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Santos TCD, Obando JMC, Leite PEC, Pereira MR, Leitão MDF, Abujadi C, Pimenta LDFL, Martins RCC, Cavalcanti DN. Approaches of marine compounds and relevant immune mediators in Autism Spectrum Disorder: Opportunities and challenges. Eur J Med Chem 2024; 266:116153. [PMID: 38277916 DOI: 10.1016/j.ejmech.2024.116153] [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: 10/09/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/28/2024]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that affects social skills, language, communication, and behavioral skills, significantly impacting the individual's quality of life. Recently, numerous works have centered on the connections between the immune and central nervous systems and the influence of neuroinflammation on autism symptomatology. Marine natural products are considered as important alternative sources of different types of compounds, including polysaccharides, polyphenols, sterols, carotenoids, terpenoids and, alkaloids. These compounds present anti-inflammatory, neuroprotective and immunomodulatory activities, exhibiting a potential for the treatment of many diseases. Although many studies address the marine compounds in the modulation of inflammatory mediators, there is a gap regarding their use in the regulation of the immune system in ASD. Thus, this review aims to provide a better understanding regarding cytokines, chemokines, growth factors and immune responses in ASD, as well as the potential of bioactive marine compounds in the immune regulation in ASD. We expect that this review would contribute to the development of therapeutic alternatives for controlling immune mediators and inflammation in ASD.
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Affiliation(s)
- Thalisia Cunha Dos Santos
- Programa de Pós-graduação em Química de Produtos Naturais, Instituto de Pesquisas de Produtos Naturais Walter Mors, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Laboratório de Produtos Naturais de Algas Marinha (ALGAMAR), Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Núcleo de Estudos e Pesquisas em Autismo (NEPA), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil.
| | - Johana Marcela Concha Obando
- Laboratório de Produtos Naturais de Algas Marinha (ALGAMAR), Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Núcleo de Estudos e Pesquisas em Autismo (NEPA), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Paulo Emílio Corrêa Leite
- Núcleo de Estudos e Pesquisas em Autismo (NEPA), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Instituto LisMAPS, Niterói, RJ, Brazil
| | - Mariana Rodrigues Pereira
- Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Instituto LisMAPS, Niterói, RJ, Brazil; Programa de Pós-graduação em Neurociências, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Mônica de Freitas Leitão
- Núcleo de Estudos e Pesquisas em Autismo (NEPA), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Faculdade de Medicina, Pontifícia Universidade Católica de Campinas (PUC-Camp), Campinas, SP, Brazil
| | - Caio Abujadi
- Núcleo de Estudos e Pesquisas em Autismo (NEPA), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Programa de Pós-graduação em Ciência, Tecnologia e Inclusão (PGCTIn), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | | | - Roberto Carlos Campos Martins
- Programa de Pós-graduação em Química de Produtos Naturais, Instituto de Pesquisas de Produtos Naturais Walter Mors, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Diana Negrão Cavalcanti
- Laboratório de Produtos Naturais de Algas Marinha (ALGAMAR), Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Núcleo de Estudos e Pesquisas em Autismo (NEPA), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil; Programa de Pós-graduação em Ciência, Tecnologia e Inclusão (PGCTIn), Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil.
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Alves J, Gaspar H, Silva J, Alves C, Martins A, Teodoro F, Susano P, Pinteus S, Pedrosa R. Unravelling the Anti-Inflammatory and Antioxidant Potential of the Marine Sponge Cliona celata from the Portuguese Coastline. Mar Drugs 2021; 19:632. [PMID: 34822503 PMCID: PMC8625174 DOI: 10.3390/md19110632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation is a double-edged sword, as it can have both protective effects and harmful consequences, which, combined with oxidative stress (OS), can lead to the development of deathly chronic inflammatory conditions. Over the years, research has evidenced the potential of marine sponges as a source of effective anti-inflammatory therapeutic agents. Within this framework, the purpose of this study was to evaluate the antioxidant and the anti-inflammatory potential of the marine sponge Cliona celata. For this purpose, their organic extracts (C1-C5) and fractions were evaluated concerning their radical scavenging activity through 2,2-diphenyl-1-picrylhydrazyl radical (DPPH), ferric reducing antioxidant power (FRAP), oxygen radical absorbance capacity (ORAC), and anti-inflammatory activity through a (lipopolysaccharides (LPS)-induced inflammation on RAW 264.7 cells) model. Compounds present in the two most active fractions (F5 and F13) of C4 were tentatively identified by gas chromatography coupled to mass spectrometry (GC-MS). Even though samples displayed low antioxidant activity, they presented a high anti-inflammatory capacity in the studied cellular inflammatory model when compared to the anti-inflammatory standard, dexamethasone. GC-MS analysis led to the identification of n-hexadecanoic acid, cis-9-hexadecenal, and 13-octadecenal in fraction F5, while two major compounds, octadecanoic acid and cholesterol, were identified in fraction F13. The developed studies demonstrated the high anti-inflammatory activity of the marine sponge C. celata extracts and fractions, highlighting its potential for further therapeutic applications.
