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Ai WJ, Li J, Cao D, Liu S, Yuan YY, Li Y, Tan GS, Xu KP, Yu X, Kang F, Zou ZX, Wang WX. A Very Deep Graph Convolutional Network for 13C NMR Chemical Shift Calculations with Density Functional Theory Level Performance for Structure Assignment. JOURNAL OF NATURAL PRODUCTS 2024; 87:743-752. [PMID: 38359467 DOI: 10.1021/acs.jnatprod.3c00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nuclear magnetic resonance (NMR) chemical shift calculations are powerful tools for structure elucidation and have been extensively employed in both natural product and synthetic chemistry. However, density functional theory (DFT) NMR chemical shift calculations are usually time-consuming, while fast data-driven methods often lack reliability, making it challenging to apply them to computationally intensive tasks with a high requirement on quality. Herein, we have constructed a 54-layer-deep graph convolutional network for 13C NMR chemical shift calculations, which achieved high accuracy with low time-cost and performed competitively with DFT NMR chemical shift calculations on structure assignment benchmarks. Our model utilizes a semiempirical method, GFN2-xTB, and is compatible with a broad variety of organic systems, including those composed of hundreds of atoms or elements ranging from H to Rn. We used this model to resolve the controversial J/K ring junction problem of maitotoxin, which is the largest whole molecule assigned by NMR calculations to date. This model has been developed into user-friendly software, providing a useful tool for routine rapid structure validation and assignation as well as a new approach to elucidate the large structures that were previously unsuitable for NMR calculations.
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Affiliation(s)
- Wen-Jing Ai
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Jing Li
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorder, in Xiangya Hospital, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Shao Liu
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorder, in Xiangya Hospital, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Yi-Yun Yuan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Yan Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Gui-Shan Tan
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorder, in Xiangya Hospital, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Xia Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Zhen-Xing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, People's Republic of China
- Hunan Prima Drug Research Center Co., Ltd, Hunan Research Center for Drug Safety Evaluation, Hunan Key Laboratory of Pharmacodynamics and Safety Evaluation of New Drugs, Changsha, Hunan 410331, People's Republic of China
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2
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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: 17] [Impact Index Per Article: 17.0] [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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3
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Nishikibe K, Nishikawa K, Kumagai M, Doe M, Morimoto Y. Asymmetric Total Syntheses, Stereostructures, and Cytotoxicities of Marine Bromotriterpenoids Aplysiol B (Laurenmariannol) and Saiyacenol A. Chem Asian J 2022; 17:e202101137. [PMID: 34704367 PMCID: PMC9299038 DOI: 10.1002/asia.202101137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Indexed: 11/29/2022]
Abstract
There are marine cytotoxic bromotriterpenoids, named the thyrsiferol family that are structurally characterized by some tetrahydropyran (THP) and tetrahydrofuran (THF) rings. The thyrsiferol family belongs to natural products that are often difficult to determine their stereostructures even by the current, highly advanced spectroscopic methods, especially in acyclic systems including stereogenic tetrasubstituted carbon centers. In such cases, it is effective to predict and synthesize the possible stereostructures. Herein, to elucidate ambiguous stereostructures and unassigned absolute configurations of aplysiol B, laurenmariannol, and saiyacenol A, members of the thyrsiferol family, we carried out their asymmetric chemical syntheses featuring 6-exo and 5-exo oxacyclizations of epoxy alcohol precursors and 6-endo bromoetherification of a bishomoallylic alcohol. In this paper, we report total assignments of their stereostructures through their asymmetric chemical syntheses and also their preliminary cytotoxic activities against some tumor cells. These results could not have been achieved without depending on asymmetric total synthesis.
