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Kwon J, Reeves HL, Wang LP, Freedberg DI. Revealing elusive conformations of sucrose from hydrogen bond J-coupling in H 2O: A combined NMR and quantum mechanics study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:742-753. [PMID: 38981694 DOI: 10.1002/mrc.5473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/11/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024]
Abstract
Hydrogen bonding is a crucial feature of biomolecules, but its characterization in glycans dissolved in aqueous solutions is challenging due to rapid hydrogen exchange between hydroxyl groups and H2O. In principle, the scalar (J) coupling constant can reveal the relative orientation of the atoms in the molecule. In contrast to J-coupling through H-bonds reported in proteins and nucleic acids, research on J-coupling through H-bonds in glycans dissolved in water is lacking. Here, we use sucrose as a model system for H-bonding studies; its structure, which consists of glucose (Glc) and fructose (Frc), is well-studied, and it is readily available. We apply the in-phase, antiphase-HSQC-TOCSY and quantify previously unreported through H-bond J-values for Frc-OH1-Glc-OH2 in H2O. While earlier reports of Brown and Levy indicate this H-bond as having only a single direction, our reported findings indicate the potential presence of two involving these same atoms, namely, G2OH ➔ F1O and F1OH ➔ G2O (where F and G stand for Frc and Glc, respectively). The calculated density functional theory J-values for the G2OH ➔ F1O agree with the experimental values. Additionally, we detected four other possible H-bonds in sucrose, which require different phi, psi (ϕ, ψ) torsion angles. The ϕ, ψ values are consistent with previous predictions of du Penhoat et al. and Venable et al. Our results will provide new insights into the molecular structure of sucrose and its interactions with proteins.
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Affiliation(s)
- Jeahoo Kwon
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hannah L Reeves
- Department of Chemistry, University of California at Davis, Davis, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California at Davis, Davis, California, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
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2
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Yao T, Tan C, Rong Y, Jie S, Zhang B, Yan J, Cao S, Qiu F. Discovery of natural AMPK activator from the fruits of Xanthium sibiricum Patr.: Xanthiumine A, protoberberine alkaloid with unique C 28 skeleton. Bioorg Chem 2024; 150:107527. [PMID: 38876005 DOI: 10.1016/j.bioorg.2024.107527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/12/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
Two protoberberine alkaloids with a unique C28 skeleton, named xanthiumines A (1) and B (2), respectively, were isolated from the fruits of Xanthium sibiricum Patr. Their structures including absolute configurations were unequivocally established by the comprehensive NMR and MS spectroscopic data analysis together with gauge-independent atomic orbital (GIAO) NMR calculations, and electronic circular dichroism (ECD) calculations. Compounds 1 and 2 are the first examples of natural protoberberine alkaloid with a phenolic acid group at C-13a. Their plausible biosynthetic pathway was proposed on the basis of the coexisting alkaloid monomer as the precursor. Furthermore, the effects and related molecular mechanism of compound 1 on hepatic lipid accumulation were also investigated in oleic acid (OA)-treated HepG2 cells.
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Affiliation(s)
- Tie Yao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Cuicui Tan
- School of Chinese Materia Medica, and Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Yifang Rong
- School of Chinese Materia Medica, and Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Shi Jie
- School of Chinese Materia Medica, and Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Bingyang Zhang
- School of Chinese Materia Medica, and Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Jiankun Yan
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang 050091, PR China
| | - Shijie Cao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China.
| | - Feng Qiu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; School of Chinese Materia Medica, and Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China.
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3
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Liu F, Qiao X, Li Q, Zhou J, Gao J, He F, Wu P, Chen C, Sun W, Zhu H, Zhang Y. Aculeatiols A-G: Lovastatin Derivatives Extracted from Aspergillus aculeatus. JOURNAL OF NATURAL PRODUCTS 2024; 87:753-763. [PMID: 38372239 DOI: 10.1021/acs.jnatprod.3c00872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
In this study, we isolated lovastatin derivatives, including aculeatiols A-G (1-7) and three known compounds (8-10), from Aspergillus aculeatus. Their structures and absolute configurations were experimentally determined by high-resolution electrospray ionization mass spectrometry, nuclear magnetic resonance spectroscopy, and X-ray diffraction analyses, and the results were corroborated by quantum-chemical calculations. As members of the lovastatin derivatives, aculeatiols A-C (1-3) possess a γ-lactone functional group in the side chain. Compound 6 represents the first example that features an undescribed aromatized heterotetracyclic 6/6/6/6 ring system. Biologically, the lipid-lowering effects of all of these compounds were evaluated by analyzing the free fatty acid-induced intracellular lipid accumulation. In addition, compound 5, which regulated the transcription of genes associated with lipid uptake and synthesis, inhibited the accumulation of lipids.
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Affiliation(s)
- Fei Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Xinyi Qiao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Qin Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Jiajun Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Jie Gao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Feng He
- Hubei Topgene Biotechnology Technical Research Institute Co., Ltd., Wuhan 430030, People's Republic of China
| | - Peng Wu
- Hubei Topgene Biotechnology Technical Research Institute Co., Ltd., Wuhan 430030, People's Republic of China
| | - Chunmei Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, People's Republic of China
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4
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Wang D, Wang H, Chen X, Xu Y, He W, Wu D, Zuo M, Zhu W, Wang L. Five previously undescribed citrinin derivatives from the endophytic fungus Penicillium citrinum GZWMJZ-836. PHYTOCHEMISTRY 2024; 220:114032. [PMID: 38369172 DOI: 10.1016/j.phytochem.2024.114032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Penicillium citrinum GZWMJZ-836 is an endophytic fungus from Drynaria roosii Nakaike. Five previously undescribed citrinin derivatives (1-5) and six intermediates related to their biosynthesis (6-11) were obtained from the extract of this strain's solid fermentation using multiple column chromatography separations, including high-performance liquid chromatography. The structures of these compounds were determined through comprehensive spectroscopic analyses, primarily using NMR and HRESIMS data. The stereochemistry was mainly confirmed by ECD calculations, and the configurations of C-7' in compounds 4 and 5 were determined using 13C NMR calculations. Compounds 4-5 and 8 showed antibacterial activity against five strains, with minimum inhibitory concentration values ranging from 7.8 to 125 μM. Compounds 4 and 7 exhibited inhibitions against three plant pathogenic fungi, with IC50 values ranging from 66.6 to 152.1 μM. Additionally, a putative biosynthetic pathway for compounds 1-5 derived from citrinin was proposed.
