1
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Cuadrado C, Cen-Pacheco F, Daranas AH. Computationally Assisted Analysis of NMR Chemical Shifts as a Tool in Conformational Analysis. Org Lett 2024; 26:6529-6534. [PMID: 38888989 PMCID: PMC11320654 DOI: 10.1021/acs.orglett.4c01642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
A key to understanding the properties of functional molecules is to determine their conformation in solution. A conformational analysis procedure that relies on quantum mechanical calculations and the widely used DP4+ probability was evaluated to decipher the structural information encoded in NMR chemical shifts. The results underscore the potential utility of using NMR chemical shifts in advancing conformational analysis studies of complex molecules in solution.
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Affiliation(s)
- Cristina Cuadrado
- Instituto
de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Francisco Cen-Pacheco
- Faculty
of Bioanalysis, Iturbide s/n, Veracruz University, 91700 Veracruz, Veracruz, México
| | - Antonio Hernández Daranas
- Instituto
de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
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2
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Rodríguez
Martín-Aragón V, Trigal Martínez M, Cuadrado C, Daranas AH, Fernández Medarde A, Sánchez
López JM. OSMAC Approach and Cocultivation for the Induction of Secondary Metabolism of the Fungus Pleotrichocladium opacum. ACS OMEGA 2023; 8:39873-39885. [PMID: 37901491 PMCID: PMC10601420 DOI: 10.1021/acsomega.3c06299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
The application of an OSMAC (One Strain-Many Compounds) approach on the fungus Pleotrichocladium opacum, isolated from a soil sample collected on the coast of Asturias (Spain), using different culture media, chemical elicitors, and cocultivation techniques resulted in the isolation and identification of nine new compounds (8, 9, 12, 15-18, 20, 21), along with 15 known ones (1-7, 10, 11, 14, 19, 22-25). Compounds 1-9 were detected in fungal extracts from JSA liquid fermentation, compounds 10-12 were isolated from a solid rice medium, whereas compounds 14 and 15 were isolated from a solid wheat medium. Addition of 5-azacytidine to the solid rice medium caused the accumulation of compounds 16-18, whereas adding N-acetyl-d-glucosamine triggered the production of two additional metabolites, 19 and 20. Finally, cocultivation of the fungus Pleotrichocladium opacum with Echinocatena sp. in a solid PDA medium led to the production of five additional natural products, 21-25. The structures of the new compounds were elucidated by HRESIMS and 1D and 2D NMR as well as by comparison with literature data. DP4+ and mix-J-DP4 computational methods were applied to determine the relative configurations of the novel compounds, and in some cases, the absolute configurations were assigned by a comparison of the optical rotations with those of related natural products.
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Affiliation(s)
| | - Mónica Trigal Martínez
- Biomar
Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4,
Armunia,León 24009, Spain
| | - Cristina Cuadrado
- Instituto
de Productos Naturales y Agrobiología, Consejo Superior de
Investigaciones Científicas (IPNA-CSIC), San Cristobal de La Laguna, Tenerife 38206, Spain
| | - Antonio Hernández Daranas
- Instituto
de Productos Naturales y Agrobiología, Consejo Superior de
Investigaciones Científicas (IPNA-CSIC), San Cristobal de La Laguna, Tenerife 38206, Spain
| | - Antonio Fernández Medarde
- Biomar
Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4,
Armunia,León 24009, Spain
| | - José M. Sánchez
López
- Biomar
Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4,
Armunia,León 24009, Spain
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3
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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: 20] [Impact Index Per Article: 20.0] [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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4
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Palivec V, Pohl R, Kaminský J, Martinez-Seara H. Efficiently Computing NMR 1H and 13C Chemical Shifts of Saccharides in Aqueous Environment. J Chem Theory Comput 2022; 18:4373-4386. [PMID: 35687789 DOI: 10.1021/acs.jctc.2c00127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Determining the structure of saccharides in their native environment is crucial to understanding their function and more accurately targeting their utilization. Nuclear magnetic resonance observables such as the nuclear Overhauser effect or spin-spin coupling constants are routinely utilized to study saccharides in their native water environment. However, while highly sensitive to the local environment, chemical shifts are mostly overlooked, despite being commonly measured for compounds identification. Although chemical shifts carry considerable structural information, their direct association with structure is notoriously difficult. This is mostly due to the similarity in the chemical nature of most saccharides causing similar physicochemical environments close to sugar C and H atoms, resulting in comparable chemical shifts. The rise of computational power allows one to compute reliable chemical shifts and use them to determine atomistic details of these sugars in solution. However, any prediction is severely limited by the computational protocol used and its accuracy. In this work, we studied a set of 31 saccharides on which we evaluated various computational protocols to calculate the total number of 375 1H and 327 13C chemical shifts of sugars in an aqueous environment. Our study proposes two cost-effective protocols for simulating 1H and 13C chemical shifts that we recommend for further use. These protocols can help with the interpretation of experimental spectra, but we also show that they are also capable of structure prediction independently. This is possible because of the low mean absolute deviations of calculated shifts from the experiment (0.06 ppm for 1H and 1.09 ppm for 13C). We explore different solvation methods, basis sets, and optimization schemes to reach such accuracy. A correct sampling of the conformation phase space of flexible sugar molecules is also key to obtaining accurately converged theoretical chemical shifts. The linear regression method was applied to convert the calculated isotropic nuclear magnetic shielding constants to simulated chemical shifts comparable with the experiment. The achieved level of accuracy can help in utilizing chemical shifts for elucidating the 3D atomistic structure of saccharides in aqueous solutions. All linear regression parameters obtained on our extensive set of sugars for all the tested protocols can be reutilized in future works.
