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Shama SM, Elissawy AM, Salem MA, Youssef FS, Elnaggar MS, El-Seedi HR, Khalifa SAM, Briki K, Hamdan DI, Singab ANB. Comparative metabolomics study on the secondary metabolites of the red alga, Corallina officinalis and its associated endosymbiotic fungi. RSC Adv 2024; 14:18553-18566. [PMID: 38903055 PMCID: PMC11187739 DOI: 10.1039/d4ra01055h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024] Open
Abstract
Marine endosymbionts have gained remarkable interest in the last three decades in terms of natural products (NPs) isolated thereof, emphasizing the chemical correlations with those isolated from the host marine organism. The current study aimed to conduct comparative metabolic profiling of the marine red algae Corallina officinalis, and three fungal endosymbionts isolated from its inner tissues namely, Aspergillus nidulans, A. flavipes and A. flavus. The ethyl acetate (EtOAc) extracts of the host organism as well as the isolated endosymbionts were analyzed using ultra-high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-MS/MS)in both positive and negative ion modes, applying both full scan (FS) and all ion fragmentation (AIF) modes. Extensive interpretation of the LC-MS/MS spectra had led to the identification of 76 metabolites belonging to different phytochemical classes including alkaloids, polyketides, sesquiterpenes, butyrolactones, peptides, fatty acids, isocoumarins, quinones, among others. Metabolites were tentatively identified by comparing the accurate mass and fragmentation pattern with metabolites previously reported in the literature, as well as bioinformatics analysis using GNPS. A relationship between the host C. officinalis and its endophytes (A. flavus, A. nidulans, and A. flavipes) was discovered. C. officinalis shares common metabolites with at least one of the three endosymbiotic fungi. Some metabolites have been identified in endophytes and do not exist in their host. Multivariate analysis (MVA) revealed discrimination of A. flavipes from Corallina officinalis and other associated endophytic Aspergillus fungi (A. flavus and A. nidulans).
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Affiliation(s)
- Sherif M Shama
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University Shibin Elkom 32511 Egypt
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University Cairo 11566 Egypt
| | - Mohamed A Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University Shibin Elkom 32511 Egypt
| | - Fadia S Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
| | - Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
| | - Hesham R El-Seedi
- Chemistry Department, Faculty of Science, Islamic University of Madinah P. O. Box: 170 Madinah 42351 Saudi Arabia
| | - Shaden A M Khalifa
- International Research Center for Food Nutrition and Safety, Jiangsu University Zhenjiang 212013 China
- Psychiatry and Neurology Department, Capio Saint Göran's Hospital Sankt Göransplan 1 112 19 Stockholm Sweden
| | - Khaled Briki
- Laboratory of Organic Chemistry and Natural Substance, University Ziane Achour Djelfa Algeria
| | - Dalia Ibrahim Hamdan
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University Shibin Elkom 32511 Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University Cairo 11566 Egypt
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2
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Pilz M, Cavelius P, Qoura F, Awad D, Brück T. Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review. Biotechnol Adv 2023; 67:108210. [PMID: 37460047 DOI: 10.1016/j.biotechadv.2023.108210] [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: 01/26/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.
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Affiliation(s)
- Melania Pilz
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Philipp Cavelius
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Farah Qoura
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
| | - Thomas Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
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3
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Jenkinson CB, Podgorny AR, Zhong C, Oakley BR. Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors. J Ind Microbiol Biotechnol 2023; 50:kuad045. [PMID: 38061800 PMCID: PMC10734572 DOI: 10.1093/jimb/kuad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023]
Abstract
Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors. ONE-SENTENCE SUMMARY A new computer-assisted approach to resistance gene-directed genome mining is reported along with its use to identify fungal biosynthetic gene clusters that putatively produce proteasome and HMG-CoA reductase inhibitors.
