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Sánchez-Suárez J, Villamil L, Coy-Barrera E, Díaz L. Photoprotection-related properties of a raw extract from Gordonia hongkongensis EUFUS-Z928: A culturable rare actinomycete associated with the Caribbean octocoral Eunicea fusca. Sci Prog 2024; 107:368504241272454. [PMID: 39119690 PMCID: PMC11311175 DOI: 10.1177/00368504241272454] [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] [Indexed: 08/10/2024]
Abstract
UV filters in current sunscreen formulations can have negative effects on human health, such as endocrine disruption and allergic reactions, as well as on the environment, including bioaccumulation and coral health toxicity. As a result, there is a need to find alternative compounds that serve as safer and more ecofriendly active ingredients. This study successfully isolated actinomycetes from the octocoral Eunicea fusca and assessed their potential as producers of photoprotective compounds. The use of bio-based chemical agents, particularly natural products, has been a highly effective strategy for discovering bioactive compounds, especially in marine invertebrates and their associated microbiota. Eighteen bacterial isolates were obtained and subsequently employed to prepare raw methanolic extracts from seven-day submerged cultures in Zobell marine broth. The resulting extracts were screened for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging capacity and characterized by total phenolic and flavonoid content measurements. After screening, the Gordonia hongkongensis EUFUS-Z928-derived raw extract exhibited the best antioxidant profile, i.e. DPPH and ABTS radical scavenging of 4.93 and 6.00 µmol Trolox per gram of extract, respectively, and selected for further photoprotection-related analysis. Thus, this extract demonstrated a UV-absorbing capacity of 46.33% of the in vitro sun protection factor calculated for 30 µg/mL oxybenzone but did not exhibit any cytotoxicity on human dermal fibroblasts (HDFa cell line) at concentrations up to 500 µg/mL. The liquid chromatography-mass spectrometry chemical characterization of this extract showed compounds with structural features associated with free radical scavenging and UV absorption (i.e. photoprotection-related activities). These findings highlighted the potential of the microbiota associated with E. fusca and confirmed the feasibility of exploiting its metabolites for photoprotection-related purposes.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Ecology and Biogeography Research Group, Department of Biology, School of Basic Sciences, Universidad de Pamplona, Pamplona, Colombia
| | - Luisa Villamil
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Luis Díaz
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
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Li ZW, Fan CL, Sun B, Huang L, Wang ZQ, Huang XJ, Zhang SQ, Ye WC, Wu ZL, Zhang XQ. Discovery of Unusual Ajmaline-Macroline Type Bisindole Alkaloids from Alstonia macrophylla by Building Blocks-Based Molecular Networking. Chemistry 2024; 30:e202303519. [PMID: 38018776 DOI: 10.1002/chem.202303519] [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: 10/25/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Three unusual ajmaline-macroline type bisindole alkaloids, alsmaphylines A-C, together with their postulated biogenetic precursors, were isolated from the stem barks and leaves of Alstonia macrophylla via the building blocks-based molecular network (BBMN) strategy. Alsmaphyline A represents a rare ajmaline-macroline type bisindole alkaloid with an S-shape polycyclic ring system. Alsmaphylines B and C are two novel ajmaline-macroline type bisindole alkaloids with N-1-C-21' linkages, and the former possesses an unconventional stacked conformation due to the presence of intramolecular noncovalent interactions. The chemical structures including absolute configurations of alsmaphylines A-C were established by comprehensive spectroscopic analyses, electronic circular dichroism (ECD) calculations, and single-crystal X-ray crystallography. In addition, a plausible biosynthetic pathway of these bisindole alkaloids as well as their ability to promote the protein synthesis on HT22 cells were discussed.
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Affiliation(s)
- Zi-Wei Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Chun-Lin Fan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Biao Sun
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Lan Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Zi-Qi Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Xiao-Jun Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Shi-Qing Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Wen-Cai Ye
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Zhen-Long Wu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
| | - Xiao-Qi Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P.R. China
- Center for Bioactive Natural Molecules and Innovative Drugs Research, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, P.R. China
- Guangdong Provincial Engineering Research Center for Modernization of TCM, College of Pharmacy, Jinan University, Guangzhou, 510632, P.R. China
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Alwali AY, Santos D, Aguilar C, Birch A, Rodriguez-Orduña L, Roberts CB, Modi R, Licona-Cassani C, Parkinson EI. Discovery of Streptomyces species CS-62, a novel producer of the Acinetobacter baumannii selective antibiotic factumycin. J Ind Microbiol Biotechnol 2024; 51:kuae014. [PMID: 38632045 PMCID: PMC11066910 DOI: 10.1093/jimb/kuae014] [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: 03/06/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
Narrow-spectrum antibiotics are of great interest given their ability to spare the microbiome and decrease widespread antibiotic resistance compared to broad-spectrum antibiotics. Herein, we screened an in-house library of Actinobacteria strains for selective activity against Acinetobacter baumannii and successfully identified Streptomyces sp. CS-62 as a producer of a natural product with this valuable activity. Analysis of the cultures via high-resolution mass spectrometry and tandem mass spectrometry, followed by comparison with molecules in the Natural Product Atlas and the Global Natural Products Social Molecular Networking platform, suggested a novel natural product. Genome mining analysis initially supported the production of a novel kirromycin derivative. Isolation and structure elucidation via mass spectrometry and Nuclear Magnetic Resonance (NMR) analyses revealed that the active natural product was the known natural product factumycin, exposing omissions and errors in the consulted databases. While public databases are generally very useful for avoiding rediscovery of known molecules, rediscovery remains a problem due to public databases either being incomplete or having errors that result in failed dereplication. Overall, the work describes the ongoing problem of dereplication and the continued need for public database curation.
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Affiliation(s)
- Amir Y Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Diane Santos
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Audrey Birch
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Lorena Rodriguez-Orduña
- Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, 64849 Monterrey, México
| | - Carson B Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Cuauhtemoc Licona-Cassani
- Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, 64849 Monterrey, México
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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Lv TM, Han JL, Yan QL, Lin B, Yao GD, Huang XX, Song SJ. Discovery of the Caged-Vibsane Norditerpenoids with Unprecedented Chemical Architectures and Exploration of Their Various Acid Tolerances. J Org Chem 2023; 88:12385-12393. [PMID: 37585921 DOI: 10.1021/acs.joc.3c01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Cyclovibsanones A-D (1-4, respectively), featuring unprecedented caged tricyclo[5.4.1.05,9]dodecane and bicyclo[4.2.1]hexane cores, were isolated from the leaves of Viburnum odoratissimum. Their structures as well as that of one chemical derivative (5), which was transformed from 2, were determined by spectroscopic data, theoretical calculations, and the ML-JDP4/MAEΔΔδ methods. In addition, compounds 1 and 2 were found to possess dissimilarities in acid tolerance during nuclear magnetic resonance (NMR) experiments. The potential mechanism was consequently postulated and further supported through NMR analysis and mechanistic calculations. Biologically, chemical derivative 5 exerted antiproliferative activity against HepG2 cells.
