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Biomolecules
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Marine Natural Compounds with Biomedical Potential: 2nd Edition
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Marine Natural Compounds with Biomedical Potential: 2nd Edition

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Natural and Bio-derived Molecules".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 16488

Special Issue Editor

Dr. Elena Leychenko

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Guest Editor
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia
Interests: marine bioprospecting; sea anemone venoms; combinatorial peptide libraries; recombinant peptides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Marine organisms are an inexhaustible source of natural compounds that are promising for the creation of drugs or biologically active additives, which is closely related to the huge biological diversity of the resources of the World Ocean. More than 99% of the studied marine natural compounds are new, having no analogues among land plants and animals. The spectrum of biological activities shown by metabolites of marine origin is extremely wide; they exhibit antitumor, cancer-preventive, analgesic, antimicrobial, neuroprotective and other actions. The probability of the release of new highly active substances from marine organisms, on the basis of which drugs for medicine and veterinary medicine can be created and the corresponding technologies for their use, is quite high.

The use of "omix" technologies, such as metabolomics, genomics, proteomics, and venomics, makes it possible to ensure the scale and maximum efficiency of studying compounds of various origins with biomedical potential using a limited initial biomaterial. This opens up new possibilities for studying the structures and biological activities of new compounds, including complete metabolomes/transcriptomes and individual minor components of complex natural mixtures.

This Special Issue covers the role of marine organisms in biomolecule production, including screening extracts or isolating new metabolites and evaluating their biological activity.

Dr. Elena Leychenko

Guest Editor

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Keywords

  • Marine organisms
  • marine natural compounds
  • secondary metabolites
  • marine toxins
  • biomedical potential

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Related Special Issue

Published Papers (9 papers)

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Editorial

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3 pages, 147 KiB  
Editorial
Marine Natural Compounds with Biomedical Potential: 2nd Edition
by Elena Leychenko
Biomolecules 2024, 14(8), 1005; https://doi.org/10.3390/biom14081005 - 14 Aug 2024
Viewed by 613
Abstract
The potential of marine natural compounds for drug design is difficult to overestimate [...] Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)