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Affiliation(s)
- Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
| | - Adam R Podgorny
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
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Robbins N, Ketela T, Kim SH, Cowen LE. Chemical-Genetic Approaches for Exploring Mode of Action of Antifungal Compounds in the Fungal Pathogen Candida albicans. Methods Mol Biol 2023; 2658:145-165. [PMID: 37024700 PMCID: PMC11019913 DOI: 10.1007/978-1-0716-3155-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Candida albicans is a prevalent fungal pathogen of humans that can cause both superficial and life-threatening disease, primarily in immunocompromised populations. Currently, antifungal drug classes available to treat fungal infections remain limited and the emergence of drug-resistant strains threatens antifungal efficacy, necessitating the discovery and development of additional therapeutics. The construction of the C. albicans double-barcoded heterozygous deletion collection (DBC) enables the rapid and systematic assessment of haploinsufficiency phenotypes in a pooled format. Specifically, this functional genomics resource can be used to identify heterozygous deletion mutants that are hypersensitive to compounds in order to define putative cellular targets and/or other modifiers of compound activity. Here, we describe protocols to characterize the mode of action of small molecules using the C. albicans DBC, including how to prepare compound-treated cultures, isolate genomic DNA, amplify strain-specific barcodes, and prepare DNA libraries for high-throughput sequencing. This technique provides a powerful approach to elucidate the compound mechanism of action in order to bolster the antifungal pipeline.
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Affiliation(s)
- Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Fungal Secondary Metabolites as Inhibitors of the Ubiquitin-Proteasome System. Int J Mol Sci 2021; 22:ijms222413309. [PMID: 34948102 PMCID: PMC8707610 DOI: 10.3390/ijms222413309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 12/19/2022] Open
Abstract
The ubiquitin–proteasome system (UPS) is the major non-lysosomal pathway responsible for regulated degradation of intracellular proteins in eukaryotes. As the principal proteolytic pathway in the cytosol and the nucleus, the UPS serves two main functions: the quality control function (i.e., removal of damaged, misfolded, and functionally incompetent proteins) and a major regulatory function (i.e., targeted degradation of a variety of short-lived regulatory proteins involved in cell cycle control, signal transduction cascades, and regulation of gene expression and metabolic pathways). Aberrations in the UPS are implicated in numerous human pathologies such as cancer, neurodegenerative disorders, autoimmunity, inflammation, or infectious diseases. Therefore, the UPS has become an attractive target for drug discovery and development. For the past two decades, much research has been focused on identifying and developing compounds that target specific components of the UPS. Considerable effort has been devoted to the development of both second-generation proteasome inhibitors and inhibitors of ubiquitinating/deubiquitinating enzymes. With the feature of unique structure and bioactivity, secondary metabolites (natural products) serve as the lead compounds in the development of new therapeutic drugs. This review, for the first time, summarizes fungal secondary metabolites found to act as inhibitors of the UPS components.
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Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
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Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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Lan N, Perlatti B, Kvitek DJ, Wiemann P, Harvey CJB, Frisvad J, An Z, Bills GF. Acrophiarin (antibiotic S31794/F-1) from Penicillium arenicola shares biosynthetic features with both Aspergillus- and Leotiomycete-type echinocandins. Environ Microbiol 2020; 22:2292-2311. [PMID: 32239586 DOI: 10.1111/1462-2920.15004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/28/2020] [Indexed: 11/30/2022]
Abstract
The antifungal echinocandin lipopeptide, acrophiarin, was circumscribed in a patent in 1979. We confirmed that the producing strain NRRL 8095 is Penicillium arenicola and other strains of P. arenicola produced acrophiarin and acrophiarin analogues. Genome sequencing of NRRL 8095 identified the acrophiarin gene cluster. Penicillium arenicola and echinocandin-producing Aspergillus species belong to the family Aspergillaceae of the Eurotiomycetes, but several features of acrophiarin and its gene cluster suggest a closer relationship with echinocandins from Leotiomycete fungi. These features include hydroxy-glutamine in the peptide core instead of a serine or threonine residue, the inclusion of a non-heme iron, α-ketoglutarate-dependent oxygenase for hydroxylation of the C3 of the glutamine, and a thioesterase. In addition, P. arenicola bears similarity to Leotiomycete echinocandin-producing species because it exhibits self-resistance to exogenous echinocandins. Phylogenetic analysis of the genes of the echinocandin biosynthetic family indicated that most of the predicted proteins of acrophiarin gene cluster exhibited higher similarity to the predicted proteins of the pneumocandin gene cluster of the Leotiomycete Glarea lozoyensis than to those of the echinocandin B gene cluster from A. pachycristatus. The fellutamide gene cluster and related gene clusters are recognized as relatives of the echinocandins. Inclusion of the acrophiarin gene cluster into a comprehensive phylogenetic analysis of echinocandin gene clusters indicated the divergent evolutionary lineages of echinocandin gene clusters are descendants from a common ancestral progenitor. The minimal 10-gene cluster may have undergone multiple gene acquisitions or losses and possibly horizontal gene transfer after the ancestral separation of the two lineages.