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Affiliation(s)
- Tian-Ming Lv
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Jin-Ling Han
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Qiu-Lin Yan
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
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5
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Chen J, Guo Y, Wu Q, Wang W, Pan J, Chen M, Jiang H, Yin Q, Zhang G, Wei B, Zhang H, Wang H. Discovery of New Siderophores from a Marine Streptomycetes sp. via Combined Metabolomics and Analysis of Iron-Chelating Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6584-6593. [PMID: 37076425 DOI: 10.1021/acs.jafc.3c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The marine-derived Streptomyces sp. FIMYZ-003 strain was found to produce novel siderophores with yields negatively correlated with the iron concentration in the medium. Mass spectrometry (MS)-based metabolomics coupled with metallophore assays identified two novel α-hydroxycarboxylate-type siderophores, fradiamines C and D (3 and 4), together with two related known siderophores, fradiamines A and B (1 and 2). Their chemical structures were elucidated by nuclear magnetic resonance (NMR) and MS experiments. The annotation of a putative fra biosynthetic gene cluster enabled us to propose the biosynthetic pathway of fradiamines A-D. Furthermore, the solution-phase iron-binding activity of fradiamines was evaluated using metabolomics, confirming them as general iron scavengers. Fradiamines A-D exhibited Fe(III) binding activity equivalent to that of deferoxamine B mesylate. Growth analysis of pathogenic microbes demonstrated that fradiamine C promoted the growth of Escherichia coli and Staphylococcus aureus, but fradiamines A, B, and D did not. The results indicate that fradiamine C may serve as a novel iron carrier applicable to antibiotic delivery strategies to treat and prevent foodborne pathogens.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yuqi Guo
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qihao Wu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiangwei Pan
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Minghong Chen
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou 350007, China
| | - Hong Jiang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou 350007, China
| | - Qunjian Yin
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000 Guangxi, China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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Antioxidant-Activity-Guided Purification and Separation of Octocrylene from Saussurea heteromalla. SEPARATIONS 2023. [DOI: 10.3390/separations10020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Plants have been a source of medicine since ancient times, and such traditional medications are widely practiced nowadays. Saussurea heteromalla is widely used in traditional medicine in the Himalayan region for the treatment of different ailments. However, despite its traditional uses, it is not widely explored for its free radical scavenging abilities and other biological activities. Thus, the current study is aimed at exploring the free radical scavenging ability of S. heteromalla extracts, along with the isolation and evaluation of its compound through bioassay-guided purification. From different solvent fractions, an n-hexane extract of a whole plant is found to be most active; thus, it is processed for large-scale extraction and column chromatography. Further, the purification of an active fraction is performed using HPLC–DAD, which led to the isolation of an active peak, identified by GC/MS, as 2-ethylhexyl 2-cyano-3, 3-diphenylprop-2-enoate. This compound, commonly known as octocrylene, is widely recommended for UV-B filter, to be used in the cosmetic industry as photoprotection products. The presence of free radical scavenging activity enhances the sun protection factor of octocrylene. The present study presents the first report on the isolation of this compound from the family Asteraceae. The compound has good free radical scavenging activity and is widely used in the cosmetic industry as a sun protectant and is much less reported from botanical sources.
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Ahmad F, Nadeem H. Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery. Methods Mol Biol 2023; 2575:77-103. [PMID: 36301472 DOI: 10.1007/978-1-0716-2716-7_5] [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] [Indexed: 06/16/2023]
Abstract
The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.
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Affiliation(s)
- Faheem Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Hera Nadeem
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.
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Affiliation(s)
- Lívia Soman de Medeiros
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil.
| | - Moysés B de Araújo Júnior
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eldrinei G Peres
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | | | - Milena Costa Bassicheto
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Giordanno Di Gioia
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Thiago André Moura Veiga
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
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9
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Quiros-Guerrero LM, Nothias LF, Gaudry A, Marcourt L, Allard PM, Rutz A, David B, Queiroz EF, Wolfender JL. Inventa: A computational tool to discover structural novelty in natural extracts libraries. Front Mol Biosci 2022; 9:1028334. [PMID: 36438653 PMCID: PMC9692083 DOI: 10.3389/fmolb.2022.1028334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 09/05/2023] Open
Abstract
Collections of natural extracts hold potential for the discovery of novel natural products with original modes of action. The prioritization of extracts from collections remains challenging due to the lack of a workflow that combines multiple-source information to facilitate the data interpretation. Results from different analytical techniques and literature reports need to be organized, processed, and interpreted to enable optimal decision-making for extracts prioritization. Here, we introduce Inventa, a computational tool that highlights the structural novelty potential within extracts, considering untargeted mass spectrometry data, spectral annotation, and literature reports. Based on this information, Inventa calculates multiple scores that inform their structural potential. Thus, Inventa has the potential to accelerate new natural products discovery. Inventa was applied to a set of plants from the Celastraceae family as a proof of concept. The Pristimera indica (Willd.) A.C.Sm roots extract was highlighted as a promising source of potentially novel compounds. Its phytochemical investigation resulted in the isolation and de novo characterization of thirteen new dihydro-β-agarofuran sesquiterpenes, five of them presenting a new 9-oxodihydro-β-agarofuran base scaffold.
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Affiliation(s)
- Luis-Manuel Quiros-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Louis-Félix Nothias
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Arnaud Gaudry
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Laurence Marcourt
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Adriano Rutz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Emerson Ferreira Queiroz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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10
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Chen Z, Yan G, Yang Y, Sun H, Zhang A, Han Y, Wang S, Wang X. Rapid characterization of chemical constituents in Naoling Pian by LC-MS combined with data processing techniques. J Sep Sci 2022; 45:3431-3442. [PMID: 35855656 DOI: 10.1002/jssc.202200244] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022]
Abstract
Naoling Pian is a prescription composed of 15 herbs, which is mainly used for the treatment of insomnia in clinical practice. However, the chemical constituents in Naoling Pian are numerous and unclear, which hinders the interpretation of its bioactive constituents and the subsequent research on the material basis for pharmacodynamics. The purpose of this study is to develop a rapid method for identifying the chemical constituents of Naoling Pian using high-throughput ultra-performance liquid chromatography quadrupole time of flight coupled with mass spectrometry combined with a software platform for data processing. The whole composition of Naoling Pian was characterized in positive and negative ion modes. In this experiment, an overall total of 201 constituents were identified by using reference standards, online and self-built databases matching, fragmentation rules analysis of mass spectrometry peaks with a software platform. Meanwhile, Naoling Pian was analyzed for the first time using LC-MS method, the constituents could be identified in a quick and accurate manner, and the results could provide a scientific basis for the follow-up research on the pharmacodynamic material basis and quality control of Naoling Pian. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zhe Chen
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
| | - Guangli Yan
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
| | - Yu Yang
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
| | - Hui Sun
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
| | - Aihua Zhang
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
| | - Ying Han
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
| | - Shugui Wang
- Wusuli River Pharmaceutical Co., Ltd., Heilongjiang, China
| | - Xijun Wang
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Functional Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, China
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11
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Wang P, Zhao YN, Xu RZ, Zhang XW, Sun YR, Feng QM, Li ZH, Xu JY, Xie ZS, Zhang ZQ, E HC. Sesquiterpene Lactams and Lactones With Antioxidant Potentials From Atractylodes macrocephala Discovered by Molecular Networking Strategy. Front Nutr 2022; 9:865257. [PMID: 35571927 PMCID: PMC9097160 DOI: 10.3389/fnut.2022.865257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/29/2022] [Indexed: 12/24/2022] Open
Abstract
Atractylodes macrocephala rhizome (called Bái-zhú in China) has a long history as a functional food and herbal medicine in East Asia, especially China. Sesquiterpenoids are one of the main active compounds of Atractylodes macrocephala rhizome. This study aimed to explore the unknown sesquiterpenoids of A. macrocephala rhizome using a molecular networking strategy. Two new nitrogen-containing sesquiterpenoids, atractylenolactam A (1) and atractylenolactam B (2), and 2 new sesquiterpene lactones, 8-methoxy-atractylenolide V (6) and 15-acetoxyl atractylenolide III (7), along with 12 known analogs (3-5 and 8-16) were discovered and isolated. All the structures were assigned based on detailed spectroscopic analyses. The absolute configurations of 1, 2, 6, and 7 were established by time-dependent density functional theory ECD (TDDFT-ECD) calculations. All these compounds had different degrees of concentration-dependent activating effects on nuclear-factor-E2-related factor-2 (Nrf2).
