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Zhao ZY, Wan J, Chen HW, Sun ZS, Tao YT, Tong Y, Zang Y, Choo YM, Wang P, Li YL, Jiang CX, Li J, Xiong J, Li J, Jin ZX, Hu JF. Major specialized natural products from the endangered plant Heptacodium miconioides, potential medicinal uses and insights into its longstanding unresolved systematic classification. PHYTOCHEMISTRY 2024; 228:114259. [PMID: 39186996 DOI: 10.1016/j.phytochem.2024.114259] [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: 05/23/2024] [Revised: 08/15/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
A comprehensive phytochemical investigation of the flower buds and leaves/twigs of Heptacodium miconioides, a cultivated ornamental plant native to China and categorized as 'vulnerable', has led to the isolation of 45 structurally diverse compounds, which comprise 18 phenylpropanoids (1-4, 7-20), 11 pentacyclic triterpenoids (5, 6, 21-29), eight secoiridoid glycosides (30-37), three quinic acid derivatives (38-40), and a few miscellaneous components (41-45). Among them, (+)-α-intermedianol (1), (+)-holophyllol A (2), and (-)-pseudolarkaemin A (3) represent previously unreported enantiomeric lignans, while (+)-7'(R)-hydroxymatairesinol (4) is an undescribed naturally occurring lignan. Heptacoacids A (5) and B (6) are undescribed 24-nor-urs-28-oic acid derivatives. Their chemical structures were determined by 2D-NMR, supplemented by evidence from specific rotations and circular dichroism spectra. Given the uncertainty surrounding the systematic position of Heptacodium, integrative taxonomy (ITA), a method utilized to define contentious species, is applied. Chemotaxonomy, a vital aspect of ITA, becomes significant. By employing hierarchical clustering analysis (HCA) and syntenic pattern analysis methods, a taxonomic examination based on the major specialized natural products from the flower buds of H. miconioides and two other Caprifoliaceae plants (i.e., Lonicera japonica and Abelia × grandiflora) could offer enhanced understanding of the systematic placement of Heptacodium. Additionally, compounds 39 and 40 displayed remarkable inhibitory activities against ATP-citrate lyase (ACL), with IC50 values of 0.11 and 1.10 μM, respectively. In summary, the discovery of medical properties and refining systematic classification can establish a sturdy groundwork for conservation efforts aimed at mitigating species diversity loss while addressing human diseases.
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Affiliation(s)
- Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiang Wan
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Hao-Wei Chen
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhong-Shuai Sun
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Yu-Tian Tao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Yingpeng Tong
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yeun-Mun Choo
- Chemistry Department, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Pan Wang
- Traditional Chinese Medicine Industry Development and Promotion Center of Pan'an County & Dapanshan National Natural Reserve, Zhejiang, 322300, China
| | - Yue-Ling Li
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Chun-Xiao Jiang
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Junming Li
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ze-Xin Jin
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; School of Pharmacy, Fudan University, Shanghai, 201203, China.
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Coals PGR, Williams VL, Benítez G, Chassagne F, Leonti M. Ethnopharmacology, ethnomedicine, and wildlife conservation. JOURNAL OF ETHNOPHARMACOLOGY 2024; 333:118399. [PMID: 38824978 DOI: 10.1016/j.jep.2024.118399] [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: 01/22/2024] [Revised: 04/16/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE There are longstanding traditions of animal-derived products being employed as medicines, and they continue to be important in many traditional cultural healthcare practices. However, the populations of numerous so-used animals are known to be threatened with extirpation by such practices. Ethnopharmacological studies documenting these animal-derived drugs are not only interesting from an anthropological standpoint, but they are also relevant from a wildlife conservation perspective - especially since ethnopharmacologists are intermediaries between indigenous and scientific communities, placing them at the forefront of being able to ethically access information to address these issues. METHODS Using the example of documenting culturally acceptable substitute materials for animal products (which ultimately also extends to flora), we explore the intersection of ethnopharmacology, biocultural resources, and wildlife conservation. RESULTS Pharmacological efficacy and symbolism are factors influencing the utilization of traditional medicines. Achieving the integration of conservation aims with ethnopharmacology requires a nuanced understanding of both factors, along with fair adjudication when conservation and cultural aims diverge. Ethnopharmacology is suitably placed for making conservation-orientated recommendations - including investigating more sustainable substitutes for animal products in the context of medical efficacy, and for engaging ethically with local communities to facilitate information generation aimed at protecting the environment and their traditions. CONCLUSION We suggest an integrative approach to ethnopharmacological studies investigating medicinal bioresource use. This approach is considerate of species' conservation profiles, the substitutability and pharmacological efficacy of biocultural resources, indigenous and cultural rights, and a collaborative ethos for stakeholder engagement.
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Affiliation(s)
- Peter G R Coals
- School of Animal, Plant & Environmental Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Vivienne L Williams
- School of Animal, Plant & Environmental Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Guillermo Benítez
- Department of Botany, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071, Granada, Spain
| | - François Chassagne
- UMR152 PharmaDev, Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Marco Leonti
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, CA, Italy.
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Zhou PJ, Zhao ZY, Zhu JX, Zang Y, Benjamin MM, Xiong J, Li J, Hu JF. Phytochemical and biological studies on rare and endangered plants endemic to China. Part XXXVI. Tsugaforrestiacids A-O: Structurally diverse C-18 carboxylated diterpenoids from the twigs and needles of the 'vulnerable' conifer Tsuga forrestii and their inhibitory effects on ATP-citrate lyase. PHYTOCHEMISTRY 2024; 226:114221. [PMID: 39002688 DOI: 10.1016/j.phytochem.2024.114221] [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: 04/24/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
An extensive phytochemical investigation on the EtOAc-soluble fraction of the 90% MeOH extract from the twigs and needles of the 'vulnerable' Chinese endemic conifer Tsuga forrestii (Forrest's hemlock) led to the isolation and characterization of 50 structurally diverse diterpenoids, including 15 unreported C-18 carboxylated ones (tsugaforrestiacids A-O, 1-15, resp.). Among them, compounds 1-7 are abieten-18-oic acids, compound 8 is an abieten-18-succinate, and compounds 10-12 are podocarpen-18-oic acids, whereas compounds 13-15 are pimarane-type, isopimarane-type, and totarane-type diterpenoid acids, respectively. Their structures and absolute configurations were determined by a combination of spectroscopic methods, GIAO NMR calculations and DP4+ probability analyses, electronic circular dichroism (ECD) data, and single crystal X-ray diffraction analyses. All the isolates were evaluated for their inhibitory activities against the ATP-citrate lyase (ACL), a key enzyme in cellular metabolism. Tsugaforrestiacids E (5) and H (8) were found to have significant inhibitory effects against ACL, with IC50 values of 5.3 and 6.2 μM, respectively. The interactions of the bioactive molecules with the ACL enzyme were examined by molecular docking studies. The isolated diterpenoids also provide chemotaxonomic evidence to support the delimitation of Tsuga from its closest sister group (Nothotsuga). The above findings highlight the importance of protecting plant species with unique and diverse secondary metabolites, which may be potential sources of new therapeutic agents for the treating ACL-associated diseases.
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Affiliation(s)
- Peng-Jun Zhou
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ze-Yu Zhao
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Jin-Xin Zhu
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, PR China
| | - Menny M Benjamin
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, PR China
| | - Jin-Feng Hu
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
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Chen HW, Yan LH, Wang XJ, Zhao ZY, Wu X, Li J, Lei XS, Xiong J, Hu JF. Undescribed polyketides from endophytes associated with the critically endangered conifer Abies beshanzuensis. Fitoterapia 2024; 177:106104. [PMID: 38950637 DOI: 10.1016/j.fitote.2024.106104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/03/2024]
Abstract
Four undescribed polyketides, beshanzones A (1) and B (2) as well as beshanhexanols A (3) and B (4), along with three known ones (5-7) were isolated from the rice fermentation of two endophytic fungi associated with the critically endangered Chinese endemic conifer Abies beshanzuensis. γ-Butyrolactone derivatives 1, 2, and 5 were isolated from Phomopsis sp. BSZ-AZ-2, an interesting strain that drawn our attention this time. The cyclohexanol derivatives 3, 4, 6, and 7 were obtained during a follow-up investigation on Penicillium commune BSZ-P-4-1. The chemical structures including absolute configurations of compounds 1-4 were determined by spectroscopic methods, Mo2(OAc)4 induced electronic circular dichroism (IECD), GIAO NMR calculations and DP4+ probability analyses. In particular, compound 2 contains a novel 5/5 bicyclic ring system, which might be biogenetically derived from the known compound 5 through hydrolysis followed by an Aldol reaction. All isolates were evaluated for their antimicrobial activities against a small panel of bacterial and fungal pathogens. Compounds 6 and 7 showed moderate inhibitory activities against Candida albicans, with MIC values of 16 and 32 μg/mL, respectively.
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Affiliation(s)
- Hao-Wei Chen
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Li-Hong Yan
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China
| | - Xue-Jiao Wang
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ze-Yu Zhao
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xiying Wu
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Jiyang Li
- School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xin-Sheng Lei
- School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| | - Jin-Feng Hu
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China.
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Davis CC, Choisy P. Medicinal plants meet modern biodiversity science. Curr Biol 2024; 34:R158-R173. [PMID: 38412829 DOI: 10.1016/j.cub.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study of medicinal plants that combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, and ethnopharmacology - is poised to facilitate new breakthroughs in science, including pharmacological discoveries and rapid advancements in human health and well-being. Such interdisciplinary research leverages data and methods spanning space, time, and species associated with medicinal plant species evolution, ecology, genomics, and metabolomic trait diversity, all of which build heavily on traditional Indigenous knowledge. Such an interdisciplinary approach contrasts sharply with most well-funded and successful medicinal plant research during the last half-century, which, despite notable advancements, has greatly oversimplified the dynamic relationships between plants and humans, kept hidden the larger human narratives about these relationships, and overlooked potentially important research and discoveries into life-saving medicines. We suggest that medicinal plants and people should be viewed as partners whose relationship involves a complicated and poorly explored set of (socio-)ecological interactions including not only domestication but also commensalisms and mutualisms. In short, medicinal plant species are not just chemical factories for extraction and exploitation. Rather, they may be symbiotic partners that have shaped modern societies, improved human health, and extended human lifespans.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Patrick Choisy
- LVMH Research, 185 Avenue de Verdun, 45804 Saint Jean de Braye CEDEX, France
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Hou D, Lin H, Feng Y, Zhou K, Li X, Yang Y, Wang S, Yang X, Wang J, Zhao H, Zhang X, Fan J, Lu S, Wang D, Zhu L, Ju D, Chen YZ, Zeng X. CMAUP database update 2024: extended functional and association information of useful plants for biomedical research. Nucleic Acids Res 2024; 52:D1508-D1518. [PMID: 37897343 PMCID: PMC10767869 DOI: 10.1093/nar/gkad921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023] Open
Abstract
Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21-107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.
