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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: 0] [Impact Index Per Article: 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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2
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Taniguchi T, Ida N, Kitahara T, Agbo DO, Monde K. Stereostructural analysis of flexible oxidized fatty acids by VCD spectroscopy. Chem Commun (Camb) 2022; 58:6116-6119. [PMID: 35506441 DOI: 10.1039/d2cc01337a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxidation of polyunsaturated fatty acids produces various oxidized lipids whose absolute configuration (AC) and conformations are difficult to analyze due to their flexibility. Through studies on hydroxy fatty acids, lipid hydroperoxides, and lipid epoxides, this work demonstrates the effectiveness of VCD spectroscopy to elucidate their AC and conformational preferences.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
| | - Naka Ida
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Takuya Kitahara
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan.
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3
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Fraga BM, Díaz CE, Bailén M, González-Coloma A. Sesquiterpene Lactones from Artemisia absinthium. Biotransformation and Rearrangement of the Insect Antifeedant 3α-hydroxypelenolide. PLANTS (BASEL, SWITZERLAND) 2021; 10:891. [PMID: 33925212 PMCID: PMC8146418 DOI: 10.3390/plants10050891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022]
Abstract
Three new compounds, the sesquiterpenes absilactone and hansonlactone and the acetophenone derivative ajenjol, have been isolated from a cultivated variety of Artemisia absinthium. In addition, the major lactone isolated, 3α-hydroxypelenolide, was biotransformed by the fungus Mucor plumbeus affording the corresponding 1β, 10α-epoxide. A cadinane derivative was formed by an acid rearrangement produced in the culture medium, but not by the enzymatic system of the fungus. Furthermore, 3α-hydroxypelenolide showed strong antifeedant effects against Leptinotarsa decemlineata and cytotoxic activity to Sf9 insect cells, while the biotransformed compounds showed antifeedant postingestive effects against Spodoptera littoralis.
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Affiliation(s)
- Braulio M. Fraga
- Instituto de Productos Naturales y Agrobiología, CSIC, Avda. Astrofísico F. Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain;
| | - Carmen E. Díaz
- Instituto de Productos Naturales y Agrobiología, CSIC, Avda. Astrofísico F. Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain;
| | - María Bailén
- Departamento de Medicina Preventiva y Salud Pública y Microbiología, Facultad de Medicina, Universidad Autónoma de Madrid, C. Arzobispo Morcillo s/n, 28049 Madrid, Spain;
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4
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del Río RE, Joseph-Nathan P. Vibrational Circular Dichroism Absolute Configuration of Natural Products From 2015 to 2019. Nat Prod Commun 2021. [DOI: 10.1177/1934578x21996166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although demonstrated in 1975, vibrational circular dichroism (VCD) finally started to popularize during this century as a reliable tool to determine the absolute configuration (AC) of organic molecules. This research field continues to be a very dynamic one, in particular for the study of natural products which are a unlimited source of chiral molecules. It therefore turns of interest to summarize the accomplishments published in recent years and to comment on some eventual difficulties that emerged in rare cases to complete the AC determination task. Therefore the aim of this review is to update VCD results for the AC assignment of natural products published from 2015 to 2019, a period in which VCD was reported in some 126 publications involving almost 300 molecules. They are organized according the type of studied metabolite allowing an easily search. The molecules correspond to 28 monoterpenes concerning 17 papers, to 42 sesquiterpenes in 14 papers, to 51 diterpenes in 19 publications, to 5 other terpenoids in three papers, to 48 aromatic molecules in 15 reports, to 20 polyketides in 10 publications, to 27 miscellaneous formulas also in 10 papers, and to 76 nitrogen containing compounds, which include alkaloids and their synthetic analogs, in 38 articles. The landscape of reviewed molecules is quite wide as it goes from simple monoterpenes, like borneol or camphor, to very relevant biological molecules like the alkaloid cocaine or tadalafil samples to distinguish genuine and counterfeit Cialis®. In addition, 5 natural products and a simple derivative published outside the reviewed period, were used to illustrate some aspects of density functional theory calculations.
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Affiliation(s)
- Rosa E. del Río
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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5
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López-Garrido L, Bañuelos-Hernández AE, Pérez-Hernández E, Tecualt-Gómez R, Quiroz-Williams J, Ariza-Castolo A, Becerra-Martínez E, Pérez-Hernández N. Metabolic profiling of serum in patients with cartilage tumours using 1 H-NMR spectroscopy: A pilot study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:65-76. [PMID: 31323132 DOI: 10.1002/mrc.4925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/15/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Cartilage-forming lesions include tumours that can vary in severity from benign enchondromas to high-grade malignant chondrosarcomas. Chondrosarcoma is the second most frequent malignant bone tumour, accounting for 20-30% of all malignant bone neoplasms. Surgery is the standard treatment for cartilage tumours (CTs); however, their incidental diagnosis and the difficult differentiation of low-grade lesions like chondrosarcoma grade I from benign entities like enchondroma are challenges for clinical management. In this sense, the search for circulating biomarkers for early detection and prognosis is an ongoing interest. Targeted metabolomics is a powerful tool that can propose potential biomarkers in biological fluids as well as help to discover disturbed metabolic pathways to reveal tumour pathogenesis. In this context, the aim of this study was to investigate the 1 H nuclear magnetic resonance metabolomic serum profile of patients with CTs contrasted with healthy controls. Forty-one metabolites were identified and quantified; the multivariate statistical methods principal component analysis and partial least squares discriminant analysis reveal a clear separation of the CT group, that is, the differential metabolites that were involved in two main metabolic pathways: the taurine and hypotaurine metabolism and synthesis and degradation of ketone bodies. Our results represent preliminary work for emergent serum-based diagnostics or prognostic methods for patients with chondrogenic tumours.
