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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Yin T, Yu Y, Liu Q, Zhu G, Bai L, Zhang W, Jiang Z. 13C-NMR-based MixONat strategy coupled with 2D NMR for rapid dereplication and identification of new secondary metabolites from Aloe vera. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2022.104975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Du Y, Yao L, Li X, Guo Y. Yonarolide A, an unprecedented furanobutenolide-containing norcembranoid derivative formed by photoinduced intramolecular [2 + 2] cycloaddition. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
BACKGROUND Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms. AIM OF REVIEW This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms. KEY SCIENTIFIC CONCEPTS OF REVIEW The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.
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Affiliation(s)
- Lina M Bayona
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Marine Biodiversity, 2333 CR, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
- College of Pharmacy, Kyung Hee University, 130-701, Seoul, Republic of Korea.
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5
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Small Molecule Accurate Recognition Technology accelerated isolation of structurally diverse sesquiterpenes from Litsea lancilimba Merr. Fitoterapia 2022; 158:105168. [DOI: 10.1016/j.fitote.2022.105168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/22/2022]
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Exploring Verrucosidin Derivatives with Glucose-Uptake-Stimulatory Activity from Penicillium cellarum Using MS/MS-Based Molecular Networking. J Fungi (Basel) 2022; 8:jof8020143. [PMID: 35205896 PMCID: PMC8878765 DOI: 10.3390/jof8020143] [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: 01/03/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Under the guidance of LC-MS/MS-based molecular networking, seven new verrucosidin derivatives, penicicellarusins A-G (3–9), were isolated together with three known analogues from the fungus Penicillium cellarum. The structures of the new compounds were determined by a combination of NMR, mass and electronic circular dichroism spectral data analysis. The absolute configuration of penicyrone A (10) was corrected based on X-ray diffraction analyses. Bioactivity screening indicated that compounds 1, 2, and 4 showed much stronger promising hypoglycemic activity than the positive drug (rosiglitazone) in the range of 25–100 μM, which represents a potential new class of hypoglycemic agents. Preliminary structure-activity relationship analysis indicates that the formation of epoxy ring on C6-C7 in the structures is important for the glucose uptake-stimulating activity. The gene cluster for the biosynthesis of 1–12 is identified by sequencing the genome of P. cellarum and similarity analysis with the gene cluster of verrucosidins in P. polonicum.
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7
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Lin X, Chai L, Zhu HR, Zhou Y, Shen Y, Chen KH, Sun F, Liu BM, Xu SH, Lin HW. Applying molecular networking for targeted isolation of depsipeptides. RSC Adv 2021; 11:2774-2782. [PMID: 35747077 PMCID: PMC9134009 DOI: 10.1039/d0ra09388b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/05/2020] [Indexed: 12/02/2022] Open
Abstract
LC-HRMS/MS molecular networking enabled the targeted isolation of three new neoantimycin analogs (1, 3, 5) and two known ones (2, 4) from the culture broth of Streptomyces conglobatus RJ8. After derivatization into C1-hydroxyl form compounds (6-10) respectively, the absolute structures of 1-5 were clearly determined by analyzing the hydrolyzed components from 6-10. Compounds 2 and 3 were confirmed to be a pair of epimers with different stereochemistry at C-2, and so were 4 and 5. This is the first report of the isolation and characterization of epimers of NATs. The most abundant eight compounds we obtained were subjected to a cytotoxicity assay, 1 and 6 exhibited excellent cytotoxicity with the lowest IC50 value in the picomolar range against six human carcinoma cell lines while 7 and 8 showed potent cytotoxicity against PC-9 and PC-9/GR cell lines.