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Affiliation(s)
- Pan Wang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
- Henan Province Technological Innovation Center for Solid Preparation of Traditional Chinese Medicine, Zhongjing Wanxi Pharmaceutical Co., Ltd., Nanyang, China
| | - Yi-nan Zhao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Rui-zhu Xu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiao-wei Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yi-ran Sun
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Qing-mei Feng
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhong-hua Li
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jiang-yan Xu
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhi-shen Xie
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
- *Correspondence: Zhi-shen Xie
| | - Zhen-qiang Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
- Zhen-qiang Zhang
| | - Heng-chao E
- Institute for Agri-Food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Heng-chao E
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12
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Xu J, Liu Z, Feng Z, Ren Y, Liu H, Wang Y. Rapid Mining of Novel α-Glucosidase and Lipase Inhibitors from Streptomyces sp. HO1518 Using UPLC-QTOF-MS/MS. Mar Drugs 2022; 20:md20030189. [PMID: 35323488 PMCID: PMC8955712 DOI: 10.3390/md20030189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
A rapid and sensitive method using ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) was applied for the analysis of the metabolic profile of acarviostatin-containing aminooligosaccharides derived from Streptomyces sp. HO1518. A total of ninety-eight aminooligosaccharides, including eighty potential new compounds, were detected mainly based on the characteristic fragment ions originating from quinovosidic bond cleavages in their molecules. Following an LC-MS-guided separation technique, seven new aminooligosaccharides (10–16) along with four known related compounds (17–20) were obtained directly from the crude extract of strain HO1518. Compounds 10–13 represent the first examples of aminooligosaccharides with a rare acarviostatin II02-type structure. In addition, all isolates displayed considerable inhibitory effects on three digestive enzymes, which revealed that the number of the pseudo-trisaccharide core(s), the feasible length of the oligosaccharides, and acyl side chain exerted a crucial influence on their bioactivities. These results demonstrated that the UPLC-QTOF-MS/MS-based metabolomics approach could be applied for the rapid identification of aminooligosaccharides and other similar structures in complex samples. Furthermore, this study highlights the potential of acylated aminooligosaccharides with conspicuous α-glucosidase and lipase inhibition for the future development of multi-target anti-diabetic drugs.
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Affiliation(s)
- Jianlin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (J.X.); (Y.R.)
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhifeng Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhanguang Feng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuhong Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (J.X.); (Y.R.)
| | - Haili Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- Correspondence: (H.L.); (Y.W.); Tel.: +86-021-5492-4295 (Y.W.)
| | - Yong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (J.X.); (Y.R.)
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (Z.L.); (Z.F.)
- Correspondence: (H.L.); (Y.W.); Tel.: +86-021-5492-4295 (Y.W.)
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13
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An in-house database-driven untargeted identification strategy for deep profiling of chemicalome in Chinese medicinal formula. J Chromatogr A 2022; 1666:462862. [DOI: 10.1016/j.chroma.2022.462862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022]
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14
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Zhao R, Fu J, Zhu L, Chen Y, Liu B. Designing strategies of small-molecule compounds for modulating non-coding RNAs in cancer therapy. J Hematol Oncol 2022; 15:14. [PMID: 35123522 PMCID: PMC8817562 DOI: 10.1186/s13045-022-01230-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been defined as a class of RNA molecules transcribed from the genome but not encoding proteins, such as microRNAs, long non-coding RNAs, Circular RNAs, and Piwi-interacting RNAs. Accumulating evidence has recently been revealing that ncRNAs become potential druggable targets for regulation of several small-molecule compounds, based on their complex spatial structures and biological functions in cancer therapy. Thus, in this review, we focus on summarizing some new emerging designing strategies, such as high-throughput screening approach, small-molecule microarray approach, structure-based designing approach, phenotypic screening approach, fragment-based designing approach, and pharmacological validation approach. Based on the above-mentioned approaches, a series of representative small-molecule compounds, including Bisphenol-A, Mitoxantrone and Enoxacin have been demonstrated to modulate or selectively target ncRNAs in different types of human cancers. Collectively, these inspiring findings would provide a clue on developing more novel avenues for pharmacological modulations of ncRNAs with small-molecule drugs for future cancer therapeutics.
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15
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Li SF, Lv TM, Li YL, Yu XQ, Yao GD, Lin B, Huang XX, Song SJ. Vibsanoids A–D, four new subtypes of vibsane diterpenoids with a distinctive tricyclo[8.2.1.0 2,9]tridecane core from Viburnum odoratissimum. Org Chem Front 2022. [DOI: 10.1039/d2qo00674j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four highly rearranged tetranorvibsane-type diterpenoids, vibsanoids A–D, with an unprecedented tricyclo[8.2.1.02,9]tridecane skeleton were isolated from Viburnum odoratissimum.
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Affiliation(s)
- Shi-Fang Li
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Tian-Ming Lv
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ya-Ling Li
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xiao-Qi Yu
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Bin Lin
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
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16
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Covington BC, Seyedsayamdost MR. MetEx, a Metabolomics Explorer Application for Natural Product Discovery. ACS Chem Biol 2021; 16:2825-2833. [PMID: 34859662 DOI: 10.1021/acschembio.1c00737] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in next-generation DNA sequencing technologies, bioinformatics, and mass spectrometry-based metabolite detection have ushered in a new era of natural product discovery. Microbial secondary metabolomes are complex, especially when otherwise silent biosynthetic genes are activated, and there is therefore a need for data analysis software to explore and map the resulting multidimensional datasets. To that end, we herein report the Metabolomics Explorer (MetEx), a publicly available web application for the analysis of parallel liquid chromatography-coupled mass spectrometry (LC-MS)-based metabolomics data. MetEx is a highly interactive application that facilitates visualization and analysis of complex metabolomics datasets, consisting of retention time, m/z, and MS intensity features, as a function of hundreds of conditions or elicitors. The software enables prioritization of leads from three-dimensional maps, extraction of two-dimensional slices from various higher order plots, organization of datasets by elicitor chemotypes, customizable library-based dereplication, and automatically scored lead selection. We describe the application of MetEx to the first UPLC-MS-guided high-throughput elicitor screen in which Burkholderia gladioli was challenged with 750 elicitors, and the resulting profiles were interrogated by UPLC-Qtof-MS and subsequently analyzed with the app. We demonstrate the utility of MetEx by reporting elicitors for several cryptic metabolite groups and by uncovering new natural products that remain to be characterized. MetEx is available at https://mo.princeton.edu/MetEx/.
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Affiliation(s)
- Brett C. Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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17
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Adegboye O, Field MA, Kupz A, Pai S, Sharma D, Smout MJ, Wangchuk P, Wong Y, Loiseau C. Natural-Product-Based Solutions for Tropical Infectious Diseases. Clin Microbiol Rev 2021; 34:e0034820. [PMID: 34494873 PMCID: PMC8673330 DOI: 10.1128/cmr.00348-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
About half of the world's population and 80% of the world's biodiversity can be found in the tropics. Many diseases are specific to the tropics, with at least 41 diseases caused by endemic bacteria, viruses, parasites, and fungi. Such diseases are of increasing concern, as the geographic range of tropical diseases is expanding due to climate change, urbanization, change in agricultural practices, deforestation, and loss of biodiversity. While traditional medicines have been used for centuries in the treatment of tropical diseases, the active natural compounds within these medicines remain largely unknown. In this review, we describe infectious diseases specific to the tropics, including their causative pathogens, modes of transmission, recent major outbreaks, and geographic locations. We further review current treatments for these tropical diseases, carefully consider the biodiscovery potential of the tropical biome, and discuss a range of technologies being used for drug development from natural resources. We provide a list of natural products with antimicrobial activity, detailing the source organisms and their effectiveness as treatment. We discuss how technological advancements, such as next-generation sequencing, are driving high-throughput natural product screening pipelines to identify compounds with therapeutic properties. This review demonstrates the impact natural products from the vast tropical biome have in the treatment of tropical infectious diseases and how high-throughput technical capacity will accelerate this discovery process.
