101
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Fu XZ, Zhang SM, Wang GF, Yang QL, Guo L, Pescitelli G, Xie ZP. Atypical Angucyclinones with Ring Expansion and Cleavage from a Marine Streptomyces sp. J Org Chem 2022; 87:15998-16010. [PMID: 36395479 DOI: 10.1021/acs.joc.2c02134] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A unique ring C-expanded angucyclinone, oxemycin A (1), and seven new ring-cleavage derivatives (2-5 and 9-11) were isolated from the marine actinomycete Streptomyces pratensis KCB-132, together with eight known analogues (6-8 and 12-16). Their structures were elucidated by spectroscopic analyses, single-crystal X-ray diffractions, and NMR and ECD calculations. Among these atypical angucyclinones, compound 1 represented the first seven-membered ketoester in the angucyclinone family, which sheds light on the origin of fragmented angucyclinones with C-ring cleavage at C-12/C-12a in the Baeyer-Villiger hypothesis, such as 2-4, while the related "nonoxidized" analogues 5-8 seem to originate from a diverse pathway within the Grob fragmentation hypothesis. Additionally, we have succeeded in the challenging separation of elmenols E and F (12) into their four stereoisomers, which remained stable in aprotic solvents but rapidly racemized under protic conditions. Furthermore, the absolute configurations of LS1924 and its isomers (14 and 15) were assigned by ECD calculations for the first time. Surprisingly, these two bicyclic acetals are susceptible to hydrolysis in solution, resulting in fragmented derivatives 17 and 18 with C-ring cleavage between C-6a and C-7. Compared with ring C-modified angucyclinones, ring A-cleaved 11 was more active to multiple resistant "ESKAPE" pathogens with MIC values ranging from 4.7 to 37.5 μg/mL.
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Affiliation(s)
- Xin-Zhen Fu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Shu-Min Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Guang-Fei Wang
- College of Life Sciences, Yantai University, Yantai 264003, China
| | - Qiao-Li Yang
- College of Life Sciences, Yantai University, Yantai 264003, China
| | - Lin Guo
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy
| | - Ze-Ping Xie
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
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102
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Otogo N'Nang E, Gallard JF, Champy P, Le Pogam P, Beniddir MA. Density functional theory-nuclear magnetic resonance-validated full structure elucidation of theionbrunonine C, an unstable N-oxide theionbrunonine from Mostuea brunonis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:1178-1184. [PMID: 35368097 DOI: 10.1002/mrc.5271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
The structure elucidation of theionbrunonine C, a thioether-bridged dimeric monoterpene indole alkaloid (MIA), and more generally, one of the very few sulfur-containing MIA, is reported after its isolation from Mostuea brunonis (Gelsemiaceae). This unstable structure had already been targeted for isolation in our former, molecular network-guided, investigation of this plant, but this compound had degraded before sufficient spectroscopic data could have been acquired for a complete structure assignment. With this constraint in mind, the rapid acquisition of nuclear magnetic resonance (NMR) data enabled retrieving sufficient spectroscopic information for full structure elucidation, although from a partial set of spectroscopic information (1 H and 13 C NMR; COSY, HSQC, and HMBC). In conjunction with biosynthetic considerations, the cursory examination of 13 C NMR data unambiguously defined the complete stereostructure of 1, as further supported by density functional theory (DFT)-NMR calculations and subsequent DP4 probability score.
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Affiliation(s)
- Elvis Otogo N'Nang
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
- Laboratoire de chimie des substances naturelles, Département Science Fondamentale de l'Ingénieur (INSAB), Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Champy
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Pierre Le Pogam
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
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103
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Tanaka N, Takahashi S, Yoshino Y, Nakatani M, Ahmed FA, Hossain GM, Chen CH, Lee KH, Kashiwada Y. Tigliane-Type Diterpene Esters from the Fruits of Shirakiopsis indica and Their Anti-HIV Activity. JOURNAL OF NATURAL PRODUCTS 2022; 85:2687-2693. [PMID: 36378070 DOI: 10.1021/acs.jnatprod.2c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Four new diterpene esters, shirakindicans A-D (1-4), along with eight related known diterpene esters (5-12), were isolated from the fruits of the Bangladeshi medicinal plant Shirakiopsis indica. The structures of 1-4 were elucidated by spectroscopic data analysis and electronic circular dichroism (ECD) calculations. Shirakindican A (1) was assigned as a tigliane-type diterpene ester possessing an unusual 6β-hydroxy-1,7-dien-3-one structure, while shirakindican B (2) exhibits a tiglia-1,5-dien-3,7-dione structure. The anti-HIV activities of the isolated diterpene esters were evaluated and showed significant activities for sapintoxins A (5) and D (11), with EC50 values of 0.0074 and 0.044 μM, respectively, and TI values of 1 100 and 5 290. Sapatoxin A (12) also exhibited anti-HIV activity with an EC50 value of 0.13 μM and a TI value of 161.
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Affiliation(s)
- Naonobu Tanaka
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Sakura Takahashi
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Yuki Yoshino
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Megumi Nakatani
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Fakhruddin Ali Ahmed
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Gazi Mosharof Hossain
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Chin-Ho Chen
- Medical Center, Duke University, Durham, North Carolina 27710, United States
| | - Kuo-Hsiung Lee
- Natural Products Laboratory, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yoshiki Kashiwada
- Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
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104
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Cuadrado C, Daranas AH, Sarotti AM. May the Force (Field) Be with You: On the Importance of Conformational Searches in the Prediction of NMR Chemical Shifts. Mar Drugs 2022; 20:699. [PMID: 36355022 PMCID: PMC9694776 DOI: 10.3390/md20110699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 09/21/2023] Open
Abstract
NMR data prediction is increasingly important in structure elucidation. The impact of force field selection was assessed, along with geometry and energy cutoffs. Based on the conclusions, we propose a new approach named mix-J-DP4, which provides a remarkable increase in the confidence level of complex stereochemical assignments-100% in our molecular test set-with a very modest increment in computational cost.
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Affiliation(s)
- Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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105
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Lee TH, Ham SL, Lee DY, Lee JR, Kim J, Kim CS. Structure Revision of Balsamisides A-D and Establishment of an Empirical Rule for Distinguishing Four Classes of Biflavonoids. JOURNAL OF NATURAL PRODUCTS 2022; 85:2461-2467. [PMID: 36222268 DOI: 10.1021/acs.jnatprod.2c00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Balsamisides A-D (1-4) are anti-inflammatory and neurotrophic biflavonoidal glycosides originally proposed to possess an epoxide functionality at the C-2/C-3 position. However, there are inconsistencies in their 13C NMR chemical shift values with those of previously reported analogs, indicating that reanalysis of NMR data for structures of 1-4 is necessary. Computational methods aided by the DP4+ probability technique and ECD calculations enabled structural reassignment of 1-4 to have a 2,3-dihydro-3-hydroxyfuran (3-DHF) instead of an epoxide. Additionally, two new biflavonoidal glycosides, balsamisides E and F (14 and 18), possessing a 2,3-dihydro-2-hydroxyfuran (2-DHF) and a 1,4-dioxane ring, respectively, were characterized by conventional NMR and MS data analysis as well as DP4+ and ECD methods. Systematic 13C NMR analysis was performed on the four aforementioned classes of biflavonoids with a 2- or 3-DHF, epoxide, or 1,4-dioxane. As a result, diagnostic 13C NMR chemical shift values of C-2/C-3 for rapid determination of these four biflavonoid classes were formulated, and based on this first empirical rule for (bi)flavonoids eight previously reported ones were structurally revised.