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Affiliation(s)
- Joana Alves
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
| | - Helena Gaspar
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Science, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Joana Silva
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
| | - Celso Alves
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
| | - Alice Martins
- MARE—Marine and Environmental Sciences Centre, Escola Superior de Turismo e Tecnologia do Mar, Politécnico de Leiria, 2520-614 Peniche, Portugal;
| | - Fernando Teodoro
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
| | - Patrícia Susano
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
| | - Susete Pinteus
- MARE—Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; (J.A.); (J.S.); (C.A.); (F.T.); (P.S.); (S.P.)
| | - Rui Pedrosa
- MARE—Marine and Environmental Sciences Centre, Escola Superior de Turismo e Tecnologia do Mar, Politécnico de Leiria, 2520-614 Peniche, Portugal;
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Burgers LD, Fürst R. Natural products as drugs and tools for influencing core processes of eukaryotic mRNA translation. Pharmacol Res 2021; 170:105535. [PMID: 34058326 DOI: 10.1016/j.phrs.2021.105535] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022]
Abstract
Eukaryotic protein synthesis is the highly conserved, complex mechanism of translating genetic information into proteins. Although this process is essential for cellular homoeostasis, dysregulations are associated with cellular malfunctions and diseases including cancer and diabetes. In the challenging and ongoing search for adequate treatment possibilities, natural products represent excellent research tools and drug leads for new interactions with the translational machinery and for influencing mRNA translation. In this review, bacterial-, marine- and plant-derived natural compounds that interact with different steps of mRNA translation, comprising ribosomal assembly, translation initiation and elongation, are highlighted. Thereby, the exact binding and interacting partners are unveiled in order to accurately understand the mode of action of each natural product. The pharmacological relevance of these compounds is furthermore assessed by evaluating the observed biological activities in the light of translational inhibition and by enlightening potential obstacles and undesired side-effects, e.g. in clinical trials. As many of the natural products presented here possess the potential to serve as drug leads for synthetic derivatives, structural motifs, which are indispensable for both mode of action and biological activities, are discussed. Evaluating the natural products emphasises the strong diversity of their points of attack. Especially the fact that selected binding partners can be set in direct relation to different diseases emphasises the indispensability of natural products in the field of drug development. Discovery of new, unique and unusual interacting partners again renders them promising tools for future research in the field of eukaryotic mRNA translation.
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Affiliation(s)
- Luisa D Burgers
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt, Germany
| | - Robert Fürst
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt, Germany; LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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Krueger K, Boehme E, Klettner AK, Zille M. The potential of marine resources for retinal diseases: a systematic review of the molecular mechanisms. Crit Rev Food Sci Nutr 2021; 62:7518-7560. [PMID: 33970706 DOI: 10.1080/10408398.2021.1915242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We rely on vision more than on any other sense to obtain information about our environment. Hence, the loss or even impairment of vision profoundly affects our quality of life. Diet or food components have already demonstrated beneficial effects on the development of retinal diseases. Recently, there has been a growing interest in resources from marine animals and plants for the prevention of retinal diseases through nutrition. Especially fish intake and omega-3 fatty acids have already led to promising results, including associations with a reduced incidence of retinal diseases. However, the underlying molecular mechanisms are insufficiently explained. The aim of this review was to summarize the known mechanistic effects of marine resources on the pathophysiological processes in retinal diseases. We performed a systematic literature review following the PRISMA guidelines and identified 107 studies investigating marine resources in the context of retinal diseases. Of these, 46 studies described the underlying mechanisms including anti-inflammatory, antioxidant, antiangiogenic/vasoprotective, cytoprotective, metabolic, and retinal function effects, which we critically summarize. We further discuss perspectives on the use of marine resources for human nutrition to prevent retinal diseases with a particular focus on regulatory aspects, health claims, safety, and bioavailability.