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Affiliation(s)
- Dongyue Hou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hanbo Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuhan Feng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Kaicheng Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xingxiu Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuan Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Shuaiqi Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xue Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiayu Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hui Zhao
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiajun Fan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - SongLin Lu
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Dan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Lyuhan Zhu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yu Zong Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
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Yang J, Wu Y, Zhang P, Ma J, Yao YJ, Ma YL, Zhang L, Yang Y, Zhao C, Wu J, Fang X, Liu J. Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family. Nat Commun 2023; 14:8457. [PMID: 38114555 PMCID: PMC10730914 DOI: 10.1038/s41467-023-44246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Hyoscyamine and scopolamine (HS), two valuable tropane alkaloids of significant medicinal importance, are found in multiple distantly related lineages within the Solanaceae family. Here we sequence the genomes of three representative species that produce HS from these lineages, and one species that does not produce HS. Our analysis reveals a shared biosynthetic pathway responsible for HS production in the three HS-producing species. We observe a high level of gene collinearity related to HS synthesis across the family in both types of species. By introducing gain-of-function and loss-of-function mutations at key sites, we confirm the reduced/lost or re-activated functions of critical genes involved in HS synthesis in both types of species, respectively. These findings indicate independent and repeated losses of the HS biosynthesis pathway since its origin in the ancestral lineage. Our results hold promise for potential future applications in the artificial engineering of HS biosynthesis in Solanaceae crops.
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Affiliation(s)
- Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Jun Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Lin Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, Ningxia, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Changmin Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jihua Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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Simoben CV, Babiaka SB, Moumbock AFA, Namba-Nzanguim CT, Eni DB, Medina-Franco JL, Günther S, Ntie-Kang F, Sippl W. Challenges in natural product-based drug discovery assisted with in silico-based methods. RSC Adv 2023; 13:31578-31594. [PMID: 37908659 PMCID: PMC10613855 DOI: 10.1039/d3ra06831e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The application of traditional medicine by humans for the treatment of ailments as well as improving the quality of life far outdates recorded history. To date, a significant percentage of humans, especially those living in developing/underprivileged communities still rely on traditional medicine for primary healthcare needs. In silico-based methods have been shown to play a pivotal role in modern pharmaceutical drug discovery processes. The application of these methods in identifying natural product (NP)-based hits has been successful. This is very much observed in many research set-ups that use rationally in silico-based methods in combination with experimental validation techniques. The combination has rendered the use of in silico-based approaches even more popular and successful in the investigation of NPs. However, identifying and proposing novel NP-based hits for experimental validation comes with several challenges such as the availability of compounds by suppliers, the huge task of separating pure compounds from complex mixtures, the quantity of samples available from the natural source to be tested, not to mention the potential ecological impact if the natural source is exhausted. Because most peer-reviewed publications are biased towards "positive results", these challenges are generally not discussed in publications. In this review, we highlight and discuss these challenges. The idea is to give interested scientists in this field of research an idea of what they can come across or should be expecting as well as prompting them on how to avoid or fix these issues.
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Affiliation(s)
- Conrad V Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Smith B Babiaka
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen 72076 Tübingen Germany
| | - Aurélien F A Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Freiburg Germany
| | - Cyril T Namba-Nzanguim
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
| | - Donatus Bekindaka Eni
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000 Mexico City 04510 Mexico
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Freiburg Germany
| | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg Halle (Saale) Germany
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9
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Moyo P, Invernizzi L, Mianda SM, Rudolph W, Andayi WA, Wang M, Crouch NR, Maharaj VJ. Leveraging off higher plant phylogenetic insights for antiplasmodial drug discovery. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:35. [PMID: 37798547 PMCID: PMC10555984 DOI: 10.1007/s13659-023-00396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/03/2023] [Indexed: 10/07/2023]
Abstract
The antimalarial drug-resistance conundrum which threatens to reverse the great strides taken to curb the malaria scourge warrants an urgent need to find novel chemical scaffolds to serve as templates for the development of new antimalarial drugs. Plants represent a viable alternative source for the discovery of unique potential antiplasmodial chemical scaffolds. To expedite the discovery of new antiplasmodial compounds from plants, the aim of this study was to use phylogenetic analysis to identify higher plant orders and families that can be rationally prioritised for antimalarial drug discovery. We queried the PubMed database for publications documenting antiplasmodial properties of natural compounds isolated from higher plants. Thereafter, we manually collated compounds reported along with plant species of origin and relevant pharmacological data. We systematically assigned antiplasmodial-associated plant species into recognised families and orders, and then computed the resistance index, selectivity index and physicochemical properties of the compounds from each taxonomic group. Correlating the generated phylogenetic trees and the biological data of each clade allowed for the identification of 3 'hot' plant orders and families. The top 3 ranked plant orders were the (i) Caryophyllales, (ii) Buxales, and (iii) Chloranthales. The top 3 ranked plant families were the (i) Ancistrocladaceae, (ii) Simaroubaceae, and (iii) Buxaceae. The highly active natural compounds (IC50 ≤ 1 µM) isolated from these plant orders and families are structurally unique to the 'legacy' antimalarial drugs. Our study was able to identify the most prolific taxa at order and family rank that we propose be prioritised in the search for potent, safe and drug-like antimalarial molecules.
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Affiliation(s)
- Phanankosi Moyo
- Biodiscovery Center, Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X 20, Hatfield, Pretoria, 0028, South Africa
| | - Luke Invernizzi
- Biodiscovery Center, Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X 20, Hatfield, Pretoria, 0028, South Africa
| | - Sephora M Mianda
- Biodiscovery Center, Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X 20, Hatfield, Pretoria, 0028, South Africa
| | - Wiehan Rudolph
- Biodiscovery Center, Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X 20, Hatfield, Pretoria, 0028, South Africa
| | - Warren A Andayi
- Department of Physical and Biological Sciences, Murang'a University of Technology, Murang'a, Kenya
| | - Mingxun Wang
- Computer Science and Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Neil R Crouch
- Biodiversity Research and Monitoring Directorate, South African National Biodiversity Institute, Berea Road, P.O. Box 52099, Durban, 4007, South Africa
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Vinesh J Maharaj
- Biodiscovery Center, Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X 20, Hatfield, Pretoria, 0028, South Africa.
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10
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Feng X, Dong Z, Li Y, Cheng Q, Xin Y, Lu Q, Xin R. MSFC: a new feature construction method for accurate diagnosis of mass spectrometry data. Sci Rep 2023; 13:15694. [PMID: 37735183 PMCID: PMC10514077 DOI: 10.1038/s41598-023-42395-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/09/2023] [Indexed: 09/23/2023] Open
Abstract
Mass spectrometry technology can realize dynamic detection of many complex matrix samples in a simple, rapid, compassionate, precise, and high-throughput manner and has become an indispensable tool in accurate diagnosis. The mass spectrometry data analysis is mainly to analyze all metabolites in the organism quantitatively and to find the relative relationship between metabolites and physiological and pathological changes. A feature construction of mass spectrometry data (MSFS) method is proposed to construct the features of the original mass spectrometry data, so as to reduce the noise in the mass spectrometry data, reduce the redundancy of the original data and improve the information content of the data. Chi-square test is used to select the optimal non-redundant feature subset from high-dimensional features. And the optimal feature subset is visually analyzed and corresponds to the original mass spectrum interval. Training in 10 kinds of supervised learning models, and evaluating the classification effect of the models through various evaluation indexes. Taking two public mass spectrometry datasets as examples, the feasibility of the method proposed in this paper is verified. In the coronary heart disease dataset, during the identification process of mixed batch samples, the classification accuracy on the test set reached 1.000; During the recognition process, the classification accuracy on the test set advanced to 0.979. On the colorectal liver metastases data set, the classification accuracy on the test set reached 1.000. This paper attempts to use a new raw mass spectrometry data preprocessing method to realize the alignment operation of the raw mass spectrometry data, which significantly improves the classification accuracy and provides another new idea for mass spectrometry data analysis. Compared with MetaboAnalyst software and existing experimental results, the method proposed in this paper has obtained better classification results.
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Affiliation(s)
- Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin, 130000, People's Republic of China
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Zheyuan Dong
- College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin, 130000, People's Republic of China
| | - Yingrui Li
- College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin, 130000, People's Republic of China
| | - Qian Cheng
- College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin, 130000, People's Republic of China
| | - Yongxian Xin
- College of Business and Economics, Australian National University, Canberra, ACT, 2601, Australia
| | - Qiaolin Lu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, People's Republic of China
| | - Ruihao Xin
- College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin, 130000, People's Republic of China.
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, People's Republic of China.
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11
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Chen HW, Jiang CX, Ma GL, Wu XY, Jiang W, Li J, Zang Y, Li J, Xiong J, Hu JF. Unprecedented spirodioxynaphthalenes from the endophytic fungus Phyllosticta ligustricola HDF-L-2 derived from the endangered conifer Pseudotsuga gaussenii. PHYTOCHEMISTRY 2023; 211:113687. [PMID: 37105348 DOI: 10.1016/j.phytochem.2023.113687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Four undescribed palmarumycin-type spirodioxynaphthalenes (phyligustricins A-D) and a known biogenetic precursor (palmarumycin BG1) were isolated from a solid fermentation of Phyllosticta ligustricola HDF-L-2, an endophyte associated with the endangered Chinese conifer Pseudotsuga gaussenii. The structures were elucidated by spectroscopic methods, single-crystal X-ray diffraction analyses, and electronic circular dichroism calculations. Both phyligustricins A and B have an unprecedented spirodioxynaphthalene-derived skeleton containing an extra 4H-furo [3,2-c]pyran-4-one moiety, while phyligustricins C and D are p-hydroxy-phenethyl substituted spirodioxynaphthalenes. The plausible biosynthetic relationships of the isolates were briefly proposed. Phyligustricins C and D and palmarumycin BG1 showed considerable antibacterial activity against Staphylococcus aureus, each with an MIC value of 16 μg/mL. Palmarumycin BG1 displayed significant inhibitory effects against ACL and ACC1, with IC50 values of 1.60 and 8.00 μM, respectively.
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Affiliation(s)
- Hao-Wei Chen
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Chun-Xiao Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, PR China
| | - Guang-Lei Ma
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Xi-Ying Wu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Wei Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Jiyang Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, PR China.
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12
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Zhao ZY, Tong YP, Jiang W, Zang Y, Xiong J, Li J, Hu JF. Structurally Diverse Triterpene-26-oic Acids as Potential Dual ACL and ACC1 Inhibitors from the Vulnerable Conifer Keteleeria fortunei. JOURNAL OF NATURAL PRODUCTS 2023; 86:1487-1499. [PMID: 37291059 DOI: 10.1021/acs.jnatprod.3c00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A preliminary phytochemical investigation on the 90% MeOH extract from the twigs and needles of the vulnerable conifer Keteleeria fortunei led to the isolation and characterization of 17 structurally diverse triterpen-26-oic acids, including nine previously undescribed ones (fortunefuroic acids A-I, 1-9) featuring a rare furoic acid moiety in the lateral chain. Among them, 1-5 are uncommon 9βH-lanostane-type triterpenoic acids. Friedo-rearranged triterpenoids 6 and 7 feature a unique 17,14-friedo-lanostane skeleton, whereas 9 possesses a rare 17,13-friedo-cycloartane-type framework. Their structures and absolute configurations were elucidated by extensive spectroscopic (e.g., detailed 2D NMR) and computational (NMR/ECD) calculations and the modified Mosher's method. In addition, the absolute structure of compound 1 was ascertained by single-crystal X-ray diffraction analyses. Fortunefuroic acids B (2), G (7), and I (9), along with isomangiferolic acid (12) and 3α,27-dihydroxycycloart-24E-en-26-oic acid (14), exhibited dual inhibitory effects against the adenosine triphosphate (ATP)-citrate lyase (ACL, IC50s: 5.7-11.4 μM) and acetyl-CoA carboxylase 1 (ACC1, IC50s: 7.5-10.5 μM), both of which are key enzymes for glycolipid metabolism. The interactions of the bioactive triterpenoids with both enzymes were examined by molecular docking studies. The above findings reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics for ACL-/ACC1-associated diseases.