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Affiliation(s)
- Dongyang Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China
| | - Huanhuan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China; School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, China
| | - Xuli Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China; School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, China
| | - Yanchao Xu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, China
| | - Wenwen He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China
| | - Dan Wu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China
| | - Mingxing Zuo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China
| | - Weiming Zhu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266003, China.
| | - Liping Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, China; Natural Product Research Center of Guizhou Province, Guiyang, 550014, China.
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5
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Passaglia L, Zanardi MM, Sarotti AM. Study of heavy atom influence on poly-halogenated compounds using DP4/MM-DP4+/DP4+: insights and trends. Org Biomol Chem 2024; 22:2435-2442. [PMID: 38416037 DOI: 10.1039/d3ob02077k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy complemented by density functional theory (DFT) calculations is a crucial tool for structural elucidation. Nevertheless, the precision of NMR predictions is influenced by the 'heavy atom effect', wherein heavy atoms affect the shielding values of neighboring light atoms (HALA effect). Standard practice in the field involves removing the conflicting signals. However, in the case of polyhalogenated molecules, this is challenging due to the significant amount of information that ends up being lost. In this study the HALA is thoroughly investigated in the context of three leading probability methods: DP4, MM-DP4+, and DP4+. The results show that DP4+ is more sensitive to C-Cl or C-Br signals, which is a consequence of the longer bond lengths computed with DFT. Removing conflicting signals is highly effective in DP4+, but has an uncertain outcome in methods based on molecular mechanics geometries, such as DP4 and MM-DP4+. A detailed investigation of the effect of bond distance on the corresponding chemical shifts has also been conducted.
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Affiliation(s)
- Lucas Passaglia
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, Argentina
| | - María M Zanardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, 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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Gasevic T, Kleine Büning JB, Grimme S, Bursch M. Benchmark Study on the Calculation of 207Pb NMR Chemical Shifts. Inorg Chem 2024; 63:5052-5064. [PMID: 38446045 PMCID: PMC10951955 DOI: 10.1021/acs.inorgchem.3c04539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
A benchmark set for the computation of 207Pb nuclear magnetic resonance (NMR) chemical shifts is presented. The PbS50 set includes conformer ensembles of 50 lead-containing molecular compounds and their experimentally measured 207Pb NMR chemical shifts. Various bonding motifs at the Pb center with up to seven bonding partners are included. Six different solvents were used in the measurements. The respective shifts lie in the range between +10745 and -5030 ppm. Several calculation settings are assessed by evaluating computed 207Pb NMR shifts for the use with different density functional approximations (DFAs), relativistic approaches, treatment of the conformational space, and levels for geometry optimization. Relativistic effects were included explicitly with the zeroth order regular approximation (ZORA), for which only the spin-orbit variant was able to yield reliable results. In total, seven GGAs and three hybrid DFAs were tested. Hybrid DFAs significantly outperform GGAs. The most accurate DFAs are mPW1PW with a mean absolute deviation (MAD) of 429 ppm and PBE0 with an MAD of 446 ppm. Conformational influences are small as most compounds are rigid, but more flexible structures still benefit from Boltzmann averaging. Including explicit relativistic treatments such as SO-ZORA in the geometry optimization does not show any significant improvement over the use of effective core potentials (ECPs).
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Affiliation(s)
- Thomas Gasevic
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Julius B. Kleine Büning
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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7
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Jiao S, Liu C, Chen P, Li J, Sun J, Gao X, Chai X. 9,9'-epoxylignans from Syringa pinnatifolia: A typical case of stereochemical assignment by a quantum chemical calculation with MAE ΔΔδ parameter. PHYTOCHEMISTRY 2024; 219:113978. [PMID: 38237843 DOI: 10.1016/j.phytochem.2024.113978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
In the current study, twenty-two stereochemical 9,9'-epoxylignans including 19 undescribed ones were isolated from the ethanol extract of Syringa pinnatifolia in our continuing effort to understand the overall chemical spectrum of this species. These isolates were structurally elucidated by extensive spectroscopic data analysis, X-ray diffraction, modified Mosher's method, and quantum chemical calculations. Meanwhile, the utilization of 13C NMR calculation and the MAEΔΔδ parameter facilitated the stereochemical assignment of groups of lignan stereoisomers. The 13C NMR data were corrected by the averaged errors at each corresponding carbon position in groups of lignan stereoisomers, which improved the theoretic 13C NMR calculation. The finding of the stereochemical structures of 9,9'-epoxylignans is significant. It is helpful to determine the absolute configurations of molecules with the similar core. In addition, these lignans exhibited potential cardioprotective activities on H9c2 cardiomyocytes in vitro and presented significant antioxidant effect.
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Affiliation(s)
- Shungang Jiao
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Changxin Liu
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Panlong Chen
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Junjun Li
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Jingjing Sun
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China; Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, PR China
| | - Xiaoli Gao
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Xingyun Chai
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, PR China.