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Affiliation(s)
- Oyelola Adegboye
- Public Health and Tropical Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
- World Health Organization Collaborating Center for Vector-Borne and Neglected Tropical Diseases, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Matt A. Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
- Garvin Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Andreas Kupz
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Saparna Pai
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Dileep Sharma
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Cairns, QLD, Australia
| | - Michael J. Smout
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Phurpa Wangchuk
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Yide Wong
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
| | - Claire Loiseau
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia
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18
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Li T, Zhang M, Tan Z, Miao J, He Y, Zhang A, Ou M, Huang D, Wu F, Wang X. Rapid characterization of the constituents in Jigucao capsule using ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry. J Sep Sci 2021; 45:677-696. [PMID: 34822724 DOI: 10.1002/jssc.202100664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
Jigucao capsule is a well-known Chinese patent medicine for the treatment of acute and chronic hepatitis and cholecystitis. The chemical components of Jigucao capsule were not clear resulting from the paucity of relevant studies, which hindered the research of the pharmacological mechanism, the comprehensive development, and utilization of Jigucao capsule in clinical studies. By establishing a high-throughput ultra-performance liquid chromatography quadrupole time of flight mass spectrometry in combination with intelligent UNIFI software data processing platform to automatically characterize and identify the chemical profile of Jigucao capsule, 144 compounds were determined rapidly, including 34 terpenoids, 25 flavonoids, 22 steroids, 21 phenylpropanoids, 10 glycosides, six alkaloids, 13 organic acids, and other 13 components. These compounds may be the active components of Jigucao capsule. In this study, a rapid and robust method for comprehensively analyzing the chemical composition of Jigucao capsule was described and established for the first time. The results will provide a reference for the quality control of Jigucao capsule and the establishment of a higher quality standard, as well as for the pharmacodynamic material basis research.
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Affiliation(s)
- Taiping Li
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China.,National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Mengli Zhang
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Zhien Tan
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Jianhua Miao
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Yanmei He
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Aihua Zhang
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Min Ou
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Danna Huang
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Fangfang Wu
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Xijun Wang
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China.,National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
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19
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Hostetler MA, Smith C, Nelson S, Budimir Z, Modi R, Woolsey I, Frerk A, Baker B, Gantt J, Parkinson EI. Synthetic Natural Product Inspired Cyclic Peptides. ACS Chem Biol 2021; 16:2604-2611. [PMID: 34699170 PMCID: PMC8610019 DOI: 10.1021/acschembio.1c00641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Natural products
are a bountiful source of bioactive molecules.
Unfortunately, discovery of novel bioactive natural products is challenging
due to cryptic biosynthetic gene clusters, low titers, and arduous
purifications. Herein, we describe SNaPP (Synthetic Natural Product
Inspired Cyclic Peptides), a method for identifying
NP-inspired bioactive peptides. SNaPP expedites bioactive molecule
discovery by combining bioinformatics predictions of nonribosomal
peptide synthetases with chemical synthesis of the predicted natural
products (pNPs). SNaPP utilizes a recently discovered cyclase, the
penicillin binding protein-like cyclase, as the lynchpin for the development
of a library of head-to-tail cyclic peptide pNPs. Analysis of 500
biosynthetic gene clusters allowed for identification of 131 novel
pNPs. Fifty-one diverse pNPs were synthesized using solid phase peptide
synthesis and solution-phase cyclization. Antibacterial testing revealed
14 pNPs with antibiotic activity, including activity against multidrug-resistant
Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining
bioinformatics predictions with chemical synthesis to accelerate the
discovery of bioactive molecules.
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Affiliation(s)
- Matthew A. Hostetler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chloe Smith
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zachary Budimir
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ian Woolsey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Autumn Frerk
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Braden Baker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jessica Gantt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth I. Parkinson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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20
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He Q, Wu Z, Li L, Sun W, Wang G, Jiang R, Hu L, Shi L, He R, Wang Y, Ye W. Discovery of Neuritogenic
Securinega
Alkaloids from
Flueggea suffruticosa
by a Building Blocks‐Based Molecular Network Strategy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qi‐Fang He
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Zhen‐Long Wu
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Liuren Li
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Wan‐Yang Sun
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Gui‐Yang Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Ren‐Wang Jiang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Li‐Jun Hu
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Lei Shi
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Rong‐Rong He
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Ying Wang
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Wen‐Cai Ye
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
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21
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He QF, Wu ZL, Li L, Sun WY, Wang GY, Jiang RW, Hu LJ, Shi L, He RR, Wang Y, Ye WC. Discovery of Neuritogenic Securinega Alkaloids from Flueggea suffruticosa by a Building Blocks-Based Molecular Network Strategy. Angew Chem Int Ed Engl 2021; 60:19609-19613. [PMID: 34196083 DOI: 10.1002/anie.202103878] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/28/2021] [Indexed: 12/22/2022]
Abstract
A combined strategy of building blocks recognition and molecular network construction, termed the building blocks-based molecular network (BBMN), was first presented to facilitate the efficient discovery of novel natural products. By mapping the BBMN of the total alkaloid fraction of Flueggea suffruticosa, three Securinega alkaloids (SEAs) with unusual chemical architectures, suffranidines A-C (1-3), were discovered and isolated. Compound 1 characterizes an unprecedented 8/5/6/5/6/6/6/6-fused octacyclic scaffold with a unique cage-shaped 3-azatricyclo[6.4.0.03,11 ]dodecane core. Compounds 2 and 3 are highly modified SEA dimers that incorporate additional C6 motifs. A hypothetical biosynthetic pathway for 1-3 was proposed. In addition, 1 significantly induced neuronal differentiation and neurite extension by upregulating eukaryotic elongation factor 2 (eEF2)-mediated protein synthesis.
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Affiliation(s)
- Qi-Fang He
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Zhen-Long Wu
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Liuren Li
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Wan-Yang Sun
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Gui-Yang Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Ren-Wang Jiang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Li-Jun Hu
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Lei Shi
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Rong-Rong He
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Ying Wang
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Wen-Cai Ye
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
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22
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Pham HT, Lee KH, Jeong E, Woo S, Yu J, Kim WY, Lim YW, Kim KH, Kang KB. Species Prioritization Based on Spectral Dissimilarity: A Case Study of Polyporoid Fungal Species. JOURNAL OF NATURAL PRODUCTS 2021; 84:298-309. [PMID: 33529025 DOI: 10.1021/acs.jnatprod.0c00977] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biological species collections are critical for natural product drug discovery programs. However, prioritization of target species in massive collections remains difficult. Here, we introduce an untargeted metabolomics-based prioritization workflow that uses MS/MS molecular networking to estimate scaffold-level distribution. As a demonstration, we applied the workflow to 40 polyporoid fungal species. Nine species were prioritized as candidates based on the chemical structural and compositional similarity (CSCS) metric. Most of the selected species showed relatively higher richness and uniqueness of metabolites than those of the others. Cryptoporus volvatus, one of the prioritized species, was investigated further. The chemical profiles of the extracts of C. volvatus culture and fruiting bodies were compared, and it was shown that derivative-level diversity was higher in the fruiting bodies; meanwhile, scaffold-level diversity was similar. This showed that the compounds found from a cultured fungus can also be isolated in wild mushrooms. Targeted isolation of the fruiting body extract yielded three unknown (1-3) and six known (4-9) cryptoporic acid derivatives, which are drimane-type sesquiterpenes with isocitric acid moieties that have been reported in this species. Cryptoporic acid T (1) is a trimeric cryptoporic acid reported for the first time. Compounds 2 and 5 exhibited cytotoxicity against HCT-116 cell lines with IC50 values of 4.3 and 3.6 μM, respectively.