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Affiliation(s)
- Ze-Yu Zhao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
| | - Ying-Peng Tong
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
| | - Wei Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei 430023, People's Republic of China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, People's Republic of China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, People's Republic of China
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
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13
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Liang KY, Li H, Zhou PJ, Zhao ZY, Zang Y, Xiong J, Li J, Hu JF. Squamabietenols A-F, undescribed abietane-O-abietane dimeric diterpenoids from the ornamental conifer Juniperus squamata and their ATP-citrate lyase inhibitory activities. PHYTOCHEMISTRY 2023; 210:113663. [PMID: 36990194 DOI: 10.1016/j.phytochem.2023.113663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Six undescribed naturally occurring abietane-O-abietane dimers (squamabietenols A-F) together with one 3,4-seco-totarane-type, a pimarane-type, and 17 related known mono-/dimeric diterpenoids were isolated and characterized from the needles and twigs of the ornamental conifer Juniperus squamata. The undescribed structures and their absolute configurations were established by extensive spectroscopic methods, GIAO NMR calculations with DP4+ probability analyses, and ECD calculations. Squamabietenols A and B showed significant inhibitory effects against ATP-citrate lyase (ACL, a novel drug target for hyperlipidemia and other metabolic disorders), with IC50 values of 8.82 and 4.49 μM, respectively. A molecular docking study corroborated the findings by highlighting the interactions between the bioactive compounds and the ACL enzyme (binding affinities: -7.1 to -9.0 kcal/mol). The unique abietane-O-abietane dimeric diterpenoids are quite rare in the vegetable kingdom, and they are of chemotaxonomic significance for the Cupressaceae family.
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Affiliation(s)
- Kai-Yuan Liang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China
| | - Hao Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Peng-Jun Zhou
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China
| | - Ze-Yu Zhao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China.
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14
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Wu X, Ma GL, Chen HW, Zhao ZY, Zhu ZP, Xiong J, Yang GX, Hu JF. Antibacterial and antibiofilm efficacy of the preferred fractions and compounds from Euphorbia humifusa (herba euphorbiae humifusae) against Staphylococcus aureus. JOURNAL OF ETHNOPHARMACOLOGY 2023; 306:116177. [PMID: 36681167 DOI: 10.1016/j.jep.2023.116177] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/07/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Euphorbia humifusa Willd., known as Di-Jin-Cao in Chinese, has long been utilized as a traditional herb for the treatment of furuncles and carbuncles mainly caused by Staphylococcus aureus infection. Despite extensive chemical and pharmacological studies reported previously for E. humifusa, the antibacterial and antibiofilm activities against S. aureus as well as the related mechanism of action (MoA) remain largely obscure. AIM OF THE STUDY To investigate the antibacterial and antibiofilm activities of the preferred fractions and compounds from E. humifusa against S. aureus and assess the associated MoA. MATERIALS AND METHODS The bioactive fractions and compounds were obtained from the 75% ethanol extract of E. humifusa (75%-EEEH) with the assistance of the related antibacterial and antibiofilm screening. Their antibacterial activities were determined using the broth microdilution method, whilst the inhibition of biofilm formation and the disruption of preformed biofilm were assessed by crystal violet staining and confocal laser scanning microscopy (CLSM). To achieve more effective therapies, the combinatory effects of different components were also studied. The biofilm metabolic activities of isolated compounds were evaluated by 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) reduction assay. The scanning electron microscopy (SEM) and quantitative real-time polymerase chain reaction (qRT-PCR) were employed to explore the antibiofilm mechanism. RESULTS Fractions DJC06 and DJC07 collected from the ethyl acetate extract of the 75%-EEEH exhibited antibacterial activity (MIC = 256 μg/mL) against S. aureus and further separation of these two fractions led to the isolation and characterization of 22 compounds. Among the isolates, luteolin (LU), quercetin (QU), and kaempferol (KA) are the verified components associated with the antibacterial and antibiofilm activities by displaying individual or combinational MIC values of 8-128 μg/mL and 70.9-99.7% inhibition for biofilm formation. Importantly, QU and KA can work in synergy with LU to significantly enhance the efficacy via destroying cell integrity, increasing membrane permeability, and down-regulating the biofilm-related gene expression. CONCLUSIONS The preferred fractions and compounds from E. humifusa exerted desired antibacterial and antibiofilm efficacy against S. aureus via a MoA involving cell morphology disruption and altered genes expression. The findings herein not only support its traditional use in the treatment of furuncles and carbuncles, but reveal E. humifusa is a potential source for producing promising antibiofilm alternatives against S. aureus and highlight the isolated components (LU, QU, KA) that can potentiate the efficacy when used in synergy.
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Affiliation(s)
- Xiying Wu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China; Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, 200443, China
| | - Guang-Lei Ma
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Hao-Wei Chen
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zi-Ping Zhu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Guo-Xun Yang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang, 318000, China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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15
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Xu H, Zhang W, Zhou Y, Yue Z, Yan T, Zhang Y, Liu Y, Hong Y, Liu S, Zhu F, Tao L. Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics. J Chem Inf Model 2023; 63:1615-1625. [PMID: 36795011 DOI: 10.1021/acs.jcim.2c01459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Natural products (NPs) have long been associated with human production and play a key role in the survival of species. Significant variations in NP content may severely affect the "return on investment" of NP-based industries and render ecological systems vulnerable. Thus, it is crucial to construct a platform that relates variations in NP content to their corresponding mechanisms. In this study, a publicly accessible online platform, NPcVar (http://npcvar.idrblab.net/), was developed, which systematically described the variations of NP contents and their corresponding mechanisms. The platform comprises 2201 NPs and 694 biological resources, including plants, bacteria, and fungi, curated using 126 diverse factors with 26,425 records. Each record contains information about the species, NP, and factors involved, as well as NP content data, parts of the plant that produce NPs, the location of the experiment, and reference information. All factors were manually curated and categorized into 42 classes which belong to four mechanisms (molecular regulation, species factor, environmental condition, and combined factor). Additionally, the cross-links of species and NP to well-established databases and the visualization of NP content under various experimental conditions were provided. In conclusion, NPcVar is a valuable resource for understanding the relationship between species, factors, and NP contents and is anticipated to serve as a promising tool for improving the yield of high-value NPs and facilitating the development of new therapeutics.
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Affiliation(s)
- Hongquan Xu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Wei Zhang
- The Second Affiliated Hospital, Zhejiang University School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Zixuan Yue
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Tianci Yan
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuanyuan Zhang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yanfeng Hong
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Shuiping Liu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Feng Zhu
- The Second Affiliated Hospital, Zhejiang University School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
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16
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Schmaltz S, Silva MA, Ninaus RG, Guedes JVC, Zabot GL, Tres MV, Mazutti MA. Biomolecules in modern and sustainable agriculture. 3 Biotech 2023; 13:70. [PMID: 36742447 PMCID: PMC9889597 DOI: 10.1007/s13205-023-03486-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
This review presents scientific findings which indicate biomolecules are excellent candidates for the development of biopesticides. Efforts are being done to find routes to increase their concentrations in the cultivation media because this concentration facilitates applications, storage, and transportation. Some of these routes are co-fermentation and ultrasound-assisted fermentation. Ultrasonication increases metabolite production and growth rates by improvement of cell permeability and nutrient uptake rates through cell membranes. For example, 24% increase in the enzymatic activity of cellulases produced by Trichoderma reesei in solid-state fermentation was achieved with ultrasonication. Also, chitinase and β-1,3-glucanase productions were stimulated by ultrasound in Beauveria bassiana cultivation, presenting positive results. The common parameters evaluated in the production of biomolecules by ultrasound-assisted fermentation are the duty cycle, time of application, power, energetic density, and how long the sonication is maintained in the fermentation media. Many successful cases are reported and discussed, which include the final formulation of bioproducts for agricultural applications. In this trend, nanotechnology is a promising tool for the development of nanoformulations. Nanoemulsification, green synthesis, biosynthesis, or biogenic synthesis are technologies used to produce such nanoformulations, allowing the controlled release of control agents, as well as the delivery of biomolecules to specific targets.
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Affiliation(s)
- Silvana Schmaltz
- Department of Chemical Engineering, Federal University of Santa Maria, 1000, Roraima Avenue, Santa Maria, RS 97105-900 Brazil
| | - Marco Antônio Silva
- São Carlos School of Engineering, University of São Paulo, 400, Trabalhador São-Carlense Avenue, São Carlos, SP 13566-590 Brazil
| | - Renata Gulart Ninaus
- Department of Chemical Engineering, Federal University of Santa Maria, 1000, Roraima Avenue, Santa Maria, RS 97105-900 Brazil
| | - Jerson Vanderlei Carus Guedes
- Department of Plant Protection, Federal University of Santa Maria, 1000, Roraima Avenue, Santa Maria, RS 97105-900 Brazil
| | - Giovani Leone Zabot
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria, 1040, Sete de Setembro St., Center DC, Cachoeira Do Sul, RS 96508-010 Brazil
| | - Marcus Vinícius Tres
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria, 1040, Sete de Setembro St., Center DC, Cachoeira Do Sul, RS 96508-010 Brazil
| | - Marcio Antonio Mazutti
- Department of Chemical Engineering, Federal University of Santa Maria, 1000, Roraima Avenue, Santa Maria, RS 97105-900 Brazil
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Awada B, Chahine DA, Derbaj G, Khalek PA, Awad MK, Fayad AA. Antimicrobial Natural Products Derived from Microorganisms Inhabiting the MENA Region. Nat Prod Commun 2023. [DOI: 10.1177/1934578x231154989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Objective/Background Natural products (NPs) derived from microorganisms are the basis of a plethora of clinically utilized medications, namely, antimicrobial remedies. Although these secondary metabolites have been extensively explored all over the planet, they remain understudied in the Middle East and North Africa (MENA) region. Methods A literature search was conducted to first find NPs that were isolated from environmental fungi and bacteria that inhabit the soils and seawater of the MENA region. Then, purified molecules with biological activity against pathogenic bacteria, biofilms, fungi, and parasites were described in terms of structure, function, and location. Moreover, the methods that could be used to ameliorate the discovery of novel NPs from this region were investigated. Results A multitude of antimicrobial molecules from various chemical classes were found to be derived from the environmental microbes of MENA. Although many were rediscovered, some represented novel structural scaffolds for novel families of antimicrobial agents. Additionally, the geographical distribution showed a high number of these NPs were unraveled in a restricted area leaving much of MENA untapped. Furthermore, as relatively traditional and low-efficiency methods were typically used in the discovery process, advanced high-throughput techniques were suggested to enhance this practice at the regional level. Conclusion MENA represents a fairly unexploited region where antimicrobial drug discovery could be performed comprehensively through the concomitant exploration of untouched geographical locations and advanced molecular techniques.