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8
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Zhao P, Xin BS, Ye L, Ma ZT, Yao GD, Shi R, He XH, Lin B, Huang XX, Song SJ. Structurally diverse rearranged sesquiterpenoids, including a pair of rare tautomers, from the aerial parts of Daphne penicillata. PHYTOCHEMISTRY 2024; 218:113950. [PMID: 38101591 DOI: 10.1016/j.phytochem.2023.113950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Eight structurally diverse rearranged sesquiterpenoids, including seven undescribed sesquiterpenoids (1a/1b and 3-8) were obtained from the aerial parts of Daphne penicillata. 1a/1b, 3, 5 and 6 possess rare rearranged guaiane skeletons and 4 represents the first example of rearranged carotene sesquiterpenoids. Their structures and absolute configurations were determined by extensive spectroscopic analyses, NMR and ECD calculations. Interestingly, 1a and 1b were a pair of magical interconverting epimers that may interconvert by retro-aldol condensation. The mechanism of interconversion has been demonstrated indirectly by 9-OH derivatization of 1a/1b and a hypothetical biogenetic pathway was proposed. All compounds were evaluated for anti-inflammatory and cytotoxic activities. Among them, 1a/1b and 2 exhibited potential inhibitory activities on the production of NO against LPS-induced BV2 microglial cells.
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Affiliation(s)
- Peng Zhao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Ben-Song Xin
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Li Ye
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Zhen-Tao Ma
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, International Ecological Foresty Research Center of Kunming, Horticulture and Landscape Architecture, Southwest Forestry University, Yunnan Kunming, 650224, China
| | - Xia-Hong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, International Ecological Foresty Research Center of Kunming, Horticulture and Landscape Architecture, Southwest Forestry University, Yunnan Kunming, 650224, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China; Basic Science Research Center Base (Pharmaceutical Science), Shandong Province, Yantai University, Yantai, 264005, China.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, China; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, China; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China.
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9
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Hansen PE. The Synergy between Nuclear Magnetic Resonance and Density Functional Theory Calculations. Molecules 2024; 29:336. [PMID: 38257249 PMCID: PMC10821511 DOI: 10.3390/molecules29020336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
This paper deals with the synergy between Nuclear Magnetic Resonance (NMR) spectroscopic investigations and DFT calculations, mainly of NMR parameters. Both the liquid and the solid states are discussed here. This text is a mix of published results supplemented with new findings. This paper deals with examples in which useful results could not have been obtained without combining NMR measurements and DFT calculations. Examples of such cases are tautomeric systems in which NMR data are calculated for the tautomers; hydrogen-bonded systems in which better XH bond lengths can be determined; cage compounds for which assignment cannot be made based on NMR data alone; revison of already published structures; ionic compounds for which reference data are not available; assignment of solid-state spectra and crystal forms; and the creation of libraries for biological molecules. In addition to these literature cases, a revision of a cage structure and substituent effects on pyrroles is also discussed.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark
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10
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Feuge N, Wilhelm R. Straightforward synthesis of chiral sulfonate-based ionic liquids from amino alcohols for chiral recognition. Chirality 2023; 35:993-1011. [PMID: 37497749 DOI: 10.1002/chir.23614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
New sulfonate-based chiral salts were prepared from amino alcohols and sodium hydroxymethanesulfonate, vinyl sulfonate, or sultone. The synthesis started with different amino acids from the chiral pool and gave the desired products in just four steps. After cation metathesis, the salts were explored as chiral solvating agents (CSAs) in NMR studies. The new chiral ionic liquids (CILs) were successfully able to interact with different chiral guest molecules and formed diastereomeric aggregates. In some cases, baseline separation was observed. The influence of the structural differences in the CIL as well as the structural requirements of the guest molecule is discussed.
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Affiliation(s)
- Niklas Feuge
- Institute of Organic Chemistry, Clausthal University of Technology, Clausthal-Zellerfeld, Germany
| | - René Wilhelm
- Institute of Organic Chemistry, Clausthal University of Technology, Clausthal-Zellerfeld, Germany
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11
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Franco BA, Luciano ER, Sarotti AM, Zanardi MM. DP4+App: Finding the Best Balance between Computational Cost and Predictive Capacity in the Structure Elucidation Process by DP4+. Factors Analysis and Automation. JOURNAL OF NATURAL PRODUCTS 2023; 86:2360-2367. [PMID: 37721602 DOI: 10.1021/acs.jnatprod.3c00566] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
DP4+ is one of the most popular methods for the structure elucidation of natural products using NMR calculations. While the method is simple and easy to implement, it requires a series of procedures that can be tedious, coupled with the fact that its computational demand can be high in certain cases. In this work, we made a substantial improvement to these limitations. First, we deeply explored the effect of molecular mechanics architecture on the DP4+ formalism (MM-DP4+). In addition, a Python applet (DP4+App) was developed to automate the entire process, requiring only the Gaussian NMR output files and a spreadsheet containing the experimental NMR data and labels. The script is designed to use the statistical parameters from the original 24 levels of theory (employing B3LYP/6-31G* geometries) and the new 36 levels explored in this work (over MMFF geometries). Furthermore, it enables the development of customizable methods using any desired level of theory, allowing for a free choice of test molecules.
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Affiliation(s)
- Bruno A Franco
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Ezequiel R Luciano
- Instituto de Investigaciones en 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
| | - María M Zanardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
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12
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Lv TM, Han JL, Yan QL, Lin B, Yao GD, Huang XX, Song SJ. Discovery of the Caged-Vibsane Norditerpenoids with Unprecedented Chemical Architectures and Exploration of Their Various Acid Tolerances. J Org Chem 2023; 88:12385-12393. [PMID: 37585921 DOI: 10.1021/acs.joc.3c01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Cyclovibsanones A-D (1-4, respectively), featuring unprecedented caged tricyclo[5.4.1.05,9]dodecane and bicyclo[4.2.1]hexane cores, were isolated from the leaves of Viburnum odoratissimum. Their structures as well as that of one chemical derivative (5), which was transformed from 2, were determined by spectroscopic data, theoretical calculations, and the ML-JDP4/MAEΔΔδ methods. In addition, compounds 1 and 2 were found to possess dissimilarities in acid tolerance during nuclear magnetic resonance (NMR) experiments. The potential mechanism was consequently postulated and further supported through NMR analysis and mechanistic calculations. Biologically, chemical derivative 5 exerted antiproliferative activity against HepG2 cells.