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Affiliation(s)
- Kristin Krueger
- Department of Marine Biotechnology, Fraunhofer Research and Development Center for Marine and Cellular Biotechnology EMB, Lübeck, Germany
| | - Elke Boehme
- Department of Marine Biotechnology, Fraunhofer Research and Development Center for Marine and Cellular Biotechnology EMB, Lübeck, Germany
| | - Alexa Karina Klettner
- Department of Ophthalmology, University Medical Center, University of Kiel, Quincke Research Center, Kiel, Germany
| | - Marietta Zille
- Department of Marine Biotechnology, Fraunhofer Research and Development Center for Marine and Cellular Biotechnology EMB, Lübeck, Germany.,Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
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5
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Application of marine natural products in drug research. Bioorg Med Chem 2021; 35:116058. [PMID: 33588288 DOI: 10.1016/j.bmc.2021.116058] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022]
Abstract
New diseases are emerging as the environment changes, so drug manufacturers are always on the lookout for new resources to develop effective and safe drugs. In recent years, many bioactive substances have been produced in the marine environment, which represents an alternative resource for new drugs used to combat major diseases such as cancer or inflammation. Many marine-derived medicinal substances are in preclinical or early stage of clinical development, and some marine drugs have been put on the market, such as ET743 (Yondelis®). This review presents the sources, activities, mechanisms of action and syntheses of bioactive substances based on marine natural products in clinical trials and on the market, which is helpful to understand the progress of drug research by application of marine natural products.
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Baldo F. Prediction of modes of action of components of traditional medicinal preparations. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2018-0115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AbstractTraditional medicine preparations are used to treat many ailments in multiple regions across the world. Despite their widespread use, the mode of action of these preparations and their constituents are not fully understood. Traditional methods of elucidating the modes of action of these natural products (NPs) can be expensive and time consuming e. g. biochemical methods, bioactivity guided fractionation, etc. In this review, we discuss some methods for the prediction of the modes of action of traditional medicine preparations, both in mixtures and as isolated NPs. These methods are useful to predict targets of NPs before they are experimentally validated. Case studies of the applications of these methods are also provided herein.
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Dolmatova LS, Dolmatov IY. Different Macrophage Type Triggering as Target of the Action of Biologically Active Substances from Marine Invertebrates. Mar Drugs 2020; 18:E37. [PMID: 31906518 PMCID: PMC7024355 DOI: 10.3390/md18010037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/28/2019] [Accepted: 12/30/2019] [Indexed: 12/11/2022] Open
Abstract
Macrophages play a fundamental role in the immune system. Depending on the microenvironment stimuli, macrophages can acquire distinct phenotypes characterized with different sets of the markers of their functional activities. Polarization of macrophages towards M1 type (classical activation) is involved in inflammation and the related progression of diseases, while, in contrast, alternatively activated M2 macrophages are associated with the anti-inflammatory mechanisms. Reprogramming macrophages to switch their phenotypes could provide a new therapeutic strategy, and targeting the M1/M2 macrophage balance is a promising current trend in pharmacology. Marine invertebrates are a vast source of the variety of structurally diverse compounds with potent pharmacological activities. For years, a large number of studies concerning the immunomodulatory properties of the marine substances have been run with using some intracellular markers of immune stimulation or suppression irrespective of the possible application of marine compounds in reprogramming of macrophage activation, and only few reports clearly demonstrated the macrophage-polarizing activities of some marine compounds during the last decade. In this review, the data on the immunomodulating effects of the extracts and pure compounds of a variety of chemical structure from species of different classes of marine invertebrates are described with focus on their potential in shifting M1/M2 macrophage balance towards M1 or M2 phenotype.
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Affiliation(s)
- Lyudmila S. Dolmatova
- V.I. Il‘ichev Pacific Oceanological Institute, Far Eastern Branch, Russian Academy of Sciences, Baltiyskaya 43, 690041 Vladivostok, Russia
| | - Igor Yu. Dolmatov
- National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevsky 17, 690041 Vladivostok, Russia;
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Marine Pharmacology in 2014-2015: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis, Antiviral, and Anthelmintic Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action. Mar Drugs 2019; 18:md18010005. [PMID: 31861527 PMCID: PMC7024264 DOI: 10.3390/md18010005] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 12/31/2022] Open
Abstract
The systematic review of the marine pharmacology literature from 2014 to 2015 was completed in a manner consistent with the 1998-2013 reviews of this series. Research in marine pharmacology during 2014-2015, which was reported by investigators in 43 countries, described novel findings on the preclinical pharmacology of 301 marine compounds. These observations included antibacterial, antifungal, antiprotozoal, antituberculosis, antiviral, and anthelmintic pharmacological activities for 133 marine natural products, 85 marine compounds with antidiabetic, and anti-inflammatory activities, as well as those that affected the immune and nervous system, and 83 marine compounds that displayed miscellaneous mechanisms of action, and may probably contribute to novel pharmacological classes upon further research. Thus, in 2014-2015, the preclinical marine natural product pharmacology pipeline provided novel pharmacology as well as new lead compounds for the clinical marine pharmaceutical pipeline, and thus continued to contribute to ongoing global research for alternative therapeutic approaches to many disease categories.
