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Wu Y, Xu ZZ, Kong C, Zhang SS, Lin XL, Zhang S, Liu LY, Sun F, Lin HW, Wang SP. Discovery of cycloheptapeptides phakefusins A-E from the marine sponge Phakellia fusca based on molecular networking. PHYTOCHEMISTRY 2024; 229:114248. [PMID: 39197714 DOI: 10.1016/j.phytochem.2024.114248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/01/2024]
Abstract
Guided by a probe-based molecular networking strategy, five undescribed cycloheptapeptides, phakefusins A-E (1-5), were isolated from the marine sponge Phakellia fusca. Compounds 1 and 2 contain the nonproteinogenic amino acid residues of dioxindolyalanine (Dioia) and β-3-oxindolylalanine (Oia), respectively. Compound 3 possesses a unique methionine sulfoxide, whereas compound 5 includes a glutamic acid ethyl ester unit. Their structures were elucidated through NMR spectroscopy, HR-MS/MS analysis, and the advanced Marfey's method. By synthesizing the (S, S/R)-Oia standard through tryptophan oxidation, we determined the configuration of this amino acid in compound 2 using the advanced Marfey's method. These cycloheptapeptides were evaluated for their antitumor, antibacterial, and antioxidant activities. Compound 1 showed moderate cytotoxicity against MCF-7 and PC9 cells, with IC50 values of 6.8 and 9.6 μM, respectively, while compounds 2-5 demonstrated potential antioxidant effects by upregulating HO-1, NQO1, and SOD2 levels, as well as inducing Nrf2 activation.
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Affiliation(s)
- Ying Wu
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zhao-Ze Xu
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Can Kong
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Shuai-Shuai Zhang
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xin-Li Lin
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Si Zhang
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li-Yun Liu
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fan Sun
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hou-Wen Lin
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Shu-Ping Wang
- Marine Drug Integrated Innovation Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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2
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Mayer AMS, Mayer VA, Swanson-Mungerson M, Pierce ML, Rodríguez AD, Nakamura F, Taglialatela-Scafati O. Marine Pharmacology in 2019-2021: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis and Antiviral Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action. Mar Drugs 2024; 22:309. [PMID: 39057418 PMCID: PMC11278370 DOI: 10.3390/md22070309] [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: 05/22/2024] [Revised: 06/22/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The current 2019-2021 marine pharmacology literature review provides a continuation of previous reviews covering the period 1998 to 2018. Preclinical marine pharmacology research during 2019-2021 was published by researchers in 42 countries and contributed novel mechanism-of-action pharmacology for 171 structurally characterized marine compounds. The peer-reviewed marine natural product pharmacology literature reported antibacterial, antifungal, antiprotozoal, antituberculosis, and antiviral mechanism-of-action studies for 49 compounds, 87 compounds with antidiabetic and anti-inflammatory activities that also affected the immune and nervous system, while another group of 51 compounds demonstrated novel miscellaneous mechanisms of action, which upon further investigation, may contribute to several pharmacological classes. Thus, in 2019-2021, a very active preclinical marine natural product pharmacology pipeline provided novel mechanisms of action as well as new lead chemistry for the clinical marine pharmaceutical pipeline targeting the therapy of several disease categories.
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Affiliation(s)
- Alejandro M. S. Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Veronica A. Mayer
- Department of Nursing Education, School of Nursing, Aurora University, 347 S. Gladstone Ave., Aurora, IL 60506, USA;
| | - Michelle Swanson-Mungerson
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Marsha L. Pierce
- Department of Pharmacology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, PR 00926, USA;
| | - Fumiaki Nakamura
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku 169-8555, Tokyo, Japan;
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3
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Zhang ZY, Gao XH, Huang Y, Fan YY, Yue JM. Drymariamides A-J, Antiadipogenic Cyclopeptides Incorporating Noncanonical Amino Acids from Drymaria cordata. JOURNAL OF NATURAL PRODUCTS 2024; 87:1441-1453. [PMID: 38722764 DOI: 10.1021/acs.jnatprod.4c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Herein, we report an extensive phytochemical study on the whole plant of Drymaria cordata, which led to the isolation of ten new orbitides, named drymariamides A-J (1-10). Compounds 2, 3, and 5 incorporate rare residues of noncanonical amino acids of kynurenine (Kyn) or 3a-hydroxypyrroloindoline (HPI). Their structures with absolute configurations were elucidated by a combination of spectroscopic analysis, advanced Marfey's method, X-ray diffraction, and electronic circular dichroism analysis. Compounds 1-10 exhibited antiadipogenic effects in 3T3-L1 adipocytes, and the most potent compound 7 showed an EC50 value of 1.17 ± 0.19 μM.
