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Kim HW, Zhang C, Reher R, Wang M, Alexander KL, Nothias LF, Han YK, Shin H, Lee KY, Lee KH, Kim MJ, Dorrestein PC, Gerwick WH, Cottrell GW. DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data. J Cheminform 2023; 15:71. [PMID: 37550756 PMCID: PMC10406729 DOI: 10.1186/s13321-023-00738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023] Open
Abstract
The identification of molecular structure is essential for understanding chemical diversity and for developing drug leads from small molecules. Nevertheless, the structure elucidation of small molecules by Nuclear Magnetic Resonance (NMR) experiments is often a long and non-trivial process that relies on years of training. To achieve this process efficiently, several spectral databases have been established to retrieve reference NMR spectra. However, the number of reference NMR spectra available is limited and has mostly facilitated annotation of commercially available derivatives. Here, we introduce DeepSAT, a neural network-based structure annotation and scaffold prediction system that directly extracts the chemical features associated with molecular structures from their NMR spectra. Using only the 1H-13C HSQC spectrum, DeepSAT identifies related known compounds and thus efficiently assists in the identification of molecular structures. DeepSAT is expected to accelerate chemical and biomedical research by accelerating the identification of molecular structures.
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Affiliation(s)
- Hyun Woo Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Gyeonggi-Do, Republic of Korea
| | - Chen Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, La Jolla, San Diego, CA, USA
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Ometa Labs LLC, San Diego, CA, USA
- Department of Computer Science, University of California Riverside, Riverside, CA, USA
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, 06108, Nice, France
| | - Yoo Kyong Han
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Hyeji Shin
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Ki Yong Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Kyu Hyeong Lee
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Gyeonggi-Do, Republic of Korea
| | - Myeong Ji Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Gyeonggi-Do, Republic of Korea
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Garrison W Cottrell
- Department of Computer Science and Engineering, University of California, La Jolla, San Diego, CA, USA.
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Sala-Carvalho WR, Montessi-Amaral FP, Esposito MP, Campestrini R, Rossi M, Peralta DF, Furlan CM. Metabolome of Ceratodon purpureus (Hedw.) Brid., a cosmopolitan moss: the influence of seasonality. PLANTA 2022; 255:77. [PMID: 35239061 DOI: 10.1007/s00425-022-03857-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Ceratodon purpureus showed changes in disaccharides, flavonoids, and carotenoids throughout annual seasons. These changes indicate harsher environmental conditions during the dry period, directing metabolic precursors to enhance the antioxidant system. Bryophytes are a group of land plants comprising mosses (Bryophyta), liverworts (Marchantyophyta), and hornworts (Antocerotophyta). This study uses the molecular networking approach to investigate the influence of seasonality (dry and rainy seasons) on the metabolome and redox status of the moss Ceratodon purpureus (Hedw.) Brid., from Campos do Jordão, Brazil. Samples of C. purpureus were submitted to three extraction methods: 80% methanol producing the soluble fraction (intracellular compounds), followed by debris hydrolysis using sodium hydroxide producing the insoluble fraction (cell wall conjugated compounds), both analyzed by HPLC-MS; and extraction using pre-cooled methanol, separated into polar and non-polar fractions, being both analyzed by GC-MS. All fractions were processed using the Global Natural Product Social Molecular Network (GNPS). The redox status was assessed by the analysis of four enzyme activities combined with the analysis of the contents of ascorbate, glutathione, carotenoids, reactive oxygen species (ROS), and malondialdehyde acid (MDA). During the dry period, there was an increase of most biflavonoids, as well as phospholipids, disaccharides, long-chain fatty acids, carotenoids, antioxidant enzymes, ROS, and MDA. Results indicate that C. purpureus is under harsher environmental conditions during the dry period, mainly due to low temperature and less water availability (low rainfall).
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Affiliation(s)
- Wilton R Sala-Carvalho
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, SP, 05508-090, Brazil
| | - Francisco P Montessi-Amaral
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, SP, 05508-090, Brazil
| | - Marisia P Esposito
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, SP, 05508-090, Brazil
| | - Richard Campestrini
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, SP, 05508-090, Brazil
| | - Magdalena Rossi
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, SP, 05508-090, Brazil
| | - Denilson F Peralta
- Instituto de Pesquisas Ambientais, Avenida Miguel Estéfano, 3687, SP, 04301-012, Brazil
| | - Claudia M Furlan
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua Do Matão, 277, SP, 05508-090, Brazil.
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Oliveira VM, Andreote FD, Cortelo PC, Castro-Gamboa I, Costa-Lotufo LV, Polizeli MDLTM, Thiemann OH, Setubal JC. Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract We present a survey of projects that have been funded by FAPESP under the BIOTA-Microorganisms program. These projects generated a wide variety of results, including the identification of novel antibacterial-producing microorganisms, the characterization of novel microbial enzymes for industrial applications, taxonomic classification of novel microorganisms in several environments, investigation of the soil and mangrove microbial ecosystems and its influence on endangered plant species, and the sequencing of novel metagenome-assembled genomes. The results surveyed demonstrate the importance of microorganisms in environments that play important roles in human activities as well as the potential that many of these microorganisms have in contributing to biotechnological applications crucial for human survival in the 21st century.
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Abstract
Phenolic compounds are plants’ bioactive metabolites that have been studied for their ability to confer extensive benefits to human health. As currently there is an increased interest in natural compounds identification and characterization, new analytical methods based on advanced technologies have been developed. This paper summarizes current advances in the state of the art for polyphenols identification and quantification. Analytical techniques ranging from high-pressure liquid chromatography to hyphenated spectrometric methods are discussed. The topic of high-resolution mass spectrometry, from targeted quantification to untargeted comprehensive chemical profiling, is particularly addressed. Structure elucidation is one of the important steps for natural products research. Mass spectral data handling approaches, including acquisition mode selection, accurate mass measurements, elemental composition, mass spectral library search algorithms and structure confirmation through mass fragmentation pathways, are discussed.
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Pesek M, Juvan A, Jakoš J, Košmrlj J, Marolt M, Gazvoda M. Database Independent Automated Structure Elucidation of Organic Molecules Based on IR, 1H NMR, 13C NMR, and MS Data. J Chem Inf Model 2021; 61:756-763. [PMID: 33378192 PMCID: PMC7903418 DOI: 10.1021/acs.jcim.0c01332] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 01/21/2023]
Abstract
Herein, we report a computational algorithm that follows a spectroscopist-driven elucidation process of the structure of an organic molecule based on IR, 1H and 13C NMR, and MS tabular data. The algorithm is independent from database searching and is based on a bottom-up approach, building the molecular structure from small structural fragments visible in spectra. It employs an analytical combinatorial approach with a graph search technique to determine the connectivity of structural fragments that is based on the analysis of the NMR spectra, to connect the identified structural fragments into a molecular structure. After the process is completed, the interface lists the compound candidates, which are visualized by the WolframAlpha computational knowledge engine within the interface. The candidates are ranked according to the predefined rules for analyzing the spectral data. The developed elucidator has a user-friendly web interface and is publicly available (http://schmarnica.si).
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Affiliation(s)
- Matevž Pesek
- Faculty
of Computer and Information Science, University
of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Andraž Juvan
- Faculty
of Computer and Information Science, University
of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Jure Jakoš
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
Pot 113, SI-1000 Ljubljana, Slovenia
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
Pot 113, SI-1000 Ljubljana, Slovenia
| | - Matija Marolt
- Faculty
of Computer and Information Science, University
of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Martin Gazvoda
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
Pot 113, SI-1000 Ljubljana, Slovenia
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