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Decyl Gallate as a Possible Inhibitor of N-Glycosylation Process in Paracoccidioides lutzii. Antimicrob Agents Chemother 2019; 63:AAC.01909-18. [PMID: 31451502 DOI: 10.1128/aac.01909-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/28/2019] [Indexed: 01/29/2023] Open
Abstract
The available antifungal therapeutic arsenal is limited. The search for alternative drugs with fewer side effects and new targets remains a major challenge. Decyl gallate (G14) is a derivative of gallic acid with a range of biological activities and broad-spectrum antifungal activity. Previously, our group demonstrated the promising anti-Paracoccidioides activity of G14. In this work, to evaluate the antifungal characteristics of G14 for Paracoccidioides lutzii, a chemical-genetic interaction analysis was conducted on a Saccharomyces cerevisiae model. N-glycosylation and/or the unfolded protein response pathway was identified as a high-confidence process for drug target prediction. The overactivation of unfolded protein response (UPR) signaling was confirmed using this model with IRE1/ATF6/PERK genes tagged with green fluorescent protein (GFP). In P. lutzii, this prediction was confirmed by the low activity of glycosylated enzymes [α-(1,3)-glucanase, N-acetyl-β-d-glucosaminidase (NAGase), and α-(1,4)-amylase], by hyperexpression of genes involved with the UPR and glycosylated enzymes, and by the reduction in the amounts of glycosylated proteins and chitin. All of these components are involved in fungal cell wall integrity and are dependent on the N-glycosylation process. This loss of integrity was confirmed by the reduction in mitochondrial activity, impaired budding, enhancement of wall permeability, and a decrease in viability. These events led to a reduction of the ability of fungi to adhere on human lung epithelial cells (A549) in vitro Therefore, G14 may have an important role in balancing the inflammatory reaction caused by fungal infection, without interfering with the microbicidal activity of nitric oxide. This work provides new information on the activity of G14, a potential anti-Paracoccidioides compound.
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Oceans as a Source of Immunotherapy. Mar Drugs 2019; 17:md17050282. [PMID: 31083446 PMCID: PMC6562586 DOI: 10.3390/md17050282] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
Marine flora is taxonomically diverse, biologically active, and chemically unique. It is an excellent resource, which offers great opportunities for the discovery of new biopharmaceuticals such as immunomodulators and drugs targeting cancerous, inflammatory, microbial, and fungal diseases. The ability of some marine molecules to mediate specific inhibitory activities has been demonstrated in a range of cellular processes, including apoptosis, angiogenesis, and cell migration and adhesion. Immunomodulators have been shown to have significant therapeutic effects on immune-mediated diseases, but the search for safe and effective immunotherapies for other diseases such as sinusitis, atopic dermatitis, rheumatoid arthritis, asthma and allergies is ongoing. This review focuses on the marine-originated bioactive molecules with immunomodulatory potential, with a particular focus on the molecular mechanisms of specific agents with respect to their targets. It also addresses the commercial utilization of these compounds for possible drug improvement using metabolic engineering and genomics.
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From Yeast to Humans: Leveraging New Approaches in Yeast to Accelerate Discovery of Therapeutic Targets for Synucleinopathies. Methods Mol Biol 2019; 2049:419-444. [PMID: 31602625 DOI: 10.1007/978-1-4939-9736-7_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Neurodegenerative diseases (ND) represent a growing, global health crisis, one that lacks any disease-modifying therapeutic strategy. This critical need for new therapies must be met with an exhaustive approach to exploit all tools available. A yeast (Saccharomyces cerevisiae) model of α-synuclein toxicity-the protein causally linked to Parkinson's disease and other synucleinopathies-offers a powerful approach that takes advantage of the unique offerings of this system: tractable genetics, robust high-throughput screening strategies, unparalleled data repositories, powerful computational tools, and extensive evolutionary conservation of fundamental biological pathways. These attributes have enabled genetic and small molecule screens that have revealed toxic phenotypes and drug targets that translate directly to patient-derived iPSC neurons. Extending these insights, recent advances in genetic network analyses have generated the first "humanized" α-synuclein network, which has identified druggable proteins and led to validation of the toxic phenotypes in patient-derived cells. Unbiased phenotypic small molecule screens can identify compounds targeting critical proteins within α-synuclein networks. While identification of direct drug targets for phenotypic screen hits represents a bottleneck, high-throughput chemical genetic methods provide a means to uncover cellular targets and pathways for large numbers of compounds in parallel. Taken together, the yeast α-synuclein model and associated tools can reveal insights into underlying cellular pathologies, lead molecules and their cognate targets, and strategies to translate mechanisms of toxicity and cytoprotection into complex neuronal systems.