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Affiliation(s)
- Tian-Ming Lv
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Jin-Ling Han
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Qiu-Lin Yan
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
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13
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Rogati F, Maioli C, Lauro G, Caprioglio D, Imperio D, Del Grosso E, Botta B, Mannina L, Bifulco G, Ingallina C, Minassi A. A Classic Photochemical Approach Inducing an Unexpected Rearrangement: Exploring the Photoreactivity of Pentacyclic Triterpenic Acids. JOURNAL OF NATURAL PRODUCTS 2023; 86:1025-1032. [PMID: 37036806 DOI: 10.1021/acs.jnatprod.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The discovery of new bioactivities is closely related to the generation of novel scaffolds, and in the past few years different strategies have been proposed to obtain unknown architectures from the manipulation of known compounds. In the present study, we exploited a vintage photochemical approach for the discovery of an unexpected pathway of reactivity related to Δ1-3-oxo-pentacyclic triterpenic acids gaining access to a new class of natural-unnatural 5(10→1)abeo-pentacyclic triterpenic acids.
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Affiliation(s)
- Federica Rogati
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Chiara Maioli
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Gianluigi Lauro
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Diego Caprioglio
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Daniela Imperio
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Erika Del Grosso
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologie del Farmaco, Università la Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Luisa Mannina
- Dipartimento di Chimica e Tecnologie del Farmaco, Università la Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Cinzia Ingallina
- Dipartimento di Chimica e Tecnologie del Farmaco, Università la Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Alberto Minassi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
- PlantaChem srls, Via Canobio 4/6, 28100 Novara, Italy
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14
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Xi YF, Bai M, Zhang X, Hou ZL, Lin B, Yao GD, Lou LL, Wang XB, Song SJ, Huang XX. Insight into tetrahydrofuran lignans from Isatis indigotica fortune with neuroprotective and acetylcholinesterase inhibitor activity. PHYTOCHEMISTRY 2023; 208:113609. [PMID: 36758886 DOI: 10.1016/j.phytochem.2023.113609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/04/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Nine tetrahydrofuran lignans, including three undescribed spiro-lignans, were isolated from Isatis indigotica Fortune (Brassicaceae). Extensive spectroscopic analyses achieved the structure elucidation of these tetrahydrofuran lignans, and quantum chemical calculation combined with the MAEΔΔδ parameter. Notably, isatispironeols A-B have a unique spiro[dienone-tetrahydrofuran] molecular core. These spiro[dienone-tetrahydrofuran] lignans showed comparable neuroprotective effects as the positive control in the H2O2-induced SH-SY5Y cells model. In addition, (-)-(7R,8S,1'R,7'R,8'R)-isatispironeol A possessed more significant AChE inhibitory activity, further interact sites were also predicted by the in silico assay.
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Affiliation(s)
- Yu-Fei Xi
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ming Bai
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xin Zhang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Zi-Lin Hou
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Bin Lin
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Li-Li Lou
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China.
| | - Xiao-Bo Wang
- Chinese People's Liberation Army Logistics Support Force No. 967 Hospital, Dalian, 116021, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China.
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15
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Naseem M, Asghar S, Farooq U, Lakhani A, Altaf Y, Hashmi MA. Determination of the Absolute Configuration of Ballonigrin Lactone A Using Density Functional Theory Calculations. ACS OMEGA 2023; 8:1923-1928. [PMID: 36687041 PMCID: PMC9850775 DOI: 10.1021/acsomega.2c03858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
We report the determination of the absolute configuration of a diterpenoid, namely, ballonigrin lactone A (BLA), by comparison of the computed optical rotations, [α]D, of its two diastereomers using density functional theory (DFT) calculations to the experimental [α]D value of +22.4. One of the diastereomers having configurations 4S, 5R, 6S, 10S, 15S was named "α-BLA," and the other one with configuration 4S, 5R, 6S, 10S, 15R was called "β-BLA". Six conformers for each diastereomer (α-BLA and β-BLA) of BLA were identified through their conformational analysis. [α]D values of these six conformations for each diastereomer were calculated using DFT at the mPW1PW91/6-311G(d,p)/SMDChloroform level of theory, leading to the conformationally averaged [α]D values of -96.8 for α-BLA and +65.1 for β-BLA. Thus, it was found that the experimental [α]D value of +22.4 was of 4S, 5R, 6S, 10S, 15R, i.e., β-BLA. Experimental and computed nuclear magnetic resonance (NMR) data were also compared, and this comparison was in accordance with the conclusion drawn from the comparison of [α]D values. Finally, the results were augmented with the calculation of the DP4 analysis, and the probability obtained also endorsed our earlier calculations.
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Affiliation(s)
- Misbah Naseem
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Saleha Asghar
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Umar Farooq
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, 22060 Abbottabad, Pakistan
| | - Ahmed Lakhani
- Department
of Biomedical and Health Sciences, Calumet
College of St. Joseph, 2400, New York Avenue, Whiting, Indiana 46394, United States
| | - Yasir Altaf
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Muhammad Ali Hashmi
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
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16
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Yoshino Y, Tanaka N, Tsuji D, Itoh K, Kashiwada Y. Communiferulins, farnesylated coumarins from the roots of Ferula communis and their anti-neuroinflammatory activity. J Nat Med 2023; 77:173-179. [PMID: 36289185 DOI: 10.1007/s11418-022-01657-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/06/2022] [Indexed: 01/06/2023]
Abstract
Three new farnesylated coumarins, communiferulins A-C (1-3), and a farnesylated chromone, ferchromone (4), were isolated from the roots of an Apiaceous plant Ferula communis. Their structures including the relative configurations were elucidated by a combination of spectroscopic analyses and calculations of the NMR data. Communiferulins A-C (1-3) had dihydrofuran rings fused to C-3 and C-4 of their coumarin moieties, while 3 possessed one additional furan ring. HPLC analyses using a chiral column showed 1-4 to be racemates, and the absolute configurations of (+)-1, (-)-1, (+)-2, and (-)-2 were deduced by comparison of their ECD spectra with TDDFT-calculated spectra. Communiferulins A (1) and B (2), and ferchromone (4) showed inhibitory activities on IL-1β production from LPS-stimulated microglial cells.