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Affiliation(s)
- Xiao Lin
- Institute of Marine Drugs, Guangxi University of Chinese Medicine Nanning 530200 P. R. China
- College of Chemistry and Materials, Jinan University Guangzhou 510632 P. R. China
- College of Pharmacy, Jinan University Guangzhou 510632 P. R. China
| | - Ling Chai
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Traditional Medical and Pharmaceutical Sciences Nanning 530022 P. R. China
| | - Hong Rui Zhu
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Yongjun Zhou
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Yaoyao Shen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Kai Hao Chen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Fan Sun
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Bu Ming Liu
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Traditional Medical and Pharmaceutical Sciences Nanning 530022 P. R. China
| | - Shi Hai Xu
- College of Chemistry and Materials, Jinan University Guangzhou 510632 P. R. China
| | - Hou Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 P. R. China
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Li SF, Yu XQ, Li YL, Bai M, Lin B, Yao GD, Song SJ. Vibsane-type diterpenoids from Viburnum odoratissimum and their cytotoxic activities. Bioorg Chem 2020; 106:104498. [PMID: 33272710 DOI: 10.1016/j.bioorg.2020.104498] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 01/03/2023]
Abstract
Seven new diterpenoids (1-7), including five 7-membered ring vibsane-type diterpenoids, vibsanolide A-E (1-5) and a pair of epimers of 14,15,16,17-tetranorvibsane-type diterpenoids possessing bicyclo[4.2.1]nonane moiety, vibsanolide F-G (6-7), together with twelve known analogues (8-19) were isolated from the crude extracts of the leaves of Viburnum odoratissimum using Small Molecule Accurate Recognition Technology (SMART). These structures including absolute configurations were elucidated by means of comprehensive analyses of spectroscopic data, as well as comparison of the experimental and calculated electronic circular dichroism (ECD) spectra. These compounds were evaluated for their cytotoxic activities against A549 and HepG2 cells by MTT assay. The results showed that compound 2 exhibited potent cytotoxic activity against A549 cells with IC50 value of 1.11 μM. Further staining experiments indicated that 2 could promote apoptosis induction, enhance reactive oxygen species (ROS) level and attenuate mitochondrial membrane potential (MMP) in A549 cells. Taken together, these findings provided new insights into understanding the cytotoxic activity of vibsane-type diterpenoids and it is meaningful to further investigate the application potential of V. odoratissimum.
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Affiliation(s)
- Shi-Fang Li
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiao-Qi Yu
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ya-Ling Li
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ming Bai
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Bin Lin
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
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9
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Targeted isolation of cytotoxic germacranolide sesquiterpenes from Elephantopus scaber L. using small molecule accurate recognition technology. Bioorg Chem 2020; 104:104314. [DOI: 10.1016/j.bioorg.2020.104314] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
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Kust A, Řeháková K, Vrba J, Maicher V, Mareš J, Hrouzek P, Chiriac MC, Benedová Z, Tesařová B, Saurav K. Insight into Unprecedented Diversity of Cyanopeptides in Eutrophic Ponds Using an MS/MS Networking Approach. Toxins (Basel) 2020; 12:E561. [PMID: 32878042 PMCID: PMC7551678 DOI: 10.3390/toxins12090561] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/18/2022] Open
Abstract
Man-made shallow fishponds in the Czech Republic have been facing high eutrophication since the 1950s. Anthropogenic eutrophication and feeding of fish have strongly affected the physicochemical properties of water and its aquatic community composition, leading to harmful algal bloom formation. In our current study, we characterized the phytoplankton community across three eutrophic ponds to assess the phytoplankton dynamics during the vegetation season. We microscopically identified and quantified 29 cyanobacterial taxa comprising non-toxigenic and toxigenic species. Further, a detailed cyanopeptides (CNPs) profiling was performed using molecular networking analysis of liquid chromatography-tandem mass spectrometry (LC-MS/MS) data coupled with a dereplication strategy. This MS networking approach, coupled with dereplication, on the online global natural product social networking (GNPS) web platform led us to putatively identify forty CNPs: fourteen anabaenopeptins, ten microcystins, five cyanopeptolins, six microginins, two cyanobactins, a dipeptide radiosumin, a cyclooctapeptide planktocyclin, and epidolastatin 12. We applied the binary logistic regression to estimate the CNPs producers by correlating the GNPS data with the species abundance. The usage of the GNPS web platform proved a valuable approach for the rapid and simultaneous detection of a large number of peptides and rapid risk assessments for harmful blooms.
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Affiliation(s)
- Andreja Kust
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (A.K.); (J.M.); (P.H.)
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic; (K.Ř.); (J.V.); (M.-C.C.)
| | - Klára Řeháková
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic; (K.Ř.); (J.V.); (M.-C.C.)
- Institute of Botany of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Jaroslav Vrba
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic; (K.Ř.); (J.V.); (M.-C.C.)
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Vincent Maicher
- Nicholas School of the Environment, Duke University, Durham, NC 27710, USA;
| | - Jan Mareš
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (A.K.); (J.M.); (P.H.)
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic; (K.Ř.); (J.V.); (M.-C.C.)
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Pavel Hrouzek
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (A.K.); (J.M.); (P.H.)