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Affiliation(s)
- Tae Hyun Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Song Lim Ham
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Da Yeong Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Ju Ryeong Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Jonghwan Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Chung Sub Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon16419, Republic of Korea
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106
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Choi YJ, Alishir A, Jang T, Kang KS, Lee S, Kim KH. Antiskin Aging Effects of Indole Alkaloid N-Glycoside from Ginkgo Fruit ( Ginkgo biloba fruit) on TNF-α-Exposed Human Dermal Fibroblasts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13651-13660. [PMID: 36251736 DOI: 10.1021/acs.jafc.2c05769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Human skin aging has internal and external factors, both of which are characterized by TNF-α overproduction. Therefore, we aimed to identify a natural product that suppresses the damage that occurs in cutaneous dermal fibroblasts exposed to TNF-α. The protective effects of the indole alkaloid N-glycoside, ginkgoside B dimethyl ester (GBDE), isolated from ginkgo fruit (Ginkgo biloba fruit) were evaluated in TNF-α stimulated human dermal fibroblasts (HDFs). GBDE inhibited TNF-α-induced MMP-1 expression to 2.2 ± 0.1-fold (p < 0.01) and reversed the decrease in collagen levels to 0.4 ± 0.00-fold (p < 0.01) at 50 μM. The effect of GBDE was due to the suppression of the phospolylaton of MAPKs (ERK, 0.47 ± 0.05; JNK, 1.21 ± 0.07; p38, 0.77 ± 0.07-folds, p < 0.001) and Akt (0.14 ± 0.03-fold, p < 0.001) compared to the TNF-α group. GBDE also reduced the expression of COX-2 to 2.06 ± 0.12-fold (p < 0.001) and increased the expression of HO-1 to 10.64 ± 0.2-fold (p < 0.001). In addition, GBDE inhibited the expression of the pro-inflammatory cytokines (IL-8, 2.2 ± 0.0; IL-1β, 1.6 ± 0.0; IL-6, 2.0 ± 0.10-folds, p < 0.05). These results provide experimental evidence that GBDE can protect against skin damage, including aging.
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Affiliation(s)
- Yea Jung Choi
- College of Korean Medicine, Gachon University, Seongnam13120, Republic of Korea
| | - Akida Alishir
- School of Pharmacy, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Taesu Jang
- Health Administration, Dankook University, Cheonan31116, Republic of Korea
| | - Ki Sung Kang
- College of Korean Medicine, Gachon University, Seongnam13120, Republic of Korea
| | - Sullim Lee
- Department of Life Science, College of Bio-Nano Technology, Gachon University, Seongnam13120, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon16419, Republic of Korea
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107
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Schuppe AW, Liu Y, Gonzalez-Hurtado E, Zhao Y, Jiang X, Ibarraran S, Huang D, Wang E, Lee J, Loria JP, Dixit VD, Li X, Newhouse TR. Unified Total Synthesis of the Limonoid Alkaloids: Strategies for the De Novo Synthesis of Highly Substituted Pyridine Scaffolds. Chem 2022; 8:2856-2887. [PMID: 37396824 PMCID: PMC10311986 DOI: 10.1016/j.chempr.2022.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Highly substituted pyridine scaffolds are found in many biologically active natural products and therapeutics. Accordingly, numerous complementary de novo approaches to obtain differentially substituted pyridines have been disclosed. This article delineates the evolution of the synthetic strategies designed to assemble the demanding tetrasubstituted pyridine core present in the limonoid alkaloids isolated from Xylocarpus granatum, including xylogranatopyridine B, granatumine A and related congeners. In addition, NMR calculations suggested structural misassignment of several limonoid alkaloids, and predicted their C3-epimers as the correct structures, which was further validated unequivocally through chemical synthesis. The materials produced in this study were evaluated for cytotoxicity, anti-oxidant effects, anti-inflammatory action, PTP1B and Nlrp3 inflammasome inhibition, which led to compelling anti-inflammatory activity and anti-oxidant effects being discovered.
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Affiliation(s)
- Alexander W. Schuppe
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Yannan Liu
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Elsie Gonzalez-Hurtado
- Department of Pathology, Immunobiology, Comparative Medicine, Yale School of Medicine, 310 Cedar Street, New Haven, Connecticut 06520, United States
| | - Yizhou Zhao
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Xuefeng Jiang
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310018, P. R. China
| | - Sebastian Ibarraran
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - David Huang
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Emma Wang
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Jaehoo Lee
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - J. Patrick Loria
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Vishwa Deep Dixit
- Department of Pathology, Immunobiology, Comparative Medicine, Yale School of Medicine, 310 Cedar Street, New Haven, Connecticut 06520, United States
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310018, P. R. China
| | - Timothy R. Newhouse
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
- Lead contact
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108
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Yao J, Qin Q, Wang Y, Zeng J, Xu J, He X. Anti-neuroinflammatory 3-hydroxycoumaronochromones and isoflavanones enantiomers from the fruits of Ficus altissima Blume. PHYTOCHEMISTRY 2022; 202:113313. [PMID: 35820504 DOI: 10.1016/j.phytochem.2022.113313] [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: 03/29/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
A phytochemical study on the fruits of Ficus altissima Blume (lofty fig) led to the isolation and structural elucidation of three pairs of enantiomeric 3-hydroxycoumaronochromones and two pairs of enantiomeric isoflavanones, including eight undescribed compounds. Their structures were determined based on a comprehensive analysis of NMR and HR-ESI-MS spectroscopic data, calculated 13C NMR-DP4 plus analysis and the comparisons of experimental measurements of ECD with calculated ECD spectra by TDDFT or ECD plots in reported protocols. The inhibitory effects of the isolated enantiomers on NO production stimulated by LPS in microglial BV-2 cells were evaluated. Among them, ficusaltin D exhibited the most potent anti-neuroinflammatory activity, which inhibited the production of NO and the expression of iNOS, IL-6 and IL-1β and suppressed the NF-κB nuclear translocation in LPS-induced BV-2 cells, while its enantiomer displayed cytotoxicity.
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Affiliation(s)
- Jiaming Yao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Qiuyi Qin
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yihai Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China; Guangdong Engineering Research Center for Lead Compounds & Drug Discovery, Guangzhou, 510006, China.
| | - Jia Zeng
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jingwen Xu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China; Guangdong Engineering Research Center for Lead Compounds & Drug Discovery, Guangzhou, 510006, China
| | - Xiangjiu He
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China; Guangdong Engineering Research Center for Lead Compounds & Drug Discovery, Guangzhou, 510006, China.