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Affiliation(s)
- Huong T Pham
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Korea
| | - Kwang Ho Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Eunah Jeong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Korea
| | - Sunmin Woo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea
| | - Jinsuh Yu
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Korea
| | - Woo-Young Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Korea
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23
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Zhao C, Li S, Zhang J, Huang Y, Zhang L, Zhao F, Du X, Hou J, Zhang T, Shi C, Wang P, Huo R, Woodman OL, Qin CX, Xu H, Huang L. Current state and future perspective of cardiovascular medicines derived from natural products. Pharmacol Ther 2020; 216:107698. [PMID: 33039419 DOI: 10.1016/j.pharmthera.2020.107698] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The contribution of natural products (NPs) to cardiovascular medicine has been extensively documented, and many have been used for centuries. Cardiovascular disease (CVD) is the leading cause of morbidity and mortality worldwide. Over the past 40 years, approximately 50% of newly developed cardiovascular drugs were based on NPs, suggesting that NPs provide essential skeletal structures for the discovery of novel medicines. After a period of lower productivity since the 1990s, NPs have recently regained scientific and commercial attention, leveraging the wealth of knowledge provided by multi-omics, combinatorial biosynthesis, synthetic biology, integrative pharmacology, analytical and computational technologies. In addition, as a crucial part of complementary and alternative medicine, Traditional Chinese Medicine has increasingly drawn attention as an important source of NPs for cardiovascular drug discovery. Given their structural diversity and biological activity NPs are one of the most valuable sources of drugs and drug leads. In this review, we briefly described the characteristics and classification of NPs in CVDs. Then, we provide an up to date summary on the therapeutic potential and the underlying mechanisms of action of NPs in CVDs, and the current view and future prospect of developing safer and more effective cardiovascular drugs based on NPs.
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Affiliation(s)
- Chunhui Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Sen Li
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Junhong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yuanyun Huang
- Biology Department, Cornell University, Ithaca, NY 14850, United States of America
| | - Luoqi Zhang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Feng Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xia Du
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Shaanxi Academy of Traditional Chinese Medicine, Xi'an 710003, China
| | - Jinli Hou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Tong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chenjing Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ping Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruili Huo
- China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Owen L Woodman
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
| | - Cheng Xue Qin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia; School of Pharmaceutical Science, Shandong University, Shandong 250100, China; Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong 250100, China.
| | - Haiyu Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; China Academy of Chinese Medical Sciences, Beijing 100700, China.
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24
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Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep 2020; 37:879-892. [PMID: 31912842 PMCID: PMC7340575 DOI: 10.1039/c9np00050j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.
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Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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25
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Grim CM, Luu GT, Sanchez LM. Staring into the void: demystifying microbial metabolomics. FEMS Microbiol Lett 2020; 366:5519856. [PMID: 31210257 DOI: 10.1093/femsle/fnz135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a 'choose your own adventure' approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.
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Affiliation(s)
- Cynthia M Grim
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Gordon T Luu
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
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26
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Lorsbach BA, Sparks TC, Cicchillo RM, Garizi NV, Hahn DR, Meyer KG. Natural products: a strategic lead generation approach in crop protection discovery. PEST MANAGEMENT SCIENCE 2019; 75:2301-2309. [PMID: 30672097 DOI: 10.1002/ps.5350] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 05/14/2023]
Abstract
With the anticipated population growth in the coming decades, the changing regulatory environment, and the continued emergence of resistance to commercial pesticides, there is a constant need to discover new lead chemistries with novel modes of action. We have established a portfolio of approaches to accelerate lead generation. One of these approaches capitalizes on the rich bioactivity of natural products (NPs), highlighted by the numerous examples of NP-based crop protection compounds. Within Corteva Agriscience and the affiliated preceding companies, NPs have been a fruitful approach, for nearly three decades, to identifying and bringing to the market crop protection products inspired by or originating from NPs, . Included in these NP-based crop protection products are the spinosyns family of insecticides, and those from more recent areas of NP-based fungicidal chemistry, as highlighted in this perspective. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Beth A Lorsbach
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Thomas C Sparks
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Robert M Cicchillo
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Negar V Garizi
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Donald R Hahn
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Kevin G Meyer
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
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27
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Fox Ramos AE, Pavesi C, Litaudon M, Dumontet V, Poupon E, Champy P, Genta-Jouve G, Beniddir MA. CANPA: Computer-Assisted Natural Products Anticipation. Anal Chem 2019; 91:11247-11252. [PMID: 31369240 DOI: 10.1021/acs.analchem.9b02216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Traditional natural products discovery workflows implying a combination of different targeting strategies, including structure- and/or bioactivity-based approaches, afford no information about new compound structures until late in the discovery pipeline. By integrating a MS/MS prediction module and a collaborative library of (bio)chemical transformations, we have developed a new platform, coined MetWork, that is capable of anticipating the structural identity of metabolites starting from any identified compound. In our quest to discover new monoterpene indole alkaloids, we demonstrate the utility of the MetWork platform by anticipating the structures of five previously undescribed sarpagine-like N-oxide alkaloids that have been targeted and isolated from the leaves of Alstonia balansae using a molecular networking-based dereplication strategy fueled by computer-generated annotations. This study constitutes the first example of nonpeptidic molecular networking-based natural product discovery workflow, in which the targeted structures were initially generated, and therefore anticipated by a computer prior to their isolation.
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Affiliation(s)
- Alexander E Fox Ramos
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Coralie Pavesi
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay , 21 avenue de la Terrasse , 91198 , Gif-sur-Yvette , France
| | - Vincent Dumontet
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay , 21 avenue de la Terrasse , 91198 , Gif-sur-Yvette , France
| | - Erwan Poupon
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Pierre Champy
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
| | - Grégory Genta-Jouve
- C-TAC UMR CNRS 8038 CiTCoM, Faculté de Pharmacie de Paris, Université Paris Descartes , 4 avenue de l'Observatoire , 75006 Paris , France.,Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245) , Sorbonne Universités, CNRS , 75006 Paris , France
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie-chimie des substances naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay , 5 rue J.-B. Clément , 92290 Châtenay-Malabry , France
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28
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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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29
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Woo S, Kang KB, Kim J, Sung SH. Molecular Networking Reveals the Chemical Diversity of Selaginellin Derivatives, Natural Phosphodiesterase-4 Inhibitors from Selaginella tamariscina. JOURNAL OF NATURAL PRODUCTS 2019; 82:1820-1830. [PMID: 31244143 DOI: 10.1021/acs.jnatprod.9b00049] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Selaginellins are unique pigments found in the genus Selaginella, the largest genus of Lycopodiophyta. Recent studies reported that some selaginellin analogues have potent phosphodiesterase-4 (PDE4) inhibitory activity. In this study, the chemical diversity of natural selaginellin derivatives was revealed by an MS/MS molecular networking-based dereplication of the Selaginella tamariscina extract. It led to the prioritization of chromatographic peaks predicted as previously unknown selaginellin derivatives. Targeted isolation of these compounds afforded two unusual selaginellin analogues with a 1H,3H-dibenzo[de,h]isochromene skeleton, namely, selariscins A (1) and B (2), along with eight new diarylfluorene derivatives, selaginpulvilins M-T (3-10), and five known analogues, 11-15. The absolute configurations of 1, 2, and 8-10 were elucidated by spectroscopic data analyses including computational electronic circular dichroism data. Compounds 1 and 3-10 showed PDE4 inhibitory activity with IC50 values in the range of 2.8-33.8 μM, and their binding modes are suggested by a molecular docking study.