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Affiliation(s)
- Bassel Awada
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Dany Abi Chahine
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
- Laboratory of Biodiversity and Functional Genomics, UR EGP, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Ghada Derbaj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Pascal Abdel Khalek
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Mireille Kallassy Awad
- Laboratory of Biodiversity and Functional Genomics, UR EGP, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Antoine Abou Fayad
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
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18
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Liu J, Li JJ, Yan YM, Bai M, Cheng YX. COX-2 and iNOS inhibitory abietane diterpenoids from Pinus yunnanensis exudates. Fitoterapia 2023; 164:105376. [PMID: 36450314 DOI: 10.1016/j.fitote.2022.105376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Pinuskesiols A-F (1-6), six new structurally diverse abietane diterpenoids were isolated from Pinus yunnanensis resins. Their structures including absolute configurations were characterized by using spectroscopic and computational methods. All the compounds bear a carbonyl functionality at C-4 with 1 and 2 behaving as a lactone thereof. The isopropyl group is attached to C-13 via O-atom in 3. In addition, the presence of a Δ5(6) double bond and a ketone at C-7 makes 2 a large conjugated system. Biological evaluation revealed that 1, 2, and 4 could concentration-dependently inhibit iNOS and COX-2 expression in lipopolysaccharide-induced RAW 264.7 cells with 2 to be the most active toward COX-2 inhibition.
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Affiliation(s)
- Jing Liu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, PR China; Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Ji-Jun Li
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Yong-Ming Yan
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Ming Bai
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, PR China.
| | - Yong-Xian Cheng
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, PR China; Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China.
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19
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Hussain A. A phylogenetic perspective of antiviral species of the genus Artemisia (Asteraceae-Anthemideae): A proposal of anti SARS-CoV-2 (COVID-19) candidate taxa. J Herb Med 2022; 36:100601. [PMID: 36188629 PMCID: PMC9514968 DOI: 10.1016/j.hermed.2022.100601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/22/2022] [Accepted: 09/21/2022] [Indexed: 01/11/2023]
Abstract
Introduction Different classes of disease-causing viruses are widely distributed universally. Plant-based medicines are anticipated to be effective cures for viral diseases including the COVID-19, instigated by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). This study displays the phylogenetic perspective of Artemisia and proposes some candidate taxa against different viral diseases, including SARS-CoV-2. Methods Data of Artemisia with antiviral activity were obtained from different published sources and electronic searches. A phylogenetic analysis of the nrDNA ITS sequences of reported antiviral Artemisia species, along with the reference species retrieved from the NCBI GenBank database, was performed using the maximum likelihood (ML) approach. Results In total, 23 Artemisia species have been documented so far with antiviral activity for 17 different types of viral diseases. 17 out of 23 antiviral Artemisia species were included in the ITS phylogeny, which presented the distribution of these antiviral Artemisia species in clades corresponding to different subgenera of the genus Artemisia. In the resultant ML tree, 10 antiviral Artemisia species appeared within the subgenus Artemisia clade, 2 species appeared within the subgenus Absinthium clade, 3 species appeared within the subgenus Dracunculus clade, and 2 species appeared within the subgenus Seriphidium clade. Discussion Artemisia species from different subgenera with antiviral activity are prevalent in the genus, with most antiviral species belonging to the subgenus Artemisia. A detailed analysis of taxa from all subgenera, particularly the subgenus Artemisia, is therefore proposed in order to discover compounds with potential anti-SARS-CoV-2 activity.
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Key Words
- Antiviral activity
- Artemisia
- Asteraceae
- BVD, Bovine viral diarrhea virus
- COVID-19
- Candidate taxa
- DEN 2, Dengue virus type 2
- FCV, Feline calci virus
- FIV, Feline immunodeficiency virus
- HBV, Hepatitis B virus
- HBeAg, Hepatitis B e-antigen
- HBsAg, Hepatitis B surface antigen
- HCV, Hepatitis C virus
- HHV (HSV), Human alphaherpesvirus (Herpes simplex virus)
- HHV-4 (EBV), Human gammaherpesvirus type 4 (Epstein-Barr virus)
- HIV-, Human immunodeficiency virus
- HeLa, Henrietta Lacks cells
- ITS Phylogeny
- IV, Influenza virus
- JUN V, Junin virus
- MDBK, Madin-Darby bovine kidney cells
- MDCK, Madin-Darby canine kidney cells
- MNV, Murine norovirus
- MTTA, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide assay
- NDV, Newcastle disease virus
- PV, Polio virus
- SARS CoV2, Severe acute respiratory syndrome corona virus 2
- SARS-CoV-2
- SV, Sindbis virus
- VERO, Verda reno cells
- YFV, Yellow fever virus
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20
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Wang H, He Y, Jian M, Fu X, Cheng Y, He Y, Fang J, Li L, Zhang D. Breaking the Bottleneck in Anticancer Drug Development: Efficient Utilization of Synthetic Biology. Molecules 2022; 27:7480. [PMID: 36364307 PMCID: PMC9656990 DOI: 10.3390/molecules27217480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 08/13/2024] Open
Abstract
Natural products have multifarious bioactivities against bacteria, fungi, viruses, cancers and other diseases due to their diverse structures. Nearly 65% of anticancer drugs are natural products or their derivatives. Thus, natural products play significant roles in clinical cancer therapy. With the development of biosynthetic technologies, an increasing number of natural products have been discovered and developed as candidates for clinical cancer therapy. Here, we aim to summarize the anticancer natural products approved from 1950 to 2021 and discuss their molecular mechanisms. We also describe the available synthetic biology tools and highlight their applications in the development of natural products.
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Affiliation(s)
- Haibo Wang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yu He
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Meiling Jian
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Xingang Fu
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yuheng Cheng
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yujia He
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Jun Fang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Lin Li
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Dan Zhang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
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21
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Jiang W, Zhao ZY, Tong YP, Ma GL, Zang Y, Osman EEA, Jin ZX, Xiong J, Li J, Hu JF. Phytochemical and biological studies on rare and endangered plants endemic to China. Part XXV. Structurally diverse triterpenoids and diterpenoids from two endangered Pinaceae plants endemic to the Chinese Qinling Mountains and their bioactivities. PHYTOCHEMISTRY 2022; 203:113366. [PMID: 35970438 DOI: 10.1016/j.phytochem.2022.113366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
A joint phytochemical investigation on the MeOH extracts of the twigs and needles of two endangered Pinaceae plants endemic to the Chinese Qinling Mountains, Picea neoveitchii (an evergreen spruce) and Larix potaninii var. chinensis (a deciduous larch), led to the isolation and characterization of 34 and 24 structurally diverse terpenoids, respectively. Among them, seven are previously undescribed, including a picane-type [i.e., 14(13 → 12)abeo-12αH-serratane] (neoveitchin A) and a serratane-type (neoveitchin B) triterpenoids, and an abietane-type (neoveitchin C) as well as four labdane-type (potalarxins A-D) diterpenoids. Their structures and absolute configurations were established by extensive spectroscopic methods and/or X-ray diffraction analyses. All isolates were evaluated for their inhibitory activities against the human protein tyrosine phosphatase 1B (PTP1B). Serrat-14-en-3α,21β-diol, betulinic acid, 3β-hydroxy-11-ursen-13(28)-olide, ursolic acid, and oleanolic acid were found to have considerable inhibitory effects against PTP1B, with IC50 values ranging from 1.1 to 18.1 μM. The interactions of the bioactive triterpenoids with PTP1B were thereafter performed by employing molecular docking studies. In addition, 7-oxo-dehydroabietic acid (an abietane-type diterpenoid) and mangiferonic acid (a cycloartane-type triterpenoid) inhibited acetyl-coenzyme A carboxylase 1 (ACC1), with IC50 values of 3.4 and 6.6 μM, respectively.
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Affiliation(s)
- Wei Jiang
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China; School of Life Science and Technology, Wuhan Polytechnic University, Hubei, 430023, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Ying-Peng Tong
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China
| | - Guang-Lei Ma
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Ezzat E A Osman
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; Department of Biochemistry, Molecular Biology and Medicinal Chemistry, Theodor Bilharz Research Institute, P. O. Box 30 Imbaba, Giza, 12411, Egypt
| | - Ze-Xin Jin
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
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22
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Wagemans J, Panda SK, Crauwels S, Lood C, Lievens B, Lavigne R, Luyten W. Identification of Spoilage Bacteria in Non-Food Products and Their Inhibition Using Botanical Extracts. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:13805-13815. [DOI: 10.1021/acssuschemeng.2c04174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Affiliation(s)
| | - Sujogya Kumar Panda
- Center of Environment, Climate Change and Public Health, RUSA 2.0, Utkal University, Bhubaneswar 751004, India
- Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Sam Crauwels
- Department of Microbial and Molecular Systems, KU Leuven, Leuven 3001, Belgium
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven 3001, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven 3001, Belgium
| | - Bart Lievens
- Department of Microbial and Molecular Systems, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven 3001, Belgium
| | - Walter Luyten
- Department of Biology, KU Leuven, Leuven 3000, Belgium
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23
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Awada B, Hamie M, El Hajj R, Derbaj G, Najm R, Makhoul P, Ali DH, Abou Fayad AG, El Hajj H. HAS 1: A natural product from soil-isolated Streptomyces species with potent activity against cutaneous leishmaniasis caused by Leishmania tropica. Front Pharmacol 2022; 13:1023114. [PMID: 36299890 PMCID: PMC9589300 DOI: 10.3389/fphar.2022.1023114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/26/2022] [Indexed: 01/19/2023] Open
Abstract
Cutaneous Leishmaniasis (CL) is a neglected tropical disease, classified by the World Health Organization (WHO) as one of the most unrestrained diseases. The Syrian war and the significant displacement of refugees aggravated the spread of this ailment into several neighboring countries in the Eastern Mediterranean Region (EMR). In Syria, Leishmania tropica is identified as one of the most aggressive and endemic identified species, causing localized or generalized lesions, often chronic or relapsing. Pentavalent antimonial drugs are currently used as first line treatment against CL. Nonetheless, these drugs exhibit several limitations, including the repetitive painful injections, high cost, poor availability, and mainly systemic toxicity. Besides, the emergence of acquired parasitic resistance hinders their potency, stressing the need for new therapies to combat CL. Natural products (NPs) epitomize a valuable source in drug discovery. NPs are secondary metabolites (SMs) produced by plants, sponges, or a wide variety of organisms, including environmental microorganisms. The EMR is characterized by its immense biodiversity, yet it remains a relatively untapped area in drug discovery. NPs of the region were explored over the last 2 decades, but their discoveries lack biogeographical diversity and are limited to the Red Sea. Here, we isolated previously uncultured environmental soil-dwelling Streptomyces sp. HAS1, from Hasbaya region in southeast Lebanon. When fermented in one of our production media named INA, HAS1 produced a crude extract with significant potency against a clinical Leishmania tropica isolate. Using bio-guided fractionation, the bioactive compound was purified and the structure was elucidated by NMR and LC-HRMS. Our findings establish NPs as strong candidates for treating Leishmania tropica and further dwells on the importance of these natural sources to combat microbial infections.
