1
|
Worayuthakarn R, Suddee N, Theppitak C, Chainok K, Ruchirawat S, Thasana N. Cascade Cyclization of o-(2-Acyl-1-ethynyl)benzaldehydes with Amino Acid Derivatives: Synthesis of Indeno[2,1- c]pyran-3-ones and 1-Oxazolonylisobenzofurans via the Erlenmeyer-Plöchl Azlactone Reaction. ACS OMEGA 2024; 9:37814-37842. [PMID: 39281931 PMCID: PMC11391571 DOI: 10.1021/acsomega.4c03842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/05/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024]
Abstract
A highly regioselective divergent approach is reported for the synthesis of both indeno[2,1-c]pyran-3-one and 1-oxazolonylisobenzofuran derivatives using the Erlenmeyer-Plöchl azlactone (EPA) reaction. This approach involves the synthesis of o-(2-acyl-1-ethynyl)benzaldehydes, which reacted with various amino acids. Reaction with N-acylglycines resulted in the formation of indeno[2,1-c]pyran-3-ones, involving the sequential formation of two C-C bonds and two C-O bonds. Conversely, when the same conditions were applied to free amino acids, 1-oxazolonylisobenzofurans were obtained. This reaction involved the formation of a C-C bond between oxazolone and o-(2-acyl-1-ethynyl)benzaldehyde, followed by the formation of a C-O bond through a selective 5-exo-dig cyclization.
Collapse
Affiliation(s)
- Rattana Worayuthakarn
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Nattanit Suddee
- Chemical Sciences Program, Chulabhorn Graduate Institute, Laksi, Bangkok 10210, Thailand
| | - Chatphorn Theppitak
- Thammasat University Research Unit in Multifunctional Crystalline Materials and Applications (TU-MCMA), Faculty of Science and Technology, Thammasat University, Pathum Thani 12121, Thailand
| | - Kittipong Chainok
- Thammasat University Research Unit in Multifunctional Crystalline Materials and Applications (TU-MCMA), Faculty of Science and Technology, Thammasat University, Pathum Thani 12121, Thailand
| | - Somsak Ruchirawat
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
- Chemical Sciences Program, Chulabhorn Graduate Institute, Laksi, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Education, Science, Research and Innovation, Bangkok 10400, Thailand
| | - Nopporn Thasana
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
- Chemical Sciences Program, Chulabhorn Graduate Institute, Laksi, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Education, Science, Research and Innovation, Bangkok 10400, Thailand
| |
Collapse
|
2
|
Lin J, Wu J, Bao MF, Kongkiatpaiboon S, Cai XH. Gelselegine-gelsedine type bisindoles as well as the units from Gelsemium elegans with promoting proliferation of oral mucosa fibroblast cells. PHYTOCHEMISTRY 2024; 222:114077. [PMID: 38615925 DOI: 10.1016/j.phytochem.2024.114077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/16/2024]
Abstract
Two undescribed bisindole alkaloids, gelseginedine A (1) and its rearranged gelseginedine B (2), and seven unreported gelselegine-type oxindole alkaloids (3-9) were isolated from the stems and leaves of Gelsemium elegans, together with five known alkaloids (10-14). Compounds 1 and 2 represented the first examples of gelselegine-gelsedine type alkaloids which bridged two units by a double bond. Their structures with absolute configurations were elucidated by means of HRESIMS, NMR and calculational chemistry. The performed bioassay revealed that 14 could promote the proliferation of human oral mucosa fibroblast cells.
Collapse
Affiliation(s)
- Jing Lin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Wu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Mei-Fen Bao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Sumet Kongkiatpaiboon
- Drug Discovery and Development Center, Office of Advanced Science and Technology, Thammasat University, Pathum Thani, 12121, Thailand.
| | - Xiang-Hai Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Hu S, Sun Q, Xu F, Jiang N, Gao J. Age-related hearing loss and its potential drug candidates: a systematic review. Chin Med 2023; 18:121. [PMID: 37730634 PMCID: PMC10512576 DOI: 10.1186/s13020-023-00825-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Age-related hearing loss (ARHL) is one of the main illnesses afflicting the aged population and has a significant negative impact on society, economy, and health. However, there is presently no appropriate therapeutic treatment of ARHL due to the absence of comprehensive trials. OBJECTIVES The goal of this review is to systematically evaluate and analyze recent statistics on the pathologic classifications, risk factors, treatment strategies, and drug candidates of ARHL, including that from traditional Chinese medicine (TCM), to provide potential new approaches for preventing and treating ARHL. METHODS Literature related to ARHL was conducted in databases such as PubMed, WOS, China National Knowledge Infrastructure (CNKI), and Wanfang from the establishment of the database to Jan, 2023. The pathology, causal factor, pathophysiological mechanism, treatment strategy, and the drug candidate of ARHL were extracted and pooled for synthesis. RESULTS Many hypotheses about the etiology of ARHL are based on genetic and environmental elements. Most of the current research on the pathology of ARHL focuses on oxidative damage, mitochondrial dysfunction, inflammation, cochlear blood flow, ion homeostasis, etc. In TCM, herbs belonging to the kidney, lung, and liver meridians exhibit good hearing protection. Seven herbs belonging to the kidney meridian, 9 belonging to the lung meridian, and 4 belonging to the liver meridian were ultimately retrieved in this review, such as Polygonum multiflorum Thunb., Panax ginseng C.A. Mey, and Pueraria lobata (Willd.) Ohwi. Their active compounds, 2,3,4',5-Tetrahydroxystilbene-2-O-D-glucoside, ginsenoside Rb1, and puerarin, may act as the molecular substance for their anti-ARHL efficacy, and show anti-oxidative, neuroprotective, anti-inflammatory, anti-apoptotic, or mitochondrial protective effects. CONCLUSION Anti-oxidants, modulators of mitochondrial function, anti-inflammation agents, vasodilators, K+ channel openers, Ca2+ channel blockers, JNK inhibitors, and nerve growth factors/neurotrophic factors all contribute to hearing protection, and herbs are an important source of potential anti-ARHL drugs.