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109
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Xian PJ, Liu SZ, Wang WJ, Yang SX, Feng Z, Yang XL. Undescribed specialised metabolites from the endophytic fungus Emericella sp. XL029 and their antimicrobial activities. PHYTOCHEMISTRY 2022; 202:113303. [PMID: 35787351 DOI: 10.1016/j.phytochem.2022.113303] [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: 01/27/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The fungus Emericella sp. XL029 isolated from leaves of Panax notoginseng was investigated for agents with potential antibacterial and antifungal activities using a one strain-many compounds (OSMAC) strategy. Fifteen compounds, including seven undescribed structures, were obtained from this species. Their structures were confirmed by extensive spectroscopic data, single-crystal X-ray crystallography and quantum chemistry calculations. Emerlactam A exhibited better antibacterial activity against multidrug-resistant Enterococcus faecium and antifungal activity against Helminthosporium maydis, with an MIC value of 12.5 μg/mL. Quiannulatic acid displayed significant antibacterial activity against multidrug-resistant Enterococcus faecium and multidrug-resistant Enterococcus faecalis with MIC values of 1.56 μg/mL and 3.13 μg/mL, respectively. 5-alkenylresorcinol exhibited significant antifungal activity against all tested phytopathogenic fungi with MIC values ranging from 6.25 to 12.5 μg/mL.
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Affiliation(s)
- Peng-Jie Xian
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Shu-Zhi Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Wen-Jing Wang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Sheng-Xiang Yang
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization & Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A & F University, Lin'an, 311300, China
| | - Zhang Feng
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| | - Xiao-Long Yang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China; The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, China.
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110
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Identifying the meta, para and ortho isomers in octa(aminophenyl)silsesquioxane (OAPS) from joint experimental characterizations and theoretical predictions of the IR and NMR spectra. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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111
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Yesiltepe Y, Govind N, Metz TO, Renslow RS. An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts. J Cheminform 2022; 14:64. [PMID: 36138446 PMCID: PMC9499888 DOI: 10.1186/s13321-022-00587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/06/2022] [Indexed: 11/24/2022] Open
Abstract
The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13C and 1H NMR spectra with respect to experimentally measured values. This leads us to the question-what accuracy is required in predicted 13C and 1H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1H and 13C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.
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Affiliation(s)
- Yasemin Yesiltepe
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Niranjan Govind
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Ryan S Renslow
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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112
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Wang C, Zhang J, Shi X, Li K, Li F, Tang X, Li G, Li P. Sarcoeleganolides C-G, Five New Cembranes from the South China Sea Soft Coral Sarcophyton elegans. Mar Drugs 2022; 20:574. [PMID: 36135763 PMCID: PMC9506240 DOI: 10.3390/md20090574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Five new cembranes, named sarcoeleganolides C-G (1-5), along with three known analogs (6-8) were isolated from soft coral Sarcophyton elegans collected from the Yagong Island, South China Sea. Their structures and absolute configurations were determined by extensive spectroscopic analysis, QM-NMR, and TDDFT-ECD calculations. In addition, compound 3 exhibited better anti-inflammation activity compared to the indomethacin as a positive control in zebrafish at 20 μM.
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Affiliation(s)
- Cili Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Jiarui Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Xing Shi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Kai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Fengling Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Xuli Tang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Guoqiang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Pinglin Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
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113
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Miao WG, Nguyen T, Iqbal J, Pierens GK, Ma L, Richardson DR, Wood SA, Mellick GD, Quinn RJ, Feng Y. Meeting the Challenge 2: Identification of Potential Chemical Probes for Parkinson's Disease from Ligusticum chuanxiong Hort Using Cytological Profiling. ACS Chem Neurosci 2022; 13:2565-2578. [PMID: 36018577 DOI: 10.1021/acschemneuro.1c00820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Traditional Chinese medicine (TCM) has been around for thousands of years and is increasingly gaining popularity in the Western world to treat various complex disorders including the incurable neurodegenerative condition, Parkinson's Disease (PD). One of the many directions in recent studies of PD is utilizing the phenotypic assay, or cytological profiling, to evaluate the phenotypic changes of PD-implicated cellular components in patient-derived olfactory neuroepithelial (hONS) cells, upon treating the cells with extracts or pure compounds. To obtain small molecules for studies utilizing PD phenotyping assays, Ligusticum chuanxiong Hort was selected for analysis as it is a popular Chinese herbal medicine used for treating PD-like symptoms. Fifty-three secondary metabolites, including six new compounds, were isolated from the ethanolic extract of L. chuanxiong; their structures were elucidated based on several spectroscopic techniques such as NMR, MS, Fourier transform infrared (FTIR), UV, and theoretical density functional theory (DFT) calculations. Cytological profiling of the afforded natural products against PD hONS cells revealed 34 compounds strongly perturbated the staining of several cellular organelles. In fact, greaterthan 1.5-fold change was observed compared to the control (dimethyl sulfoxide; DMSO), with early endosome, lysosome, and autophagosome (LC3b) being particularly affected. Given these biological compartments are closely related to PD pathogenesis, the results helped rationalize the traditional medicinal use of L. chuanxiong in PD treatment. Further, the hit compounds can serve as chemical probes to map the molecular pathways underlying PD, potentially leading to new therapeutic targets for PD.
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Affiliation(s)
- William Gang Miao
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Jamila Iqbal
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Linlin Ma
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Des R Richardson
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia.,School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
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114
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Youn I, Han KY, Gurgul A, Wu Z, Lee H, Che CT. Chemical constituents of Entandrophragma angolense and their anti-inflammatory activity. PHYTOCHEMISTRY 2022; 201:113276. [PMID: 35714737 DOI: 10.1016/j.phytochem.2022.113276] [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: 01/24/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
From the stem bark of Entandrophragma angolense, six undescribed compounds were isolated, including seco-tirucallane type triterpenoids, limonoids, and a catechin glucoside, along with nineteen known structures. All structures were determined by interpretation of spectroscopic and HRMS data, and absolute configuration was confirmed with the aid of electronic circular dichroism. The isolated compounds were tested for LPS-induced NO inhibition in RAW 264.7 macrophages and EC50 values for moluccensin O and (-)-catechin were 81 μM and 137 μM, respectively.
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Affiliation(s)
- Isoo Youn
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Kyu-Yeon Han
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Aleksandra Gurgul
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Zhenlong Wu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States; Biophysics Core at Research Resource Center, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Chun-Tao Che
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States.
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115
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Zhang JJ, Wang DW, Peng YL, Katta MK, Dong HQ, Cheng YX. Structural characterization of minor optically pure and impure meroterpenoid-type compounds in Ganoderma lucidum and structure revision of spirolingzhine D. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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116
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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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117
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Masi M, Castaldi S, Sautua F, Pescitelli G, Carmona MA, Evidente A. Truncatenolide, a Bioactive Disubstituted Nonenolide Produced by Colletotrichum truncatum, the Causal Agent of Anthracnose of Soybean in Argentina: Fungal Antagonism and SAR Studies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9834-9844. [PMID: 35925677 PMCID: PMC9389607 DOI: 10.1021/acs.jafc.2c02502] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
A bioactive disubstituted nonenolide, named truncatenolide, was produced by Colletotrichum truncatum, which was collected from infected tissues of soybean showing anthracnose symptoms in Argentina. This is a devastating disease that drastically reduces the yield of soybean production in the world. The fungus also produced a new trisubstituted oct-2-en-4-one, named truncatenone, and the well-known tyrosol and N-acetyltyramine. Truncatenolide and truncatenone were characterized by spectroscopic (essentially one-dimensional (1D) and two-dimensional (2D) 1H and 13C NMR and HR ESIMS) and chemical methods as (5E,7R,10R)-7-hydroxy-10-methyl-3,4,7,8,9,10-hexahydro-2H-oxecin-2-one and (Z)-6-hydroxy-3,5-dimethyloct-2-en-4-one, respectively. The geometry of the double bond of truncatenolide was assigned by the value of olefinic proton coupling constant and that of truncatenone by the correlation observed in the corresponding NOESY spectrum. The relative configuration of each stereogenic center was assigned with the help of 13C chemical shift and 1H-1H scalar coupling DFT calculations, while the absolute configuration assignment of truncatenolide was performed by electronic circular dichroism (ECD). When tested on soybean seeds, truncatenolide showed the strongest phytotoxic activity. Tyrosol and N-acetyltyramine also showed phytotoxicity to a lesser extent, while truncatenone weakly stimulated the growth of the seed root in comparison to the control. When assayed against Macrophomina phaseolina and Cercospora nicotianae, other severe pathogens of soybean, truncatenolide showed significant activity against M. phaseolina and total inhibition of C. nicotianae. Thus, some other fungal nonenolides and their derivatives were assayed for their antifungal activity against both fungi in comparison with truncatenolide. Pinolidoxin showed to a less extent antifungal activity against both fungi, while modiolide A selectively and totally inhibited only the growth of C. nicotianae. The SAR results and the potential of truncatenolide, modiolide A, and pinolidoxin as biofungicides were also discussed.
