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Chu MJ, Li M, Zhao Y. Dimeric pyrrole-imidazole alkaloids: sources, structures, bioactivities and biosynthesis. Bioorg Chem 2023; 133:106332. [PMID: 36773454 DOI: 10.1016/j.bioorg.2022.106332] [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: 10/24/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Pyrrole-imidazole alkaloids (PIAs) constitute a highly diverse and densely functionalized subclass of marine natural products. Among them, the uncommon dimeric PIAs with ornate molecular architectures, attractive biological properties and interesting biosynthetic origin have spurred a considerable interest of chemists and biologists. The present review comprehensively summarized 84 dimeric PIAs discovered during the period from 1981 to September 2022, covering their source organisms, chemical structures, biological activities as well as biosynthesis. For a better understanding, these structurally intricate PIA dimers are firstly classified and presented according to their carbon skeleton features as well as biosynthesis pathways. Furthermore, relevant summaries focusing on the source organisms and the associated bioactivities of these compounds belonging to different chemical classes are also provided, which will help elucidate the fascinating chemistry and biology of these unusual PIA dimers.
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Affiliation(s)
- Mei-Jun Chu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Meng Li
- Department of Pharmacy, Qingdao Central Hospital, Qingdao 266042, China
| | - Yongda Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
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Limited Metabolomic Overlap between Commensal Bacteria and Marine Sponge Holobionts Revealed by Large Scale Culturing and Mass Spectrometry-Based Metabolomics: An Undergraduate Laboratory Pedagogical Effort at Georgia Tech. Mar Drugs 2023; 21:md21010053. [PMID: 36662226 PMCID: PMC9862627 DOI: 10.3390/md21010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies.
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A Series of New Pyrrole Alkaloids with ALR2 Inhibitory Activities from the Sponge Stylissa massa. Mar Drugs 2022; 20:md20070454. [PMID: 35877747 PMCID: PMC9320028 DOI: 10.3390/md20070454] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 12/05/2022] Open
Abstract
Twelve new and four known alkaloids including five different structural scaffolds were isolated from the sponge Stylissa massa collected in the South China Sea. Compound 1 is the first identified precursor metabolite of the classic 5/7/5 tricyclic skeleton with unesterified guanidine and carboxyl groups, compounds 2–5 and 13–15 belong to the spongiacidin-type pyrrole imidazole alkaloids (PIAs). Z- and E-configurations of the spongiacidin-type PIAs often appeared concomitantly and were distinguished by the chemical shift analysis of 13C NMR spectra. The structures of all twelve new compounds were determined by NMR, MS, and ECD analysis combined with single-crystal data of compounds 1, 5, and 10. In the aldose reductase (ALR2) inhibitory assay, six 5/7/5 tricyclic compounds (2–5, 13–15) displayed significant activities. Compounds 13 and 14, as the representative members of spongiacidin-PIAs, demonstrated their ALR2-targeted activities in SPR experiments with KD values of 12.5 and 6.9 µM, respectively.
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Chu MJ, Li M, Ma H, Li PL, Li GQ. Secondary metabolites from marine sponges of the genus Agelas: a comprehensive update insight on structural diversity and bioactivity. RSC Adv 2022; 12:7789-7820. [PMID: 35424773 PMCID: PMC8982468 DOI: 10.1039/d1ra08765g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/03/2022] [Indexed: 01/07/2023] Open
Abstract
As one of the most common marine sponges in tropical and subtropical oceans, the sponges of the genus Agelas, have emerged as unique and yet under-investigated pools for discovery of natural products with fabulous molecular diversity and myriad interesting biological activities. The present review highlights the chemical structure and biological activity of 355 compounds that have been isolated and characterized from the members of Agelas sponges, over the period of about five decades (from 1971 to November 2021). For a better understanding, these numerous compounds are firstly classified and presented according to their carbon skeleton as well as their biosynthetic origins. Relevant summaries focusing on the source organism and the associated bioactivity of these compounds belonging to different chemical classes are also provided. This review highlights sponges of the genus Agelas as exciting source for discovery of intriguing natural compounds.