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Affiliation(s)
- Kento Nishikibe
- Department of ChemistryGraduate School of ScienceOsaka City University Sumiyoshi-kuOsaka558–8585Japan
| | - Keisuke Nishikawa
- Department of ChemistryGraduate School of ScienceOsaka City University Sumiyoshi-kuOsaka558–8585Japan
| | - Momochika Kumagai
- Department of ChemistryGraduate School of ScienceOsaka City University Sumiyoshi-kuOsaka558–8585Japan
- Faculty of FisheriesKagoshima University ShimoarataKagoshima8900056Japan
| | - Matsumi Doe
- Department of ChemistryGraduate School of ScienceOsaka City University Sumiyoshi-kuOsaka558–8585Japan
| | - Yoshiki Morimoto
- Department of ChemistryGraduate School of ScienceOsaka City University Sumiyoshi-kuOsaka558–8585Japan
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4
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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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Marcarino MO, Cicetti S, Zanardi MM, Sarotti AM. A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide. Nat Prod Rep 2021; 39:58-76. [PMID: 34212963 DOI: 10.1039/d1np00030f] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.
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Affiliation(s)
- Maribel O Marcarino
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - Soledad Cicetti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - María M Zanardi
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, 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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6
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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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7
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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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8
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Li QJ, Tang PF, Zhou X, Lu WJ, Xu WJ, Luo J, Kong LY. Elodeoidins A–H, acylphloroglucinol meroterpenoids possessing diverse rearranged skeletons from Hypericum elodeoides. Org Chem Front 2021. [DOI: 10.1039/d0qo01118e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Inspired by the biosynthetic fragment (9), the first example of rearranged dimethylated acylphloroglucinol and monoterpene adducts, elodeoidins A–H (1–8) representing four skeletons and two rearranged pathways were authenticated from H. elodeoides.
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Affiliation(s)
- Qi-Ji Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Peng-Fei Tang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Xin Zhou
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Wei-Jia Lu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Wen-Jun Xu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
| | - Ling-Yi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 210009
- People's Republic of China
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9
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Daranas AH, Sarotti AM. Are Computational Methods Useful for Structure Elucidation of Large and Flexible Molecules? Belizentrin as a Case Study. Org Lett 2020; 23:503-507. [PMID: 33382270 DOI: 10.1021/acs.orglett.0c04016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantum mechanical NMR methods are progressively becoming decisive in structure elucidation. However, problems arise using low-level calculations for complex molecules, whereas methods using higher levels of theory are not practical for large molecules. This report outlines a synergistic effort employing computationally inexpensive quantum mechanical NMR calculations with conformer selection incorporating 3JHH values as a way to solve the structure of large, complex, and highly flexible molecules using readily available computational resources with belizentrin as a case study.
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Affiliation(s)
- Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna 38206, Tenerife, Spain
| | - 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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10
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Domínguez HJ, Cabrera-García D, Cuadrado C, Novelli A, Fernández-Sánchez MT, Fernández JJ, Daranas AH. Prorocentroic Acid, a Neuroactive Super-Carbon-Chain Compound from the Dinoflagellate Prorocentrum hoffmannianum. Org Lett 2020; 23:13-18. [DOI: 10.1021/acs.orglett.0c03437] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Humberto J. Domínguez
- Instituto Universitario de Bio-Orgánica Antonio González, University of La Laguna, 38206, Tenerife, Spain
| | - David Cabrera-García
- Department of Biochemistry and Molecular Biology and University Institute of Biotechnology of Asturias (IUBA), Campus “El Cristo”, University of Oviedo, 33006 Oviedo, Oviedo, Spain
| | - Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206, Tenerife, Spain
| | - Antonello Novelli
- Department of Psychology and University Institute of Biotechnology of Asturias (IUBA), Campus “El Cristo”, University of Oviedo; Institute for Sanitary Research of the Princedom of Asturias (ISPA), 33006 Oviedo, Oviedo, Spain
| | - M. Teresa Fernández-Sánchez
- Department of Biochemistry and Molecular Biology and University Institute of Biotechnology of Asturias (IUBA), Campus “El Cristo”, University of Oviedo, 33006 Oviedo, Oviedo, Spain
| | - José J. Fernández
- Instituto Universitario de Bio-Orgánica Antonio González, University of La Laguna, 38206, Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206, Tenerife, Spain
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11
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Li SW, Cuadrado C, Huan XJ, Yao LG, Miao ZH, Hernandez Daranas A, Guo YW. Rare new bicyclic cembranoid ethers and a novel trihydroxy prenylated guaiane from the Xisha soft coral Lobophytum sp. Bioorg Chem 2020; 103:104223. [DOI: 10.1016/j.bioorg.2020.104223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