Research

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24 pages, 28885 KiB  
Article
Dimerization of the β-Hairpin Membrane-Active Cationic Antimicrobial Peptide Capitellacin from Marine Polychaeta: An NMR Structural and Thermodynamic Study
by Pavel A. Mironov, Alexander S. Paramonov, Olesya V. Reznikova, Victoria N. Safronova, Pavel V. Panteleev, Ilia A. Bolosov, Tatiana V. Ovchinnikova and Zakhar O. Shenkarev
Biomolecules 2024, 14(3), 332; https://doi.org/10.3390/biom14030332 - 11 Mar 2024
Cited by 3 | Viewed by 1829
Abstract
Capitellacin is the β-hairpin membrane-active cationic antimicrobial peptide from the marine polychaeta Capitella teleta. Capitellacin exhibits antibacterial activity, including against drug-resistant strains. To gain insight into the mechanism of capitellacin action, we investigated the structure of the peptide in the membrane-mimicking environment [...] Read more.
Capitellacin is the β-hairpin membrane-active cationic antimicrobial peptide from the marine polychaeta Capitella teleta. Capitellacin exhibits antibacterial activity, including against drug-resistant strains. To gain insight into the mechanism of capitellacin action, we investigated the structure of the peptide in the membrane-mimicking environment of dodecylphosphocholine (DPC) micelles using high-resolution NMR spectroscopy. In DPC solution, two structural forms of capitellacin were observed: a monomeric β-hairpin was in equilibrium with a dimer formed by the antiparallel association of the N-terminal β-strands and stabilized by intermonomer hydrogen bonds and Van der Waals interactions. The thermodynamics of the enthalpy-driven dimerization process was studied by varying the temperature and molar ratios of the peptide to detergent. Cooling the peptide/detergent system promoted capitellacin dimerization. Paramagnetic relaxation enhancement induced by lipid-soluble 12-doxylstearate showed that monomeric and dimeric capitellacin interacted with the surface of the micelle and did not penetrate into the micelle interior, which is consistent with the “carpet” mode of membrane activity. An analysis of the known structures of β-hairpin AMP dimers showed that their dimerization in a membrane-like environment occurs through the association of polar or weakly hydrophobic surfaces. A comparative analysis of the physicochemical properties of β-hairpin AMPs revealed that dimer stability and hemolytic activity are positively correlated with surface hydrophobicity. An additional positive correlation was observed between hemolytic activity and AMP charge. The data obtained allowed for the provision of a more accurate description of the mechanism of the oligomerization of β-structural peptides in biological membranes. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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18 pages, 2393 KiB  
Article
Phanogracilins A–C, New Bibenzochromenones of Crinoid Phanogenia gracilis (Hartlaub, 1890)
by Elena A. Vasileva, Dmitrii V. Berdyshev, Natalia P. Mishchenko, Andrey V. Gerasimenko, Ekaterina S. Menchinskaya, Evgeniy A. Pislyagin, Ekaterina A. Chingizova, Leonid A. Kaluzhskiy, Salim Sh. Dautov and Sergey A. Fedoreyev
Biomolecules 2024, 14(2), 151; https://doi.org/10.3390/biom14020151 - 26 Jan 2024
Cited by 1 | Viewed by 1387
Abstract
Three new bibenzochromenones named phanogracilins A–C (1–3) were isolated from the crinoid Phanogenia gracilis. The structure of 1 was established using X-ray crystallography as 5,5′,6,6′,8,8′-hexahydroxy-2,2′-dipropyl-4H,4′H-[7,9′-bibenzo[g]chromene]-4,4′-dione. This allowed us to assign reliably 2D NMR signals for compound 1 and [...] Read more.
Three new bibenzochromenones named phanogracilins A–C (1–3) were isolated from the crinoid Phanogenia gracilis. The structure of 1 was established using X-ray crystallography as 5,5′,6,6′,8,8′-hexahydroxy-2,2′-dipropyl-4H,4′H-[7,9′-bibenzo[g]chromene]-4,4′-dione. This allowed us to assign reliably 2D NMR signals for compound 1 and subsequently for its isomer 2 that differed in the connecting position of two benzochromenone moieties (7,10′ instead of 7,9′), and compound for 3 that differed in the length of the aliphatic chain of one of the fragments. Compound 4 was derived from 1 in alkaline conditions, and its structure was elucidated as 5,5′,6′,8,8′-pentahydroxy-2,2′-dipropyl-4H,4′H-[7,9′-bibenzo[g]chromene]-4,4′,6,9-tetraone. Even though compounds 1–4 did not contain stereo centers, they possessed notable optical activity due to sterical hindrances, which limited the internal rotation of two benzochromenone fragments around C(7)–C(9′/10′) bonds. Isolated bibenzochromenones 1–4 were tested for their antiradical, neuroprotective and antimicrobial activities. Compounds 1, 3 and 4 demonstrated significant antiradical properties towards ABTS radicals higher than the positive control trolox. Compounds 1 and 4 exhibited moderate neuroprotective activity, increasing the viability of rotenone-treated Neuro-2a cells at a concentration of 1 µM by 9.8% and 11.8%, respectively. Compounds 1 and 3 at concentrations from 25 to 100 μM dose-dependently inhibited the growth of Gram-positive bacteria S. aureus and yeast-like fungi C. albicans, and they also prevented the formation of their biofilms. Compounds 2 and 4 exhibited low antimicrobial activity. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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18 pages, 14486 KiB  