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Affiliation(s)
- Zong-Yi Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Xin-Hua Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
| | - Yi Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Yao-Yue Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, 198 East Binhai Road, Yantai, Shandong 264117, People's Republic of China
| | - Jian-Min Yue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People's Republic of China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, 198 East Binhai Road, Yantai, Shandong 264117, People's Republic of China
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4
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Kong C, Wu Y, Zhao HM, Zhang SS, Wu ZM, Li XB, Liu KC, Lin HW, Wang SP. Phakellisins A-E, cyclopeptides from a marine sponge Phakellia sp. guided by LC-MS. Bioorg Chem 2023; 139:106699. [PMID: 37390633 DOI: 10.1016/j.bioorg.2023.106699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
A chemical investigation of the marine sponge Phakellia sp. from the South China Sea yielded five new cyclopeptides, phakellisins A-E (1-5). Structures of these compounds were determined by comprehensive analysis of 1D/2D NMR, HRESIMS/MS spectroscopic data and the advanced Marfey's method. All compounds were evaluated for their cytotoxic activity. Compound 1 showed a strong inhibitory activity against WSU-DLCL-2 cells with an IC50 value of 5.25 ± 0.2 μM by induction of G0/G1 cell cycle arrest and apoptosis.
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Affiliation(s)
- Can Kong
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Key Laboratory for Biosensor of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, Shandong, People's Republic of China
| | - Ying Wu
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Hui-Min Zhao
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Shuai-Shuai Zhang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, People's Republic of China
| | - Zong-Mei Wu
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiao-Bin Li
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Key Laboratory for Biosensor of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, Shandong, People's Republic of China
| | - Ke-Chun Liu
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Key Laboratory for Biosensor of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, Shandong, People's Republic of China
| | - Hou-Wen Lin
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong Province, Key Laboratory for Biosensor of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, Shandong, People's Republic of China; Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
| | - Shu-Ping Wang
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China.
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Hegde M, Girisa S, Naliyadhara N, Kumar A, Alqahtani MS, Abbas M, Mohan CD, Warrier S, Hui KM, Rangappa KS, Sethi G, Kunnumakkara AB. Natural compounds targeting nuclear receptors for effective cancer therapy. Cancer Metastasis Rev 2023; 42:765-822. [PMID: 36482154 DOI: 10.1007/s10555-022-10068-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/03/2022] [Indexed: 12/13/2022]
Abstract
Human nuclear receptors (NRs) are a family of forty-eight transcription factors that modulate gene expression both spatially and temporally. Numerous biochemical, physiological, and pathological processes including cell survival, proliferation, differentiation, metabolism, immune modulation, development, reproduction, and aging are extensively orchestrated by different NRs. The involvement of dysregulated NRs and NR-mediated signaling pathways in driving cancer cell hallmarks has been thoroughly investigated. Targeting NRs has been one of the major focuses of drug development strategies for cancer interventions. Interestingly, rapid progress in molecular biology and drug screening reveals that the naturally occurring compounds are promising modern oncology drugs which are free of potentially inevitable repercussions that are associated with synthetic compounds. Therefore, the purpose of this review is to draw our attention to the potential therapeutic effects of various classes of natural compounds that target NRs such as phytochemicals, dietary components, venom constituents, royal jelly-derived compounds, and microbial derivatives in the establishment of novel and safe medications for cancer treatment. This review also emphasizes molecular mechanisms and signaling pathways that are leveraged to promote the anti-cancer effects of these natural compounds. We have also critically reviewed and assessed the advantages and limitations of current preclinical and clinical studies on this subject for cancer prophylaxis. This might subsequently pave the way for new paradigms in the discovery of drugs that target specific cancer types.