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12
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Li SW, Cuadrado C, Yao LG, Daranas AH, Guo YW. Quantum Mechanical–NMR-Aided Configuration and Conformation of Two Unreported Macrocycles Isolated from the Soft Coral Lobophytum sp.: Energy Calculations versus Coupling Constants. Org Lett 2020; 22:4093-4096. [DOI: 10.1021/acs.orglett.0c01155] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Song-Wei Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Li-Gong Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Antonio Hernandez Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
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13
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Zanardi MM, Marcarino MO, Sarotti AM. Redefining the Impact of Boltzmann Analysis in the Stereochemical Assignment of Polar and Flexible Molecules by NMR Calculations. Org Lett 2019; 22:52-56. [DOI: 10.1021/acs.orglett.9b03866] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- María M. Zanardi
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Maribel O. Marcarino
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - 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, Argentina
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14
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Díaz-Marrero AR, López-Arencibia A, Bethencout-Estrella CJ, Cen-Pacheco F, Sifaoui I, Hernández Creus A, Duque-Ramírez MC, Souto ML, Hernández Daranas A, Lorenzo-Morales J, Piñero JE, Fernández JJ. Antiprotozoal activities of marine polyether triterpenoids. Bioorg Chem 2019; 92:103276. [PMID: 31539745 DOI: 10.1016/j.bioorg.2019.103276] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 01/29/2023]
Abstract
Chagas disease and leishmaniasis are tropical neglected diseases caused by kinetoplastids protozoan parasites of Trypanosoma and Leishmania genera, and a public health burden with high morbidity and mortality rates in developing countries. Among difficulties with their epidemiological control, a major problem is their limited and toxic treatments to attend the affected populations; therefore, new therapies are needed in order to find new active molecules. In this work, sixteen Laurencia oxasqualenoid metabolites, natural compounds 1-11 and semisynthetic derivatives 12-16, were tested against Leishmania amazonensis, Leishmania donovani and Trypanosoma cruzi. The results obtained point out that eight substances possess potent activities, with IC50 values in the range of 5.40-46.45 µM. The antikinetoplastid action mode of the main metabolite dehydrothyrsiferol (1) was developed, also supported by AFM images. The semi-synthetic active compound 28-iodosaiyacenol B (15) showed an IC50 5.40 µM against Leishmania amazonensis, turned to be non-toxic against the murine macrophage cell line J774A.1 (CC50 > 100). These values are comparable with the reference compound miltefosine IC50 6.48 ± 0.24 and CC50 72.19 ± 3.06 μM, suggesting that this substance could be scaffold for development of new antikinetoplastid drugs.
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Affiliation(s)
- Ana R Díaz-Marrero
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain
| | - Atteneri López-Arencibia
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain
| | - Carlos J Bethencout-Estrella
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain
| | - Francisco Cen-Pacheco
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain; Facultad de Bioanálisis, Campus-Veracruz, Universidad Veracruzana (UV), Veracruz 91700, Mexico
| | - Ines Sifaoui
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain
| | - Alberto Hernández Creus
- Departamento de Química, Área de Química Física, Instituto de Materiales y Nanotecnología, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 Tenerife, Spain
| | - María Clara Duque-Ramírez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain
| | - María L Souto
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain; Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain; Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), Avda. Astrofísico F. Sánchez s/n, 38206 Tenerife, Spain
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain
| | - José E Piñero
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - José J Fernández
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain; Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
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15
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Evaluation of Oxasqualenoids from the Red Alga Laurencia viridis against Acanthamoeba. Mar Drugs 2019; 17:md17070420. [PMID: 31331002 PMCID: PMC6669608 DOI: 10.3390/md17070420] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023] Open
Abstract
Acanthamoeba genus is a widely distributed and opportunistic parasite with increasing importance worldwide as an emerging pathogen in the past decades. This protozoan has an active trophozoite stage, a cyst stage, and is dormant and very resistant. It can cause Acanthamoeba keratitis, an ocular sight-threatening disease, and granulomatous amoebic encephalitis, a chronic, very fatal brain pathology. In this study, the amoebicidal activity of sixteen Laurencia oxasqualenoid metabolites and semisynthetic derivatives were tested against Acanthamoeba castellanii Neff. The results obtained point out that iubol (3) and dehydrothyrsiferol (1) possess potent activities, with IC50 values of 5.30 and 12.83 µM, respectively. The hydroxylated congeners thyrsiferol (2) and 22-hydroxydehydrothyrsiferol (4), active in the same value range at IC50 13.97 and 17.00 µM, are not toxic against murine macrophages; thus, they are solid candidates for the development of new amoebicidal therapies.