Article
New Anti-Hypoxic Metabolites from Co-Culture of Marine-Derived Fungi Aspergillus carneus KMM 4638 and Amphichorda sp. KMM 4639
by Elena B. Belousova, Olesya I. Zhuravleva, Ekaterina A. Yurchenko, Galina K. Oleynikova, Alexandr S. Antonov, Natalya N. Kirichuk, Viktoria E. Chausova, Yuliya V. Khudyakova, Alexander S. Menshov, Roman S. Popov, Ekaterina S. Menchinskaya, Evgeny A. Pislyagin, Valery V. Mikhailov and Anton N. Yurchenko
Biomolecules 2023, 13(5), 741; https://doi.org/10.3390/biom13050741 - 25 Apr 2023
Cited by 6 | Viewed by 2022
Abstract
The KMM 4639 strain was identified as Amphichorda sp. based on two molecular genetic markers: ITS and β-tubulin regions. Chemical investigation of co-culture marine-derived fungi Amphichorda sp. KMM 4639 and Aspergillus carneus KMM 4638 led to the identification of five new quinazolinone alkaloids [...] Read more.
The KMM 4639 strain was identified as Amphichorda sp. based on two molecular genetic markers: ITS and β-tubulin regions. Chemical investigation of co-culture marine-derived fungi Amphichorda sp. KMM 4639 and Aspergillus carneus KMM 4638 led to the identification of five new quinazolinone alkaloids felicarnezolines A–E (1–5), a new highly oxygenated chromene derivative oxirapentyn M (6) and five previously reported related compounds. Their structures were established using spectroscopic methods and by comparison with related known compounds. The isolated compounds showed low cytotoxicity against human prostate and breast cancer cells but felicarnezoline B (2) protected rat cardiomyocytes H9c2 and human neuroblastoma SH-SY5Y cells against CoCl2-induced damage. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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17 pages, 2387 KiB  
Article
Phytoceramides from the Marine Sponge Monanchora clathrata: Structural Analysis and Cytoprotective Effects
by Elena A. Santalova, Alexandra S. Kuzmich, Ekaterina A. Chingizova, Ekaterina S. Menchinskaya, Evgeny A. Pislyagin and Pavel S. Dmitrenok
Biomolecules 2023, 13(4), 677; https://doi.org/10.3390/biom13040677 - 14 Apr 2023
Cited by 3 | Viewed by 2021
Abstract
In our research on sphingolipids from marine invertebrates, a mixture of phytoceramides was isolated from the sponge Monanchora clathrata (Western Australia). Total ceramide, ceramide molecular species (obtained by RP-HPLC, high-performance liquid chromatography on reversed-phase column) and their sphingoid/fatty acid components were analyzed by [...] Read more.
In our research on sphingolipids from marine invertebrates, a mixture of phytoceramides was isolated from the sponge Monanchora clathrata (Western Australia). Total ceramide, ceramide molecular species (obtained by RP-HPLC, high-performance liquid chromatography on reversed-phase column) and their sphingoid/fatty acid components were analyzed by NMR (nuclear magnetic resonance) spectroscopy and mass spectrometry. Sixteen new (1b, 3a, 3c, 3d, 3f, 3g, 5c, 5d, 5f, 5g, 6b–g) and twelve known (2b, 2e, 2f, 3b, 3e, 4a–c, 4e, 4f, 5b, 5e) compounds were shown to contain phytosphingosine-type backbones i-t17:0 (1), n-t17:0 (2), i-t18:0 (3), n-t18:0 (4), i-t19:0 (5), or ai-t19:0 (6), N-acylated with saturated (2R)-2-hydroxy C21 (a), C22 (b), C23 (c), i-C23 (d), C24 (e), C25 (f), or C26 (g) acids. The used combination of the instrumental and chemical methods permitted the more detailed investigation of the sponge ceramides than previously reported. It was found that the cytotoxic effect of crambescidin 359 (alkaloid from M. clathrata) and cisplatin decreased after pre-incubation of MDA-MB-231 and HL-60 cells with the investigated phytoceramides. In an in vitro paraquat model of Parkinson’s disease, the phytoceramides decreased the neurodegenerative effect and ROS (reactive oxygen species) formation induced by paraquat in neuroblastoma cells. In general, the preliminary treatment (for 24 or 48 h) of the cells with the phytoceramides of M. clathrata was necessary for their cytoprotective functions, otherwise the additive damaging effect of these sphingolipids and cytotoxic compounds (crambescidin 359, cisplatin or paraquat) was observed. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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18 pages, 3799 KiB  
