of Denver, Denver, Colorado 80208, United States
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14
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Bañuelos-Hernández AE, Mendoza-Espinoza JA. Synthesis of the 2,3,4-triacetyl-1,6-dideoxy-L-mannose and tetracetyl-3,6-dideoxy-L-mannitol and the study of the reaction mechanism by molecular modeling. RUSS J GEN CHEM+ 2014. [DOI: 10.1134/s1070363214070342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Bañuelos-Hernández AE, Mendoza-Espinoza JA, Pereda-Miranda R, Cerda-García-Rojas CM. Studies of (−)-Pironetin Binding to α-Tubulin: Conformation, Docking, and Molecular Dynamics. J Org Chem 2014; 79:3752-64. [DOI: 10.1021/jo500420j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Angel E. Bañuelos-Hernández
- Departamento
de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A. P. 14-740, México D. F. 07000, Mexico
| | - José Alberto Mendoza-Espinoza
- Departamento
de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A. P. 14-740, México D. F. 07000, Mexico
| | - Rogelio Pereda-Miranda
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria, México D. F. 04510, Mexico
| | - Carlos M. Cerda-García-Rojas
- Departamento
de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A. P. 14-740, México D. F. 07000, Mexico
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16
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Lokesh N, Chaudhari SR, Suryaprakash N. Quick re-introduction of selective scalar interactions in a pure-shift NMR spectrum. Chem Commun (Camb) 2014; 50:15597-600. [DOI: 10.1039/c4cc06772j] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new 1D NMR experiment cited as ‘Quick G-SERF’, which re-introduces selective proton–proton scalar interactions in a pure shift spectrum during real time data acquisition, is reported.
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Affiliation(s)
- N. Lokesh
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012, India
| | - Sachin Rama Chaudhari
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012, India
| | - N. Suryaprakash
- NMR Research Centre and Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012, India
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17
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Madariaga-Mazón A, González-Andrade M, González MDC, Glenn AE, Cerda-García-Rojas CM, Mata R. Absolute configuration of acremoxanthone C, a potent calmodulin inhibitor from Purpureocillium lilacinum. JOURNAL OF NATURAL PRODUCTS 2013; 76:1454-1460. [PMID: 23876004 DOI: 10.1021/np4002477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bioassay-guided fractionation of an extract prepared from the culture medium and mycelium of Purpureocillium lilacinum allowed the isolation of two calmodulin (CaM) inhibitors, namely, acremoxanthone C (1) and acremonidin A (2). The absolute configuration of 1 was established as 2R, 3R, 1'S, 11'S, and 14'R through extensive NMR spectroscopy and molecular modeling calculations at the DFT B3LYP/DGDZVP level, which included the comparison between theoretical and experimental specific rotation, ³J(C,H), and ³J(H,H) values. Compounds 1 and 2 bind to the human calmodulin (hCaM) biosensor hCaM M124C-mBBr, with dissociation constants (Kd) of 18.25 and 19.40 nM, respectively, 70-fold higher than that of chlorpromazine (Kd = 1.24 μM), used as positive control. Docking analysis using AutoDock 4.2 predicted that 1 and 2 bind to CaM at a similar site to that which KAR-2 binds, which is unusual. Furthermore, a novel, sensible, and specific fluorescent biosensor of hCaM, i.e., hCaM T110C-mBBr, was constructed; this device is labeled at a site where classical inhibitors do not interact and was successfully applied to measure the interaction of 1 with CaM. This is the first report of xanthone-anthraquinone heterodimers in species of Paecilomyces or Purpureocillium genera.
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Zhang J, Tang X, Li J, Li P, de Voogd NJ, Ni X, Jin X, Yao X, Li P, Li G. Cytotoxic polyketide derivatives from the South China Sea sponge Plakortis simplex. JOURNAL OF NATURAL PRODUCTS 2013; 76:600-606. [PMID: 23806071 DOI: 10.1021/np300771p] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Five new polyketides, plakortoxides A (1) and B (2), simplextones C (3) and D (4), and plakorsin D (5), together with six known analogues (6-11) were isolated from the South China Sea sponge Plakortis simplex. Their structures were identified by spectroscopic and chemical methods, including NMR, MS, and IR. Experimental and calculated ECD spectra and the modified Mosher's method were used to determine the absolute configurations. Structurally, both plakortoxides A and B feature a butenolide coupled to an epoxide moiety, while simplextones C and D consist of γ-butyrolactone and cyclopentane moieties, and plakorsin D is a furan acetic acid polyketide. The cytotoxic activities of the isolates were tested, and compounds 8, 10, and 11 showed potent cytotoxicity against both K562 and HeLa tumor cell lines with IC50 values ranging from 0.8 to 5.3 μM. Compound 3 showed significant inhibitory activity against c-Met kinase.