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Affiliation(s)
- Marco Masi
- Dipartimento
di Scienze Chimiche, Università di
Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Stefany Castaldi
- Dipartimento
di Biologia, Università di Napoli
Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Francisco Sautua
- Cátedra
de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSE Buenos Aires, Argentina
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Marcelo Anibal Carmona
- Cátedra
de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSE Buenos Aires, Argentina
| | - Antonio Evidente
- Dipartimento
di Scienze Chimiche, Università di
Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy
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118
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Mills MD, Sonstrom RE, Vang ZP, Neill JL, Scolati HN, West CT, Pate BH, Clark JR. Enantioselective Synthesis of Enantioisotopomers with Quantitative Chiral Analysis by Chiral Tag Rotational Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202207275. [PMID: 35700045 PMCID: PMC9403034 DOI: 10.1002/anie.202207275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 01/13/2023]
Abstract
Fundamental to the synthesis of enantioenriched chiral molecules is the ability to assign absolute configuration at each stereogenic center, and to determine the enantiomeric excess for each compound. While determination of enantiomeric excess and absolute configuration is often considered routine in many facets of asymmetric synthesis, the same determinations for enantioisotopomers remains a formidable challenge. Here, we report the first highly enantioselective metal-catalyzed synthesis of enantioisotopomers that are chiral by virtue of deuterium substitution along with the first general spectroscopic technique for assignment of the absolute configuration and quantitative determination of the enantiomeric excess of isotopically chiral molecules. Chiral tag rotational spectroscopy uses noncovalent chiral derivatization, which eliminates the possibility of racemization during derivatization, to perform the chiral analysis without the need of reference samples of the enantioisotopomer.
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Affiliation(s)
| | | | - Zoua Pa Vang
- Department of ChemistryMarquette UniversityMilwaukeeWI 53233USA
| | - Justin L. Neill
- BrightSpec Inc.770 Harris Street Suite 104bCharlottesvilleVA 22903USA
| | - Haley N. Scolati
- Department of ChemistryUniversity of VirginiaCharlottesvilleVA 22904USA
| | - Channing T. West
- Department of ChemistryUniversity of VirginiaCharlottesvilleVA 22904USA
| | - Brooks H. Pate
- Department of ChemistryUniversity of VirginiaCharlottesvilleVA 22904USA
| | - Joseph R. Clark
- Department of ChemistryMarquette UniversityMilwaukeeWI 53233USA
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119
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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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120
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Gao Y, Zhou JS, Liu HC, Zhang Y, Yin WH, Liu QF, Wang GW, Zhao JX, Yue JM. Phonerilins A–K, cytotoxic ingenane and ingol diterpenoids from Euphorbia neriifolia. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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121
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Li J, Tan YF, Liu S, Wu XQ, Wang J, Xu KP, Tan GS, Zou ZX, Wang WX. Reassignment of the structures of pestalopyrones A-D. PHYTOCHEMISTRY 2022; 200:113205. [PMID: 35436477 DOI: 10.1016/j.phytochem.2022.113205] [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: 01/28/2022] [Revised: 03/10/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Pestalopyrones A-D are four unusual tricyclic pyrone derivatives with flexible chiral structures, isolated from the endophytic fungus Pestalotiopsis neglecta S3. The full elucidation of their structures was a challenging task, and remained unsolved in the original article. Herein, the relative configurations of pestalopyrones A and pestalopyrones B were unambiguously assigned by detailed analyses on spectroscopic data and GIAO 13C NMR calculation method with sorted training sets (STS). The planar structures of pestalopyrones C and pestalopyrones D were revised by reinterpretation of their reported spectroscopic data, and then their relative configurations were deduced by STS GIAO 13C NMR calculation and NOE analysis. The absolute configurations of all the mentioned compounds were determined by the comparison of their experimental and calculated ECD curves.
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Affiliation(s)
- Jing Li
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Gui-Shan Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Zhen-Xing Zou
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China.
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122
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Cho HM, Park EJ, Park YJ, Ponce-Zea J, Mai VH, Doan TP, Ryu B, Chin YW, Oh WK. Sesquiterpene lactone and its unique proaporphine hybrids from Magnolia grandiflora L. and their anti-inflammatory activity. PHYTOCHEMISTRY 2022; 200:113211. [PMID: 35490776 DOI: 10.1016/j.phytochem.2022.113211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Two undescribed sesquiterpene lactone-proaporphine hybrid skeletons, two undescribed sesquiterpenes, and four known compounds were isolated from the aerial part of Magnolia grandiflora L. The structures of isolated compounds were unambiguously determined based on the interpretation of a combination of NMR spectroscopy, HRESIMS, DP4+ probability calculation of carbon data, X-ray crystallographic analyses, and ECD calculation. The isolated compounds were investigated for their anti-inflammatory activity against nitric oxide production and the protein expression of COX-2 in LPS-stimulated RAW 264.7 cells.
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Affiliation(s)
- Hyo Moon Cho
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun Jin Park
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeon Joo Park
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jorge Ponce-Zea
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van Hieu Mai
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Thi Phuong Doan
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byeol Ryu
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Won Chin
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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123
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Kanehara R, Tonouchi A, Konno K, Koshino H, Hashimoto M. Isolation of cyclohumulanoids from Daedaleopsis tricolor and their biosynthesis based on in silico simulations. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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124
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Li XL, Ru T, Navarro-Vázquez A, Lindemann P, Nazaré M, Li XW, Guo YW, Sun H. Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D. JOURNAL OF NATURAL PRODUCTS 2022; 85:1730-1737. [PMID: 35792821 DOI: 10.1021/acs.jnatprod.2c00257] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).