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Sponges: A Reservoir of Genes Implicated in Human Cancer. Mar Drugs 2018; 16:md16010020. [PMID: 29320389 PMCID: PMC5793068 DOI: 10.3390/md16010020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/21/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
Recently, it was shown that the majority of genes linked to human diseases, such as cancer genes, evolved in two major evolutionary transitions—the emergence of unicellular organisms and the transition to multicellularity. Therefore, it has been widely accepted that the majority of disease-related genes has already been present in species distantly related to humans. An original way of studying human diseases relies on analyzing genes and proteins that cause a certain disease using model organisms that belong to the evolutionary level at which these genes have emerged. This kind of approach is supported by the simplicity of the genome/proteome, body plan, and physiology of such model organisms. It has been established for quite some time that sponges are an ideal model system for such studies, having a vast variety of genes known to be engaged in sophisticated processes and signalling pathways associated with higher animals. Sponges are considered to be the simplest multicellular animals and have changed little during evolution. Therefore, they provide an insight into the metazoan ancestor genome/proteome features. This review compiles current knowledge of cancer-related genes/proteins in marine sponges.
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Wyche TP, Ramos Alvarenga RF, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin. ACS Chem Biol 2017; 12:2287-2295. [PMID: 28708379 PMCID: PMC5697710 DOI: 10.1021/acschembio.7b00388] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A polyether antibiotic, ecteinamycin (1), was isolated from a marine Actinomadura sp., cultivated from the ascidian Ecteinascidia turbinata. 13C enrichment, high resolution NMR spectroscopy, and molecular modeling enabled elucidation of the structure of 1, which was validated on the basis of comparisons with its recently reported crystal structure. Importantly, ecteinamycin demonstrated potent activity against the toxigenic strain of Clostridium difficile NAP1/B1/027 (MIC = 59 ng/μL), as well as other toxigenic and nontoxigenic C. difficile isolates both in vitro and in vivo. Additionally, chemical genomics studies using Escherichia coli barcoded deletion mutants led to the identification of sensitive mutants such as trkA and kdpD involved in potassium cation transport and homeostasis supporting a mechanistic proposal that ecteinamycin acts as an ionophore antibiotic. This is the first antibacterial agent whose mechanism of action has been studied using E. coli chemical genomics. On the basis of these data, we propose ecteinamycin as an ionophore antibiotic that causes C. difficile detoxification and cell death via potassium transport dysregulation.
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Affiliation(s)
- Thomas P. Wyche
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - René F. Ramos Alvarenga
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | | | - Megan N. Duster
- Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Simone R. Warrack
- Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Travis J. De Wolfe
- Department of Food Science, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yanpeng Hou
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gregory A. Ellis
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Scott W. Simpkins
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Justin Nelson
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James Steele
- Department of Food Science, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Nasia Safdar
- Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Scott R. Rajski
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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14
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Yang H, Fung SY, Bao A, Li Q, Turvey SE. Screening Bioactive Nanoparticles in Phagocytic Immune Cells for Inhibitors of Toll-like Receptor Signaling. J Vis Exp 2017. [PMID: 28784964 DOI: 10.3791/56075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pharmacological regulation of Toll-like receptor (TLR) responses holds great promise in the treatment of many inflammatory diseases. However, there have been limited compounds available so far to attenuate TLR signaling and there have been no clinically approved TLR inhibitors (except the anti-malarial drug hydroxychloroquine) in clinical use. In light of rapid advances in nanotechnology, manipulation of immune responsiveness using nano-devices may provide a new strategy to treat these diseases. Herein, we present a high throughput screening method for quickly identifying novel bioactive nanoparticles that inhibit TLR signaling in phagocytic immune cells. This screening platform is built on THP-1 cell-based reporter cells with colorimetric and luciferase assays. The reporter cells are engineered from the human THP-1 monocytic cell line by stable integration of two inducible reporter constructs. One expresses a secreted embryonic alkaline phosphatase (SEAP) gene under the control of a promoter inducible by the transcription factors NF-κB and AP-1, and the other expresses a secreted luciferase reporter gene under the control of promoters inducible by interferon regulatory factors (IRFs).Upon TLR stimulation, the reporter cells activate transcription factors and subsequently produce SEAP and/or luciferase, which can be detected using their corresponding substrate reagents. Using a library of peptide-gold nanoparticle (GNP) hybrids established in our previous studies as an example, we identified one peptide-GNP hybrid that could effectively inhibit the two arms of TLR4 signaling cascade triggered by its prototypical ligand, lipopolysaccharide (LPS). The findings were validated by standard biochemical techniques including immunoblotting. Further analysis established that this lead hybrid had a broad inhibitory spectrum, acting on multiple TLR pathways, including TLR2, 3, 4, and 5. This experimental approach allows a rapid assessment of whether a nanoparticle (or other therapeutic compounds) can modulate specific TLR signaling in phagocytic immune cells.