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Affiliation(s)
- Liliana López-Garrido
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de México, Mexico
| | - Angel E Bañuelos-Hernández
- Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Elizabeth Pérez-Hernández
- Instituto Mexicano del Seguro Social, UMAE de Traumatología, Ortopedia y Rehabilitación "Dr. Victorio de la Fuente Narváez", Ciudad de México, Mexico
| | - Romeo Tecualt-Gómez
- Instituto Mexicano del Seguro Social, UMAE de Traumatología, Ortopedia y Rehabilitación "Dr. Victorio de la Fuente Narváez", Ciudad de México, Mexico
| | - Jorge Quiroz-Williams
- Instituto Mexicano del Seguro Social, UMAE de Traumatología, Ortopedia y Rehabilitación "Dr. Victorio de la Fuente Narváez", Ciudad de México, Mexico
| | - Armando Ariza-Castolo
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Elvia Becerra-Martínez
- Instituto Politécnico Nacional, Centro de Nanociencias y Micro y Nanotecnologías, Ciudad de México, Mexico
| | - Nury Pérez-Hernández
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de México, Mexico
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Polavarapu PL, Santoro E. Vibrational optical activity for structural characterization of natural products. Nat Prod Rep 2020; 37:1661-1699. [DOI: 10.1039/d0np00025f] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.
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Pino-Otín MR, Val J, Ballestero D, Navarro E, Sánchez E, Mainar AM. Impact of Artemisia absinthium hydrolate extracts with nematicidal activity on non-target soil organisms of different trophic levels. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:565-574. [PMID: 31129435 DOI: 10.1016/j.ecoenv.2019.05.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Natural pesticides are considered a good alternative to synthetic pesticides to reduce environmental impacts. However, biopesticides may have unknown effects on the environment, and can affect non-target organisms. In this study, the ecotoxicological effects of an aqueous extract (hydrolate) from Spanish populations of Artemisia absinthium (var. Candial) showing a promising biopesticide activity, were evaluated on non-target soil organisms from different trophic levels (natural microbial communities characterized through 16S rRNA gene sequencing, the earthworm Eisenia fetida and the plant Allium cepa). The hydrolate usually was considered as a by-product of the distillation to obtain essential oils. However, recently has been found to have nematicide properties. The hydrolate caused acute toxicity at values of LC50 of 3.87% v/v for A. cepa and 0.07 mL/g for E. fetida. All the concentrations except for the most diluted (1% v/v) reduced the bacterial physiological activity compared to controls (LC50 = 25.72% v/v after 24 h of exposure). The hydrolate also slightly altered the ability of the microbial community to degrade carbon substrates. These results indicate that the hydrolate from A. absinthium may affect the survival and metabolic abilities of key soil organisms.
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Affiliation(s)
- M Rosa Pino-Otín
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain.
| | - Jonatan Val
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain; Colegio Internacional Ánfora, c/ Pirineos, 8, 50410, Cuarte de Huerva, Zaragoza, Spain
| | - Diego Ballestero
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain
| | - Enrique Navarro
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciónes Científicas, Av. Montañana 1005, 50059, Zaragoza, Spain
| | - Esther Sánchez
- Colegio Internacional Ánfora, c/ Pirineos, 8, 50410, Cuarte de Huerva, Zaragoza, Spain
| | - Ana M Mainar
- I3A, Universidad de Zaragoza, c/ Mariano Esquillor s/n, 50018, Zaragoza, Spain
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Ortega AR, Pérez-Hernández N, Joseph-Nathan P. Piscicartone, a Rotenoid From Piscidia carthagenensis. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The bark of the roots of Piscidia carthagenensis afforded the known insecticides rotenone (1) and millettone (2), as well as the new rotenoid piscicartone (3). The structure of 3 followed from nuclear magnetic resonance studies, while its absolute configuration (AC) was determined by vibrational circular dichroism (VCD) measurements in comparison with discrete Fourier transform B3LYP/DGDZVPcalculated spectra using the Compare VOA software. In addition, the AC of 1 and 2 was verified using the same VCD methodology.