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Affiliation(s)
- Jinrong Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
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19
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Suárez-Ortiz GA, Cerda-García-Rojas CM, Hernández-Rojas A, Pereda-Miranda R. Absolute configuration and conformational analysis of brevipolides, bioactive 5,6-dihydro-α-pyrones from Hyptis brevipes. JOURNAL OF NATURAL PRODUCTS 2013; 76:72-78. [PMID: 23282042 DOI: 10.1021/np300740h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The (6'S)-configuration of brevipolides A-J (1-10), isolated from Hyptis brevipes, was established by X-ray diffraction analysis of 9 in conjunction with Mosher's ester analysis of the tetrahydro derivative 11 obtained from both geometric isomers 8 and 9 as well as by chemical correlations. The structure of the new brevipolide J (10) was characterized through NMR and MS data as having the same 6-heptyl-5,6-dihydro-2H-pyran-2-one framework possessing the cyclopropane moiety of all brevipolides but substituted by an isoferuloyl group instead of the p-methoxycinnamoyl moiety found in 8 and 9. Conformational analysis of these cytotoxic 6-heptyl-5,6-dihydro-α-pyrones was carried out on compound 9 by application of a protocol based on comparison between experimental and DFT-calculated vicinal (1)H-(1)H NMR coupling constants. Molecular modeling was used to correlate minimum energy conformers and observed electronic circular dichroism transitions for the isomeric series of brevipolides. Compounds 7-10 exhibited moderate activity (ED(50) 0.3-8.0 μg/mL) against a variety of tumor cell lines.
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Affiliation(s)
- G Alejandra Suárez-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria, México City, D. F. 04510 México
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20
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Leyte-Lugo M, González-Andrade M, González MDC, Glenn AE, Cerda-García-Rojas CM, Mata R. (+)-Ascosalitoxin and vermelhotin, a calmodulin inhibitor, from an endophytic fungus isolated from Hintonia latiflora. JOURNAL OF NATURAL PRODUCTS 2012; 75:1571-1577. [PMID: 22924467 DOI: 10.1021/np300327y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Chemical investigation of the endophytic MEXU 26343, isolated from the medicinal plant Hintonia latiflora, yielded the known polyketide vermelhotin (1) and a new salicylic aldehyde derivative, namely, 9S,11R-(+)-ascosalitoxin (2). The structure and absolute configuration of the new compound were established through extensive NMR spectroscopy and molecular modeling calculations at the DFT B3LYP/DGDZVP level, which included the comparison between theoretical and experimental optical rotation values. In addition, chemical transformations of 2 yielded suitable derivatives for NOESY and (1)H-(1)H NMR coupling constant analyses, which reinforce the stereochemical assignment. The potential affinity of 1 and 2 with (Ca(2+))(4)-hCaM in solution was measured using the fluorescent biosensor hCaM M124C-mBBr. The results showed that 1 bound to the protein with a dissociation constant (K(d)) of 0.25 ± 0.04 μM, close to that of chlorpromazine (K(d) = 0.64 ± 0.03 μM), a classical CaM inhibitor. The stoichiometry ratio of 1 to (Ca(2+))(4)-hCaM was 1:4, similar to other well-known CaM ligands.
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Affiliation(s)
- Martha Leyte-Lugo
- Facultad de Química, Universidad Nacional Autónoma de México, México DF 04510, Mexico
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21
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Hersh WH, Lam ST, Moskovic DJ, Panagiotakis AJ. A non-Karplus effect: evidence from phosphorus heterocycles and DFT calculations of the dependence of vicinal phosphorus-hydrogen NMR coupling constants on lone-pair conformation. J Org Chem 2012; 77:4968-79. [PMID: 22612503 DOI: 10.1021/jo3003776] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In contrast to literature reports of a Karplus-type curve that correlates (3)J(PH) with phosphorus-hydrogen dihedral angle, a recently reported glycine-derived 1,3,2-oxazaphospholidine (7c) has two hydrogen atoms on the ring with identical PNCH dihedral angles but measured coupling constants of ∼6 and 1.5 Hz. DFT calculations were in accord with these values and suggested that the smaller coupling constant is negative. Experimental evidence of the opposite signs of these coupling constants was obtained by analysis of the ABX NMR spectrum of the new glycine-derived N-p-toluenesulfonyl phosphorus heterocycle 6c. DFT calculations on 6c and on Me(2)NPCl(2) and t-BuPCl(2) were also in accord with NMR data and allowed confirmation of unusual features including a lone pair effect on (3)J(PH), the negative coupling constant, temperature-dependent chemical shifts due to rotation about the sulfonamide S-N bond, and vicinal phosphorus-hydrogen coupling constants over 40 Hz. Calculation of phosphorus-hydrogen coupling constants both as a function of PYCH dihedral angle θ (Y = O, N, C) and lone pair-PYC dihedral angle ω shows similar θ,ω surfaces for (3)J(PH) with a range of (3)J(PH) from -4.4 to +51 Hz and demonstrates the large non-Karplus effect of lone-pair conformation on vicinal phosphorus-hydrogen coupling constants.
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Affiliation(s)
- William H Hersh
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, Flushing, New York 11367-1597, United States.
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