Collapse
Affiliation(s)
- Shiyu Hu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Qingru Sun
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Fei Xu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Ninghua Jiang
- Department of Pharmacy, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Jianli Gao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China.
| |
Collapse
|
5
|
Dimeric alkaloids from the barks of Erythrina variegata as well as their occurrence. Fitoterapia 2022; 166:105408. [PMID: 36586624 DOI: 10.1016/j.fitote.2022.105408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Thirteen undescribed dimeric Erythrina alkaloids, named as erythrivarines A1-A13, were isolated from the barks of Erythrina variegata L. and. Their structures were determined on the basis of NMR, UV and mass spectral analyses. Dimeric Erythrina alkaloid with a C-8/8' linkage in erythrivarine A1 was not yet reported. Representative dimers from titled plant were used to prove their occurrence as natural products by LC - MS detection. Additionally, simultaneous investigation enabled us to propose the natural property of seemingly artificial Erythrina alkaloid with acetonyl group.
Collapse
|
6
|
Yu GX, Yu Y, Zeng LH, Schinnerl J, Cai XH. Cephalotaxine homologous alkaloids from seeds of Cephalotaxus oliveri Mast. PHYTOCHEMISTRY 2022; 200:113220. [PMID: 35513135 DOI: 10.1016/j.phytochem.2022.113220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Six undescribed isoquinoline alkaloids, named as cephaloliverines A-F, were isolated from the seeds of Cephalotaxus oliveri. They were identified by NMR and MS spectroscopic data analyses, combined with the time-dependent density functional theory ECD calculation for cephaloliverines A and B and also by X-ray crystal diffraction for cephaloliverine E. Biosynthetic considerations suggest that cephaloliverines A-D are homologous of cephalotaxine-, homoerythrina- and Erythrina-type alkaloids. The performed bioassay revealed no cytotoxic activity against cancer cells and no neuroprotective properties on HEI-OC-1 cells model.
Collapse
Affiliation(s)
- Guang-Xing Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yang Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Ling-Hui Zeng
- Zhejiang University City College, Hangzhou, 310015, China.
| | - Johann Schinnerl
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
| | - Xiang-Hai Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China.
| |
Collapse
|
7
|
Yu GX, Wu J, Shi BB, Bao MF, Cai XH. Enantiomeric Cephalotaxus alkaloids from seeds of Cephalotaxus oliveri. NATURAL PRODUCTS AND BIOPROSPECTING 2022; 12:24. [PMID: 35778536 PMCID: PMC9249953 DOI: 10.1007/s13659-022-00344-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Five undescribed alkaloids were isolated from the seeds of Cephalotaxus oliveri along with 27 known ones. The new structures were elucidated based on spectroscopic data including 1D and 2D NMR, MS and calculated ECD spectra. Among them, (+)-acetylcephalofortine C was an enantiomeric Cephalotaxine alkaloids. The performed bioassay revealed that those alkaloids were not cytotoxic against cancer cells and had no neuroprotective properties in the HEI-OC-1 cells model.
Collapse
Affiliation(s)
- Guang-Xing Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Jing Wu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Bao-Bao Shi
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Mei-Fen Bao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Xiang-Hai Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China.
| |
Collapse
|
8
|
Tang YT, Wu J, Bao MF, Tan QG, Cai XH. Dimeric Erythrina alkaloids as well as their key units from Erythrina variegata. PHYTOCHEMISTRY 2022; 198:113160. [PMID: 35292327 DOI: 10.1016/j.phytochem.2022.113160] [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: 11/23/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Ten dimeric and two monomeric Erythrina alkaloids, all of them are undescribed, were isolated from the bark of Erythrina variegata L. and named as erythrivarines O-Z. Their structures were determined on the basis of NMR and UV-spectroscopy and mass spectrometry. Dimeric Erythrina alkaloids with a C-10/11' linkage in erythrivarine O and a C-7/10' connectivity in erythrivarines P-U are not yet reported. The two identified monomeric alkaloids may be the precursors of the described dimeric derivatives. These co-occurring dimeric and monomeric alkaloids enabled us to propose a possible biosynthetic pathway leading to these dimers. Their effects of preventing hearing loss were additionally evaluated and erythrivarine T showed as a potential protector of the House Ear Institute-Organ of Corti 1 (HEI-OC-1) cells against neomycin.
Collapse
Affiliation(s)
- Yu-Ting Tang
- School of Pharmaceutical Sciences, Guilin Medical University, Guilin, 541199, PR China; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Jing Wu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Mei-Fen Bao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Qin-Gang Tan
- School of Pharmaceutical Sciences, Guilin Medical University, Guilin, 541199, PR China.
| | - Xiang-Hai Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China.
| |
Collapse
|
9
|
Capecchi A, Reymond JL. Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning. J Cheminform 2021; 13:82. [PMID: 34663470 PMCID: PMC8524952 DOI: 10.1186/s13321-021-00559-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/02/2021] [Indexed: 01/13/2023] Open
Abstract
Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin ( https://tm.gdb.tools/map4/coconut_tmap/ ), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance ( https://np-svm-map4.gdb.tools/ ). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.
Collapse
Affiliation(s)
- Alice Capecchi
- 1 Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- 1 Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
| |
Collapse
|