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Affiliation(s)
- Xiao-Lu Li
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Tong Ru
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Peter Lindemann
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Marc Nazaré
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
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125
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Gao X, Wang X, Zhou J, Zhang Y, Liu H, Zhou B, Yue J. Rearranged Dichapetalin‐type Triterpenoids with Cytotoxic Activity from
Dichapetalum gelonioides. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xin‐Hua Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
| | - Xi‐Yuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
| | - Jun‐Su Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
| | - Yan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
| | - Hong‐Chun Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
| | - Bin Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
- Shandong Laboratory of Yantai Drug Discovery Bohai Rim Advanced Research Institute for Drug Discovery Yantai Shandong 264117 People's Republic of China
| | - Jian‐Min Yue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 People's Republic of China
- Research Units of Discovery of New Drug Lead Molecules Chinese Academy of Medical Sciences People's Republic of China
- Shandong Laboratory of Yantai Drug Discovery Bohai Rim Advanced Research Institute for Drug Discovery Yantai Shandong 264117 People's Republic of China
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126
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Fuentes-Monteverde JCC, Nath N, Forero AM, Balboa EM, Navarro-Vázquez A, Griesinger C, Jiménez C, Rodríguez J. Connection of Isolated Stereoclusters by Combining 13C-RCSA, RDC, and J-Based Configurational Analyses and Structural Revision of a Tetraprenyltoluquinol Chromane Meroterpenoid from Sargassum muticum. Mar Drugs 2022; 20:462. [PMID: 35877755 PMCID: PMC9319238 DOI: 10.3390/md20070462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/06/2022] [Accepted: 07/15/2022] [Indexed: 12/10/2022] Open
Abstract
The seaweed Sargassum muticum, collected on the southern coast of Galicia, yielded a tetraprenyltoluquinol chromane meroditerpene compound known as 1b, whose structure is revised. The relative configuration of 1b was determined by J-based configurational methodology combined with an iJ/DP4 statistical analysis and further confirmed by measuring two anisotropic properties: carbon residual chemical shift anisotropies (13C-RCSAs) and one-bond 1H-13C residual dipolar couplings (1DCH-RDCs). The absolute configuration of 1b was deduced by ECD/OR/TD-DFT methods and established as 3R,7S,11R.
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Affiliation(s)
- Juan Carlos C. Fuentes-Monteverde
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
- NMR Based Structural Biology, MPI for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Nilamoni Nath
- Department of Chemistry, Gauhati University, Gopinath Bardoloi Nagar, Guwahati 781014, India;
| | - Abel M. Forero
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
| | - Elena M. Balboa
- Department of Chemical Engineering, Faculty of Science, Campus Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain;
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Cidade Universitária, Recife 50740-550, Brazil;
| | - Christian Griesinger
- NMR Based Structural Biology, MPI for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carlos Jiménez
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
| | - Jaime Rodríguez
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
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127
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Elyashberg M, Novitskiy IM, Bates RW, Kutateladze AG, Williams CM. Reassignment of Improbable Natural Products Identified through Chemical Principle Screening. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development Inc. (ACD/Labs) Toronto ON, M5C 1B5 Canada
| | - Ivan M. Novitskiy
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Roderick W. Bates
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Andrei G. Kutateladze
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Queensland Australia
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128
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Kang S, Han J, Jang SC, An JS, Kang I, Kwon Y, Nam SJ, Shim SH, Cho JC, Lee SK, Oh DC. Epoxinnamide: An Epoxy Cinnamoyl-Containing Nonribosomal Peptide from an Intertidal Mudflat-Derived Streptomyces sp. Mar Drugs 2022; 20:md20070455. [PMID: 35877748 PMCID: PMC9321520 DOI: 10.3390/md20070455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/09/2022] [Accepted: 07/09/2022] [Indexed: 12/03/2022] Open
Abstract
Cinnamoyl-containing nonribosomal peptides (CCNPs) form a unique family of actinobacterial secondary metabolites and display various biological activities. A new CCNP named epoxinnamide (1) was discovered from intertidal mudflat-derived Streptomyces sp. OID44. The structure of 1 was determined by the analysis of one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) data along with a mass spectrum. The absolute configuration of 1 was assigned by the combination of advanced Marfey’s method, 3JHH and rotating-frame overhauser effect spectroscopy (ROESY) analysis, DP4 calculation, and genomic analysis. The putative biosynthetic pathway of epoxinnamide (1) was identified through the whole-genome sequencing of Streptomyces sp. OID44. In particular, the thioesterase domain in the nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster was proposed as a bifunctional enzyme, which catalyzes both epimerization and macrocyclization. Epoxinnamide (1) induced quinone reductase (QR) activity in murine Hepa-1c1c7 cells by 1.6-fold at 5 μM. It also exhibited effective antiangiogenesis activity in human umbilical vein endothelial cells (IC50 = 13.4 μM).
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Affiliation(s)
- Sangwook Kang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (J.-C.C.)
| | - Yun Kwon
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea;
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea;
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (J.-C.C.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
- Correspondence: ; Tel.: +82-880-2491; Fax: +82-762-8322
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129
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Asperopiperazines A and B: Antimicrobial and Cytotoxic Dipeptides from a Tunicate-Derived Fungus Aspergillus sp. DY001. Mar Drugs 2022; 20:md20070451. [PMID: 35877744 PMCID: PMC9319533 DOI: 10.3390/md20070451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 02/06/2023] Open
Abstract
Investigation of the cytotoxic fractions of the ethyl acetate extract of the fermentation broth of the tunicate-derived Aspergillus sp. DY001 afforded two new dipeptides, asperopiperazines A and B (1 and 2), along with the previously reported compounds (+)-citreoisocoumarin (3) and (−)-6,8-di-O-methylcitreoisocoumarin (4). Analyses of the 1D and 2D NMR spectroscopic data of the compounds supported their structural assignments. Asperopiperazine A (1) is a cyclic dipeptide of leucine and phenylalanine moieties, which are substituted with an N-methyl and an N-acetyl group, respectively. On the other hand, asperopiperazine B (2) is a cyclic dipeptide of proline and phenylalanine moieties with a hydroxyl group at C-2 of the proline part. The absolute configuration of the amino acid moieties in 1 and 2 were determined by Marfey’s analyses and DFT NMR chemical shift calculations, leading to their assignment as cyclo(l-NMe-Leu-l-NAc-Phe) and cyclo(d-6-OH-Pro-l-Phe), respectively. Asperopiperazines A and B displayed higher antimicrobial effects against Escherichia coli and Staphylococcus aureus than Candida albicans. Furthermore, compounds 1–4 displayed variable growth inhibitory effects towards HCT 116 and MDA-MB-231 cells, with asperopiperazine A as the most active one towards HCT 116.
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130
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Taguchi R, Iwasaki A, Ebihara A, Jeelani G, Nozaki T, Suenaga K. Isolation and Total Synthesis of Beru'amide, an Antitrypanosomal Polyketide from a Marine Cyanobacterium Okeania sp. Org Lett 2022; 24:4710-4714. [PMID: 35713470 DOI: 10.1021/acs.orglett.2c02013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A 68 μg amount of an acyclic polyketide, named beru'amide, was isolated from a marine cyanobacterium Okeania sp. Beru'amide contains six unique moieties in its relatively small skeleton. By applying several cutting-edge techniques, including DFT-based chemical shift calculations, we achieved the structure determination and the total synthesis of this highly functionalized scarce natural product. Furthermore, beru'amide was shown to have strong antitrypanosomal activity.