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Affiliation(s)
- Hong Yang
- Department of Respiratory Medicine, Shanghai First People's Hospital, Shanghai Jiaotong University School of Medicine;
| | - Shan Yu Fung
- Department of Pediatrics, BC Children's Hospital and University of British Columbia
| | - Aihua Bao
- Department of Respiratory Medicine, Shanghai First People's Hospital, Shanghai Jiaotong University School of Medicine
| | - Qiang Li
- Department of Respiratory Medicine, Shanghai First People's Hospital, Shanghai Jiaotong University School of Medicine
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital and University of British Columbia
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15
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Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C. A global genetic interaction network maps a wiring diagram of cellular function. Science 2017; 353:353/6306/aaf1420. [PMID: 27708008 DOI: 10.1126/science.aaf1420] [Citation(s) in RCA: 809] [Impact Index Per Article: 101.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.
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Affiliation(s)
- Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Simons Center for Data Analysis, Simons Foundation, 160 Fifth Avenue, New York, NY 10010, USA
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Matej Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Julia Hanchard
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Susan D Lee
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Erin B Styles
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Maximilian Billmann
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Jolanda van Leeuwen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Nydia van Dyk
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto ON, Canada
| | - Elena Kuzmin
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Justin Nelson
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Program in Biomedical Informatics and Computational Biology, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Jeff S Piotrowski
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan
| | - Tharan Srikumar
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto ON, Canada
| | - Sondra Bahr
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Yiqun Chen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Christoph F Kurat
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Sheena C Li
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan
| | - Zhijian Li
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Mojca Mattiazzi Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561
| | - Natasha Pascoe
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Sara Sharifpoor
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Emira Shuteriqi
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Scott W Simpkins
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Program in Biomedical Informatics and Computational Biology, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Jamie Snider
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Harsha Garadi Suresh
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Yizhao Tan
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Hongwei Zhu
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Noel Malod-Dognin
- Computer Science Deptartment, University College London, London WC1E 6BT, UK
| | - Vuk Janjic
- Department of Computing, Imperial College London, UK
| | - Natasa Przulj
- Computer Science Deptartment, University College London, London WC1E 6BT, UK. School of Computing (RAF), Union University, Belgrade, Serbia
| | - Olga G Troyanskaya
- Simons Center for Data Analysis, Simons Foundation, 160 Fifth Avenue, New York, NY 10010, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Igor Stagljar
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Tian Xia
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, China, 430074
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto ON, Canada
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany. Department of Genetics, School of Medicine and Stanford Genome Technology Center Stanford University, Palo Alto, CA 94304, USA
| | - Claire L Moore
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Adam P Rosebrock
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Amy A Caudy
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. Program in Biomedical Informatics and Computational Biology, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.
| | - Brenda Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1.
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto ON, Canada M5S 3E1. Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan.
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16
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Gomes NGM, Dasari R, Chandra S, Kiss R, Kornienko A. Marine Invertebrate Metabolites with Anticancer Activities: Solutions to the "Supply Problem". Mar Drugs 2016; 14:E98. [PMID: 27213412 PMCID: PMC4882572 DOI: 10.3390/md14050098] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/29/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023] Open
Abstract
Marine invertebrates provide a rich source of metabolites with anticancer activities and several marine-derived agents have been approved for the treatment of cancer. However, the limited supply of promising anticancer metabolites from their natural sources is a major hurdle to their preclinical and clinical development. Thus, the lack of a sustainable large-scale supply has been an important challenge facing chemists and biologists involved in marine-based drug discovery. In the current review we describe the main strategies aimed to overcome the supply problem. These include: marine invertebrate aquaculture, invertebrate and symbiont cell culture, culture-independent strategies, total chemical synthesis, semi-synthesis, and a number of hybrid strategies. We provide examples illustrating the application of these strategies for the supply of marine invertebrate-derived anticancer agents. Finally, we encourage the scientific community to develop scalable methods to obtain selected metabolites, which in the authors' opinion should be pursued due to their most promising anticancer activities.