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Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
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5
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Semenov VA, Krivdin LB. Computational NMR of natural products. RUSSIAN CHEMICAL REVIEWS 2022. [DOI: 10.1070/rcr5027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Cen-Pacheco F, Santiago-Benítez AJ, Tsui KY, Tantillo DJ, Fernández JJ, Daranas AH. Structure and Computational Basis for Backbone Rearrangement in Marine Oxasqualenoids. J Org Chem 2021; 86:2437-2446. [PMID: 33369417 DOI: 10.1021/acs.joc.0c02600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Six novel oxasqualenoids (polyether triterpenes) were isolated from the red alga Laurencia viridis. Laurokanols A-E (1-5) comprise an unreported tricyclic core with a [6,6]-spiroketal system. Yucatecone (6) shows a biogenetically intriguing epimerization at C14. Quantum mechanical calculations were used to corroborate their structures and to explain key steps involved in the biogenetic mechanisms proposed for the formation of oxasqualenoids.
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Affiliation(s)
- Francisco Cen-Pacheco
- Instituto Universitario de Bio-Organica Antonio González (IUBO-AG), Departmento de Química Orgánica, University of La Laguna, Av. Astrofísico Francisco Sánchez 2, 38206 Tenerife, Spain.,Facultad de Bioanálisis, Campus-Veracruz, Universidad Veracruzana, 91700 Veracruz, México
| | - Adrián J Santiago-Benítez
- Instituto Universitario de Bio-Organica Antonio González (IUBO-AG), Departmento de Química Orgánica, University of La Laguna, Av. Astrofísico Francisco Sánchez 2, 38206 Tenerife, Spain
| | - Ka Yi Tsui
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - José J Fernández
- Instituto Universitario de Bio-Organica Antonio González (IUBO-AG), Departmento de Química Orgánica, University of La Laguna, Av. Astrofísico Francisco Sánchez 2, 38206 Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
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7
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Casabianca LB. Calculating nuclear magnetic resonance chemical shifts in solvated systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:611-624. [PMID: 31916612 DOI: 10.1002/mrc.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
The nuclear magnetic resonance (NMR) chemical shift is extremely sensitive to molecular geometry, hydrogen bonding, solvent, temperature, pH, and concentration. Calculated magnetic shielding constants, converted to chemical shifts, can be valuable aids in NMR peak assignment and can also give detailed information about molecular geometry and intermolecular effects. Calculating chemical shifts in solution is complicated by the need to include solvent effects and conformational averaging. Here, we review the current state of NMR chemical shift calculations in solution, beginning with an introduction to the theory of calculating magnetic shielding in general, then covering methods for inclusion of solvent effects and conformational averaging, and finally discussing examples of applications using calculated chemical shifts to gain detailed structural information.