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Affiliation(s)
- Yuki Yoshino
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, 770-8505, Japan
| | - Naonobu Tanaka
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, 770-8505, Japan.
| | - Daisuke Tsuji
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, 770-8505, Japan.,Faculty of Pharmacy, Yasuda Women's University, Hiroshima, 731-0153, Japan
| | - Kohji Itoh
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, 770-8505, Japan
| | - Yoshiki Kashiwada
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, 770-8505, Japan
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17
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Dong SH, Duan ZK, Ai YF, Zhou XF, Zhang X, Lian MY, Huang XX, Bai M, Song SJ. Guaiane-type sesquiterpenoids with various ring skeletons from Daphne bholua uncovered by molecular networking and structural revisions of previously reported analogues. Bioorg Chem 2022; 129:106208. [DOI: 10.1016/j.bioorg.2022.106208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2022]
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18
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Deng Q, Jiang L, Yu Y, Yang Y. Theoretical exploration of the mechanism of α-pinene hydrogenation. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Precisely predicting the 1H and 13C NMR chemical shifts in new types of nerve agents and building spectra database. Sci Rep 2022; 12:20288. [PMID: 36434133 PMCID: PMC9700684 DOI: 10.1038/s41598-022-24647-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
Abstract
Following the recent terrorist attacks using Novichok agents and the subsequent decomposition operations, understanding the chemical structures of nerve agents has become important. To mitigate the ever-evolving threat of new variants, the Organization for the Prohibition of Chemical Weapons has updated the list of Schedule 1 substances defined by the Chemical Weapons Convention. However, owing to the several possible structures for each listed substance, obtaining an exhaustive dataset is almost impossible. Therefore, we propose a nuclear magnetic resonance-based prediction method for 1H and 13C NMR chemical shifts of Novichok agents based on conformational and density functional study calculations. Four organophosphorus compounds and five G- and V-type nerve agents were used to evaluate the accuracy of the proposed procedure. Moreover, 1H and 13C NMR prediction results for an additional 83 Novichok candidates were compiled as a database to aid future research and identification. Further, this is the first study to successfully predict the NMR chemical shifts of Novichok agents, with an exceptional agreement between predicted and experimental data. The conclusions enable the prediction of all possible structures of Novichok agents and can serve as a firm foundation for preparation against future terrorist attacks using new variants of nerve agents.
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20
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Serusi L, Zebrowski P, Schörgenhumer J, Massa A, Waser M. Stereoselective Syntheses of Masked β-Amino Acid Containing Phthalides. Helv Chim Acta 2022; 105:e202200110. [PMID: 36845268 PMCID: PMC7614226 DOI: 10.1002/hlca.202200110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We herein report a protocol for the asymmetric aldol-initiated cascade addition of isoxazolidin-5-ones to ortho-cyanobenzaldehydes by using Takemoto's bifunctional organocatalyst. This approach allows for the synthesis of various novel β2,2-amino acid-phthalide conjugates with good enantio- and diastereoselectivities in reasonable yields and the further ring-opening of these compounds to acyclic carboxylic acid derivatives was demonstrated too.
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Affiliation(s)
- Lorenzo Serusi
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstr. 69, AT-4040 Linz, Austria,Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, IT-84084-Fisciano (SA), Italy
| | - Paul Zebrowski
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstr. 69, AT-4040 Linz, Austria
| | - Johannes Schörgenhumer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Antonio Massa
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, IT-84084-Fisciano (SA), Italy
| | - Mario Waser
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstr. 69, AT-4040 Linz, Austria,
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21
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Zhao P, Huang XX, Song SJ. The hypothesis of tautomeric equilibrium between epimers in ciquitins A and B. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2022; 24:1052-1057. [PMID: 34871119 DOI: 10.1080/10286020.2021.2009464] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Recently, ciquitins A and B isolated from the powdered and defatted airdried aerial parts of Leucophyllum ambiguum were reported as a mixture of conformers in a solution at room temperature. Considering the existence of a hemiacetal hydroxyl fragment in the ciquitins A and B, they are more likely to exist in the form of epimer rather than the mixture of conformers. To confirm this hypothesis, the NMR calculations of two epimers at C-9 (1-a and 1-b) were performed and the results matched well with experimental NMR data of mixtures (1). Moreover, a brief discussion on the reason for this hypothesis was also presented.
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Affiliation(s)
- Peng Zhao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
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22
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Merrill AT, Tantillo DJ. Reconsideration of the Structures of Stemara-13(14)-en-18-ol and Related Diterpene Natural Products: Vinylic Hydrogen Chemical Shifts Are Key. JOURNAL OF NATURAL PRODUCTS 2022; 85:1912-1917. [PMID: 35952375 DOI: 10.1021/acs.jnatprod.1c00923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The reported synthesis of stemara-13(14)-en-18-ol, which revealed that the structure of this natural product was misassigned, prompted an investigation using density functional theory methods into the structural reassignment of this natural product and related diterpenoids extracted from Calceolaria plants. 1H and 13C chemical shift predictions led to the reassignment of relative configuration, and in one case the carbon skeleton, of several diterpenoids from Calceolaria. In many of these cases, the chemical shift of the vinylic hydrogen was found to be diagnostic.