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Affiliation(s)
- Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy , Sookmyung Women's University , Seoul 04310 , Republic of Korea
| | - Jinwoong Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
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30
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Caesar LK, Cech NB. Synergy and antagonism in natural product extracts: when 1 + 1 does not equal 2. Nat Prod Rep 2019; 36:869-888. [PMID: 31187844 PMCID: PMC6820002 DOI: 10.1039/c9np00011a] [Citation(s) in RCA: 345] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 2000 to 2019 According to a 2012 survey from the Centers for Disease Control and Prevention, approximately 18% of the U.S. population uses natural products (including plant-based or botanical preparations) for treatment or prevention of disease. The use of plant-based medicines is even more prevalent in developing countries, where for many they constitute the primary health care modality. Proponents of the medicinal use of natural product mixtures often claim that they are more effective than purified compounds due to beneficial "synergistic" interactions. A less-discussed phenomenon, antagonism, in which effects of active constituents are masked by other compounds in a complex mixture, also occurs in natural product mixtures. Synergy and antagonism are notoriously difficult to study in a rigorous fashion, particularly given that natural products chemistry research methodology is typically devoted to reducing complexity and identifying single active constituents for drug development. This report represents a critical review with commentary about the current state of the scientific literature as it relates to studying combination effects (including both synergy and antagonism) in natural product extracts. We provide particular emphasis on analytical and Big Data approaches for identifying synergistic or antagonistic combinations and elucidating the mechanisms that underlie their interactions. Specific case studies of botanicals in which synergistic interactions have been documented are also discussed. The topic of synergy is important given that consumer use of botanical natural products and associated safety concerns continue to garner attention by the public and the media. Guidance by the natural products community is needed to provide strategies for effective evaluation of safety and toxicity of botanical mixtures and to drive discovery in botanical natural product research.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
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31
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Fox Ramos AE, Evanno L, Poupon E, Champy P, Beniddir MA. Natural products targeting strategies involving molecular networking: different manners, one goal. Nat Prod Rep 2019; 36:960-980. [PMID: 31140509 DOI: 10.1039/c9np00006b] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2019Landmark advances in bioinformatics tools have recently enhanced the field of natural products research, putting today's natural product chemists in the enviable position of being able to perform the efficient targeting/discovery of previously undescribed molecules by expediting the prioritization of the isolation workflow. Among these advances, MS/MS molecular networking has appeared as a promising approach to dereplicate complex natural product mixtures, leading to a real revolution in the "art of natural product isolation" by accelerating the pace of research of this field. This review illustrates through selected cornerstone studies the new thinking in natural product isolation by drawing a parallel between the different underlying philosophies behind the use of molecular networking in targeting natural products.
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Affiliation(s)
- Alexander E Fox Ramos
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Laurent Evanno
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Erwan Poupon
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Pierre Champy
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
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Lee HJ, Dhodary B, Lee JY, An JP, Ryu YK, Kim KS, Lee CH, Oh WK. Dereplication of Components Coupled with HPLC-qTOF-MS in the Active Fraction of Humulus japonicus and It's Protective Effects against Parkinson's Disease Mouse Model. Molecules 2019; 24:E1435. [PMID: 30979037 PMCID: PMC6480934 DOI: 10.3390/molecules24071435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022] Open
Abstract
Humulus japonicus is an annual plant belonging to the Cannabacea family, and it has been traditionally used to treat pulmonary tuberculosis, dysentery, chronic colitis, and hypertension. We investigated the active components against Parkinson's disease from H. japonicus fraction (HJF) using high performance liquid chromatography (HPLC) coupled with quadruple-time-of-flight mass spectroscopy (qTOF-MS) and NMR. Fourteen compounds were isolated from HJF, including one new compound, using HPLC-qTOF-MS and NMR. The major compounds of HJF were luteolin-7-O-glucoside and apigenin-7-O-glucoside, and there was approximately 12.57- and 9.68-folds increase in the contents of these flavonoids compared to those of the 70% EtOH extract. Apigenin and luteolin exhibited the strongest inhibitory effects on monoamine oxidase (MAO) B enzyme activity. In animal studies, limb-use behavior was significantly reduced by unilateral 6-OHDA lesion and ipsilateral rotations. These results indicated that oral administration of 300 mg/kg HJF resulted in the improvement of motor asymmetry and motor impairment in unilateral 6-OHDA-lesioned mice. HJF, including active components leads to an improvement of motor behavior in a Parkinson's disease mouse model.
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Affiliation(s)
- Hee Ju Lee
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, Korea.
| | - Basanta Dhodary
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Ju Yong Lee
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Jin-Pyo An
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Young-Kyoung Ryu
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
| | - Kyoung-Shim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
| | - Won Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
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Afzan A, Kasim N, Ismail NH, Azmi N, Ali AM, Mat N, Wolfender JL. Differentiation of Ficus deltoidea varieties and chemical marker determination by UHPLC-TOFMS metabolomics for establishing quality control criteria of this popular Malaysian medicinal herb. Metabolomics 2019; 15:35. [PMID: 30830457 DOI: 10.1007/s11306-019-1489-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Ficus deltoidea Jack (Moraceae) is a plant used in Malaysia for various diseases including as a supplement in diabetes management. Morphology distinction of the 7 main varieties (var. angustifolia, var. bilobata, var. deltoidea, var. intermedia, var. kunstleri, var. motleyana and var. trengganuensis) is challenging due to the extreme leaf heterophylly and unclear varietal boundaries, making it difficult for quality control of F. deltoidea products. OBJECTIVE We aimed to compare the phytochemical composition of 7 varieties growing in different conditions at various geographical locations. We also aimed to establish the quality control markers for the authentication of these varieties. METHODS We applied untargeted UHPLC-TOFMS metabolomics to discriminate 100 leaf samples of F. deltoidea collected from 6 locations in Malaysia. A genetic analysis on 21 leaf samples was also performed to validate the chemotaxonomy differentiation. RESULTS The PCA and HCA analysis revealed the existence of 3 chemotypes based on the differentiation in the flavonoid content. The PLS-DA analysis identified 15 glycosylated flavone markers together with 1 furanocoumarin. These markers were always consistent for the respective varieties, regardless of the geographical locations and growing conditions. The chemotaxonomy differentiation was in agreement with the DNA sequencing. In particular, var. bilobata accession which showed divergent morphology was also differentiated by the chemical fingerprints and genotype. CONCLUSION Chemotype differentiation based on the flavonoid fingerprints along with the proposed markers provide a powerful identification tool to complement morphology and genetic analyses for the quality control of raw materials and products from F. deltoidea.
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Affiliation(s)
- Adlin Afzan
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Rue Michel-Servet 1, 1206, Geneva, Switzerland
- Phytochemistry Unit, Herbal Medicine Research Center, Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
| | - Noraini Kasim
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA, Kampus Puncak Alam, 42300, Selangor, Malaysia
| | - Nor Hadiani Ismail
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA, Kampus Puncak Alam, 42300, Selangor, Malaysia
| | - Norfaizura Azmi
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia
- Institute of Agropolis, Universiti Sultan Zainal Abidin, Campus Besut, 22200, Besut, Terengganu, Malaysia
- Natural Medicine Center, Universiti Islam, Cyberjaya, 63000, Cyberjaya, Selangor, Malaysia
| | - Nashriyah Mat
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Rue Michel-Servet 1, 1206, Geneva, Switzerland.
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Kempa EE, Hollywood KA, Smith CA, Barran PE. High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis. Analyst 2019; 144:872-891. [DOI: 10.1039/c8an01448e] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.
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Affiliation(s)
- Emily E. Kempa
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
| | - Katherine A. Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Clive A. Smith
- Sphere Fluidics Limited
- The Jonas-Webb Building
- Babraham Research Campus
- Cambridge
- UK
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
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Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Anal Chem 2018; 91:704-742. [DOI: 10.1021/acs.analchem.8b05112] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | | | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 44035 Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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36
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Zhang A, Sun H, Wang X. Mass spectrometry-driven drug discovery for development of herbal medicine. MASS SPECTROMETRY REVIEWS 2018; 37:307-320. [PMID: 28009933 DOI: 10.1002/mas.21529] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Herbal medicine (HM) has made a major contribution to the drug discovery process with regard to identifying products compounds. Currently, more attention has been focused on drug discovery from natural compounds of HM. Despite the rapid advancement of modern analytical techniques, drug discovery is still a difficult and lengthy process. Fortunately, mass spectrometry (MS) can provide us with useful structural information for drug discovery, has been recognized as a sensitive, rapid, and high-throughput technology for advancing drug discovery from HM in the post-genomic era. It is essential to develop an efficient, high-quality, high-throughput screening method integrated with an MS platform for early screening of candidate drug molecules from natural products. We have developed a new chinmedomics strategy reliant on MS that is capable of capturing the candidate molecules, facilitating their identification of novel chemical structures in the early phase; chinmedomics-guided natural product discovery based on MS may provide an effective tool that addresses challenges in early screening of effective constituents of herbs against disease. This critical review covers the use of MS with related techniques and methodologies for natural product discovery, biomarker identification, and determination of mechanisms of action. It also highlights high-throughput chinmedomics screening methods suitable for lead compound discovery illustrated by recent successes.