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Affiliation(s)
- Bassel Awada
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Maguy Hamie
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Rana El Hajj
- Department of Biological Sciences, Beirut Arab University, Beirut, Lebanon
| | - Ghada Derbaj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Rania Najm
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Perla Makhoul
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Dima Hajj Ali
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Antoine G. Abou Fayad
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
- *Correspondence: Antoine G. Abou Fayad, ; Hiba El Hajj,
| | - Hiba El Hajj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
- *Correspondence: Antoine G. Abou Fayad, ; Hiba El Hajj,
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24
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Pirintsos S, Panagiotopoulos A, Bariotakis M, Daskalakis V, Lionis C, Sourvinos G, Karakasiliotis I, Kampa M, Castanas E. From Traditional Ethnopharmacology to Modern Natural Drug Discovery: A Methodology Discussion and Specific Examples. Molecules 2022; 27:4060. [PMID: 35807306 PMCID: PMC9268545 DOI: 10.3390/molecules27134060] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Ethnopharmacology, through the description of the beneficial effects of plants, has provided an early framework for the therapeutic use of natural compounds. Natural products, either in their native form or after crude extraction of their active ingredients, have long been used by different populations and explored as invaluable sources for drug design. The transition from traditional ethnopharmacology to drug discovery has followed a straightforward path, assisted by the evolution of isolation and characterization methods, the increase in computational power, and the development of specific chemoinformatic methods. The deriving extensive exploitation of the natural product chemical space has led to the discovery of novel compounds with pharmaceutical properties, although this was not followed by an analogous increase in novel drugs. In this work, we discuss the evolution of ideas and methods, from traditional ethnopharmacology to in silico drug discovery, applied to natural products. We point out that, in the past, the starting point was the plant itself, identified by sustained ethnopharmacological research, with the active compound deriving after extensive analysis and testing. In contrast, in recent years, the active substance has been pinpointed by computational methods (in silico docking and molecular dynamics, network pharmacology), followed by the identification of the plant(s) containing the active ingredient, identified by existing or putative ethnopharmacological information. We further stress the potential pitfalls of recent in silico methods and discuss the absolute need for in vitro and in vivo validation as an absolute requirement. Finally, we present our contribution to natural products' drug discovery by discussing specific examples, applying the whole continuum of this rapidly evolving field. In detail, we report the isolation of novel antiviral compounds, based on natural products active against influenza and SARS-CoV-2 and novel substances active on a specific GPCR, OXER1.
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Affiliation(s)
- Stergios Pirintsos
- Department of Biology, School of Sciences and Technology, University of Crete, 71409 Heraklion, Greece;
- Botanical Garden, University of Crete, 74100 Rethymnon, Greece
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
| | - Athanasios Panagiotopoulos
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71409 Heraklion, Greece;
| | - Michalis Bariotakis
- Department of Biology, School of Sciences and Technology, University of Crete, 71409 Heraklion, Greece;
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol 3603, Cyprus;
| | - Christos Lionis
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Clinic of Social and Family Medicine, School of Medicine, University of Crete, 71409 Heraklion, Greece
| | - George Sourvinos
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71409 Heraklion, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Marilena Kampa
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71409 Heraklion, Greece;
| | - Elias Castanas
- Nature Crete Pharmaceuticals, 71305 Heraklion, Greece; (C.L.); (G.S.); (M.K.)
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, 71409 Heraklion, Greece;
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25
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Li H, Tang Y, Liang KY, Zang Y, Osman EEA, Jin ZX, Li J, Xiong J, Li J, Hu JF. Phytochemical and biological studies on rare and endangered plants endemic to China. Part XXII. Structurally diverse diterpenoids from the leaves and twigs of the endangered conifer Torreya jackii and their bioactivities. PHYTOCHEMISTRY 2022; 198:113161. [PMID: 35283166 DOI: 10.1016/j.phytochem.2022.113161] [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: 12/05/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
A phytochemical investigation on the MeOH extract of the leaves and twigs of the endangered conifer Torreya jackii Chun led to the isolation and characterization of 21 structurally diverse diterpenoids. Among them, six are previously undescribed, including four abietane-type (torreyins A-D, resp.) and two labdane-type diterpenoids (torreyins E and F). Their structures and absolute configurations were determined by a combination of spectroscopic methods, calculated/experimental electronic circular dichroism (ECD) data, and single-crystal X-ray diffraction analyses. In particular, torreyins A-C are rare 11,12-seco-abietane type diterpenoids possessing a dilactone moiety, and their biosynthetic pathway starting from a co-occurring abietane derivative (i.e., cyrtophyllone B) was briefly proposed. Among the isolates, 7-oxo-dehydroabietic acid and 15-methoxy-7,13-abietadien-18-oic acid showed considerable inhibitory effects against acetyl-coenzyme A carboxylase 1 (ACC1) and protein tyrosine phosphatase 1 B (PTP1B), with IC50 values of 3.1 and 6.8 μM, respectively.
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Affiliation(s)
- Hao Li
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China; School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Yu Tang
- School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Kai-Yuan Liang
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China; School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Ezzat E A Osman
- School of Pharmacy, Fudan University, Shanghai, 201203, PR China; Department of Biochemistry, Molecular Biology and Medicinal Chemistry, Theodor Bilharz Research Institute, P. O. Box 30 Imbaba, Giza, 12411, Egypt
| | - Ze-Xin Jin
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
| | - Junmin Li
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China.
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang, 318000, PR China; School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
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26
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Boosted machine learning model for predicting intradialytic hypotension using serum biomarkers of nutrition. Comput Biol Med 2022; 147:105752. [DOI: 10.1016/j.compbiomed.2022.105752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/22/2022]
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27
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Chen Z, Yan D, Zhang M, Han W, Wang Y, Xu S, Tang K, Gao J, Cao Z. MetNC: Predicting Metabolites in vivo for Natural Compounds. Front Chem 2022; 10:881975. [PMID: 35646826 PMCID: PMC9135178 DOI: 10.3389/fchem.2022.881975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Natural compounds (NCs) undergo complicated biotransformation in vivo to produce diverse forms of metabolites dynamically, many of which are of high medicinal value. Predicting the profiles of chemical products may help to narrow down possible candidates, yet current computational methods for predicting biotransformation largely focus on synthetic compounds. Here, we proposed a method of MetNC, a tailor-made method for NC biotransformation prediction, after exploring the overall patterns of NC in vivo metabolism. Based on 850 pairs of the biotransformation dataset validated by comprehensive in vivo experiments with sourcing compounds from medicinal plants, MetNC was designed to produce a list of potential metabolites through simulating in vivo biotransformation and then prioritize true metabolites into the top list according to the functional groups in compound structures and steric hindrance around the reaction sites. Among the well-known peers of GLORYx and BioTransformer, MetNC gave the highest performance in both the metabolite coverage and the ability to short-list true products. More importantly, MetNC seemed to display an extra advantage in recommending the microbiota-transformed metabolites, suggesting its potential usefulness in the overall metabolism estimation. In summary, complemented to those techniques focusing on synthetic compounds, MetNC may help to fill the gap of natural compound metabolism and narrow down those products likely to be identified in vivo.
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Affiliation(s)
- Zikun Chen
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Deyu Yan
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Mou Zhang
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenhao Han
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuan Wang
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shudi Xu
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kailin Tang
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jian Gao
- International Human Phenome Institutes, Shanghai, China
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- *Correspondence: Zhiwei Cao, ; Jian Gao,
| | - Zhiwei Cao
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
- *Correspondence: Zhiwei Cao, ; Jian Gao,
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28
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Zhang C, Mou M, Zhou Y, Zhang W, Lian X, Shi S, Lu M, Sun H, Li F, Wang Y, Zeng Z, Li Z, Zhang B, Qiu Y, Zhu F, Gao J. Biological activities of drug inactive ingredients. Brief Bioinform 2022; 23:6582006. [PMID: 35524477 DOI: 10.1093/bib/bbac160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
In a drug formulation (DFM), the major components by mass are not Active Pharmaceutical Ingredient (API) but rather Drug Inactive Ingredients (DIGs). DIGs can reach much higher concentrations than that achieved by API, which raises great concerns about their clinical toxicities. Therefore, the biological activities of DIG on physiologically relevant target are widely demanded by both clinical investigation and pharmaceutical industry. However, such activity data are not available in any existing pharmaceutical knowledge base, and their potentials in predicting the DIG-target interaction have not been evaluated yet. In this study, the comprehensive assessment and analysis on the biological activities of DIGs were therefore conducted. First, the largest number of DIGs and DFMs were systematically curated and confirmed based on all drugs approved by US Food and Drug Administration. Second, comprehensive activities for both DIGs and DFMs were provided for the first time to pharmaceutical community. Third, the biological targets of each DIG and formulation were fully referenced to available databases that described their pharmaceutical/biological characteristics. Finally, a variety of popular artificial intelligence techniques were used to assess the predictive potential of DIGs' activity data, which was the first evaluation on the possibility to predict DIG's activity. As the activities of DIGs are critical for current pharmaceutical studies, this work is expected to have significant implications for the future practice of drug discovery and precision medicine.
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Affiliation(s)
- Chenyang Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Wei Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shuiyang Shi
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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29
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An efficient rotational direction heap-based optimization with orthogonal structure for medical diagnosis. Comput Biol Med 2022; 146:105563. [PMID: 35551010 DOI: 10.1016/j.compbiomed.2022.105563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/24/2022] [Accepted: 04/24/2022] [Indexed: 12/17/2022]
Abstract
The heap-based optimizer (HBO) is an optimization method proposed in recent years that may face local stagnation problems and show slow convergence speed due to the lack of detailed analysis of optimal solutions and a comprehensive search. Therefore, to mitigate these drawbacks and strengthen the performance of the algorithm in the field of medical diagnosis, a new MGOHBO method is proposed by introducing the modified Rosenbrock's rotational direction method (MRM), an operator from the grey wolf optimizer (GWM), and an orthogonal learning strategy (OL). The MGOHBO is compared with eleven famous and improved optimizers on IEEE CEC 2017. The results on benchmark functions indicate that the boosted MGOHBO has several significant advantages in terms of convergence accuracy and speed of the process. Additionally, this article analyzed the diversity and balance of MGOHBO in detail. Finally, the proposed MGOHBO algorithm is utilized to optimize the kernel extreme learning machines (KELM), and a new MGOHBO-KELM is proposed. To validate the performance of MGOHBO-KELM, seven disease diagnostic questions were introduced for testing in this work. In contrast to advanced models such as HBO-KELM and BP, it can be concluded that the MGOHBO-KELM model can achieve optimal results, which also proves that it has practical significance in solving medical diagnosis problems.
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30
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Stalin A, Daniel Reegan A, Rajiv Gandhi M, Saravanan RR, Balakrishna K, Hesham AEL, Ignacimuthu S, Zhang Y. Mosquitocidal efficacy of embelin and its derivatives against Aedes aegypti L. and Culex quinquefasciatus Say. (Diptera: Culicidae) and computational analysis of acetylcholinesterase 1 (AChE1) inhibition. Comput Biol Med 2022; 146:105535. [PMID: 35487124 DOI: 10.1016/j.compbiomed.2022.105535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022]
Abstract
Embelin was isolated from the chloroform extract of Embelia ribes (Burm.f.) fruits; its derivative compounds 6-bromoembelin and vilangin were prepared, and they were evaluated for mosquitocidal activities against the third instar larvae and pupae of Aedes aegypti L. and Culex quinquefasciatus Say. (Diptera: Culicidae). The concentrations used were 0.5, 1.0, 1.5, and 2.0 ppm. Embelin recorded LC50 values of 5.79 and 5.54 ppm against the larvae of Ae. aegypti and Cx. quinquefasciatus, respectively. Similarly, the LC50 values of embelin were 10.23 and 6.93 ppm against the pupae of Ae. aegypti and Cx. quinquefasciatus, respectively. Of the two derivatives tested, vilangin showed the highest larvicidal activity with LC50 values of 1.38 and 1.28 ppm against the larvae of Ae. aegypti and Cx. quinquefasciatus, respectively. Similarly, the LC50 values of vilangin were 1.60 and 1.43 ppm against the pupae of Ae. aegypti and Cx. quinquefasciatus, respectively. The LC50 values of 6-bromoembelin were 3.30 and 2.83 ppm against the larvae and 4.40 and 4.30 ppm against the pupae of Ae. aegypti and Cx. quinquefasciatus, respectively. The histopathological results displayed significant damage on cuboidal cells of the midgut (CU) in vilangin treated larvae of Ae. aegypti and Cx. quinquefasciatus at a concentration of 2.0 ppm. Similarly, peritrophic membrane (PM) was completely impaired in vilangin-treated larvae of Cx. quinquefasciatus and midgut content (MC) was very low in vilangin-treated larvae of Cx. quinquefasciatus. In addition, molecular docking and molecular dynamics studies demonstrated the efficacy of vilangin on the inhibition of acetylcholinesterase (AChE1) in Ae. aegypti and Cx. quinquefasciatus. The present results suggest that vilangin could be used to develop a natural active product against mosquito larvae.