Article
Combined Radiomodifying Effect of Fucoidan from the Brown Alga Saccharina cichorioides and Pacificusoside D from the Starfish Solaster pacificus in the Model of 3D Melanoma Cells
by Olesya S. Malyarenko, Timofey V. Malyarenko, Roza V. Usoltseva, Alla A. Kicha, Natalia V. Ivanchina and Svetlana P. Ermakova
Biomolecules 2023, 13(3), 419; https://doi.org/10.3390/biom13030419 - 23 Feb 2023
Cited by 5 | Viewed by 2059
Abstract
Cancer is one of the main causes of human mortality worldwide. Despite the advances in the diagnostics, surgery, radiotherapy, and chemotherapy, the search for more effective treatment regimens and drug combinations are relevant. This work aimed to assess the radiomodifying effect and molecular [...] Read more.
Cancer is one of the main causes of human mortality worldwide. Despite the advances in the diagnostics, surgery, radiotherapy, and chemotherapy, the search for more effective treatment regimens and drug combinations are relevant. This work aimed to assess the radiomodifying effect and molecular mechanism of action of fucoidan from the brown alga Saccharina cichorioides (ScF) and product of its autohydrolysis (ScF_AH) in combination with pacificusoside D from the starfish Solaster pacificus (SpD) on the model of viability and invasion of three-dimension (3D) human melanoma cells SK-MEL-2. The cytotoxicity of ScF (IC50 JB6 Cl41 > 800 µg/mL; IC50 SK-MEL-2 = 685.7 µg/mL), ScF_AH (IC50 JB6 Cl41/SK-MEL-2 > 800 µg/mL), SpD (IC50 JB6 Cl41 = 22 µM; IC50 SK-MEL-2 = 5.5 µM), and X-ray (ID50 JB6 Cl41 = 11.7 Gy; ID50 SK-MEL-2 = 6.7 Gy) was determined using MTS assay. The efficiency of two-component treatment of 3D SK-MEL-2 cells was revealed for ScF in combination with SpD or X-ray but not for the combination of fucoidan derivative ScF_AH with SpD or X-ray. The pre-treatment of spheroids with ScF, followed by cell irradiation with X-ray and treatment with SpD (three-component treatment) at low non-toxic concentrations, led to significant inhibition of the spheroids’ viability and invasion and appeared to be the most effective therapeutic scheme for SK-MEL-2 cells. The molecular mechanism of radiomodifying effect of ScF with SpD was associated with the activation of the initiator and effector caspases, which in turn caused the DNA degradation in SK-MEL-2 cells as determined by the Western blotting and DNA comet assays. Thus, the combination of fucoidan from brown algae and triterpene glycoside from starfish with radiotherapy might contribute to the development of highly effective method for melanoma therapy. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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16 pages, 4196 KiB  
Communication
First Anti-Inflammatory Peptide AnmTX Sco 9a-1 from the Swimming Sea Anemone Stomphia coccinea
by Rimma S. Kalina, Irina N. Gladkikh, Anna A. Klimovich, Yulia V. Kozhevnikova, Aleksandra N. Kvetkina, Eugene A. Rogozhin, Sergey G. Koshelev, Sergey A. Kozlov and Elena V. Leychenko
Biomolecules 2022, 12(11), 1705; https://doi.org/10.3390/biom12111705 - 17 Nov 2022
Cited by 4 | Viewed by 1803
Abstract
A novel peptide AnmTX Sco 9a-1 with the β-hairpin fold was isolated from the swimming sea anemone Stomphia coccinea (Actinostolidae family). The peptide consists of 28 amino acid residues, including modified hydroxyproline residue, and its measured molecular mass is 2960 Da. The peptide [...] Read more.
A novel peptide AnmTX Sco 9a-1 with the β-hairpin fold was isolated from the swimming sea anemone Stomphia coccinea (Actinostolidae family). The peptide consists of 28 amino acid residues, including modified hydroxyproline residue, and its measured molecular mass is 2960 Da. The peptide was not toxic on mice; however, it stimulated their exploratory motivation and active search behavior, and demonstrated an anti-anxiety effect. AnmTX Sco 9a-1 at doses of 0.1 and 1 mg/kg reduced the volume of edema during 24 h better than the nonsteroidal anti-inflammatory drug, Diclofenac, at dose of 1 mg/kg in a model of acute local λ-carrageenan-induced inflammation. ELISA analysis of the animal’s blood showed that peptide at a dose of 1 mg/kg reduced the content of tumor necrosis factor-α (TNF-α), a pro-inflammatory mediator responsible in the edema development, up to the level of TNF-α in the intact group. Besides, AnmTX Sco 9a-1 demonstrated a significant analgesic effect on acute pain sensitivity in the carrageenan-induced thermal hyperalgesia model at doses of 0.1 and 1 mg/kg. Activity of AnmTX Sco 9a-1 was shown not to be associated with modulation of nociceptive ASIC channels. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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Review