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Affiliation(s)
- Mei-Jun Chu
- College of Veterinary Medicine, Qingdao Agricultural University Qingdao 266109 China
| | - Meng Li
- Department of Pharmacy, Qingdao Central Hospital Qingdao 266042 China
| | - He Ma
- College of Veterinary Medicine, Qingdao Agricultural University Qingdao 266109 China
| | - Ping-Lin Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China Qingdao 266003 China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology Qingdao 266235 China
| | - Guo-Qiang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China Qingdao 266003 China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology Qingdao 266235 China
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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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Mohanty I, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N, Agarwal V. Stereochemical Assignment and Absolute Abundance of Nonproteinogenic Amino Acid Homoarginine in Marine Sponges. ACS OMEGA 2021; 6:33200-33205. [PMID: 34901671 PMCID: PMC8656204 DOI: 10.1021/acsomega.1c05685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Together with arginine, the nonproteinogenic amino acid homoarginine is a substrate for the production of vasodilator nitric oxide in the human body. In marine sponges, homoarginine has been postulated to serve as a precursor for the biosynthesis of pyrrole-imidazole alkaloid and bromotyrosine alkaloid classes of natural products. The absolute abundance of homoarginine, its abundance relative to arginine, and its stereochemical assignment in marine sponges are not known. Here, using stable isotope dilution mass spectrometry, we quantify the absolute abundances of homoarginine and arginine in marine sponges. We find that the abundance of homoarginine is highly variable and can far exceed the concentration of arginine, even in sponges where incorporation of homoarginine in natural products cannot be rationalized. The [homoarginine]/[arginine] ratio in marine sponges is greater than that in human analytes. By derivatization of sponge extracts with Marfey's reagent and comparison with authentic standards, we determine the l-isomer of homoarginine to be exclusively present in sponges. Our results shed light on the presence of the high abundance of homoarginine in marine sponge metabolomes and provide the foundation to investigate the biosynthetic routes and physiological roles of this nonproteinogenic amino acid in sponge physiology.
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Affiliation(s)
- Ipsita Mohanty
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Samuel G. Moore
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jason S. Biggs
- University
of Guam Marine Laboratory, UOG Station, Mangilao, Guam 96923, United States
| | - Christopher J. Freeman
- Department
of Biology, College of Charleston, Charleston, South Carolina 29424, United States
- Smithsonian
Marine Station, Ft. Pierce, Florida 34949, United States
| | - David A. Gaul
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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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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Mohanty I, Tapadar S, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N, Agarwal V. Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures. mSystems 2021; 6:e01387-20. [PMID: 33727403 PMCID: PMC8547014 DOI: 10.1128/msystems.01387-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023] Open
Abstract
Marine sponge holobionts are prolific sources of natural products. One of the most geographically widespread classes of sponge-derived natural products is the bromotyrosine alkaloids. A distinguishing feature of bromotyrosine alkaloids is that they are present in phylogenetically disparate sponges. In this study, using sponge specimens collected from Guam, the Solomon Islands, the Florida Keys, and Puerto Rico, we queried whether the presence of bromotyrosine alkaloids potentiates metabolomic and microbiome conservation among geographically distant and phylogenetically different marine sponges. A multi-omic characterization of sponge holobionts revealed vastly different metabolomic and microbiome architectures among different bromotyrosine alkaloid-harboring sponges. However, we find statistically significant correlations between the microbiomes and metabolomes, signifying that the microbiome plays an important role in shaping the overall metabolome, even in low-microbial-abundance sponges. Molecules mined from the polar metabolomes of these sponges revealed conservation of biosynthetic logic between bromotyrosine alkaloids and brominated pyrrole-imidazole alkaloids, another class of marine sponge-derived natural products. In light of prior findings postulating the sponge host itself to be the biosynthetic source of bromotyrosine alkaloids, our data now set the stage for investigating the causal relationships that dictate the microbiome-metabolome interconnectedness for marine sponges in which the microbiome may not contribute to natural product biogenesis.IMPORTANCE Our work demonstrates that phylogenetically and geographically distant sponges with very different microbiomes can harbor natural product chemical classes that are united in their core chemical structures and biosynthetic logic. Furthermore, we show that independent of geographical dispersion, natural product chemistry, and microbial abundance, overall sponge metabolomes tightly correlate with their microbiomes.
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Affiliation(s)
- Ipsita Mohanty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Subhasish Tapadar
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Samuel G Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, Guam
| | - Christopher J Freeman
- Department of Biology, College of Charleston, Charleston, South Carolina, USA
- Smithsonian Marine Station, Ft. Pierce, Florida, USA
| | - David A Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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