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Affiliation(s)
- Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610 054, China.
| | - Appadurai Daniel Reegan
- National Centre for Disease Control, Bengaluru Branch, No:8, NTI Campus, Bellary Road, Bengaluru, 560 003, Karnataka, India; Xavier Research Foundation, St. Xavier's College, Affiliated to the Manonmaniam Sundaranar University, Palayamkottai, 627 002, Tamil Nadu, India.
| | - Munusamy Rajiv Gandhi
- National Biodiversity Authority, 5th Floor, CSIR Road, TICEL Bio Park, Taramani, Chennai, 600 113, India
| | - R R Saravanan
- Department of Physics, Meenakshi Chandrasekaran College of Arts and Science, Karambayam, Pattukkottai, Thanjavur, 614 626, India
| | - Kedike Balakrishna
- Entomology Research Institute, Loyola College, Affiliated to the University of Madras, Chennai, 600 034, Tamil Nadu, India
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Savarimuthu Ignacimuthu
- Xavier Research Foundation, St. Xavier's College, Affiliated to the Manonmaniam Sundaranar University, Palayamkottai, 627 002, Tamil Nadu, India
| | - Ying Zhang
- Department of Anesthesiology, Hospital (T.C.M) Affiliated To Southwest Medical University, Luzhou, China.
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31
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Jiang W, Tang Y, Tong YP, Zhao ZY, Jin ZX, Li J, Zang Y, Li J, Xiong J, Hu JF. Structurally diverse mono-/dimeric triterpenoids from the vulnerable conifer Pseudotsuga gaussenii and their PTP1B inhibitory effects. The Role of Protecting Species Diversity in Support of Chemical Diversity. Bioorg Chem 2022; 124:105825. [DOI: 10.1016/j.bioorg.2022.105825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022]
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32
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Lei Y, Meng Y, Guo X, Ning K, Bian Y, Li L, Hu Z, Anashkina AA, Jiang Q, Dong Y, Zhu X. Overview of structural variation calling: Simulation, identification, and visualization. Comput Biol Med 2022; 145:105534. [DOI: 10.1016/j.compbiomed.2022.105534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/09/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
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33
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Zhu YX, Ding W, Hu JF, Xiong J, Li J. Beshanzuamide A, an unprecedented prenylated indole alkaloid produced by Aspergillus sp. Y-2 from the critically endangered conifer Abies beshanzuensis. RSC Adv 2022; 12:10534-10539. [PMID: 35425024 PMCID: PMC8985211 DOI: 10.1039/d2ra01578a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 12/25/2022] Open
Abstract
A structurally unprecedented prenylated indole alkaloid, beshanzuamide A (1), together with five known analogues (2–6) were isolated and identified from the endophytic fungus derived from the needles of the critically endangered conifer Abies beshanzuensis. The new structure was determined by extensive spectroscopic methods and quantum chemical calculations of NMR and electronic circular dichroism (ECD) data. Compound 1 features a unique N,O-spiroketal/δ-lactone motif connected to a pyranoindole-derived bicyclo[2.2.2]diazaoctane ring. A plausible biogenetic pathway for the assembly of 1 was proposed. A structurally unprecedented prenylated indole alkaloid, together with five known analogues, was isolated from an endophytic fungus associated with the endangered conifer Abies beshanzuensis.![]()
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Affiliation(s)
- Yuan-Xing Zhu
- Department of Biological Medicines, School of Pharmacy, Fudan University Shanghai 201203 China
| | - Wenxin Ding
- Department of Biological Medicines, School of Pharmacy, Fudan University Shanghai 201203 China
| | - Jin-Feng Hu
- Department of Natural Medicines, School of Pharmacy, Fudan University Shanghai 201203 China
| | - Juan Xiong
- Department of Natural Medicines, School of Pharmacy, Fudan University Shanghai 201203 China
| | - Jiyang Li
- Department of Biological Medicines, School of Pharmacy, Fudan University Shanghai 201203 China
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34
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Xia W, Zheng L, Fang J, Li F, Zhou Y, Zeng Z, Zhang B, Li Z, Li H, Zhu F. PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods. Comput Biol Med 2022; 145:105465. [PMID: 35366467 DOI: 10.1016/j.compbiomed.2022.105465] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
Bioinformatic annotation of protein function is essential but extremely sophisticated, which asks for extensive efforts to develop effective prediction method. However, the existing methods tend to amplify the representativeness of the families with large number of proteins by misclassifying the proteins in the families with small number of proteins. That is to say, the ability of the existing methods to annotate proteins in the 'rare classes' remains limited. Herein, a new protein function annotation strategy, PFmulDL, integrating multiple deep learning methods, was thus constructed. First, the recurrent neural network was integrated, for the first time, with the convolutional neural network to facilitate the function annotation. Second, a transfer learning method was introduced to the model construction for further improving the prediction performances. Third, based on the latest data of Gene Ontology, the newly constructed model could annotate the largest number of protein families comparing with the existing methods. Finally, this newly constructed model was found capable of significantly elevating the prediction performance for the 'rare classes' without sacrificing that for the 'major classes'. All in all, due to the emerging requirements on improving the prediction performance for the proteins in 'rare classes', this new strategy would become an essential complement to the existing methods for protein function prediction. All the models and source codes are freely available and open to all users at: https://github.com/idrblab/PFmulDL.
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Affiliation(s)
- Weiqi Xia
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Jiebin Fang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China.
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35
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Chen Y, Yang XH, Wei Z, Heidari AA, Zheng N, Li Z, Chen H, Hu H, Zhou Q, Guan Q. Generative Adversarial Networks in Medical Image augmentation: A review. Comput Biol Med 2022; 144:105382. [PMID: 35276550 DOI: 10.1016/j.compbiomed.2022.105382] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/31/2022]
Abstract
OBJECT With the development of deep learning, the number of training samples for medical image-based diagnosis and treatment models is increasing. Generative Adversarial Networks (GANs) have attracted attention in medical image processing due to their excellent image generation capabilities and have been widely used in data augmentation. In this paper, a comprehensive and systematic review and analysis of medical image augmentation work are carried out, and its research status and development prospects are reviewed. METHOD This paper reviews 105 medical image augmentation related papers, which mainly collected by ELSEVIER, IEEE Xplore, and Springer from 2018 to 2021. We counted these papers according to the parts of the organs corresponding to the images, and sorted out the medical image datasets that appeared in them, the loss function in model training, and the quantitative evaluation metrics of image augmentation. At the same time, we briefly introduce the literature collected in three journals and three conferences that have received attention in medical image processing. RESULT First, we summarize the advantages of various augmentation models, loss functions, and evaluation metrics. Researchers can use this information as a reference when designing augmentation tasks. Second, we explore the relationship between augmented models and the amount of the training set, and tease out the role that augmented models may play when the quality of the training set is limited. Third, the statistical number of papers shows that the development momentum of this research field remains strong. Furthermore, we discuss the existing limitations of this type of model and suggest possible research directions. CONCLUSION We discuss GAN-based medical image augmentation work in detail. This method effectively alleviates the challenge of limited training samples for medical image diagnosis and treatment models. It is hoped that this review will benefit researchers interested in this field.
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Affiliation(s)
- Yizhou Chen
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Xu-Hua Yang
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Zihan Wei
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Ali Asghar Heidari
- School of Surveying and Geospatial Engineering, College of Engineering, University of Tehran, Tehran, Iran; Department of Computer Science, School of Computing, National University of Singapore, Singapore, Singapore.
| | - Nenggan Zheng
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Zhicheng Li
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Huiling Chen
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, Zhejiang, 325035, China.
| | - Haigen Hu
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Qianwei Zhou
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Qiu Guan
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
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36
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Li F, Zhou Y, Zhang Y, Yin J, Qiu Y, Gao J, Zhu F. POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability. Brief Bioinform 2022; 23:6532538. [PMID: 35183059 DOI: 10.1093/bib/bbac040] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 12/17/2022] Open
Abstract
Mass spectrometry-based proteomic technique has become indispensable in current exploration of complex and dynamic biological processes. Instrument development has largely ensured the effective production of proteomic data, which necessitates commensurate advances in statistical framework to discover the optimal proteomic signature. Current framework mainly emphasizes the generalizability of the identified signature in predicting the independent data but neglects the reproducibility among signatures identified from independently repeated trials on different sub-dataset. These problems seriously restricted the wide application of the proteomic technique in molecular biology and other related directions. Thus, it is crucial to enable the generalizable and reproducible discovery of the proteomic signature with the subsequent indication of phenotype association. However, no such tool has been developed and available yet. Herein, an online tool, POSREG, was therefore constructed to identify the optimal signature for a set of proteomic data. It works by (i) identifying the proteomic signature of good reproducibility and aggregating them to ensemble feature ranking by ensemble learning, (ii) assessing the generalizability of ensemble feature ranking to acquire the optimal signature and (iii) indicating the phenotype association of discovered signature. POSREG is unique in its capacity of discovering the proteomic signature by simultaneously optimizing its reproducibility and generalizability. It is now accessible free of charge without any registration or login requirement at https://idrblab.org/posreg/.
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Affiliation(s)
- Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Ying Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Jianqing Gao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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37
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Abstract
The dragonfly algorithm is a swarm intelligence optimization algorithm based on simulating the swarming behavior of dragonfly individuals. An efficient algorithm must have a symmetry of information between the participating entities. An improved dragonfly algorithm is proposed in this paper to further improve the global searching ability and the convergence speed of DA. The improved DA is named GGBDA, which adds Gaussian mutation and Gaussian barebone on the basis of DA. Gaussian mutation can randomly update the individual positions to avoid the algorithm falling into a local optimal solution. Gaussian barebone can quicken the convergent speed and strengthen local exploitation capacities. Enhancing algorithm efficiency relative to the symmetric concept is a critical challenge in the field of engineering design. To verify the superiorities of GGBDA, this paper sets 30 benchmark functions, which are taken from CEC2014 and 4 engineering design problems to compare GGBDA with other algorithms. The experimental result show that the Gaussian mutation and Gaussian barebone can effectively improve the performance of DA. The proposed GGBDA, similar to the DA, presents improvements in global optimization competence, search accuracy, and convergence performance.