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16
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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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17
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Pérez-Victoria I, Oves-Costales D, Lacret R, Martín J, Sánchez-Hidalgo M, Díaz C, Cautain B, Vicente F, Genilloud O, Reyes F. Structure elucidation and biosynthetic gene cluster analysis of caniferolides A–D, new bioactive 36-membered macrolides from the marine-derived Streptomyces caniferus CA-271066. Org Biomol Chem 2019; 17:2954-2971. [DOI: 10.1039/c8ob03115k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structures of caniferolides A–D have been determined combining NMR and bioinformatics prediction of the absolute configuration.
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18
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Zanardi MM, Biglione FA, Sortino MA, Sarotti AM. General Quantum-Based NMR Method for the Assignment of Absolute Configuration by Single or Double Derivatization: Scope and Limitations. J Org Chem 2018; 83:11839-11849. [DOI: 10.1021/acs.joc.8b01749] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- María M. Zanardi
- Área Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Franco A. Biglione
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Maximiliano A. Sortino
- Área Farmacognosia, 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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19
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Tarazona G, Benedit G, Fernández R, Pérez M, Rodríguez J, Jiménez C, Cuevas C. Can Stereoclusters Separated by Two Methylene Groups Be Related by DFT Studies? The Case of the Cytotoxic Meroditerpenes Halioxepines. JOURNAL OF NATURAL PRODUCTS 2018; 81:343-348. [PMID: 29393646 DOI: 10.1021/acs.jnatprod.7b00807] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
QM/NMR-DFT (quantum mechanics combined with nuclear magnetic resonance parameters calculated by density functional theory approximations) studies allowed us to link two stereoclusters separated by two methylene groups present in the new meroditerpenes halioxepine B (2) and halioxepine C (3) and the known halioxepine (1), isolated from two Indonesian sponges of the genus Haliclona (Reniera). DP4 and DP4+ probabilities were used to discriminate the two diastereotopic arrangements of the two stereoclusters, whose unconnected relative configurations were determined by ROESY and J-based configurational analysis. To confirm the DFT studies, the full relative configuration of 1 was deduced using a mixture of benzene-d6 and pyridine-d5 as the NMR solvent. ROESY measurements connected the two stereoclusters and demonstrated that DFT calculations accurately predict the configuration when two methylenes separate the two stereoclusters. The different arrangements of the distant stereoclusters C-1/C-2/C-7 and C-10/C-15 for compounds 2 and 3 were deduced by DFT calculations and explained the opposite optical rotations observed for the two compounds. Halioxepines B (2) and C (3) display moderate cytotoxicity against different human cancer cell lines.
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Affiliation(s)
- Guillermo Tarazona
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Gonzalo Benedit
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Rogelio Fernández
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Marta Pérez
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
| | - Jaime Rodríguez
- Departamento de Química, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña , 15071, A Coruña, Spain
| | - Carlos Jiménez
- Departamento de Química, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña , 15071, A Coruña, Spain
| | - Carmen Cuevas
- Medicinal Chemistry Department, PharmaMar S. A. , Pol. Ind. La Mina Norte, Avenida de los Reyes 1, 28770, Colmenar Viejo (Madrid), Spain
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20
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Riveira MJ, Sarotti AM. NMR and experimental reinvestigation of the condensation reaction between γ-methylene-α,β-unsaturated aldehydes and propargyl aldehydes. Org Biomol Chem 2018; 16:1442-1447. [DOI: 10.1039/c7ob03110f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An experimental and computational study of the reaction between γ-methylene enals and propargyl aldehydes uncovered a deconjugative aldol condensation.