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Affiliation(s)
- Raimu Taguchi
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Arihiro Iwasaki
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Akira Ebihara
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Ghulam Jeelani
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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131
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Xia D, Wang ZH, Jiang JM, Yang XW, Gao Y, Xu YY, Chang LY, Zhu D, Zhao BJ, Zhu XL, Zhang J, Yin ZQ, Pan K. Lycojapomines A-E: Lycopodium Alkaloids with Anti-Renal Fibrosis Potential from Lycopodium japonicum. Org Lett 2022; 24:4684-4688. [PMID: 35724994 DOI: 10.1021/acs.orglett.2c01877] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Five Lycopodium alkaloids featuring novel C17N2 (1 and 2), C29N3 (3 and 4), and C15N2 (5) skeletons were isolated from Lycopodium japonicum. Compound 1 is the first natural product containing a 3-aza[3.3.3]propellane motif. The structures of these compounds were elucidated by spectroscopic analysis, X-ray crystallography, and computational methods. Compounds 1 and 3-5 significantly inhibited TGF-β1-induced fibronectin deposition in HK-2 cells at a nontoxic concentration of 20 μM.
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Affiliation(s)
- Dan Xia
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Zi-Han Wang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jia-Meng Jiang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xue-Wen Yang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yue Gao
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yin-Ying Xu
- Nephrology Department, Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing 211200, China
| | - Lin-Yue Chang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Dan Zhu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Bao-Jun Zhao
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xin-Liu Zhu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jian Zhang
- Nephrology Department, Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing 211200, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Zhi-Qi Yin
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Ke Pan
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
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132
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Cank KB, Shepherd RA, Knowles SL, Rangel-Grimaldo M, Raja HA, Bunch ZL, Cech NB, Rice CA, Kyle DE, Falkinham JO, Burdette JE, Oberlies NH. Polychlorinated cyclopentenes from a marine derived Periconia sp. (strain G1144). PHYTOCHEMISTRY 2022; 199:113200. [PMID: 35421431 PMCID: PMC9173697 DOI: 10.1016/j.phytochem.2022.113200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Studies on an organic extract of a marine fungus, Periconia sp. (strain G1144), led to the isolation of three halogenated cyclopentenes along with the known and recently reported rhytidhyester D; a series of spectrometric and spectroscopic techniques were used to elucidate these structures. Interestingly, two of these compounds represent tri-halogenated cyclopentene derivatives, which have been observed only rarely from Nature. The relative and absolute configurations of the compounds were established via mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, Mosher's esters method, optical rotation and GIAO NMR calculations, including correlation coefficient calculations and the use of both DP4+ and dJ DP4 analyses. Several of the isolated compounds were tested for activity in anti-parasitic, antimicrobial, quorum sensing inhibition, and cytotoxicity assays and were shown to be inactive.
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Affiliation(s)
- Kristóf B Cank
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Robert A Shepherd
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Manuel Rangel-Grimaldo
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Zoie L Bunch
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Nadja B Cech
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA
| | - Christopher A Rice
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, 724 Biological Sciences Building, University of Georgia, Athens, GA, 30602-2607, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, 335 Coverdell Center 500 D.W. Brooks Drive, Athens, GA, 30602-7399, USA.
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, 335 Coverdell Center 500 D.W. Brooks Drive, Athens, GA, 30602-7399, USA.
| | - Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech Center for Drug Discovery, Derring Hall Room 2125, 926 West Campus Drive, Mail Code 0406, Blacksburg, VA, 24061, USA.
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 South Wood Street, 333 PHARM, MC 781, Chicago, IL, 60612, USA.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 435 Patricia A. Sullivan Science Building, Greensboro, NC, 27402-6170, USA.
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133
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Bergstrom BD, Merrill AT, Fettinger JC, Tantillo DJ, Shaw JT. Divergent Asymmetric Synthesis of Panowamycins, TM‐135, and Veramycin F Using C−H Insertion with Donor/Donor Carbenes. Angew Chem Int Ed Engl 2022; 61:e202203072. [DOI: 10.1002/anie.202203072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Benjamin D. Bergstrom
- Department of Chemistry University of California, Davis One Shields Ave. Davis CA 95161 USA
| | - Amy T. Merrill
- Department of Chemistry University of California, Davis One Shields Ave. Davis CA 95161 USA
| | - James C. Fettinger
- Department of Chemistry University of California, Davis One Shields Ave. Davis CA 95161 USA
| | - Dean J. Tantillo
- Department of Chemistry University of California, Davis One Shields Ave. Davis CA 95161 USA
| | - Jared T. Shaw
- Department of Chemistry University of California, Davis One Shields Ave. Davis CA 95161 USA
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134
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Pate BH, Mills MD, Sonstrom RE, Vang ZP, Neill JL, Scolati HN, West CT, Clark JR. Enantioselective Synthesis of Enantioisotopomers with Quantitative Chiral Analysis by Chiral Tag Rotational Spectroscopy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Brooks H. Pate
- University of Virginia Department of Chemistry McCormick RoadP.O. Box 400319 22904-4319 Charlottesville UNITED STATES
| | | | | | | | - Justin L. Neill
- BrightSpec NA 770 Harris St.Suite 104b 22903 Charlottesville UNITED STATES
| | | | | | - Joseph R. Clark
- Marquette University Chemistry Department of ChemistryMarquette University 53233 Milwaukee UNITED STATES
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135
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Kurisawa N, Iwasaki A, Teranuma K, Dan S, Toyoshima C, Hashimoto M, Suenaga K. Structural Determination, Total Synthesis, and Biological Activity of Iezoside, a Highly Potent Ca 2+-ATPase Inhibitor from the Marine Cyanobacterium Leptochromothrix valpauliae. J Am Chem Soc 2022; 144:11019-11032. [DOI: 10.1021/jacs.2c04459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naoaki Kurisawa
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Arihiro Iwasaki
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kazuya Teranuma
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Shingo Dan
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Chikashi Toyoshima
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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136
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Lam N, Paterson I. Deep‐sea discovery and detective work: towards solving the hemicalide structural enigma through computational NMR analysis and stereocontrolled synthesis. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nelson Lam
- University of Cambridge Chemistry UNITED KINGDOM
| | - Ian Paterson
- Cambridge University Department of Chemistry Lensfield Road CB2 1EW Cambridge UNITED KINGDOM
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137
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Huo ZQ, Zhu F, Zhang XW, Zhang X, Liang HB, Yao JC, Liu Z, Zhang GM, Yao QQ, Qin GF. Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects. Mar Drugs 2022; 20:333. [PMID: 35621984 PMCID: PMC9143581 DOI: 10.3390/md20050333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, in turn, have led to obstacles in druggability research. To resolve this issue, the comprehensive use of multiple methods is necessary. Additionally, configuration assignment methods, such as X-ray single-crystal diffraction (crystalline derivatives, crystallization chaperones, and crystalline sponges), NMR-based methods (JBCA and Mosher's method), circular dichroism-based methods (ECCD and ICD), quantum computational chemistry-based methods (NMR calculations, ECD calculations, and VCD calculations), and chemical transformation-based methods should be summarized. This paper reviews the basic principles, characteristics, and applicability of the methods mentioned above as well as application examples to broaden the research and applications of these methods and to provide a reference for the configuration determinations of flexible MNPs.
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Affiliation(s)
- Zong-Qing Huo
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Feng Zhu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Xing-Wang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiao Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Hong-Bao Liang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Jing-Chun Yao
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Zhong Liu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Gui-Min Zhang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Qing-Qiang Yao
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China;
| | - Guo-Fei Qin
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
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138
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Tsai YH, Amichetti M, Zanardi MM, Grimson R, Daranas AH, Sarotti AM. ML- J-DP4: An Integrated Quantum Mechanics-Machine Learning Approach for Ultrafast NMR Structural Elucidation. Org Lett 2022; 24:7487-7491. [PMID: 35508069 DOI: 10.1021/acs.orglett.2c01251] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new tool, ML-J-DP4, provides an efficient and accurate method for determining the most likely structure of complex molecules within minutes using standard computational resources. The workflow involves combining fast Karplus-type J calculations with NMR chemical shifts predictions at the cheapest HF/STO-3G level enhanced using machine learning (ML), all embedded in the J-DP4 formalism. Our ML provides accurate predictions, which compare favorably alongside with other ML methods.