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31 pages, 3013 KiB  
Review
Sulfated Galactans from Agarophytes: Review of Extraction Methods, Structural Features, and Biological Activities
by Khosook Chumsook, Jantana Praiboon and Xiaoting Fu
Biomolecules 2023, 13(12), 1745; https://doi.org/10.3390/biom13121745 - 5 Dec 2023
Cited by 1 | Viewed by 2124
Abstract
Agarophytes are important seaweeds of the Rhodophyta type, which have been highly exploited for industrial use as sources of a widely consumed polysaccharide of agar. In addition to that, sulfated galactans (SGs) from agarophytes, which consist of various functional sulfate groups, have attracted [...] Read more.
Agarophytes are important seaweeds of the Rhodophyta type, which have been highly exploited for industrial use as sources of a widely consumed polysaccharide of agar. In addition to that, sulfated galactans (SGs) from agarophytes, which consist of various functional sulfate groups, have attracted the attention of scientists in current studies. SGs possess various biological activities, such as anti-tumor, anticoagulant, anti-inflammatory, antioxidant, anti-obesity, anti-diabetic, anti-microbial, anti-diarrhea, and gut microbiota regulation properties. Meanwhile, the taxonomy, ecological factors, i.e., environmental factors, and harvest period, as well as preparation methods, i.e., the pretreatment, extraction, and purification conditions, have been found to influence the chemical compositions and fine structures of SGs, which have, further, been shown to have an impact on their biological activities. However, the gaps in the knowledge of the properties of SGs due to the above complex factors have hindered their industrial application. The aim of this paper is to collect and systematically review the scientific evidence about SGs and, thus, to pave the way for broader and otherwise valuable industrial applications of agarophytes for human enterprise. In the future, this harvested biomass could be sustainably used not only as a source of agar production but also as natural materials in functional food and pharmaceutical industries. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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20 pages, 3464 KiB  
Review
Genus Acrostalagmus: A Prolific Producer of Natural Products
by Ting Shi, Han Wang, Yan-Jing Li, Yi-Fei Wang, Qun Pan, Bo Wang and Er-Lei Shang
Biomolecules 2023, 13(8), 1191; https://doi.org/10.3390/biom13081191 - 30 Jul 2023
Cited by 3 | Viewed by 1542
Abstract
Acrostalagmus is known for its ability to produce numerous bioactive natural products, making it valuable in drug development. This review provides information on the sources, distribution, chemical structure types, biosynthesis, and biological activities of the compounds isolated from the genus Acrostalagmus in the [...] Read more.
Acrostalagmus is known for its ability to produce numerous bioactive natural products, making it valuable in drug development. This review provides information on the sources, distribution, chemical structure types, biosynthesis, and biological activities of the compounds isolated from the genus Acrostalagmus in the family Plectosphaerellaceae from 1969 to 2022. The results show that 50% of the compounds isolated from Acrostalagmus are new natural products, and 82% of the natural products derived from this genus are from the marine Acrostalagmus. The compounds isolated from Acrostalagmus exhibit diverse structures, with alkaloids being of particular importance, accounting for 56% of the natural products derived from this genus. Furthermore, within the alkaloid class, 61% belong to the epipolythiodioxopiperazine family, highlighting the significance of epipolythiodioxopiperazine as a key characteristic structure within Acrostalagmus. Seventy-two percent of natural products derived from Acrostalagmus display bioactivities, with 50% of the bioactive compounds exhibiting more significant or comparable activities than their positive controls. Interestingly, 89% of potent active compounds are derived from marine fungi, demonstrating their promising potential for development. These findings underscore Acrostalagmus, particularly the marine-derived genus Acrostalagmusas, a valuable source of new bioactive secondary metabolites, and emphasize the vast resource importance of the ocean. Full article
(This article belongs to the Special Issue Marine Natural Compounds with Biomedical Potential: 2nd Edition)
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