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Xue W, Fu T, Deng S, Yang F, Yang J, Zhu F. Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram. ACS Chem Neurosci 2022; 13:340-351. [PMID: 35041375 DOI: 10.1021/acschemneuro.1c00694] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human serotine transporter (hSERT) is one of the most influential drug targets, and its allosteric modulators (e.g., escitalopram) have emerged to be the next-generation medication for psychiatric disorders. However, the molecular mechanism underlying the allosteric modulation of hSERT is still elusive. Here, the simulation strategies of conventional (cMD) and steered (SMD) molecular dynamics were applied to investigate this molecular mechanism from distinct perspectives. First, cMD simulations revealed that escitalopram's binding to hSERT's allosteric site simultaneously enhanced its binding to the orthosteric site. Then, SMD simulation identified that the occupation of hSERT's allosteric site by escitalopram could also block its dissociation from the orthosteric site. Finally, by comparing the simulated structures of two hSERT-escitalopram complexes with and without allosteric modulation, a new conformational coupling between an extracellular (Arg104-Glu494) and an intracellular (Lys490-Glu494) salt bridge was identified. In summary, this study explored the mechanism underlying the allosteric modulation of hSERT by collectively applying two MD simulation strategies, which could facilitate our understanding of the allosteric modulations of not only hSERT but also other clinically important therapeutic targets.
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Affiliation(s)
- Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Central Nervous System Drug Key Laboratory of Sichuan Province, Luzhou 646000, China
| | - Tingting Fu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Shengzhe Deng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Fengyuan Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jingyi Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Anticancer Activities of Mushrooms: A Neglected Source for Drug Discovery. Pharmaceuticals (Basel) 2022; 15:ph15020176. [PMID: 35215289 PMCID: PMC8876642 DOI: 10.3390/ph15020176] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 01/08/2023] Open
Abstract
Approximately 270 species of mushrooms have been reported as potentially useful for human health. However, few mushrooms have been studied for bioactive compounds that can be helpful in treating various diseases. Like other natural regimens, the mushroom treatment appears safe, as could be expected from their long culinary and medicinal use. This review aims to provide a critical discussion on clinical trial evidence for mushrooms to treat patients with diverse types of cancer. In addition, the review also highlights the identified bioactive compounds and corresponding mechanisms of action among the explored mushrooms. Furthermore, it also discusses mushrooms with anticancer properties, demonstrated either in vitro and/or in vivo models, which have never been tested in clinical studies. Several mushrooms have been tested in phase I or II clinical trials, mostly for treating breast cancer (18.6%), followed by colorectal (14%) and prostate cancer (11.6%). The majority of clinical studies were carried out with just 3 species: Lentinula edodes (22.2%), Coriolus versicolor, and Ganoderma lucidum (both 13.9%); followed by two other species: Agaricus bisporus and Grifola frondosa (both 11.1%). Most in vitro cell studies use breast cancer cell lines (43.9%), followed by lung (14%) and colorectal cancer cell lines (13.1%), while most in vivo animal studies are performed in mice tumor models (58.7%). Although 32 species of mushrooms at least show some promise for the treatment of cancer, only 11 species have been tested clinically thus far. Moreover, most clinical studies have investigated fewer numbers of patients, and have been limited to phase III or IV. Therefore, despite the promising preclinical and clinical data publication, more solid scientific efforts are required to clarify the therapeutic value of mushrooms in oncology.
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Wainwright CL, Teixeira MM, Adelson DL, Buenz EJ, David B, Glaser KB, Harata-Lee Y, Howes MJR, Izzo AA, Maffia P, Mayer AM, Mazars C, Newman DJ, Nic Lughadha E, Pimenta AM, Parra JA, Qu Z, Shen H, Spedding M, Wolfender JL. Future Directions for the Discovery of Natural Product-Derived Immunomodulating Drugs. Pharmacol Res 2022; 177:106076. [PMID: 35074524 DOI: 10.1016/j.phrs.2022.106076] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 02/06/2023]
Abstract
Drug discovery from natural sources is going through a renaissance, having spent many decades in the shadow of synthetic molecule drug discovery, despite the fact that natural product-derived compounds occupy a much greater chemical space than those created through synthetic chemistry methods. With this new era comes new possibilities, not least the novel targets that have emerged in recent times and the development of state-of-the-art technologies that can be applied to drug discovery from natural sources. Although progress has been made with some immunomodulating drugs, there remains a pressing need for new agents that can be used to treat the wide variety of conditions that arise from disruption, or over-activation, of the immune system; natural products may therefore be key in filling this gap. Recognising that, at present, there is no authoritative article that details the current state-of-the-art of the immunomodulatory activity of natural products, this in-depth review has arisen from a joint effort between the International Union of Basic and Clinical Pharmacology (IUPHAR) Natural Products and Immunopharmacology, with contributions from a Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation number of world-leading researchers in the field of natural product drug discovery, to provide a "position statement" on what natural products has to offer in the search for new immunomodulatory argents. To this end, we provide a historical look at previous discoveries of naturally occurring immunomodulators, present a picture of the current status of the field and provide insight into the future opportunities and challenges for the discovery of new drugs to treat immune-related diseases.
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Affiliation(s)
- Cherry L Wainwright
- Centre for Natural Products in Health, Robert Gordon University, Aberdeen, UK.
| | - Mauro M Teixeira
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Brazil.
| | - David L Adelson
- Molecular & Biomedical Science, University of Adelaide, Australia.
| | - Eric J Buenz
- Nelson Marlborough Institute of Technology, New Zealand.
| | - Bruno David
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | - Keith B Glaser
- AbbVie Inc., Integrated Discovery Operations, North Chicago, USA.
| | - Yuka Harata-Lee
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Melanie-Jayne R Howes
- Royal Botanic Gardens Kew, Richmond, Surrey, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, UK.
| | - Angelo A Izzo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy.
| | - Pasquale Maffia
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
| | - Alejandro Ms Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, IL, USA.
| | - Claire Mazars
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | | | | | - Adriano Mc Pimenta
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - John Aa Parra
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Zhipeng Qu
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Hanyuan Shen
- Molecular & Biomedical Science, University of Adelaide, Australia
| | | | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.
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Chen HW, Jiang CX, Li J, Li N, Zang Y, Wu XY, Chen WX, Xiong J, Li J, Hu JF. Beshanzoides A-D, unprecedented cycloheptanone-containing polyketides from Penicillium commune P-4-1, an endophytic fungus of the endangered conifer Abies beshanzuensis. RSC Adv 2021; 11:39781-39789. [PMID: 35494150 PMCID: PMC9044568 DOI: 10.1039/d1ra08377e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/07/2021] [Indexed: 12/18/2022] Open
Abstract
A number of previously undescribed (1–7) and structurally related known (8–17) isobenzofuran-type polyketides were obtained from the fermentation of Penicillium commune P-4-1, an endophytic fungus isolated from the fresh trunk bark of the critically endangered conifer Abies beshanzuensis. Beshanzoides A–D (1–4, resp.) feature a cycloheptanone-containing isobenzofuran ring system hitherto unknown, which might be biosynthesized via two steps of aldol reactions starting from a common co-occurring isobenzofuran-type polyketide as the precursor. The new structures were elucidated by spectroscopic methods, electronic circular dichroism data, and single crystal X-ray diffraction analyses. Beshanzoide E (5) showed antimicrobial activity (MIC: 16 μg mL−1) against Staphylococcus aureus, whereas (±)-strobide A (10) inhibited (MIC: 16 μg mL−1) Candida albicans. Cyclopaldic acid (12) and 3-O-methyl-cyclopaldic acid (13) exhibited inhibitory effects against acetyl-CoA carboxylase 1 (ACC1) with IC50 values of 0.96 and 11.77 μM, respectively. Compound 12 also inhibited (IC50: 7.56 μM) ATP-citrate lyase (ACL). Four unprecedented cycloheptanone-containing and some related known bioactive polyketides were isolated from an endophytic fungus associated with the critically endangered conifer Abies beshanzuensis.![]()
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Affiliation(s)
- Hao-Wei Chen
- Department of Natural Medicine, School of Pharmacy, Fudan University Shanghai 201203 PR China .,School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University Zhejiang 318000 PR China
| | - Chun-Xiao Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University Shanghai 201203 PR China .,School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University Zhejiang 318000 PR China
| | - Jiyang Li
- Department of Natural Medicine, School of Pharmacy, Fudan University Shanghai 201203 PR China
| | - Na Li
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University Zhejiang 318000 PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 PR China
| | - Xi-Ying Wu
- Department of Natural Medicine, School of Pharmacy, Fudan University Shanghai 201203 PR China .,Shanghai Skin Disease Hospital, School of Medicine, Tongji University Shanghai 200443 PR China
| | - Wen-Xue Chen
- Department of Chemistry, Fudan University Shanghai 200438 PR China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University Shanghai 201203 PR China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 PR China
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University Shanghai 201203 PR China .,School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University Zhejiang 318000 PR China
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Zaman W, Ye J, Saqib S, Liu Y, Shan Z, Hao D, Chen Z, Xiao P. Predicting potential medicinal plants with phylogenetic topology: Inspiration from the research of traditional Chinese medicine. JOURNAL OF ETHNOPHARMACOLOGY 2021; 281:114515. [PMID: 34388416 DOI: 10.1016/j.jep.2021.114515] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/06/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Plants are a dominant source of pharmacological drugs for the treatment and cure of different disorders and diseases. However, selecting the most biologically active plant species for further screening is still challenging. Phylogeny has strong explanatory powers and provides predictive perspectives that are not available in traditional plant classifications. China, which is endowed with a diverse set of therapeutic cures from Mother Nature, represents an ideal environment for the phylogenetic analysis of potential medicinal plants. MATERIALS AND METHODS Herein, we prepared a database of 7,451 traditional Chinese medicinal (TCM) plants, including species with therapeutic effects grouped in 14 categories. To limit our exploration of novel therapeutic species, we plotted the medicinal effects on the phylogenetic tree of almost 30,000 species of China to find hot nodes of therapeutic effects. We used the net relatedness index (NRI) and the nearest taxon index (NTI) to identify clustering and overdispersion of the phylogenetic distribution of TCM plants. RESULTS The NRI and NTI analyses highlighted 3,392 hot node species with single therapeutic effects within 507 genera and 89 families on the phylogenetic tree and about 70% of the 14 medicinal categories clusters identified. The general pattern of the hot nodes on the phylogenetic tree indicates that basal angiosperms and basal eudicots radiated for therapeutic effects. CONCLUSIONS Our study may provide a more targeted way to discover phylogeny-guided drugs in the early screening stage, which may lead to a higher discovery efficiency of new drugs with meaningful biological activities. Phylogenetic studies of plants that are richer in bioactive compounds can set the ground for the identification and discovery of alternative drugs.
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Affiliation(s)
- Wajid Zaman
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianfei Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Saddam Saqib
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yun Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhangjian Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dacheng Hao
- School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, 116028, China.
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193, China.