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Affiliation(s)
- Aihua Zhang
- Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of TCM State Administration, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hui Sun
- Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of TCM State Administration, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xijun Wang
- Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of TCM State Administration, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, China
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Nothias LF, Nothias-Esposito M, da Silva R, Wang M, Protsyuk I, Zhang Z, Sarvepalli A, Leyssen P, Touboul D, Costa J, Paolini J, Alexandrov T, Litaudon M, Dorrestein PC. Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation. JOURNAL OF NATURAL PRODUCTS 2018; 81:758-767. [PMID: 29498278 DOI: 10.1021/acs.jnatprod.7b00737] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s) may not be isolated during subsequent bioassay-guided purification. Herein, we present the concept of bioactive molecular networking to find candidate active molecules directly from fractionated bioactive extracts. By employing tandem mass spectrometry, it is possible to accelerate the dereplication of molecules using molecular networking prior to subsequent isolation of the compounds, and it is also possible to expose potentially bioactive molecules using bioactivity score prediction. Indeed, bioactivity score prediction can be calculated with the relative abundance of a molecule in fractions and the bioactivity level of each fraction. For that reason, we have developed a bioinformatic workflow able to map bioactivity score in molecular networks and applied it for discovery of antiviral compounds from a previously investigated extract of Euphorbia dendroides where the bioactive candidate molecules were not discovered following a classical bioassay-guided fractionation procedure. It can be expected that this approach will be implemented as a systematic strategy, not only in current and future bioactive lead discovery from natural extract collections but also for the reinvestigation of the untapped reservoir of bioactive analogues in previous bioassay-guided fractionation efforts.
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Affiliation(s)
- Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301 , Université Paris-Sud , 91198 , Gif-sur-Yvette , France
| | - Mélissa Nothias-Esposito
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301 , Université Paris-Sud , 91198 , Gif-sur-Yvette , France
- Laboratoire de Chimie des Produits Naturels, CNRS, UMR SPE 6134 , University of Corsica , 20250 , Corte , France
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ivan Protsyuk
- European Molecular Biology Laboratory, EMBL , Heidelberg , Germany
| | - Zheng Zhang
- Collaborative Mass Spectrometry Innovation Center , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Abi Sarvepalli
- Collaborative Mass Spectrometry Innovation Center , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Pieter Leyssen
- Laboratory for Virology and Experimental Chemotherapy, Rega Institute for Medical Research , KU Leuven , 3000 Leuven , Belgium
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301 , Université Paris-Sud , 91198 , Gif-sur-Yvette , France
| | - Jean Costa
- Laboratoire de Chimie des Produits Naturels, CNRS, UMR SPE 6134 , University of Corsica , 20250 , Corte , France
| | - Julien Paolini
- Laboratoire de Chimie des Produits Naturels, CNRS, UMR SPE 6134 , University of Corsica , 20250 , Corte , France
| | - Theodore Alexandrov
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
- European Molecular Biology Laboratory, EMBL , Heidelberg , Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301 , Université Paris-Sud , 91198 , Gif-sur-Yvette , France
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
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Netzker T, Flak M, Krespach MK, Stroe MC, Weber J, Schroeckh V, Brakhage AA. Microbial interactions trigger the production of antibiotics. Curr Opin Microbiol 2018; 45:117-123. [PMID: 29702423 DOI: 10.1016/j.mib.2018.04.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 11/30/2022]
Abstract
Since the discovery of penicillin, antibiotics have been instrumental in treating infectious diseases. However, emerging antibiotic multi-resistance coinciding with a nearly exhausted drug pipeline is a major concern for the future of the therapy of infections. A novel approach for the discovery of antibiotics relies on the analysis of microbial consortia in their ecological context, taking into account the potential natural role of antibiotics. Co-cultivations of microorganisms have been successfully applied for the isolation of unknown secondary metabolites including antibiotics, and, thus, open new avenues to the production of bioactive compounds while at the same time providing insight into the natural function of the produced molecules and the regulation of their formation.
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Affiliation(s)
- Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Michal Flak
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Mario Kc Krespach
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Maria C Stroe
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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39
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Olivon F, Apel C, Retailleau P, Allard PM, Wolfender JL, Touboul D, Roussi F, Litaudon M, Desrat S. Searching for original natural products by molecular networking: detection, isolation and total synthesis of chloroaustralasines. Org Chem Front 2018. [DOI: 10.1039/c8qo00429c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Four unprecedented chlorinated monoterpenyl quinolones have been isolated using a molecular networking based prioritisation strategy. The bio-inspired total synthesis of chloroaustralasine A involving a chloroperoxydase-mediated hydroxychlorination is described.
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Affiliation(s)
- F. Olivon
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
| | - C. Apel
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
| | - P. Retailleau
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
| | - P. M. Allard
- School of Pharmaceutical Sciences
- University of Geneva
- University of Lausanne
- 1211 Geneva 11
- Switzerland
| | - J. L. Wolfender
- School of Pharmaceutical Sciences
- University of Geneva
- University of Lausanne
- 1211 Geneva 11
- Switzerland
| | - D. Touboul
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
| | - F. Roussi
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
| | - M. Litaudon
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
| | - S. Desrat
- Institut de Chimie des Substances Naturelles
- CNRS-ICSN
- UPR 2301
- Université Paris-Saclay
- Gif-sur-Yvette
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Vaniya A, Samra SN, Palazoglu M, Tsugawa H, Fiehn O. Using MS-FINDER for identifying 19 natural products in the CASMI 2016 contest. PHYTOCHEMISTRY LETTERS 2017; 21:306-312. [PMID: 31576201 PMCID: PMC6771281 DOI: 10.1016/j.phytol.2016.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In its fourth year, the CASMI 2016 contest was organized to evaluate current chemical structure identification strategies for 19 natural products using high-resolution LC-MS and LC-MS/MS challenge datasets using automated methods with or without the combination of other tools. These natural products originate from plants, fungi, marine sponges, algae, or micro-algae. Every compound annotation workflow must start with determination of elemental compositions. Of these 19 challenges, one was excluded by the organizers after submission. For the remaining 18 challenges, three software programs were used. MS-FINDER version 1.62 was able to correctly identify 89% of the molecular formulas using an internal database that comprised of 13 metabolomics repositories with 45,181 formulas. SIRIUS correctly identified 61% compositions using PubChem formulas and Seven Golden Rules correctly identified 83% by using the Dictionary of Natural Products as a targeted database. Next, we performed structural dereplication for which we used the consensus formula from the three software programs. We submitted two solution sets for these challenges. In the first solution set, avaniya001, we only used the internal MS-FINDER functions for predicting and ranking structures, correctly identifying 53% of the structures as top-hit, 72% within the top-3 structures, and 78% within the top-10 hits. For our second set, avaniya002, we used both MS-FINDER predictions as well as MS/MS queries against the commercial NIST 14, METLIN, and the public MassBank of North America libraries. Here we correctly identified 78% of the structures as top-hit and 83% within the top-3 hits. Three challenge spectra remained unidentified in either of our submissions within the top-10 hits.
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Affiliation(s)
- Arpana Vaniya
- University of California Davis, West Coast Metabolomics Center, Genome Center, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Stephanie N Samra
- University of California Davis, West Coast Metabolomics Center, Genome Center, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Mine Palazoglu
- University of California Davis, West Coast Metabolomics Center, Genome Center, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Oliver Fiehn
- University of California Davis, West Coast Metabolomics Center, Genome Center, 451 Health Sciences Drive, Davis, CA 95616, USA
- King Abdulaziz University, Biochemistry Department, Jeddah, Saudi-Arabia
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41
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Recent developments and emerging trends of mass spectrometry for herbal ingredients analysis. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu CC, Keller NP, Kelleher NL. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol 2017; 13:895-901. [PMID: 28604695 PMCID: PMC5577364 DOI: 10.1038/nchembio.2408] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/13/2017] [Indexed: 12/02/2022]
Abstract
The genomes of filamentous fungi contain up to 90 biosynthetic gene clusters (BGCs) encoding diverse secondary metabolites-an enormous reservoir of untapped chemical potential. However, the recalcitrant genetics, cryptic expression, and unculturability of these fungi prevent scientists from systematically exploiting these gene clusters and harvesting their products. As heterologous expression of fungal BGCs is largely limited to the expression of single or partial clusters, we established a scalable process for the expression of large numbers of full-length gene clusters, called FAC-MS. Using fungal artificial chromosomes (FACs) and metabolomic scoring (MS), we screened 56 secondary metabolite BGCs from diverse fungal species for expression in Aspergillus nidulans. We discovered 15 new metabolites and assigned them with confidence to their BGCs. Using the FAC-MS platform, we extensively characterized a new macrolactone, valactamide A, and its hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS). The ability to regularize access to fungal secondary metabolites at an unprecedented scale stands to revitalize drug discovery platforms with renewable sources of natural products.