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Affiliation(s)
- Alfredo R. Ortega
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
| | - Nury Pérez-Hernández
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado, Mexico City, Mexico
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Pino-Otín MR, Ballestero D, Navarro E, González-Coloma A, Val J, Mainar AM. Ecotoxicity of a novel biopesticide from Artemisia absinthium on non-target aquatic organisms. CHEMOSPHERE 2019; 216:131-146. [PMID: 30366267 DOI: 10.1016/j.chemosphere.2018.09.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Biopesticides are increasingly being used to replace synthetic pesticides for pest control. This change raises concern for its environmental impacts, especially on non-target organisms. In this study, the ecotoxicological effects of a potential nematicide from Spanish populations of Artemisia absinthium (var. Candial) were evaluated on freshwater and aquatic non-target organisms. The study focused on the aqueous extract (hydrolate), the principal component of which ((-) -(Z) -2,6-dimethylocta-5,7-diene-2,3-diol) is responsible for its nematicidal effect. Until now, the hydrolate has been considered a byproduct of the process used to obtain essential oils, and there are no studies on its ecotoxicity from any plant with biopesticide properties. Our results indicated that A. absinthium hydrolate caused acute toxicity for non-target organisms at dilutions as low as 0.2%. The sensitivity of the organisms, from the most to the least sensitive, was: Daphnia magna (LC50 = 0,236%) > Vibrio fisheri (LC50 = 1,85%) > Chlamydomonas reinhardtii (LC50 = 16,49). Moreover, the A. absinthium organic extract was highly toxic to D. magna (LC50 = 0,093 mg/L). A. absinthium hydrolate toxicity was also tested on a natural river microbial community. Bacterial growth was not affected; the physiology of the community was only slightly modified, namely through an increased ability to degrade different substrates, mainly carbohydrates. This study provides for the first time an exhaustive assessment of the environmental exposure of a plant-derived biopesticide and shows that these products may cause a broad range of toxicity on non-target aquatic organisms.
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Affiliation(s)
- Ma Rosa Pino-Otín
- Universidad San Jorge, Villanueva de Gállego, 50830 Zaragoza, Spain.
| | - Diego Ballestero
- Universidad San Jorge, Villanueva de Gállego, 50830 Zaragoza, Spain.
| | - Enrique Navarro
- Instituto Pirenaico de Ecología, CSIC, Av. Montañana 1005, 50059 Zaragoza, Spain.
| | | | - Jonatan Val
- Universidad San Jorge, Villanueva de Gállego, 50830 Zaragoza, Spain.
| | - Ana M Mainar
- I3A, Universidad de Zaragoza, c/ Mariano Esquillor s/n, 50018 Zaragoza, Spain.
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Pérez-Hernández N, Becerra-Martínez E, Joseph-Nathan P. Complete 1H NMR assignment of cholesteryl benzoate. Steroids 2018; 138:72-81. [PMID: 30033341 DOI: 10.1016/j.steroids.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
The 750 MHz 1H NMR spectrum of cholesteryl benzoate (1b) could be assigned completely, which means all chemical shifts and all coupling constants, including some long-range values, were established. This task was possible by extracting many approximate coupling constant values in the overlapped spectrum region from an HSQC experiment, and using these values in the 1H iterative full spin analysis integrated in the PERCH NMR software. The task was facilitated using our published data for 3β-acetoxypregna-5,16-dien-20-one (3), the assignment data of the sesquiterpene benzoquinone dihydroperezone (2), also performed in the present study, which contains the same carbon atoms chain than cholesterol (1a), and an HSQC study of (25R)-27-deuteriocholesterol (1c) we prepared some 40 years ago. The HSQC values of 1c in combination with the coupling constants of 1b also allowed to completely assigning the spectrum of 1c. The complete assignment of 1b and 1c further provided the opportunity to estimate the hydrogen shifts induced upon benzoylation of cholesterol. Comparison of the experimental vicinal coupling constants of 1b with the values calculated using the Altona software provides an excellent correlation. In addition, a single crystal X-ray diffraction study of 1b provided the molecular conformation in the solid state, which revealed the side chain adopts an extended conformation.
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Affiliation(s)
- Nury Pérez-Hernández
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Mexico City 07738, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico.
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Ortega AR, Burgueño-Tapia E, Joseph-Nathan P. Difficulties to Determine the Absolute Configuration of Guaiaretic Acid. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An account of the difficulties to determine the absolute configuration (AC) of guaiaretic acid (1a), using contemporary methodology, is described in commemoration of the century of its structure elucidation. In fact, the herein studied molecule was the derived diacetate 1b, since the natural lignan slowly decomposes upon manipulation. Single crystal X-ray diffraction of 1b demonstrated the structure, but calculation of Flack and Hooft parameters to know the AC was unsuccessful since the crystals were triclinic, P-1, which is a centro-symmetric space group. In turn, manual band to band comparison of experimental and DFT B3LYP/DGDZVP calculated VCD spectra of 1b allowed ascertaining its AC, although automatic comparison using the Compare VOA software was not very successful. This behavior is associated to the fact that the studied molecule has a sole stereogenic center located on the acyclic portion of a carbon chain possessing two quite similar substituents. The behavior is discussed in relation to cases where the molecular flexibility also generates a very large number of conformers.
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Affiliation(s)
- Alfredo R. Ortega
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, 04510 Mexico
| | - Eleuterio Burgueño-Tapia
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Santo Tomás, Mexico City, 11340 Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City, 07000 Mexico
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