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Zhou PJ, Zang Y, Li C, Yuan L, Zeng H, Li J, Hu JF, Xiong J. Forrestiacids C and D, unprecedented triterpene-diterpene adducts from Pseudotsuga forrestii. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Sena PHA, Gonçalves‐Souza T, Gonçalves PHS, Ferreira PSM, Gusmão RAF, Melo FPL. Biocultural restoration improves delivery of ecosystem services in social‐ecological landscapes. Restor Ecol 2021. [DOI: 10.1111/rec.13599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pedro H. A. Sena
- Laboratório de Ecologia Aplicada, Centro de Biociências Universidade Federal de Pernambuco Av Prof Moraes Rego SN Recife Brasil 50670901 Brazil
- Laboratório de Síntese Ecológica e Conservação da Biodiversidade, Departamento de Biologia Universidade Federal Rural de Pernambuco Recife 52171‐900 Brazil
| | - Thiago Gonçalves‐Souza
- Laboratório de Síntese Ecológica e Conservação da Biodiversidade, Departamento de Biologia Universidade Federal Rural de Pernambuco Recife 52171‐900 Brazil
| | - Paulo H. S. Gonçalves
- Laboratório de Ecologia e Evolução de Sistemas Socioecológicos, Departamento de Botânica Universidade Federal de Pernambuco Av Prof Moraes Rego SN Recife Brasil 50670901 Brazil
| | - Paulo S. M. Ferreira
- Programa de Pós‐graduação em Ecologia e Recursos Naturais Universidade Federal do Ceará Fortaleza 60020‐181 Brazil
| | - Reginaldo A. F. Gusmão
- Laboratório de Síntese Ecológica e Conservação da Biodiversidade, Departamento de Biologia Universidade Federal Rural de Pernambuco Recife 52171‐900 Brazil
| | - Felipe P. L. Melo
- Laboratório de Ecologia Aplicada, Centro de Biociências Universidade Federal de Pernambuco Av Prof Moraes Rego SN Recife Brasil 50670901 Brazil
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Milliken W, Walker BE, Howes MJR, Forest F, Nic Lughadha E. Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines. JOURNAL OF ETHNOPHARMACOLOGY 2021; 279:114221. [PMID: 34029639 DOI: 10.1016/j.jep.2021.114221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Malaria remains a serious and challenging disease. Traditional antimalarial medicines are largely based on plants, and ethnopharmacological research has inspired the development of antimalarial pharmaceuticals such as artemisinin. Antimalarial drug resistance is an increasing problem in Plasmodium species, and new therapeutic strategies to combat malaria are needed. Although the number of malaria cases has been decreasing in Latin America, malaria remains a significant threat in many regions. Local people in Latin America have been using numerous plant species to treat malaria, some of which have been scientifically studied, but many others have not. AIM OF THE STUDY Our principal objective is to harness ethnobotanical data on species used traditionally to treat malaria, combined with phylogenetic approaches, to understand how ethnobotany could help identify plant genera as potential sources of new medicines. MATERIALS AND METHODS Plants used to treat malaria in Latin America were compiled from published and grey literature, unpublished data, and herbarium specimens. Initial assessment of potentially important species/genera/families included compiling the number of species used within the genus, the number of use reports per genus and species, and the geographic distribution of their use. The analysis of taxonomic distribution of species reported as antimalarial in Latin America (excluding the Southern Cone) was conducted, to determine which genera and families with reputed antimalarial properties are over-represented, and phylogenetic analyses were performed to identify if there was evidence for antimalarial species being dispersed/clustered throughout the tree or at its tips. This approach enabled 'hot-nodes' in certain families to be identified, to predict new genera with potential antimalarial properties. RESULTS Over 1000 plant species have been used to treat malaria in Latin America, of which over 600 species were cited only once. The genera with the highest number of antimalarial species were Aspidosperma, Solanum, Piper, Croton and Aristolochia. In terms of geographic distribution, the most widely used genera were Aspidosperma, Momordica, Cinchona, Senna and Stachytarpheta. Significant phylogenetic signal was detected in the distribution of native species used for malaria, analysed in a genus-level phylogenetic framework. The eudicot and magnoliidae lineages were over-represented, while monocots were not. CONCLUSION Analysis of ethnobotanical use reports in a phylogenetic framework reveals the existence of hot nodes for malaria across the Latin American flora. We demonstrate how species and genera currently lacking such reports could be pinpointed as of potential interest based on their evolutionary history. Extending this approach to other regions of the world and other diseases could accelerate the discovery of novel medicines and enhance healthcare in areas where new therapeutic strategies are needed.
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Affiliation(s)
| | | | - Melanie-Jayne R Howes
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, SE1 9NH, UK.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
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Xiong J, Zhou PJ, Jiang HW, Huang T, He YH, Zhao ZY, Zang Y, Choo YM, Wang X, Chittiboyina AG, Pandey P, Hamann MT, Li J, Hu JF. Forrestiacids A and B, Pentaterpene Inhibitors of ACL and Lipogenesis: Extending the Limits of Computational NMR Methods in the Structure Assignment of Complex Natural Products. Angew Chem Int Ed Engl 2021; 60:22270-22275. [PMID: 34374477 PMCID: PMC11173361 DOI: 10.1002/anie.202109082] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 12/30/2022]
Abstract
Forrestiacids A (1) and B (2) are a novel class of [4+2] type pentaterpenoids derived from a rearranged lanostane moiety (dienophile) and an abietane unit (diene). These unprecedented molecules were isolated using guidance by molecular ion networking (MoIN) from Pseudotsuga forrestii, an endangered member of the Asian Douglas Fir Family. The intermolecular hetero-Diels-Alder adducts feature an unusual bicyclo[2.2.2]octene ring system. Their structures were elucidated by spectroscopic analysis, GIAO NMR calculations and DP4+ probability analyses, electronic circular dichroism calculations, and X-ray diffraction analysis. This unique addition to the pentaterpene family represents the largest and the most complex molecule successfully assigned using computational approaches to predict accurately chemical shift values. Compounds 1 and 2 exhibited potent inhibitory activities (IC50 s <5 μM) of ATP-citrate lyase (ACL), a new drug target for the treatment of glycolipid metabolic disorders including hyperlipidemia. Validating this activity 1 effectively attenuated the de novo lipogenesis in HepG2 cells. These findings provide a new chemical class for developing potential therapeutic agents for ACL-related diseases with strong links to traditional medicines.
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Affiliation(s)
- Juan Xiong
- School of Pharmacy, Fudan University, Shanghai, 201203, P. R. China
| | - Peng-Jun Zhou
- School of Pharmacy, Fudan University, Shanghai, 201203, P. R. China
| | - Hao-Wen Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
| | - Ting Huang
- School of Pharmacy, Fudan University, Shanghai, 201203, P. R. China
| | - Yu-Hang He
- School of Pharmacy, Fudan University, Shanghai, 201203, P. R. China
| | - Ze-Yu Zhao
- School of Pharmacy, Fudan University, Shanghai, 201203, P. R. China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
| | - Yeun-Mun Choo
- Chemistry Department, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Xiaojuan Wang
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, Gansu, P. R. China
| | - Amar G Chittiboyina
- National Center for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA
| | - Pankaj Pandey
- National Center for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA
| | - Mark T Hamann
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, SC, 29425-5700, USA
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, Shanghai, 201203, P. R. China
- School of Advanced Study, Taizhou University, Taizhou, 318000, Zhejiang, P. R. China
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Forrestiacids A and B, Pentaterpene Inhibitors of ACL and Lipogenesis: Extending the Limits of Computational NMR Methods in the Structure Assignment of Complex Natural Products. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109082] [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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Chen K, Wu W, Hou X, Yang Q, Li Z. A review: antimicrobial properties of several medicinal plants widely used in Traditional Chinese Medicine. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
Due to the dramatic increase in the use of antibiotics and growing health threat of bacterial resistance to many commonly used antibiotics, many studies have been directed at developing new and effective antibacterial compounds, among which many new, natural, and effective antibacterial compounds discovered from medicinal plants have drawn great interest and raised new hope for treating the challenges of antibiotic resistance. This review aimed to summarize the most important and widely used medicinal plants that were reported to have antibacterial activities. A general literature search from 2010 to 2020 was conducted using different databases, including Science Direct, Web of Science, and PubMed. According to the literature, three medicinal plants with outstanding antibacterial activities, Taraxacum officinale, Coptis Rhizome, and Scutellaria baicalensis, were screened and reviewed by prioritization. The extraction methods, antibacterial activities of different parts of plants or the plant-derived compounds, spectra of antibacterial activities, and toxicity were described, respectively. However, the antibacterial activities of the extracts or pure compounds as reported in the reviewed literature were mostly based on in vitro assays, and moreover, the deeper antibacterial mechanisms have not been elucidated clearly. Therefore, further studies are required in the fields of purification and identification of the antibacterial compounds, its mechanisms of action, and synergistic effects in combination with other antibacterial drugs, which may be helpful in the development of new antibacterial drugs.
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Liana D, Rungsihirunrat K. Phytochemical screening, antimalarial activities, and genetic relationship of 16 indigenous Thai Asteraceae medicinal plants: A combinatorial approach using phylogeny and ethnobotanical bioprospecting in antimalarial drug discovery. J Adv Pharm Technol Res 2021; 12:254-260. [PMID: 34345604 PMCID: PMC8300331 DOI: 10.4103/japtr.japtr_238_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/22/2021] [Accepted: 04/26/2021] [Indexed: 11/08/2022] Open
Abstract
Emergence of artemisinin resistance leads the people to discover the new candidate for antimalarial drug. Combinatorial phylogeny and ethnobotanical approach may be useful to minimize the expenditure and time in laboratory testing. Seven hundred and thirty-three ethnomedicinal plants were listed from literature search. Obtained 340 internal transcribed spacer (ITS) sequences of plant list which met criteria were retrieved from GenBank NCBI and analyzed by MUSCLE and maximum likelihood phylogenetic test to generate the phylogenetic tree. Interactive phylogenetic tree was generated by Interactive Tree of Life (ITOL, https://itol.embl.de) and showed strong clustered pattern on Asteraceae. Afterward, 16 species of Asteraceae were selected to investigate the antimalarial activity, phytochemical, and genetic diversity. The presence of phytochemical was determined by standard method. DNA fluorescence-based assay was performed to determine the antimalarial activity against 3D7 Plasmodium falciparum. IC50μg/mL was used to categorize antimalarial activity. On the other hand, ITS universal primer was used to amplify and sequence the obtained extracted DNA of tested plant by cetyltrimethylammonium bromide method. Phylogenetic analyses were performed by MAFFT and RAxML with automatic bootstrapping. ITOL and Adobe Illustrator were used to generate interactive phylogenetic tree. All species tested showed the presence of phenolics and flavonoids, whereas alkaloids and terpenoids were shown vary among tested extracts. Among 16 species tested, 1 species exhibited good-moderate (Sphaeranthus indicus, IC506.59 μg/mL), 4 weak (Artemisia chinensis, Artemisia vulgaris, Tridax procumbens, and Blumea balsamifera), and 3 very weak (Eupatorium capillifolium, Wedelia trilobata, and Vernonia cinerea). Generated phylogenetic tree by ITS data was able to separate the tested species into their tribal classification. In addition, new medicinal properties of A. chinensis were discovered. Combining phylogeny approach with ethnobotanical data is useful to narrow down the selection of antimalarial plants candidate.
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Affiliation(s)
- Desy Liana
- Department of Public Health Sciences, College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanchana Rungsihirunrat
- Department of Public Health Sciences, College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
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Zhang Y, Deng T, Sun L, Landis JB, Moore MJ, Wang H, Wang Y, Hao X, Chen J, Li S, Xu M, Puno PT, Raven PH, Sun H. Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant 'tree of life'. Natl Sci Rev 2021; 8:nwaa105. [PMID: 34691607 PMCID: PMC8288438 DOI: 10.1093/nsr/nwaa105] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 11/13/2022] Open
Abstract
To evaluate the phylogenetic patterns of the distribution and evolution of plant secondary metabolites (PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. A significant phylogenetic signal was detected in 17 of the 18 tested seed-plant clades for at least 1 of the 8 PSM classes using the D statistic. The phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed-plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSMs, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSMs seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes.
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Affiliation(s)
- Yongzeng Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lu Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yuehua Wang
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Xiaojiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jijun Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Shenghong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Maonian Xu
- Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland
| | - Pema-Tenzin Puno
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | | | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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