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Affiliation(s)
- Kenneth D Clevenger
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rosa Ye
- Intact Genomics, Inc., St. Louis, Missouri, USA
| | - Galen P Miley
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Maria H Verdan
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Thomas Velk
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - KaHoua Yang
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Peng Gao
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | | | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | | | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, Wisconsin, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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Abstract
With the advent of very rapid and cheap genome analyses and the linkage of these plus microbial metabolomics to potential compound structures came the realization that there was an immense sea of novel agents to be mined and tested. In addition, it is now recognized that there is significant microbial involvement in many natural products isolated from “nominally non-microbial sources”. This short review covers the current screening methods that have evolved and one might even be tempted to say “devolved” in light of the realization that target-based screens had problems when the products entered clinical testing, with off-target effects being the major ones. Modern systems include, but are not limited to, screening in cell lines utilizing very modern techniques (a high content screen) that are designed to show interactions within cells when treated with an “agent”. The underlying principle(s) used in such systems dated back to unpublished attempts in the very early 1980s by the pharmaceutical industry to show toxic interactions within animal cells by using automated light microscopy. Though somewhat successful, the technology was not adequate for any significant commercialization. Somewhat later, mammalian cell lines that were “genetically modified” to alter signal transduction cascades, either up or down, and frequently linked to luciferase readouts, were then employed in a 96-well format. In the case of microbes, specific resistance parameters were induced in isogenic cell lines from approximately the mid-1970s. In the latter two cases, comparisons against parent and sibling cell lines were used in order that a rapid determination of potential natural product “hits” could be made. Obviously, all of these assay systems could also be, and were, used for synthetic molecules. These methods and their results have led to a change in what the term “screening for bioactivity” means. In practice, versions of phenotypic screening are returning, but in a dramatically different scientific environment from the 1970s, as I hope to demonstrate in the short article that follows.
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Hautbergue T, Puel O, Tadrist S, Meneghetti L, Péan M, Delaforge M, Debrauwer L, Oswald IP, Jamin EL. Evidencing 98 secondary metabolites of Penicillium verrucosum using substrate isotopic labeling and high-resolution mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1071:29-43. [PMID: 28351740 DOI: 10.1016/j.jchromb.2017.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/06/2017] [Accepted: 03/10/2017] [Indexed: 12/23/2022]
Abstract
Industrial applications of fungal compounds, coupled with the emergence of fungal threats to natural ecosystems and public health, have increased interest in filamentous fungi. Among all pathogenic fungi, Penicillium verrucosum is one of the most common mold-infecting stored cereals in temperate regions. However, it is estimated that 80% of fungal secondary metabolites remain unknown. To detect new P. verrucosum compounds, an untargeted metabolomic approach was applied to fungus grown on wheat grains labeled with stable isotopes: (i) natural grains (99% 12C); (ii) grains enriched with 97% of 13C; and (iii) grains enriched with 53% of 13C and 97% of 15N. Analyses performed by high-performance liquid chromatography coupled with high-resolution mass spectrometry (HPLC-HRMS) enabled the specific detection of fungal metabolites, and the unambiguous characterization of their chemical formulas. In this way, 98 secondary metabolites were detected and their chemical formulas were determined. Of these, only 18 identifications could be made based on databases, the literature and mass spectrometry fragmentation experiments, with the result that 80 were totally unknown. Molecular networks were generated to analyze these results, leading to the characterization by MSn experiments of a new fungisporin produced by P. verrucosum. More generally, this article provides precise mass spectrometric data about all these compounds for further studies of the Penicillium metabolome.
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Affiliation(s)
- Thaïs Hautbergue
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France; Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31027 Toulouse, France
| | - Olivier Puel
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France.
| | - Souria Tadrist
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Lauriane Meneghetti
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France; Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31027 Toulouse, France
| | - Michel Péan
- Groupe de Recherches Appliquées en Phytotechnologie, CEA, IBEB, Cadarache, FR 13108 Saint-Paul-les-Durance, France; UMR Biologie Végétale et Microbiologie Environnementale, CNRS, FR 13108 Saint-Paul-les-Durance, France; Université d'Aix-Marseille, FR 13007 Marseille, France
| | | | - Laurent Debrauwer
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France; Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31027 Toulouse, France
| | - Isabelle P Oswald
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Emilien L Jamin
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France; Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31027 Toulouse, France
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Ren H, Wang B, Zhao H. Breaking the silence: new strategies for discovering novel natural products. Curr Opin Biotechnol 2017; 48:21-27. [PMID: 28288336 DOI: 10.1016/j.copbio.2017.02.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/17/2017] [Indexed: 12/31/2022]
Abstract
Natural products have been a prolific source of antibacterial and anticancer drugs for decades. One of the major challenges in natural product discovery is that the vast majority of natural product biosynthetic gene clusters (BGCs) have not been characterized, partially due to the fact that they are either transcriptionally silent or expressed at very low levels under standard laboratory conditions. Here we describe the strategies developed in recent years (mostly between 2014-2016) for activating silent BGCs. These strategies can be broadly divided into two categories: approaches in native hosts and approaches in heterologous hosts. In addition, we briefly discuss recent advances in developing new computational tools for identification and characterization of BGCs and high-throughput methods for detection of natural products.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Bin Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Departments of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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Zhang JG, Geng CA, Huang XY, Chen XL, Ma YB, Zhang XM, Chen JJ. Chemical and biological comparison of different sections of Uncaria rhynchophylla (Gou-Teng). EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:11-21. [PMID: 28657449 DOI: 10.1177/1469066717694044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Uncaria rhynchophylla (Gou-Teng in Chinese) is officially documented in Chinese pharmacopoeia as one of the authentic sources for the crude drug of Gou-Teng which has long been used for mental and cardiovascular diseases. Indole alkaloids are the characteristic constituents responsible for the desired hypotensive effect; however, the psychiatric active constituents of Gou-Teng are still unclear. According to traditional Chinese medicine theory, only the hook-bearing stems of U. rhynchophylla are used as the crude materials for Gou-Teng, while its leaves and fruits are scarcely used. The present study aimed to compare the metabolic fingerprints of different parts (hooks, stems, leaves and fruits) of U. rhynchophylla by LC-DAD-MS/MS analysis and further evaluate their psychiatric activities on HEK293 cell line in vitro. A total of 38 constituents including 26 alkaloids, six flavonoids, two triterpenoids, two chlorogenic acid analogs and two other compounds were characterized. The different parts of U. rhynchophylla can be well differentiated from their chemical profiles. Leaves displayed the most potent activity on both MT1 and MT2 receptors, with agonistic rates of 39.7% and 97.6%. For 5-HT1A and 5-HT2C receptors, hooks showed the strongest activity with agonistic rates of 92.6% and 83.1%, respectively. This investigation provided valuable information for understanding the chemical divergence between different parts of U. rhynchophylla, and their substantial bases for psychiatric purposes.
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Affiliation(s)
- Jian-Gang Zhang
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- 2 University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chang-An Geng
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Xiao-Yan Huang
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Xing-Long Chen
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- 2 University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yun-Bao Ma
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Xue-Mei Zhang
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Ji-Jun Chen
- 1 State Key Laboratory of Phytochemistry and Plant Resources in West China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
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