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Affiliation(s)
- Nelson G M Gomes
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira No. 228, 4050-313 Porto, Portugal.
| | - Ramesh Dasari
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Sunena Chandra
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Robert Kiss
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Campus de la Plaine, CP205/1, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Alexander Kornienko
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
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17
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Abstract
This review covers the literature published in 2014 for marine natural products (MNPs), with 1116 citations (753 for the period January to December 2014) 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 (1378 in 456 papers for 2014), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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18
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Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, Boone C, Coon JJ, Hebert A, Sato TK, Landick R, Piotrowski JS. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain. Microb Cell Fact 2016; 15:17. [PMID: 26790958 PMCID: PMC4721058 DOI: 10.1186/s12934-016-0417-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/08/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property for strain engineering. To enable rational engineering, we used chemical genomic profiling to understand the effects of IILs on S. cerevisiae. RESULTS We found that IILs likely target mitochondria as their chemical genomic profiles closely resembled that of the mitochondrial membrane disrupting agent valinomycin. Further, several deletions of genes encoding mitochondrial proteins exhibited increased sensitivity to IIL. High-throughput chemical proteomics confirmed effects of IILs on mitochondrial protein levels. IILs induced abnormal mitochondrial morphology, as well as altered polarization of mitochondrial membrane potential similar to valinomycin. Deletion of the putative serine/threonine kinase PTK2 thought to activate the plasma-membrane proton efflux pump Pma1p conferred a significant IIL-fitness advantage. Conversely, overexpression of PMA1 conferred sensitivity to IILs, suggesting that hydrogen ion efflux may be coupled to influx of the toxic imidazolium cation. PTK2 deletion conferred resistance to multiple IILs, including [EMIM]Cl, [BMIM]Cl, and [EMIM]Ac. An engineered, xylose-converting ptk2∆ S. cerevisiae (Y133-IIL) strain consumed glucose and xylose faster and produced more ethanol in the presence of 1 % [BMIM]Cl than the wild-type PTK2 strain. We propose a model of IIL toxicity and resistance. CONCLUSIONS This work demonstrates the utility of chemical genomics-guided biodesign for development of superior microbial biocatalysts for the ever-changing landscape of fermentation inhibitors.
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Affiliation(s)
- Quinn Dickinson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Scott Bottoms
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Li Hinchman
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Sean McIlwain
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Sheena Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
| | - Charles Boone
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Joshua J Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Alexander Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, WI, USA.
| | - Jeff S Piotrowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
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19
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Abstract
The ubiquitin–proteasome system has been recognized as fundamental toward protein turnover in eukaryotic cells. The system comprises the ubiquitin conjugation machinery consisting of an enzyme cascade of E1, E2, and E3 enzymes, the deubiquitinases (DUBs) and the proteasome, a multisubunit protease complex acting through an N-terminal threonine protease mechanism. A number of natural product inhibitors of the proteasome have been studied in detail and these inhibitors and their derivatives have been highly valuable in developing our understanding of this system. These efforts culminated in the successful development of bortezomib as a pharmacological agent used clinically as a cancer therapeutic in the treatment of multiple myeloma. This review is focused on natural product inhibitors of the enzymes involved in intracellular ubiquitin conjugation (ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, ubiquitin ligase E3) and ubiquitin deconjugation (DUBs). Members of both of these enzyme systems have been proposed as pharmacological targets for cancer therapy and several other diseases. Furthermore compounds with activities toward enzymes from the analogous ubiquitin-like (Ubl) protein families have been identified for SUMO and NEDD8. To date natural product inhibitors have been described for members of each of these protein families and were isolated from plant, fungal, animal, and microbial sources. Insights into the mechanism of action of natural products and their derivatives will enhance our understanding of this complex system and will improve our ability to rationally design novel inhibitors. The increased availability of assays and research tools for the study of protein ubiquitination, deubiquitination, and Ubl proteins will contribute to the discovery of more potent and selective compounds. We expect that these studies will stimulate development of further potential pharmacological agents in this area.
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20
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Kurita KL, Linington RG. Connecting phenotype and chemotype: high-content discovery strategies for natural products research. JOURNAL OF NATURAL PRODUCTS 2015; 78:587-96. [PMID: 25728167 PMCID: PMC7505086 DOI: 10.1021/acs.jnatprod.5b00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In recent years, the field of natural products has seen an explosion in the breadth, resolution, and accuracy of profiling platforms for compound discovery, including many new chemical and biological annotation methods. With these new tools come opportunities to examine extract libraries using systematized profiling approaches that were not previously available to the field and which offer new approaches for the detailed characterization of the chemical and biological attributes of complex natural products mixtures. This review will present a summary of some of these untargeted profiling methods and provide perspective on the future opportunities offered by integrating these tools for novel natural products discovery.