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Affiliation(s)
- Amy T Merrill
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
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23
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Alvarenga ES, Pinto BNS, Santos AR, Oliveira WF, de Paula VF, Oliveira MN, Junior JMB, Batista ANDL. Structural elucidation by NMR assisted by DFT calculations of a novel natural product from Conchocarpus mastigophorus (Rutaceae). ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elson Santiago Alvarenga
- Universidade Federal de Vicosa Chemistry Av P H Rolfs s/n36570-900Brasil 36570-900 Viçosa BRAZIL
| | | | - Anderson Ramos Santos
- Universidade Estadual do Sudoeste da Bahia Department of Science and Technology BRAZIL
| | | | | | - Márcio Neri Oliveira
- Universidade Estadual do Sudoeste da Bahia Department of Biological Science BRAZIL
| | - João Marcos Batista Junior
- Universidade Federal de São Paulo: Universidade Federal de Sao Paulo Institute of Science and Technology BRAZIL
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24
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Sosa-Rueda J, Domínguez-Meléndez V, Ortiz-Celiseo A, López-Fentanes FC, Cuadrado C, Fernández JJ, Daranas AH, Cen-Pacheco F. Squamins C-F, four cyclopeptides from the seeds of Annona globiflora. PHYTOCHEMISTRY 2022; 194:112839. [PMID: 34332784 DOI: 10.1016/j.phytochem.2021.112839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/22/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Four cyclic octapeptides, squamins C-F, were isolated from the seeds of Annona globiflora Schltdl. These compounds share part of their amino acid sequence, -Pro-Met(O)-Tyr-Gly-Thr-, with previously reported squamins A and B. Their structures were determined using NMR spectroscopic techniques together with quantum mechanical calculations (QM-NMR), ESI-HRMS data and a modified version of Marfey's chromatographic method. All compounds showed cytotoxic activity against DU-145 (human prostate cancer) and HeLa (human cervical carcinoma) cell lines. Clearly, A. globiflora is an important source of bioactive molecules, which could promote the sustainable exploitation of this undervalued specie.
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Affiliation(s)
- Javier Sosa-Rueda
- Facultad de Bioanálisis, Veracruz University, Iturbide s/n, 91700, Veracruz, Ver., Mexico
| | | | - Araceli Ortiz-Celiseo
- Facultad de Bioanálisis, Veracruz University, Iturbide s/n, 91700, Veracruz, Ver., Mexico; Instituto Tecnológico de Orizaba, Tecnológico Nacional de México Oriente 9, Emiliano Zapata, 94320, Orizaba, Ver., Mexico
| | | | - Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206, Tenerife, Spain
| | - José J Fernández
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO-AG), Departamento 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
| | - Francisco Cen-Pacheco
- Facultad de Bioanálisis, Veracruz University, Iturbide s/n, 91700, Veracruz, Ver., Mexico; Instituto Universitario de Bio-Orgánica Antonio González (IUBO-AG), Departamento de Química Orgánica, University of La Laguna, Av. Astrofísico Francisco Sánchez 2, 38206, Tenerife, Spain.
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25
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Zhao P, Li ZY, Qin SY, Xin BS, Liu YY, Lin B, Yao GD, Huang XX, Song SJ. Three Unusual Sesquiterpenes with Distinctive Ring Skeletons from Daphne penicillata Uncovered by Molecular Networking Strategies. J Org Chem 2021; 86:15298-15306. [PMID: 34612634 DOI: 10.1021/acs.joc.1c01880] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Daphnenoids A-C (1-3), three unusual sesquiterpenes with distinctive ring skeletons, together with a biogenetically related daphnenoid D (4) were obtained from the herb of Daphne penicillata by molecular networking strategies. Daphnenoid A (1) possesses a unique caged tetracyclo [5.3.2.01,6.04,11] dodecane scaffold by unexpected cyclizations of C-1/C-11 and C-2/C-14. Daphnenoids B and C (2 and 3) were the first discovered natural sesquiterpenes with unique 5/5 spirocyclic systems in nature. Their structures were determined by NMR spectroscopic analysis, computer-assisted structure elucidation methods, quantum chemical calculations, and X-ray diffraction. A hypothetical biogenetic pathway begins with typical guaiane sesquiterpene (a), including a key intermediate (4) was proposed. Daphnenoids B and C (2 and 3) exhibited potential inhibitory activities on the production of NO against LPS-induced BV2 microglial cells.
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Affiliation(s)
- Peng Zhao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Zhi-Yuan Li
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Shu-Yan Qin
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Ben-Song Xin
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Yu-Yang Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Bin Lin
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research and Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
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Chini MG, Lauro G, Bifulco G. Addressing the Target Identification and Accelerating the Repositioning of Anti‐Inflammatory/Anti‐Cancer Organic Compounds by Computational Approaches. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone 86090 Pesche (IS) Italy
| | - Gianluigi Lauro
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Giuseppe Bifulco
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
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28
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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Gupta A, Chakraborty S, Ramakrishnan R. Revving up 13C NMR shielding predictions across chemical space: benchmarks for atoms-in-molecules kernel machine learning with new data for 134 kilo molecules. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abe347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
The requirement for accelerated and quantitatively accurate screening of nuclear magnetic resonance spectra across the small molecules chemical compound space is two-fold: (1) a robust ‘local’ machine learning (ML) strategy capturing the effect of the neighborhood on an atom’s ‘near-sighted’ property—chemical shielding; (2) an accurate reference dataset generated with a state-of-the-art first-principles method for training. Herein we report the QM9-NMR dataset comprising isotropic shielding of over 0.8 million C atoms in 134k molecules of the QM9 dataset in gas and five common solvent phases. Using these data for training, we present benchmark results for the prediction transferability of kernel-ridge regression models with popular local descriptors. Our best model, trained on 100k samples, accurately predicts isotropic shielding of 50k ‘hold-out’ atoms with a mean error of less than 1.9 ppm. For the rapid prediction of new query molecules, the models were trained on geometries from an inexpensive theory. Furthermore, by using a Δ-ML strategy, we quench the error below 1.4 ppm. Finally, we test the transferability on non-trivial benchmark sets that include benchmark molecules comprising 10–17 heavy atoms and drugs.