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Affiliation(s)
- Martín J. Riveira
- Instituto de Química Rosario
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario-CONICET
- Rosario
- Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario-CONICET
- Rosario
- Argentina
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21
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Sarotti AM. Structural revision of two unusual rhamnofolane diterpenes, curcusones I and J, by means of DFT calculations of NMR shifts and coupling constants. Org Biomol Chem 2018; 16:944-950. [DOI: 10.1039/c7ob02916k] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The structures of two unusual rhamnofolane diterpenes, curcusones I and J, have been revised using quantum calculations of NMR shifts.
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Affiliation(s)
- Ariel M. Sarotti
- Instituto de Química Rosario (CONICET)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario 2000
- Argentina
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22
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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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23
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Zanardi MM, Suárez AG, Sarotti AM. Determination of the Relative Configuration of Terminal and Spiroepoxides by Computational Methods. Advantages of the Inclusion of Unscaled Data. J Org Chem 2016; 82:1873-1879. [DOI: 10.1021/acs.joc.6b02129] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- María M. Zanardi
- Instituto
de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
- Facultad
de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av Pellegrini 3314, Rosario 2000, Argentina
| | - Alejandra G. Suárez
- 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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24
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Rodríguez J, Jiménez C, Blanco M, Tarazona G, Fernández R, Cuevas C. Lanesoic Acid: A Cytotoxic Zwitterion from Theonella sp. Org Lett 2016; 18:5832-5835. [PMID: 27802052 DOI: 10.1021/acs.orglett.6b02832] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lanesoic acid (1) was isolated and characterized from Theonella sp. during PharmaMar's ongoing program to study cytotoxic substances from marine sources. Its planar structure, elucidated by spectral analysis (NMR, IR, UV, and MS), possesses an unusual skeleton containing a tetrahydropyrimidine cation that is stabilized as a zwitterion by an internal carboxylate counterion. The stereostructure of 1 was deduced from ROESY-NOESY, J-based configurational analysis (JBCA), and density functional theory (DFT) computational calculations fitted using the recently published DP4+ parameter. Compound 1 was moderately active and selective against pancreas PSN1 cells (IC50 = 8.9 μg/mL) and inactive against colon HT-29, breast MD-MB-23, and NSCLC lung tumor cells.
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Affiliation(s)
- Jaime Rodríguez
- Departamento de Química Fundamental, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Rua As Carballeiras s/n, Universidade da Coruña , 15071 A Coruña, Spain
| | - Carlos Jiménez
- Departamento de Química Fundamental, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Rua As Carballeiras s/n, Universidade da Coruña , 15071 A Coruña, Spain
| | - María Blanco
- Departamento de Química Fundamental, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Rua As Carballeiras s/n, Universidade da Coruña , 15071 A Coruña, Spain
| | - Guillermo Tarazona
- Natural Products Department, PharmaMar S.A., Pol. Ind. La Mina Norte , Avda de los Reyes 1, 28770 Colmenar Viejo, Spain
| | - Rogelio Fernández
- Natural Products Department, PharmaMar S.A., Pol. Ind. La Mina Norte , Avda de los Reyes 1, 28770 Colmenar Viejo, Spain
| | - Carmen Cuevas
- Natural Products Department, PharmaMar S.A., Pol. Ind. La Mina Norte , Avda de los Reyes 1, 28770 Colmenar Viejo, Spain
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25
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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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26
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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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27
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Grimblat N, Zanardi MM, Sarotti AM. Beyond DP4: an Improved Probability for the Stereochemical Assignment of Isomeric Compounds using Quantum Chemical Calculations of NMR Shifts. J Org Chem 2015; 80:12526-34. [PMID: 26580165 DOI: 10.1021/acs.joc.5b02396] [Citation(s) in RCA: 851] [Impact Index Per Article: 94.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The DP4 probability is one of the most sophisticated and popular approaches for the stereochemical assignment of organic molecules using GIAO NMR chemical shift calculations when only one set of experimental data is available. In order to improve the performance of the method, we have developed a modified probability (DP4+), whose main differences from the original DP4 are the inclusion of unscaled data and the use of higher levels of theory for the NMR calculation procedure. With these modifications, a significant improvement in the overall performance was achieved, providing accurate and confident results in establishing the stereochemistry of 48 challenging isomeric compounds.
