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van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup T, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EML, Duncan KR, Linington RG. The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res 2022; 50:D1317-D1323. [PMID: 34718710 PMCID: PMC8728154 DOI: 10.1093/nar/gkab941] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 12/15/2022] Open
Abstract
Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.
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Affiliation(s)
- Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ella F Poynton
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dasha Iskakova
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Emily McMann
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Trevor N Clark
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Claire H Fergusson
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David P Fewer
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Alison H Hughes
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0RE, UK
| | - Caitlin A McCadden
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0RE, UK
| | - Sylvia Soldatou
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Elisabeth M-L Janssen
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Duebendorf, Switzerland
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0RE, UK
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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van Santen J, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, Neto FC, Castaño-Espriu L, Chang C, Clark TN, Cleary Little JL, Delgadillo DA, Dorrestein PC, Duncan KR, Egan JM, Galey MM, Haeckl FJ, Hua A, Hughes AH, Iskakova D, Khadilkar A, Lee JH, Lee S, LeGrow N, Liu DY, Macho JM, McCaughey CS, Medema MH, Neupane RP, O’Donnell TJ, Paula JS, Sanchez LM, Shaikh AF, Soldatou S, Terlouw BR, Tran TA, Valentine M, van der Hooft JJJ, Vo DA, Wang M, Wilson D, Zink KE, Linington RG. The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery. ACS Cent Sci 2019; 5:1824-1833. [PMID: 31807684 PMCID: PMC6891855 DOI: 10.1021/acscentsci.9b00806] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Indexed: 05/06/2023]
Abstract
Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.
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Affiliation(s)
- Jeffrey
A. van Santen
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Grégoire Jacob
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Amrit Leen Singh
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Victor Aniebok
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 65064, United States
| | - Marcy J. Balunas
- Division
of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Derek Bunsko
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Fausto Carnevale Neto
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Physics
and Chemistry Department, School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São
Paulo 14040, Brazil
- Northwest
Metabolomics Research Center, Department of Anesthesiology and Pain
Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Laia Castaño-Espriu
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Chen Chang
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Trevor N. Clark
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jessica L. Cleary Little
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David A. Delgadillo
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 65064, United States
| | - Pieter C. Dorrestein
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, La Jolla, California 92037, United States
| | - Katherine R. Duncan
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Joseph M. Egan
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Melissa M. Galey
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - F.P. Jake Haeckl
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Alex Hua
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Alison H. Hughes
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Dasha Iskakova
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Aswad Khadilkar
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 65064, United States
| | - Jung-Ho Lee
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Sanghoon Lee
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Nicole LeGrow
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dennis Y. Liu
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jocelyn M. Macho
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 65064, United States
| | - Catherine S. McCaughey
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Marnix H. Medema
- Bioinformatics
Group, Wageningen University, 6700 AP Wageningen, The Netherlands
| | - Ram P. Neupane
- Department
of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Timothy J. O’Donnell
- Department
of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Jasmine S. Paula
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Laura M. Sanchez
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Anam F. Shaikh
- Department
of Biochemistry, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United
States
| | - Sylvia Soldatou
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Barbara R. Terlouw
- Bioinformatics
Group, Wageningen University, 6700 AP Wageningen, The Netherlands
| | - Tuan Anh Tran
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Institute of Marine Biochemistry, Vietnam
Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Mercia Valentine
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | | | - Duy A. Vo
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 65064, United States
| | - Mingxun Wang
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, La Jolla, California 92037, United States
| | - Darryl Wilson
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Katherine E. Zink
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Roger G. Linington
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- E-mail: . Tel: +1-778-7823517
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