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Cloutier M, Prévost MJ, Lavoie S, Feroldi T, Piochon M, Groleau MC, Legault J, Villaume S, Crouzet J, Dorey S, Dìaz De Rienzo MA, Déziel E, Gauthier C. Total synthesis, isolation, surfactant properties, and biological evaluation of ananatosides and related macrodilactone-containing rhamnolipids. Chem Sci 2021; 12:7533-7546. [PMID: 34163844 PMCID: PMC8171317 DOI: 10.1039/d1sc01146d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/22/2021] [Indexed: 01/20/2023] Open
Abstract
Rhamnolipids are a specific class of microbial surfactants, which hold great biotechnological and therapeutic potential. However, their exploitation at the industrial level is hampered because they are mainly produced by the opportunistic pathogen Pseudomonas aeruginosa. The non-human pathogenic bacterium Pantoea ananatis is an alternative producer of rhamnolipid-like metabolites containing glucose instead of rhamnose residues. Herein, we present the isolation, structural characterization, and total synthesis of ananatoside A, a 15-membered macrodilactone-containing glucolipid, and ananatoside B, its open-chain congener, from organic extracts of P. ananatis. Ananatoside A was synthesized through three alternative pathways involving either an intramolecular glycosylation, a chemical macrolactonization or a direct enzymatic transformation from ananatoside B. A series of diasteroisomerically pure (1→2), (1→3), and (1→4)-macrolactonized rhamnolipids were also synthesized through intramolecular glycosylation and their anomeric configurations as well as ring conformations were solved using molecular modeling in tandem with NMR studies. We show that ananatoside B is a more potent surfactant than its macrolide counterpart. We present evidence that macrolactonization of rhamnolipids enhances their cytotoxic and hemolytic potential, pointing towards a mechanism involving the formation of pores into the lipidic cell membrane. Lastly, we demonstrate that ananatoside A and ananatoside B as well as synthetic macrolactonized rhamnolipids can be perceived by the plant immune system, and that this sensing is more pronounced for a macrolide featuring a rhamnose moiety in its native 1 C 4 conformation. Altogether our results suggest that macrolactonization of glycolipids can dramatically interfere with their surfactant properties and biological activity.
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Affiliation(s)
- Maude Cloutier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
| | - Marie-Joëlle Prévost
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
| | - Serge Lavoie
- Laboratoire d'Analyse et de Séparation des Essences Végétales (LASEVE), Département des Sciences Fondamentales, Université du Québec à Chicoutimi 555, Boulevard de l'Université Chicoutimi (Québec) G7H 2B1 Canada
| | - Thomas Feroldi
- Laboratoire d'Analyse et de Séparation des Essences Végétales (LASEVE), Département des Sciences Fondamentales, Université du Québec à Chicoutimi 555, Boulevard de l'Université Chicoutimi (Québec) G7H 2B1 Canada
| | - Marianne Piochon
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
| | - Jean Legault
- Laboratoire d'Analyse et de Séparation des Essences Végétales (LASEVE), Département des Sciences Fondamentales, Université du Québec à Chicoutimi 555, Boulevard de l'Université Chicoutimi (Québec) G7H 2B1 Canada
| | - Sandra Villaume
- Université de Reims Champagne-Ardenne, INRAE, USC RIBP 1488, SFR Condorcet-FR CNRS 3417 51100 Reims France
| | - Jérôme Crouzet
- Université de Reims Champagne-Ardenne, INRAE, USC RIBP 1488, SFR Condorcet-FR CNRS 3417 51100 Reims France
| | - Stéphan Dorey
- Université de Reims Champagne-Ardenne, INRAE, USC RIBP 1488, SFR Condorcet-FR CNRS 3417 51100 Reims France
| | - Mayri Alejandra Dìaz De Rienzo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University L3 3AF Liverpool UK
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
| | - Charles Gauthier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS) 531, Boulevard des Prairies Laval (Québec) H7V 1B7 Canada
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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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32
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A theoretical study to the loliolide molecule and its isomers: a study by circular dichroism, QTAIM, and NMR theoretical methods. J Mol Model 2021; 27:116. [PMID: 33788017 DOI: 10.1007/s00894-021-04725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
The determination of an absolute configuration is a challenge in the structure elucidation of chiral natural products. With advancements in computational chemistry of chiroptical spectroscopy, the time-dependent density functional theory (TDDFT) calculation has emerged as a very promising tool. This paper attempts to illustrate the applicability of computational approaches in comparison with experimental data to understand the conformation, interaction, and stabilization of the loliolide's isomers. The quantum chemical calculations were used from optimized geometries of the (6R,7aS)-, (6S,7aR)-, (6R,7aR)-, and (6S,7aS)-6-hydroxy-4,4,7a-trimethyl-6,7-dihydro-5H-1-benzofuran-2-one. The spectroscopic values were obtained for 13C NMR isotropic shielding by GIAO method in mPW1PW91/cc-pVTZ level, in TDDFT at the ωB97X-D/cc-pVTZ level to the circular dichroism, and in theoretical analyses of non-covalent interaction to study the isomer's stability. The TDDFT calculation of circular dichroism can be used to quantify the individual isomers and the nature of excitation in the molecule. The (6R,7aS) and (6R,7aR) isomers present a higher stability due to electronegativity associated at the hydroxyl group.