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Affiliation(s)
- Nicolás Grimblat
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Suipacha 531, Rosario 2000, Argentina
| | - María M Zanardi
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Suipacha 531, Rosario 2000, Argentina.,Facultad de Química e Ingeniería "Fray Rogelio Bacón", Pontificia Universidad Católica Argentina , Av. Pellegrini 3314, 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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28
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Novaes LFT, Sarotti AM, Pilli RA. Total Synthesis and Tentative Structural Elucidation of Cryptomoscatone E3: Interplay of Experimental and Computational Studies. J Org Chem 2015; 80:12027-37. [DOI: 10.1021/acs.joc.5b01956] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luiz F. T. Novaes
- Departamento
de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas (Unicamp), CP 6154, CEP 13084-971, Campinas, SP Brazil
| | - Ariel M. Sarotti
- Instituto
de Química Rosario, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha
531, S2002LRK Rosario, Argentina
| | - Ronaldo A. Pilli
- Departamento
de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas (Unicamp), CP 6154, CEP 13084-971, Campinas, SP Brazil
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29
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Zanardi MM, Sarotti AM. GIAO C–H COSY Simulations Merged with Artificial Neural Networks Pattern Recognition Analysis. Pushing the Structural Validation a Step Forward. J Org Chem 2015; 80:9371-8. [DOI: 10.1021/acs.joc.5b01663] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- María M. Zanardi
- Instituto
de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Suipacha
531, Rosario 2000, Argentina
- Facultad
de Química e Ingeniería “Fray Rogelio Bacón”, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, 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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30
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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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31
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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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32
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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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33
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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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34
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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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35
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Stereochemistry of complex marine natural products by quantum mechanical calculations of NMR chemical shifts: solvent and conformational effects on okadaic acid. Mar Drugs 2014; 12:176-92. [PMID: 24402177 PMCID: PMC3917268 DOI: 10.3390/md12010176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 12/29/2022] Open
Abstract
Marine organisms are an increasingly important source of novel metabolites, some of which have already inspired or become new drugs. In addition, many of these molecules show a high degree of novelty from a structural and/or pharmacological point of view. Structure determination is generally achieved by the use of a variety of spectroscopic methods, among which NMR (nuclear magnetic resonance) plays a major role and determination of the stereochemical relationships within every new molecule is generally the most challenging part in structural determination. In this communication, we have chosen okadaic acid as a model compound to perform a computational chemistry study to predict 1H and 13C NMR chemical shifts. The effect of two different solvents and conformation on the ability of DFT (density functional theory) calculations to predict the correct stereoisomer has been studied.
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36
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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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37
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Di Micco S, Zampella A, D’Auria MV, Festa C, De Marino S, Riccio R, Butts CP, Bifulco G. Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of (13)C chemical shifts. Beilstein J Org Chem 2013; 9:2940-9. [PMID: 24454574 PMCID: PMC3896268 DOI: 10.3762/bjoc.9.331] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/30/2013] [Indexed: 11/23/2022] Open
Abstract
In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of (13)C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of (13)C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.
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Affiliation(s)
- Simone Di Micco
- Dipartimento di Farmacia, Università di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Angela Zampella
- Dipartimento di Farmacia, Università di Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Maria Valeria D’Auria
- Dipartimento di Farmacia, Università di Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Festa
- Dipartimento di Farmacia, Università di Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Simona De Marino
- Dipartimento di Farmacia, Università di Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Raffaele Riccio
- Dipartimento di Farmacia, Università di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Craig P Butts
- Department of Chemistry, University of Bristol, Cantocks Close, BS8 1TS Bristol, United Kingdom
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
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