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Affiliation(s)
- Yi-Hsuan Tsai
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Milagros Amichetti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - María Marta 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
| | - Rafael Grimson
- Instituto de Investigación e Ingeniería Ambiental (IIIA), Universidad Nacional de San Martín (UNSAM) y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1650, Argentina
| | - Antonio Hernandez Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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139
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Zhang R, Wang H, Chen B, Dai H, Sun J, Han J, Liu H. Discovery of Anti-MRSA Secondary Metabolites from a Marine-Derived Fungus Aspergillus fumigatus. Mar Drugs 2022; 20:302. [PMID: 35621953 PMCID: PMC9146929 DOI: 10.3390/md20050302] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 12/30/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a WHO high-priority pathogen that can cause great harm to living beings, is a primary cause of death from antibiotic-resistant infections. In the present study, six new compounds, including fumindoline A-C (1-3), 12β, 13β-hydroxy-asperfumigatin (4), 2-epi-tryptoquivaline F (17) and penibenzophenone E (37), and thirty-nine known ones were isolated from the marine-derived fungus Aspergillus fumigatus H22. The structures and the absolute configurations of the new compounds were unambiguously assigned by spectroscopic data, mass spectrometry (MS), electronic circular dichroism (ECD) spectroscopic analyses, quantum NMR and ECD calculations, and chemical derivatizations. Bioactivity screening indicated that nearly half of the compounds exhibit antibacterial activity, especially compounds 8 and 11, and 33-38 showed excellent antimicrobial activities against MRSA, with minimum inhibitory concentration (MIC) values ranging from 1.25 to 2.5 μM. In addition, compound 8 showed moderate inhibitory activity against Mycobacterium bovis (MIC: 25 μM), compound 10 showed moderate inhibitory activity against Candida albicans (MIC: 50 μM), and compound 13 showed strong inhibitory activity against the hatching of a Caenorhabditis elegans egg (IC50: 2.5 μM).
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Affiliation(s)
- Rui Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Education, College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (R.Z.); (H.W.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (B.C.); (H.D.); (J.S.)
| | - Haifeng Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Education, College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (R.Z.); (H.W.)
| | - Baosong Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (B.C.); (H.D.); (J.S.)
| | - Huanqin Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (B.C.); (H.D.); (J.S.)
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (B.C.); (H.D.); (J.S.)
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (B.C.); (H.D.); (J.S.)
| | - Hongwei Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Education, College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (R.Z.); (H.W.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (B.C.); (H.D.); (J.S.)
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140
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Divergent Asymmetric Synthesis of Panowamycins, TM‐135, and Veramycin F Using C−H Insertion with Donor/Donor Carbenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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141
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Yan W, Xu X. Accurate Prediction of Nuclear Magnetic Resonance Parameters via the XYG3 Type of Doubly Hybrid Density Functionals. J Chem Theory Comput 2022; 18:2931-2946. [PMID: 35467852 DOI: 10.1021/acs.jctc.2c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful and versatile tools in elucidating molecular structures. To eliminate ambiguities of experimental assignments, accurate calculations of NMR spectra are of great importance. Here, a method for theoretical evaluation of the NMR shielding constants by analytic derivatives using gauge including atomic orbitals (GIAO) has been implemented for the XYG3 type of doubly hybrid density functionals (xDH), namely, the GIAO-xDH method. Benchmark calculations on shielding constants and chemical shifts demonstrate the remarkable accuracy of the GIAO-xDH method, compared to the accurate CCSD(T) references. It is shown here that the XYGJ-OS functional is able to give a mean absolute deviation (MAD) of ∼3.0 ppm in the calculated shielding constants for 13C, 15N, 17O, 19F, while both XYGJ-OS and xDH-PBE0 functionals are able to provide a satisfactory estimation of chemical shifts with MADs of ∼0.03 and 1.0 ppm for 1H and 13C, respectively. The basis set influence upon the method has been examined and a computational scheme considering both accuracy and efficiency has been proposed and tested to predict the experimental 13C chemical shifts of five medium-sized natural product molecules, yielding a MAD of ∼1.0 ppm, which demonstrates the practical feasibility of the GIAO-xDH method.
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Affiliation(s)
- Wenjie Yan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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142
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Jones TH, Harrison DP, Menegatti C, Mevers E, Knott K, Marek P, Hennen DA, Kasson MT, Macias AM, Lovett B, Saporito RA. Deoxybuzonamine Isomers from the Millipede Brachycybe lecontii (Platydesmida: Andrognathidae). JOURNAL OF NATURAL PRODUCTS 2022; 85:1134-1140. [PMID: 35389651 DOI: 10.1021/acs.jnatprod.2c00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Millipedes (Diplopoda) are well known for their toxic or repellent defensive secretions. Here, we describe (6aR,10aS,10bR)-8,8-dimethyldodecahydropyrrolo[2,1-a]isoquinoline [trans-anti-trans-deoxybuzonamine (1a)] and (rel-6aR,10aR,10bR)-8,8-dimethyldodecahydropyrrolo[2,1-a]isoquinoline [trans-syn-cis-deoxybuzonamine (1b)], two isomers of deoxybuzonamine found in the chemical defense secretions of the millipede Brachycybe lecontii Wood (Colobognatha, Platydesmida, Andrognathidae). The carbon-nitrogen skeleton of these compounds was determined from their MS and GC-FTIR spectra obtained from the MeOH extract of whole millipedes, along with a subsequent selective synthesis. Their structures were established from their 1D (1H, 13C) and 2D NMR (COSY, NOESY, multiplicity-edited HSQC, HSQC-TOCSY, HMBC) spectra. Additionally, computational chemistry (DFT and DP4) was used to identify the relative configurations of 1a and 1b by comparing predicted 13C data to their experimental values, and the absolute configuration of 1a was determined by comparing its experimental specific rotation with that of the computationally calculated value. This is the first report of dodecahydropyrrolo[2,1-a]isoquinoline alkaloids from a platydesmidan millipede.