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Affiliation(s)
- Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sosmitha Girisa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Nikunj Naliyadhara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Aviral Kumar
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Mohammed S Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, 61421, Saudi Arabia
- BioImaging Unit, Space Research Centre, University of Leicester, Michael Atiyah Building, Leicester, LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, 61421, Saudi Arabia
- Electronics and Communications Department, College of Engineering, Delta University for Science and Technology, 35712, Gamasa, Egypt
| | | | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, School of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560065, India
- Cuor Stem Cellutions Pvt Ltd, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560065, India
| | - Kam Man Hui
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, 169610, Singapore
| | | | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Fernandes C, Ribeiro R, Pinto M, Kijjoa A. Absolute Stereochemistry Determination of Bioactive Marine-Derived Cyclopeptides by Liquid Chromatography Methods: An Update Review (2018-2022). Molecules 2023; 28:615. [PMID: 36677673 PMCID: PMC9867211 DOI: 10.3390/molecules28020615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Cyclopeptides are considered as one of the most important classes of compounds derived from marine sources, due to their structural diversity and a myriad of their biological and pharmacological activities. Since marine-derived cyclopeptides consist of different amino acids, many of which are non-proteinogenic, they possess various stereogenic centers. In this respect, the structure elucidation of new molecular scaffolds obtained from natural sources, including marine-derived cyclopeptides, can become a very challenging task. The determination of the absolute configurations of the amino acid residues is accomplished, in most cases, by performing acidic hydrolysis, followed by analyses by liquid chromatography (LC). In a continuation with the authors' previous publication, and to analyze the current trends, the present review covers recently published works (from January 2018 to November 2022) regarding new cyclopeptides from marine organisms, with a special focus on their biological/pharmacological activities and the absolute stereochemical assignment of the amino acid residues. Ninety-one unreported marine-derived cyclopeptides were identified during this period, most of which displayed anticancer or antimicrobial activities. Marfey's method, which involves LC, was found to be the most frequently used for this purpose.
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Affiliation(s)
- Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Ricardo Ribeiro
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Madalena Pinto
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Anake Kijjoa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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7
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Lv LX, Wu Y, He HX, Li NP, Zhao W, Fan YQ, Wei X, Su JC, Wang Q, Gu JH. Acronyrones A-C, unusual prenylated acetophenones from Acronychia pedunculata. Fitoterapia 2022; 163:105303. [PMID: 36152926 DOI: 10.1016/j.fitote.2022.105303] [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: 08/11/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022]
Abstract
Two novel prenylated acetophenones with new carbon skeletons, acronyrones A and B (1 and 2), and a new analogue, acronyrone C (3), together with two known compounds (4 and 5) were isolated from the leaves of Acronychia pedunculata. Their structures with absolute configurations were identified by interpretation of spectroscopic data, single crystal X-ray diffraction, and electronic circular dichroism (ECD) calculations. Compounds 1 and 2 represent the first example of prenylated acetophenones possessed a C7 (1) and a C6 (2) side chain, forming a 4-isobutylchroman-2-one unit and a 3-(2-methylpropylidene)benzofuran-2(3H)-one moiety with the acetophenone core, respectively. In addition, compound 4 exhibited significant dose-dependent transcriptional activation effect against retinoid X receptor-α (RXRα), and could be regarded as a new type of non-classical RXR ligand.
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Affiliation(s)
- Li-Xia Lv
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China
| | - Yan Wu
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, People's Republic of China
| | - Hao-Xuan He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China
| | - Ni-Ping Li
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, People's Republic of China
| | - Wei Zhao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China
| | - Yun-Qi Fan
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China
| | - Xia Wei
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China
| | - Jun-Cheng Su
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China.
| | - Ji-Hong Gu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, People's Republic of China.
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8
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Yan H, Chen F. Recent Progress in Solid‐Phase Total Synthesis of Naturally Occurring Small Peptides. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hong Yan
- Institute of Pharmaceutical Science and Technology College of Chemistry Fuzhou University Fuzhou 350108 People's Republic of China
| | - Fen‐Er Chen
- Institute of Pharmaceutical Science and Technology College of Chemistry Fuzhou University Fuzhou 350108 People's Republic of China
- Engineering Center of Catalysis and Synthesis for Chiral Molecules Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 People's Republic of China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs Fudan University 220 Handan Road Shanghai 200433 People's Republic of China
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9
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Abstract
Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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10
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Wu Y, Wu ZM, Zhang SS, Liu LY, Sun F, Jiao WH, Wang SP, Lin HW. Axinellasins A-D, Immunosuppressive Cycloheptapeptide Diastereomers, Discovered via a Precursor Ion Scanning-Supercritical Fluid Chromatography Strategy from the Marine Sponge Axinella species. Org Lett 2022; 24:934-938. [PMID: 35044186 DOI: 10.1021/acs.orglett.1c04309] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The precursor ion scanning-supercritical fluid chromatography (PI-SFC) method was applied to explore new methionine sulfoxide-containing cycloheptapeptides, axinellasins A-D (1-4), from the marine sponge Axinella sp. Their structures, including absolute configurations, were elucidated by detailed spectroscopic analyses and X-ray crystallography. The total synthesis of 4 was completed via an Fmoc solid/solution-phase synthesis. Compounds 1-4 exhibited immunosuppressive effects via inhibition of T and B cell proliferation, and 1 and 4 showed better inhibitory activities than their corresponding diastereomers.