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Affiliation(s)
- Kenji L. Kurita
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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21
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Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Higbee AJ, Ulbrich A, Coon JJ, Deshpande R, Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y. Plant-derived antifungal agent poacic acid targets β-1,3-glucan. Proc Natl Acad Sci U S A 2015; 112:E1490-7. [PMID: 25775513 PMCID: PMC4378397 DOI: 10.1073/pnas.1410400112] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rise in resistance to current antifungals necessitates strategies to identify alternative sources of effective fungicides. We report the discovery of poacic acid, a potent antifungal compound found in lignocellulosic hydrolysates of grasses. Chemical genomics using Saccharomyces cerevisiae showed that loss of cell wall synthesis and maintenance genes conferred increased sensitivity to poacic acid. Morphological analysis revealed that cells treated with poacic acid behaved similarly to cells treated with other cell wall-targeting drugs and mutants with deletions in genes involved in processes related to cell wall biogenesis. Poacic acid causes rapid cell lysis and is synergistic with caspofungin and fluconazole. The cellular target was identified; poacic acid localized to the cell wall and inhibited β-1,3-glucan synthesis in vivo and in vitro, apparently by directly binding β-1,3-glucan. Through its activity on the glucan layer, poacic acid inhibits growth of the fungi Sclerotinia sclerotiorum and Alternaria solani as well as the oomycete Phytophthora sojae. A single application of poacic acid to leaves infected with the broad-range fungal pathogen S. sclerotiorum substantially reduced lesion development. The discovery of poacic acid as a natural antifungal agent targeting β-1,3-glucan highlights the potential side use of products generated in the processing of renewable biomass toward biofuels as a source of valuable bioactive compounds and further clarifies the nature and mechanism of fermentation inhibitors found in lignocellulosic hydrolysates.
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Affiliation(s)
- Jeff S Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703;
| | - Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561
| | - Fachuang Lu
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Sheena C Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan 351-0198
| | - Li Hinchman
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | | | | | - Alan J Higbee
- Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Arne Ulbrich
- Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Joshua J Coon
- Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455; and
| | - Yury V Bukhman
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Sean McIlwain
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Irene M Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455; and
| | - Charles Boone
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan 351-0198; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | - John Ralph
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53703
| | | | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan 277-8561;
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22
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Piotrowski JS, Simpkins SW, Li SC, Deshpande R, McIlwain SJ, Ong IM, Myers CL, Boone C, Andersen RJ. Chemical genomic profiling via barcode sequencing to predict compound mode of action. Methods Mol Biol 2015; 1263:299-318. [PMID: 25618354 DOI: 10.1007/978-1-4939-2269-7_23] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemical genomics is an unbiased, whole-cell approach to characterizing novel compounds to determine mode of action and cellular target. Our version of this technique is built upon barcoded deletion mutants of Saccharomyces cerevisiae and has been adapted to a high-throughput methodology using next-generation sequencing. Here we describe the steps to generate a chemical genomic profile from a compound of interest, and how to use this information to predict molecular mechanism and targets of bioactive compounds.
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Affiliation(s)
- Jeff S Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WEI4152, 1552 University Ave., Madison, WI, 53726, USA,
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Wyche TP, Piotrowski JS, Hou Y, Braun D, Deshpande R, McIlwain S, Ong IM, Myers CL, Guzei IA, Westler WM, Andes DR, Bugni TS. Forazoline A: marine-derived polyketide with antifungal in vivo efficacy. Angew Chem Int Ed Engl 2014; 53:11583-6. [PMID: 25197007 PMCID: PMC4215405 DOI: 10.1002/anie.201405990] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/10/2022]
Abstract
Forazoline A, a novel antifungal polyketide with in vivo efficacy against Candida albicans, was discovered using LCMS-based metabolomics to investigate marine-invertebrate-associated bacteria. Forazoline A had a highly unusual and unprecedented skeleton. Acquisition of (13)C-(13)C gCOSY and (13)C-(15)N HMQC NMR data provided the direct carbon-carbon and carbon-nitrogen connectivity, respectively. This approach represents the first example of determining direct (13)C-(15)N connectivity for a natural product. Using yeast chemical genomics, we propose that forazoline A operated through a new mechanism of action with a phenotypic outcome of disrupting membrane integrity.
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Affiliation(s)
- Thomas P. Wyche
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Jeff S. Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (USA)
| | - Yanpeng Hou
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Doug Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455 (USA)
| | - Sean McIlwain
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (USA)
| | - Irene M. Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (USA)
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455 (USA)
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA)
| | - William M. Westler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA)
| | - David R. Andes
- School of Medicine, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison Madison, WI 53705 (USA)
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Wyche TP, Piotrowski JS, Hou Y, Braun D, Deshpande R, McIlwain S, Ong IM, Myers CL, Guzei IA, Westler WM, Andes DR, Bugni TS. Forazoline A: Marine-Derived Polyketide with Antifungal In Vivo Efficacy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405990] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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