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Maria-Cecilia Chiriac
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic; (K.Ř.); (J.V.); (M.-C.C.)
| | - Zdeňka Benedová
- ENKI, o.p.s. Třeboň, Dukelská 145, 37901 Třeboň, Czech Republic; (Z.B.); (B.T.)
| | - Blanka Tesařová
- ENKI, o.p.s. Třeboň, Dukelská 145, 37901 Třeboň, Czech Republic; (Z.B.); (B.T.)
- Faculty of Agriculture, University of South Bohemia, Applied Ecology Laboratory, 37005 České Budějovice, Czech Republic
| | - Kumar Saurav
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, 37901 Třeboň, Czech Republic; (A.K.); (J.M.); (P.H.)
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11
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Tan LT, Phyo MY. Marine Cyanobacteria: A Source of Lead Compounds and their Clinically-Relevant Molecular Targets. Molecules 2020; 25:E2197. [PMID: 32397127 PMCID: PMC7249205 DOI: 10.3390/molecules25092197] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
The prokaryotic filamentous marine cyanobacteria are photosynthetic microbes that are found in diverse marine habitats, ranging from epiphytic to endolithic communities. Their successful colonization in nature is largely attributed to genetic diversity as well as the production of ecologically important natural products. These cyanobacterial natural products are also a source of potential drug leads for the development of therapeutic agents used in the treatment of diseases, such as cancer, parasitic infections and inflammation. Major sources of these biomedically important natural compounds are found predominately from marine cyanobacterial orders Oscillatoriales, Nostocales, Chroococcales and Synechococcales. Moreover, technological advances in genomic and metabolomics approaches, such as mass spectrometry and NMR spectroscopy, revealed that marine cyanobacteria are a treasure trove of structurally unique natural products. The high potency of a number of natural products are due to their specific interference with validated drug targets, such as proteasomes, proteases, histone deacetylases, microtubules, actin filaments and membrane receptors/channels. In this review, the chemistry and biology of selected potent cyanobacterial compounds as well as their synthetic analogues are presented based on their molecular targets. These molecules are discussed to reflect current research trends in drug discovery from marine cyanobacterial natural products.
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Affiliation(s)
- Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore;
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12
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Duggan BM, Cullum R, Fenical W, Amador LA, Rodríguez AD, La Clair JJ. Searching for Small Molecules with an Atomic Sort. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California, San Diego La Jolla CA 92093-0204 USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California, San Diego La Jolla CA 92093-0204 USA
| | - Luis A. Amador
- Molecular Sciences Research Center University of Puerto Rico 1390 Ponce de León Avenue San Juan 00926 Puerto Rico
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center University of Puerto Rico 1390 Ponce de León Avenue San Juan 00926 Puerto Rico
| | - James J. La Clair
- Department of Chemistry and Biochemistry University of California San Diego 9500 Gilman Drive, La Jolla CA 92093 USA
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13
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Duggan BM, Cullum R, Fenical W, Amador LA, Rodríguez AD, La Clair JJ. Searching for Small Molecules with an Atomic Sort. Angew Chem Int Ed Engl 2020; 59:1144-1148. [PMID: 31696595 PMCID: PMC6942196 DOI: 10.1002/anie.201911862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/24/2019] [Indexed: 12/14/2022]
Abstract
The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom-based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.
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Affiliation(s)
- Brendan M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0204, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0204, USA
| | - Luis A Amador
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, 00926, Puerto Rico
| | - Abimael D Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, 00926, Puerto Rico
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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14
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Meyer JG, Liu S, Miller IJ, Coon JJ, Gitter A. Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests. J Chem Inf Model 2019; 59:4438-4449. [PMID: 31518132 PMCID: PMC6819987 DOI: 10.1021/acs.jcim.9b00236] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Indexed: 02/08/2023]
Abstract
Empirical testing of chemicals for drug efficacy costs many billions of dollars every year. The ability to predict the action of molecules in silico would greatly increase the speed and decrease the cost of prioritizing drug leads. Here, we asked whether drug function, defined as MeSH "therapeutic use" classes, can be predicted from only a chemical structure. We evaluated two chemical-structure-derived drug classification methods, chemical images with convolutional neural networks and molecular fingerprints with random forests, both of which outperformed previous predictions that used drug-induced transcriptomic changes as chemical representations. This suggests that the structure of a chemical contains at least as much information about its therapeutic use as the transcriptional cellular response to that chemical. Furthermore, because training data based on chemical structure is not limited to a small set of molecules for which transcriptomic measurements are available, our strategy can leverage more training data to significantly improve predictive accuracy to 83-88%. Finally, we explore use of these models for prediction of side effects and drug-repurposing opportunities and demonstrate the effectiveness of this modeling strategy for multilabel classification.