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Affiliation(s)
- Ying Wu
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zong-Mei Wu
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuai-Shuai Zhang
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Li-Yun Liu
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Sun
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei-Hua Jiao
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shu-Ping Wang
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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11
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Akbarian M, Khani A, Eghbalpour S, Uversky VN. Bioactive Peptides: Synthesis, Sources, Applications, and Proposed Mechanisms of Action. Int J Mol Sci 2022; 23:ijms23031445. [PMID: 35163367 PMCID: PMC8836030 DOI: 10.3390/ijms23031445] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Bioactive peptides are a group of biological molecules that are normally buried in the structure of parent proteins and become active after the cleavage of the proteins. Another group of peptides is actively produced and found in many microorganisms and the body of organisms. Today, many groups of bioactive peptides have been marketed chemically or recombinantly. This article reviews the various production methods and sources of these important/ubiquitous and useful biomolecules. Their applications, such as antimicrobial, antihypertensive, antioxidant activities, blood-lipid-lowering effect, opioid role, antiobesity, ability to bind minerals, antidiabetic, and antiaging effects, will be explored. The types of pathways proposed for bioactive applications will be in the next part of the article, and at the end, the future perspectives of bioactive peptides will be reviewed. Reading this article is recommended for researchers interested in various fields of physiology, microbiology, biochemistry, and nanotechnology and food industry professionals.
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Affiliation(s)
- Mohsen Akbarian
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan;
| | - Ali Khani
- Department of Radiation Sciences, Faculty of Applied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran;
| | - Sara Eghbalpour
- Department of Obstetrics and Gynecology Surgery, Babol University of Medical Sciences, Babol 4717647745, Iran;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-(813)-974-5816
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12
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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.
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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.
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13
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He Q, Wu Z, Li L, Sun W, Wang G, Jiang R, Hu L, Shi L, He R, Wang Y, Ye W. Discovery of Neuritogenic
Securinega
Alkaloids from
Flueggea suffruticosa
by a Building Blocks‐Based Molecular Network Strategy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qi‐Fang He
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Zhen‐Long Wu
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Liuren Li
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Wan‐Yang Sun
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Gui‐Yang Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Ren‐Wang Jiang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Li‐Jun Hu
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Lei Shi
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
| | - Rong‐Rong He
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Ying Wang
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
| | - Wen‐Cai Ye
- Center for Bioactive Natural Molecules and Innovative Drugs Research College of Pharmacy Jinan University Guangzhou 510632 China
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research Jinan University Guangzhou 510632 China
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14
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Mohanty I, Nguyen NA, Moore SG, Biggs JS, Gaul DA, Garg N, Agarwal V. Enzymatic Synthesis Assisted Discovery of Proline-Rich Macrocyclic Peptides in Marine Sponges. Chembiochem 2021; 22:2614-2618. [PMID: 34185944 PMCID: PMC8415105 DOI: 10.1002/cbic.202100275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/25/2021] [Indexed: 11/10/2022]
Abstract
Proline-rich macrocyclic peptides (PRMPs) are natural products present in geographically and phylogenetically dispersed marine sponges. The large diversity and low abundance of PRMPs in sponge metabolomes precludes isolation and structure elucidation of each individual PRMP congener. Here, using standards developed via biomimetic enzymatic synthesis of PRMPs, a mass spectrometry-based workflow to sequence PRMPs was developed and validated to reveal that the diversity of PRMPs in marine sponges is much greater than that has been realized by natural product isolation-based strategies. Findings are placed in the context of diversity-oriented transamidative macrocyclization of peptide substrates in sponge holobionts.