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Affiliation(s)
- Leah B Casabianca
- Department of Chemistry, Clemson University, Clemson, South Carolina
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8
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Grimblat N, Gavín JA, Hernández Daranas A, Sarotti AM. Combining the Power of J Coupling and DP4 Analysis on Stereochemical Assignments: The J-DP4 Methods. Org Lett 2019; 21:4003-4007. [DOI: 10.1021/acs.orglett.9b01193] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolás Grimblat
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
| | - José A. Gavín
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, 38206 Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, 38206 Tenerife, Spain
- Instituto de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Ariel M. Sarotti
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
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9
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Kato T, Saito M, Nagae M, Fujita K, Watai M, Igarashi T, Yasumoto T, Inagaki M. Absolute Quantification of Lipophilic Shellfish Toxins by Quantitative Nuclear Magnetic Resonance Using Removable Internal Reference Substance with SI Traceability. ANAL SCI 2018; 32:729-34. [PMID: 27396652 DOI: 10.2116/analsci.32.729] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Okadaic acid (OA), a lipophilic shellfish toxin, was accurately quantified using quantitative nuclear magnetic resonance with internal standards for the development of an authentic reference standard. Pyridine and the residual proton in methanol-d4 were used as removable internal standards to limit any contamination. They were calibrated based on a maleic acid certified reference material. Thus, the concentration of OA was traceable to the SI units through accurate quantitative NMR with an internal reference substance. Signals from the protons on the oxygenated and unsaturated carbons of OA were used for quantification. A reasonable accuracy was obtained by integrating between the lower and upper (13)C satellite signal range when more than 4 mg of OA was used. The best-determined purity was 97.4% (0.16% RSD) when 20 mg of OA was used. Dinophysistoxin-1, a methylated analog of OA having an almost identical spectrum, was also quantified by using the same methodology.
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10
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Oliveira RP, Demuner AJ, Alvarenga ES, Barbosa LCA, de Melo Silva T. A novel alkaloid isolated from Crotalaria paulina and identified by NMR and DFT calculations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.09.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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De Souza LA, Dos Santos HF, Costa LT, De Almeida WB. Inclusion complexes between cisplatin and oxidized carbon nanostructures: A theoretical approach. J Inorg Biochem 2018; 178:134-143. [DOI: 10.1016/j.jinorgbio.2017.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/05/2017] [Accepted: 10/30/2017] [Indexed: 11/26/2022]
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12
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Pinnatifidenyne-Derived Ethynyl Oxirane Acetogenins from Laurencia viridis. Mar Drugs 2017; 16:md16010005. [PMID: 29286293 PMCID: PMC5793053 DOI: 10.3390/md16010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 01/03/2023] Open
Abstract
Red algae of Laurencia continue to provide wide structural diversity and complexity of halogenated C15 acetogenin medium-ring ethers. Here, we described the isolation of three new C15 acetogenins (3–5), and one truncated derivative (6) from Laurencia viridis collected on the Canary Islands. These compounds are interesting variations on the pinnatifidenyne structure that included the first examples of ethynyl oxirane derivatives (3–4). The structures were elucidated by extensive study of NMR (Nuclear Magnetic Resonance) data, J-based configuration analysis and DFT (Density Functional Theory) calculations. Their antiproliferative activity against six human solid tumor cell lines was evaluated.
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13
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Grimblat N, Sarotti AM. Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations. Chemistry 2016; 22:12246-61. [DOI: 10.1002/chem.201601150] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Nicolas Grimblat
- Instituto de Química Rosario CONICET Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Suipacha 531 Rosario 2000) Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario CONICET Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Suipacha 531 Rosario 2000) Argentina
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14
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Ermanis K, Parkes KEB, Agback T, Goodman JM. Expanding DP4: application to drug compounds and automation. Org Biomol Chem 2016; 14:3943-9. [DOI: 10.1039/c6ob00015k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The DP4 parameter, which provides a confidence level for NMR assignment, has been widely used to help assign the structures of many stereochemically-rich molecules.
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Affiliation(s)
- Kristaps Ermanis
- Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | | | | | - Jonathan M. Goodman
- Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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15
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Li K, Chung-Davidson YW, Bussy U, Li W. Recent advances and applications of experimental technologies in marine natural product research. Mar Drugs 2015; 13:2694-713. [PMID: 25939037 PMCID: PMC4446601 DOI: 10.3390/md13052694] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/02/2015] [Accepted: 04/14/2015] [Indexed: 11/16/2022] Open
Abstract
Marine natural products are a rich source of novel and biologically active compounds. The number of identified marine natural compounds has grown 20% over the last five years from 2009 to 2013. Several challenges, including sample collection and structure elucidation, have limited the development of this research field. Nonetheless, new approaches, such as sampling strategies for organisms from extreme ocean environments, nanoscale NMR and computational chemistry for structural determination, are now available to overcome the barriers. In this review, we highlight the experimental technology innovations in the field of marine natural products, which in our view will lead to the development of many new drugs in the future.