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Affiliation(s)
- Tappey H Jones
- Department of Chemistry, Virginia Military Institute, Lexington, Virginia 24450, United States
| | - Daniel P Harrison
- Department of Chemistry, Virginia Military Institute, Lexington, Virginia 24450, United States
| | - Carla Menegatti
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Emily Mevers
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Kenneth Knott
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Paul Marek
- Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Derek A Hennen
- Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Matt T Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Angie M Macias
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Brian Lovett
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Ralph A Saporito
- Department of Biology, John Carroll University, University Heights, Ohio 44118, United States
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143
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An JS, Kim MS, Han J, Jang SC, Im JH, Cui J, Lee Y, Nam SJ, Shin J, Lee SK, Yoon YJ, Oh DC. Nyuzenamide C, an Antiangiogenic Epoxy Cinnamic Acid-Containing Bicyclic Peptide from a Riverine Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:804-814. [PMID: 35294831 DOI: 10.1021/acs.jnatprod.1c00837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new nonribosomal peptide, nyuzenamide C (1), was discovered from riverine sediment-derived Streptomyces sp. DM14. Comprehensive analysis of the spectroscopic data of nyuzenamide C (1) revealed that 1 has a bicyclic backbone composed of six common amino acid residues (Asn, Leu, Pro, Gly, Val, and Thr) and four nonproteinogenic amino acid units, including hydroxyglycine, β-hydroxyphenylalanine, p-hydroxyphenylglycine, and 3,β-dihydroxytyrosine, along with 1,2-epoxypropyl cinnamic acid. The absolute configuration of 1 was proposed by J-based configuration analysis, the advanced Marfey's method, quantum mechanics-based DP4 calculations, and bioinformatic analysis of its nonribosomal peptide synthetase biosynthetic gene cluster. Nyuzenamide C (1) displayed antiangiogenic activity in human umbilical vein endothelial cells and induced quinone reductase in murine Hepa-1c1c7 cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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144
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Sternberg U, Farès C. Statistical evaluation of simulated NMR data of flexible molecules. Phys Chem Chem Phys 2022; 24:9608-9618. [PMID: 35403649 DOI: 10.1039/d2cp00330a] [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 new probability score-named χ-probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the χ-probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the χ-probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility. The NMR data (which include RDCs, NOE distances and 3J couplings) are calculated from MDOC (Molecular Dynamics with Orientational Constraints) trajectories and are investigated against experimentally measured data. It is demonstrated that this approach singles out the correct stereochemical configuration with probabilities more than 98%, even for highly mobile molecules. In more demanding cases, a decisive χ-probability test requires that the datasets include high-quality NOE distances in addition to RDC values.
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Affiliation(s)
- Ulrich Sternberg
- Research Partner of Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,COSMOS-Software, Jena, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany.
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145
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Hong X, Guan X, Lai Q, Yu D, Chen Z, Fu X, Zhang B, Chen C, Shao Z, Xia J, Qin JJ, Wang W. Characterization of a bioactive meroterpenoid isolated from the marine-derived fungus Talaromyces sp. Appl Microbiol Biotechnol 2022; 106:2927-2935. [PMID: 35416486 DOI: 10.1007/s00253-022-11914-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 02/06/2023]
Abstract
A new meroterpenoid, taladrimanin A (1), was isolated from a marine-derived fungus Talaromyces sp. HM6-1-1, together with eleven biogenetically related compounds (2-12). A plausible biosynthetic pathway for the meroterpenoids (1-4) was proposed. The planar structure of 1 was assigned by HRESIMS and NMR. Its relative configuration was established by quantum chemical NMR calculation of two possible isomers and analyzed by DP4 + method. Finally, X-ray diffraction unambiguously confirmed the relative configuration and revealed the absolute configuration of compound 1. 2-12 were assigned by comparing their NMR data with those reported in the literature. 1 was the first drimane-type meroterpenoid with a C10 polyketide unit bearing an 8R-configuration. In the bioactive assay, 1 exhibited antitumor activity against gastric cancer cells MGC803 and MKN28; it also inhibited the colony formation and induced apoptosis in MGC803 cells both in a concentration-dependent manner. Additionally, 1 displayed selective antibacterial activity against Staphylococcus aureus 6538P, and low activities towards strains of Vibrio parahaemolyticus and Escherichia coli in this study. KEY POINTS: • Twelve compounds were obtained from Talaromyces sp., including four meroterpenoids, one of which was new. • The new compound taladrimanin A (1) inhibits the growth of gastric cancer cells MGC803 and MKN28 as well as the pathogenic bacteria Staphylococcus aureus 6538P. • The biosynthetic pathway of the meroterpenoids was proposed.
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Affiliation(s)
- Xuan Hong
- Fujian Universities and Colleges Engineering Research Center of Marine Biopharmaceutical Resources, Xiamen Medical College, 361023, Xiamen, China
| | - Xiaoqing Guan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China
| | - Dehua Yu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Zhongwei Chen
- Fujian Universities and Colleges Engineering Research Center of Marine Biopharmaceutical Resources, Xiamen Medical College, 361023, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China
| | - Beibei Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China
| | - Changkun Chen
- Fujian Universities and Colleges Engineering Research Center of Marine Biopharmaceutical Resources, Xiamen Medical College, 361023, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China
| | - Jinmei Xia
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China.
| | - Jiang-Jiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
| | - Weiyi Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China.
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146
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Immel S, Köck M, Reggelin M. Bayesian Inference Applied to NMR-Based Configurational Assignments by Floating Chirality Distance Geometry Calculations. J Am Chem Soc 2022; 144:6830-6838. [PMID: 35412312 DOI: 10.1021/jacs.2c00813] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the quality and probability of structural elucidations using Bayesian inference in combination with floating chirality distance geometry simulations. Here, we will discuss the configurational analysis of three complex natural products including isopinocampheol (1), plakilactone H (2), and iodocallophycoic acid A (3) using NMR restraints of various types and in different combinations (residual dipolar couplings (RDCs) and NOE-derived distances). Our results quantitatively demonstrate how reliably molecular geometries can be inferred from experimental NMR data, unequivocally unveiling remaining assignment ambiguities. The methodology presented here can dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data in chemistry.
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Affiliation(s)
- Stefan Immel
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar- and Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Michael Reggelin
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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147
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Pinto BN, Moura GA, Demuner AJ, Alvarenga ES. Structural elucidation of a novel pyrrolizidine alkaloid isolated from Crotalaria retusa L. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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148
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Hayasaka A, Hashimoto K, Konno K, Tanaka K, Hashimoto M. Isolation, Identification, and DFT-based Conformational Analysis of Sesquikarahanadienone and its Congeners from Freshwater Dothideomycetes Neohelicascus aquaticus KT4120. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ayane Hayasaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Kazuki Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Katsuhiro Konno
- Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Kazuaki Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
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149
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Howarth A, Goodman JM. The DP5 probability, quantification and visualisation of structural uncertainty in single molecules. Chem Sci 2022; 13:3507-3518. [PMID: 35432857 PMCID: PMC8943899 DOI: 10.1039/d1sc04406k] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Whenever a new molecule is made, a chemist will justify the proposed structure by analysing the NMR spectra. The widely-used DP4 algorithm will choose the best match from a series of possibilities, but draws no conclusions from a single candidate structure. Here we present the DP5 probability, a step-change in the quantification of molecular uncertainty: given one structure and one 13C NMR spectra, DP5 gives the probability of the structure being correct. We show the DP5 probability can rapidly differentiate between structure proposals indistinguishable by NMR to an expert chemist. We also show in a number of challenging examples the DP5 probability may prevent incorrect structures being published and later reassigned. DP5 will prove extremely valuable in fields such as discovery-driven automated chemical synthesis and drug development. Alongside the DP4-AI package, DP5 can help guide synthetic chemists when resolving the most subtle structural uncertainty. The DP5 system is available at https://github.com/Goodman-lab/DP5.
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Affiliation(s)
- Alexander Howarth
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jonathan M Goodman
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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150
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Marcourt L, Massiot G. The structure of hemicalide from the marine sponge Hemimycale sp. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Georges Massiot
- Université de Reims Champagne-Ardenne: Universite de Reims Champagne-Ardenne chemistry chemin des rouliers 51100 Reims FRANCE
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