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Affiliation(s)
- Ipsita Mohanty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nguyet A Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Samuel G Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, Guam 96923, USA
| | - David A Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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15
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He QF, Wu ZL, Li L, Sun WY, Wang GY, Jiang RW, Hu LJ, Shi L, He RR, Wang Y, Ye WC. Discovery of Neuritogenic Securinega Alkaloids from Flueggea suffruticosa by a Building Blocks-Based Molecular Network Strategy. Angew Chem Int Ed Engl 2021; 60:19609-19613. [PMID: 34196083 DOI: 10.1002/anie.202103878] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/28/2021] [Indexed: 12/22/2022]
Abstract
A combined strategy of building blocks recognition and molecular network construction, termed the building blocks-based molecular network (BBMN), was first presented to facilitate the efficient discovery of novel natural products. By mapping the BBMN of the total alkaloid fraction of Flueggea suffruticosa, three Securinega alkaloids (SEAs) with unusual chemical architectures, suffranidines A-C (1-3), were discovered and isolated. Compound 1 characterizes an unprecedented 8/5/6/5/6/6/6/6-fused octacyclic scaffold with a unique cage-shaped 3-azatricyclo[6.4.0.03,11 ]dodecane core. Compounds 2 and 3 are highly modified SEA dimers that incorporate additional C6 motifs. A hypothetical biosynthetic pathway for 1-3 was proposed. In addition, 1 significantly induced neuronal differentiation and neurite extension by upregulating eukaryotic elongation factor 2 (eEF2)-mediated protein synthesis.
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Affiliation(s)
- Qi-Fang He
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Zhen-Long Wu
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Liuren Li
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Wan-Yang Sun
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Gui-Yang Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Ren-Wang Jiang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Li-Jun Hu
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Lei Shi
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Rong-Rong He
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Ying Wang
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
| | - Wen-Cai Ye
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM & New Drugs Research, Jinan University, Guangzhou, 510632, China
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16
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Sun C, Zhang Z, Ren Z, Yu L, Zhou H, Han Y, Shah M, Che Q, Zhang G, Li D, Zhu T. Antibacterial Cyclic Tripeptides from Antarctica-Sponge-Derived Fungus Aspergillus insulicola HDN151418. Mar Drugs 2020; 18:md18110532. [PMID: 33114712 PMCID: PMC7694092 DOI: 10.3390/md18110532] [Citation(s) in RCA: 16] [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: 10/07/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/11/2022] Open
Abstract
Three new aspochracin-type cyclic tripeptides, sclerotiotides M–O (1–3), together with three known analogues, sclerotiotide L (4), sclerotiotide F (5), and sclerotiotide B (6), were obtained from the ethyl acetate extract of the fungus Aspergillus insulicola HDN151418, which was isolated from an unidentified Antarctica sponge. Spectroscopic and chemical approaches were used to elucidate their structures. The absolute configuration of the side chain in compound 4 was elucidated for the first time. Compounds 1 and 2 showed broad antimicrobial activity against a panel of pathogenic strains, including Bacillus cereus, Proteus species, Mycobacterium phlei, Bacillus subtilis, Vibrio parahemolyticus, Edwardsiella tarda, MRCNS, and MRSA, with MIC values ranging from 1.56 to 25.0 µM.
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Affiliation(s)
- Chunxiao Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Ziping Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Zilin Ren
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Liu Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Huan Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Yaxin Han
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Mudassir Shah
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: (D.L.); (T.Z.); Tel.: +86-532-82031619 (D.L.); +86-532-82031632 (T.Z.)
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (C.S.); (Z.Z.); (Z.R.); (L.Y.); (H.Z.); (Y.H.); (M.S.); (Q.C.); (G.Z.)
- Correspondence: (D.L.); (T.Z.); Tel.: +86-532-82031619 (D.L.); +86-532-82031632 (T.Z.)
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17
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Capecchi A, Reymond JL. Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning. Biomolecules 2020; 10:E1385. [PMID: 32998475 PMCID: PMC7600738 DOI: 10.3390/biom10101385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial natural products (NPs) are an important source of drugs, however, their structural diversity remains poorly understood. Here we used our recently reported MinHashed Atom Pair fingerprint with diameter of four bonds (MAP4), a fingerprint suitable for molecules across very different sizes, to analyze the Natural Products Atlas (NPAtlas), a database of 25,523 NPs of bacterial or fungal origin. To visualize NPAtlas by MAP4 similarity, we used the dimensionality reduction method tree map (TMAP). The resulting interactive map organizes molecules by physico-chemical properties and compound families such as peptides and glycosides. Remarkably, the map separates bacterial and fungal NPs from one another, revealing that these two compound families are intrinsically different despite their related biosynthetic pathways. We used these differences to train a machine learning model capable of distinguishing between NPs of bacterial or fungal origin.
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Affiliation(s)
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland;
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