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Affiliation(s)
- Jesse G. Meyer
- Department
of Chemistry, Department of Biomolecular Chemistry, National Center for
Quantitative Biology of Complex Systems, Department of Computer Sciences, Morgridge Institute
for Research, DOE Great Lakes Bioenergy Research Center, and Department of Biostatistics and
Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Shengchao Liu
- Department
of Chemistry, Department of Biomolecular Chemistry, National Center for
Quantitative Biology of Complex Systems, Department of Computer Sciences, Morgridge Institute
for Research, DOE Great Lakes Bioenergy Research Center, and Department of Biostatistics and
Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Ian J. Miller
- Department
of Chemistry, Department of Biomolecular Chemistry, National Center for
Quantitative Biology of Complex Systems, Department of Computer Sciences, Morgridge Institute
for Research, DOE Great Lakes Bioenergy Research Center, and Department of Biostatistics and
Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, Department of Biomolecular Chemistry, National Center for
Quantitative Biology of Complex Systems, Department of Computer Sciences, Morgridge Institute
for Research, DOE Great Lakes Bioenergy Research Center, and Department of Biostatistics and
Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Anthony Gitter
- Department
of Chemistry, Department of Biomolecular Chemistry, National Center for
Quantitative Biology of Complex Systems, Department of Computer Sciences, Morgridge Institute
for Research, DOE Great Lakes Bioenergy Research Center, and Department of Biostatistics and
Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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Hanif N, Murni A, Tanaka C, Tanaka J. Marine Natural Products from Indonesian Waters. Mar Drugs 2019; 17:md17060364. [PMID: 31248122 PMCID: PMC6627775 DOI: 10.3390/md17060364] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Natural products are primal and have been a driver in the evolution of organic chemistry and ultimately in science. The chemical structures obtained from marine organisms are diverse, reflecting biodiversity of genes, species and ecosystems. Biodiversity is an extraordinary feature of life and provides benefits to humanity while promoting the importance of environment conservation. This review covers the literature on marine natural products (MNPs) discovered in Indonesian waters published from January 1970 to December 2017, and includes 732 original MNPs, 4 structures isolated for the first time but known to be synthetic entities, 34 structural revisions, 9 artifacts, and 4 proposed MNPs. Indonesian MNPs were found in 270 papers from 94 species, 106 genera, 64 families, 32 orders, 14 classes, 10 phyla, and 5 kingdoms. The emphasis is placed on the structures of organic molecules (original and revised), relevant biological activities, structure elucidation, chemical ecology aspects, biosynthesis, and bioorganic studies. Through the synthesis of past and future data, huge and partly undescribed biodiversity of marine tropical invertebrates and their importance for crucial societal benefits should greatly be appreciated.
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Affiliation(s)
- Novriyandi Hanif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia.
| | - Anggia Murni
- Tropical Biopharmaca Research Center, IPB University (Bogor Agricultural University), Bogor 16128, Indonesia.
| | - Chiaki Tanaka
- Department of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
| | - Junichi Tanaka
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
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16
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Ternon E, Wang Y, Coyne KJ. Small Polar Molecules: A Challenge in Marine Chemical Ecology. Molecules 2018; 24:molecules24010135. [PMID: 30602708 PMCID: PMC6337545 DOI: 10.3390/molecules24010135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 12/17/2022] Open
Abstract
Due to increasing evidence of key chemically mediated interactions in marine ecosystems, a real interest in the characterization of the metabolites involved in such intra and interspecific interactions has emerged over the past decade. Nevertheless, only a small number of studies have succeeded in identifying the chemical structure of compounds of interest. One reason for this low success rate is the small size and extremely polar features of many of these chemical compounds. Indeed, a major challenge in the search for active metabolites is the extraction of small polar compounds from seawater. Yet, a full characterization of those metabolites is necessary to understand the interactions they mediate. In this context, the study presented here aims to provide a methodology for the characterization of highly polar, low molecular weight compounds in a seawater matrix that could provide guidance for marine ecologists in their efforts to identify active metabolites. This methodology was applied to the investigation of the chemical structure of an algicidal compound secreted by the bacteria Shewanella sp. IRI-160 that was previously shown to induce programmed cell death in dinoflagellates. The results suggest that the algicidal effects may be attributed to synergistic effects of small amines (ammonium, 4-aminobutanal) derived from the catabolization of putrescine produced in large quantities (0.05–6.5 fmol/cell) by Shewanella sp. IRI-160.