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33
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Six new degraded steroids including an unprecedented 4-methyl-androstane with oxabicyclo[3.2.1]octane moiety from Nodulisporium sp. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Benzannulated 5,5-spiroketal sesquiterpenes from the roots of Angelica Pubescens. Bioorg Chem 2020; 107:104604. [PMID: 33422712 DOI: 10.1016/j.bioorg.2020.104604] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022]
Abstract
Two new tetrahydrobenzannulated 5,5-spiroketal sesquiterpenes (1 and 2) and three novel benzannulated 5,5-spiroketal sesquiterpenes (3-5) namely angepubesins A-E, together with a new heliannane-type benzannulated sesquiterpene namely angepubesin F (6) and two known monoterpenes (7 and 8), were isolated from the roots of Angelica Pubescens. Their structures were identified by various spectroscopic analyses (NMR, MS, UV, IR), in combination with 13C NMR calculation as well as MAE, CMAE, DP4 + and MAEΔΔδ values analyses. The absolute configurations of 1-6 were determined by modified Mosher's method, ECD calculation and single-crystal X-ray diffraction (Cu Kα). Furthermore, the inhibitory activities of these isolated compounds against nitric oxide (NO) production induced by lipopolysaccharide (LPS) in RAW264.7 macrophage cells were evaluated. The results showed that compounds 2-4, 6 and 7, especially 6, displayed markedly inhibitory effects on NO production in a concentration-dependent manner. Mechanical study revealed that compound 6 could significantly inhibit the expression of nitric oxide synthase (iNOS) protein at a concentration of 10 μM. In addition, compound 6 suppressed the activation of JAK-STAT and NF-κB pathways.
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35
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Zhang WY, Zhong Y, Yu Y, Shi DF, Huang HY, Tang XL, Wang YH, Chen GD, Zhang HP, Liu CL, Hu D, Gao H, Yao XS. 4-Hydroxy Pyridones from Heterologous Expression and Cultivation of the Native Host. JOURNAL OF NATURAL PRODUCTS 2020; 83:3338-3346. [PMID: 33095987 DOI: 10.1021/acs.jnatprod.0c00675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
4-Hydroxy pyridones are a class of fungi-derived polyketide-nonribosomal peptide products featuring a core of 4-hydroxy-2-pyridone which have a wide range of biological activities. Genome mining of in-house strains using polyketide synthase-nonribosomal peptide synthase as a query identified an endophyte Tolypocladium sp. 49Y, which possesses a potential 4-hydroxy pyridone biosynthetic gene cluster. Heterologous expression in Aspergillus oryzae NSAR1 revealed that this gene cluster is functional and able to produce a rare type of 4-hydroxy pyridones called tolypyridones (compounds 3 and 4). Tolypocladium sp. 49Y was grown in a variety of media which led to the isolation of six 4-hydroxy pyridones (5-10) and one pyrrolidone (11) from a rice culture, and compounds 3 and 9 showed antifungal activity. These latter compounds are different from those obtained by heterologous expression. This study shows that both heterologous expression and cultivation of the native host are complementary approaches to discover new natural products.
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Affiliation(s)
- Wei-Yang Zhang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yue Zhong
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yang Yu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Dan-Feng Shi
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hui-Yun Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Xiao-Long Tang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yong-Heng Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hui-Ping Zhang
- RIKEN SPring-8 Center, Yokohama, Kanagawa 2300045, Japan
| | - Chen-Li Liu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drug Research, Jinan University, Guangzhou 510632, People's Republic of China
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Kato S, Mizukami D, Sugai T, Tsuda M, Fuwa H. Total synthesis and complete configurational assignment of amphirionin-2. Chem Sci 2020; 12:872-879. [PMID: 34163854 PMCID: PMC8179035 DOI: 10.1039/d0sc06021f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Amphirionin-2 is a linear polyketide metabolite that exhibits potent and selective cytotoxic activity against certain human cancer cell lines. We disclose herein the first total synthesis of amphirionin-2 and determination of its absolute configuration. Our synthesis featured an extensive use of cobalt-catalyzed Mukaiyama-type cyclization of γ-hydroxy olefins for stereoselective formation of all the tetrahydrofuran rings found in the natural product, and a late-stage Stille-type coupling for convergent assembly of the entire carbon backbone. Four candidate diastereomers of amphirionin-2 were synthesized in a unified, convergent manner, and their spectroscopic/chromatographic properties were compared with those of the authentic material. The present study culminated in the reassignment of the C5/C7 relative configuration, assignment of the C12/C18 relative configuration, and determination of the absolute configuration of amphirionin-2.
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Affiliation(s)
- Shota Kato
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Daichi Mizukami
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Tomoya Sugai
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Masashi Tsuda
- Center for Advanced Marine Core Research and Department of Agriculture and Marine Science, Kochi University Nankoku Kochi 783-8502 Japan
| | - Haruhiko Fuwa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
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37
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Ji X, Gonnella NC, Xin D. Deconvolution of fast exchange equilibrium states in NMR spectroscopy using virtual reference standards and probability theory. Org Biomol Chem 2020; 18:6927-6934. [PMID: 32936188 DOI: 10.1039/d0ob01459a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A methodology for deconvolution of fast exchange equilibrium states in NMR spectroscopy (DFEQNMR) was developed based on DFT-GIAO NMR chemical shift prediction and a probability theory algorithm. Proof-of-concept studies were performed to estimate the protonation state of N-containing organic molecules involving fast proton exchange equilibrium and evaluate the solution tautomerism of a purine derivative. DFT-GIAO calculations were optimized to achieve good accuracy in 13C, 1H and 15N chemical shift prediction for protonated species. The probability theory algorithm enabled the determination of solution species ratios and yielded 95% confidence regions by comparing experimental and simulated chemical shift data sets. The calculation showed good accuracy for model partial salts with various functionalities and application in structure elucidation of complex natural product partial salts was also demonstrated. This method showed promising potential in acquisition of important insight into fast exchange equilibrium systems with only one experimental NMR chemical shift data set.
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Affiliation(s)
- Xiaozhou Ji
- Department of Chemistry, Texas A&M University, College Station, TX, USA
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38
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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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