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Affiliation(s)
- Ke Li
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
| | - Ugo Bussy
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
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16
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Cen-Pacheco F, Santiago-Benítez AJ, García C, Álvarez-Méndez SJ, Martín-Rodríguez AJ, Norte M, Martín VS, Gavín JA, Fernández JJ, Daranas AH. Oxasqualenoids from Laurencia viridis: Combined Spectroscopic-Computational Analysis and Antifouling Potential. JOURNAL OF NATURAL PRODUCTS 2015; 78:712-721. [PMID: 25781558 DOI: 10.1021/np5008922] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The chemical study of the red alga Laurencia viridis has led to the isolation of four new polyether triterpenoids: 28-hydroxysaiyacenol B (2), saiyacenol C (3), 15,16-epoxythyrsiferol A (4), and 15,16-epoxythyrsiferol B (5). The structures of 2 and 3 were established mainly by NMR data analysis and comparison with the well-known metabolite dehydrothyrsiferol (1). However, due to the existence of a nonprotonated carbon within the epoxide functionality, stereochemical assignments in 4 and 5 required an in-depth structural study that included NOESY data, J-based configuration analysis, comparison with synthetic models, and DFT calculations. The biological activities of the new metabolites and other related oxasqualenoids were evaluated for the first time against a panel of relevant biofouling marine organisms, and structure-activity conclusions were obtained.
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Affiliation(s)
- Francisco Cen-Pacheco
- ‡Faculty of Bioanalysis, Campus-Veracruz, Universidad Veracruzana, 91700, Veracruz, México
| | | | | | | | - Alberto J Martín-Rodríguez
- ⊥Oceanic Platform of the Canary Islands (PLOCAN), Carretera de Taliarte s/n, 35214, Telde, Gran Canaria, Spain
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17
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Domínguez HJ, Napolitano JG, Fernández-Sánchez MT, Cabrera-García D, Novelli A, Norte M, Fernández JJ, Daranas AH. Belizentrin, a Highly Bioactive Macrocycle from the Dinoflagellate Prorocentrum belizeanum. Org Lett 2014; 16:4546-9. [DOI: 10.1021/ol502102f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Humberto J. Domínguez
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - José G. Napolitano
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - M. Teresa Fernández-Sánchez
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - David Cabrera-García
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - Antonello Novelli
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - Manuel Norte
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - José J. Fernández
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
| | - Antonio Hernández Daranas
- Institute
for Bio-Organic Chemistry “Antonio González”,
Center for Biomedical Research of the Canary Islands,
and ∥Department of Chemical
Engineering and Pharmaceutical Technology, Faculty of Pharmacy, University of La Laguna, 38206 La Laguna, Tenerife, Spain
- Department
of Biochemistry and Molecular Biology, and §Department of Psychology, Institute
of Biotechnology of Asturias, Campus “El Cristo”, University of Oviedo, Oviedo 33006, Spain
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18
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Gutiérrez-Cepeda A, Daranas AH, Fernández JJ, Norte M, Souto ML. Stereochemical determination of five-membered cyclic ether acetogenins using a spin-spin coupling constant approach and DFT calculations. Mar Drugs 2014; 12:4031-44. [PMID: 24988069 PMCID: PMC4113813 DOI: 10.3390/md12074031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/28/2014] [Accepted: 04/10/2014] [Indexed: 01/31/2023] Open
Abstract
Five-membered rings are of particular interest, due to their presence in some of the most common molecules in chemistry and biology. Despite their apparent simplicity, the structural resolution of these rings is complex, due to their inherent conformational flexibility. Here, we describe an application of a recently reported simple and efficient NMR protocol based on the measurement of spin-spin coupling constants to achieve the challenging relative configurations of five new halogenated C15 tetrahydrofuranyl-acetogenins, marilzafurollenes A–D (1–4) and 12-acetoxy-marilzafurenyne (5), isolated from the red alga, Laurencia marilzae. Although DFT chemical shift calculations were used to connect remote stereocenters, the NMR-based approach seems advantageous over computational techniques in this context, as the presence of halogens may interfere with reliable calculations.
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Affiliation(s)
- Adrián Gutiérrez-Cepeda
- University Institute of Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), University of La Laguna, Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain.
| | - Antonio Hernández Daranas
- University Institute of Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), University of La Laguna, Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain.
| | - José J Fernández
- University Institute of Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), University of La Laguna, Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain.
| | - Manuel Norte
- University Institute of Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), University of La Laguna, Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain.
| | - María L Souto
- University Institute of Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), University of La Laguna, Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain.
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19
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Cen-Pacheco F, Norte M, Fernández JJ, Daranas AH. Zoaramine, a Zoanthamine-like Alkaloid with a New Skeleton. Org Lett 2014; 16:2880-3. [DOI: 10.1021/ol500860v] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francisco Cen-Pacheco
- Faculty
of Bioanalysis Campus-Veracruz, Universidad Veracruzana, 91700 Veracruz, Mexico
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