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Affiliation(s)
- Eva Ternon
- College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, Lewes, DE 19958, USA.
- Université Côte d'Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, 06560 Valbonne, France.
| | - Yanfei Wang
- College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, Lewes, DE 19958, USA.
| | - Kathryn J Coyne
- College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, Lewes, DE 19958, USA.
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17
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Ding CYG, Pang LM, Liang ZX, Goh KKK, Glukhov E, Gerwick WH, Tan LT. MS/MS-Based Molecular Networking Approach for the Detection of Aplysiatoxin-Related Compounds in Environmental Marine Cyanobacteria. Mar Drugs 2018; 16:md16120505. [PMID: 30551660 PMCID: PMC6315786 DOI: 10.3390/md16120505] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022] Open
Abstract
Certain strains of cyanobacteria produce a wide array of cyanotoxins, such as microcystins, lyngbyatoxins and aplysiatoxins, that are associated with public health issues. In this pilot study, an approach combining LC-MS/MS and molecular networking was employed as a rapid analytical method to detect aplysiatoxins present in four environmental marine cyanobacterial samples collected from intertidal areas in Singapore. Based on 16S-ITS rRNA gene sequences, these filamentous cyanobacterial samples collected from Pulau Hantu were determined as Trichodesmium erythraeum, Oscillatoria sp. PAB-2 and Okeania sp. PNG05-4. Organic extracts were prepared and analyzed on LC-HRMS/MS and Global Natural Product Social Molecular Networking (GNPS) for the presence of aplysiatoxin-related molecules. From the molecular networking, six known compounds, debromoaplysiatoxin (1), anhydrodebromoaplysiatoxin (2), 3-methoxydebromoaplysiatoxin (3), aplysiatoxin (4), oscillatoxin A (5) and 31-noroscillatoxin B (6), as well as potential new analogues, were detected in these samples. In addition, differences and similarities in molecular networking clusters related to the aplysiatoxin molecular family were observed in extracts of Trichodesmium erythraeum collected from two different locations and from different cyanobacterial species found at Pulau Hantu, respectively.
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Affiliation(s)
- Chi Ying Gary Ding
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Kau Kiat Kelvin Goh
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, (K.K.K.G.).
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
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18
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Zhang Y, Zhang R, Nazari M, Bagley MC, Miller ES, Williams PG, Muddiman DC, Lindsey JS. Mass spectrometric detection of chlorophyll a and the tetrapyrrole secondary metabolite tolyporphin A in the filamentous cyanobacterium HT-58-2. Approaches to high-throughput screening of intact cyanobacteria. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s108842461750078x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tolyporphins are unusual tetrapyrrole macrocycles produced by the filamentous cyanobacterium–microbial community HT-58-2, the only known source to date. Numerous cyanobacterial samples have been collected worldwide but most have not been screened for secondary metabolites. Identification of tolyporphins typically has entailed lipophilic extraction followed by chromatographic fractionation and spectroscopic and/or mass spectrometric analysis. For quantitation, lengthy lipophilic extraction, sample processing and HPLC separation are needed. Examination by MALDI-TOF-MS (with the matrix 1,5-diaminonaphthalene) of lipophilic crude extracts of small-scale HT-58-2 samples (2 mL) without chromatographic fractionation enabled semi-quantitation of tolyporphin A over a 41-day growth period. Screening for tolyporphin A in intact or slightly sheared and vortexed HT-58-2 samples (no lipophilic extraction), and confirmation of identity by tandem MS, were carried out by IR-MALDESI-FTMS. Tolyporphin A was identified by the molecular ion and four characteristic fragments. The molecular ion of chlorophyll [Formula: see text] also was observed. The sheared and vortexed sample contained substantial numbers of intact cells as demonstrated by regrowth of the filamentous cyanobacterium–microbial culture. The semi-quantitative and rapid qualitative methods developed herein should facilitate examination of other tolyporphin-producing organisms among the vast worldwide strains of cyanobacteria as well as investigation of the biosynthesis of tolyporphins.
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Affiliation(s)
- Yunlong Zhang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Milad Nazari
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Michael C. Bagley
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Eric S. Miller
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Philip G. Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822-2275, USA
| | - David C. Muddiman
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
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