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Affiliation(s)
- Nan Lan
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Bruno Perlatti
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | | | | | | | - Jens Frisvad
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
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8
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Perlatti B, Lan N, Jiang Y, An Z, Bills G. Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining. Molecules 2020; 25:molecules25040913. [PMID: 32085602 PMCID: PMC7071103 DOI: 10.3390/molecules25040913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/14/2020] [Indexed: 11/16/2022] Open
Abstract
Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A.nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus.
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Affiliation(s)
- Bruno Perlatti
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
- Correspondence:
| | - Nan Lan
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| | - Yongying Jiang
- Institute for Applied Cancer Science, M.D. Anderson Cancer Center, Houston, TX 77054, USA;
| | - Zhiqiang An
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| | - Gerald Bills
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
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Patel KD, De Zoysa GH, Kanamala M, Patel K, Pilkington LI, Barker D, Reynisson J, Wu Z, Sarojini V. Novel Cell-Penetrating Peptide Conjugated Proteasome Inhibitors: Anticancer and Antifungal Investigations. J Med Chem 2019; 63:334-348. [DOI: 10.1021/acs.jmedchem.9b01694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kamal D. Patel
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Gayan Heruka De Zoysa
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Manju Kanamala
- School of Pharmacy, University of Auckland, Auckland 1142, New Zealand
| | - Krunal Patel
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Lisa I. Pilkington
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - David Barker
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Hornbeam Building, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Zimei Wu
- School of Pharmacy, University of Auckland, Auckland 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
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Zhao P, Xue Y, Li X, Li J, Zhao Z, Quan C, Gao W, Zu X, Bai X, Feng S. Fungi-derived lipopeptide antibiotics developed since 2000. Peptides 2019; 113:52-65. [PMID: 30738838 DOI: 10.1016/j.peptides.2019.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/12/2022]
Abstract
Lipopeptide antibiotics have linear or cyclic structures with one or more hydrocarbon tails linked to the N-terminus of a short oligopeptide that may be chemically modified and/or contain unusual amino acid residues in their structures. They possess huge potential as pharmaceutical drugs and biocontrol agents, and ˜30 representative genera of fungi are known to produce them. Some chemically synthesised derivatives have already been developed into commercial products or subjected to clinical trials, including cilofungin, caspofungin, micafungin, anidulafungin, rezafungin, emodepside, fusafungine and destruxins. This review summarizes 200 fungi-derived compounds reported since 2000, including 95 cyclic depsipeptides, 67 peptaibiotics (including 35 peptaibols, eight lipoaminopeptides, and five lipopeptaibols), and 38 non-depsipeptide and non-peptaibiotic lipopeptides. Their sources, structural sequences, antibiotic activities (e.g. antibacterial, antifungal, antiviral, antimycobacterial, antimycoplasmal, antimalarial, antileishmanial, insecticidal, antitrypanosomal and nematicidal), structure-activity relationships, mechanisms of action, and specific relevance are discussed. These compounds have attracted considerable interest within the pharmaceutical and agrochemical industries.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Xin Li
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Zhanqin Zhao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
| | - Chunshan Quan
- Department of Life Science, Dalian Nationalities University, Dalian, 116600, China
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shuxiao Feng
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471023, China
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11
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Xu LL, Hai P, Zhang SB, Xiao JF, Gao Y, Ma BJ, Fu HY, Chen YM, Yang XL. Prenylated Indole Diterpene Alkaloids from a Mine-Soil-Derived Tolypocladium sp. JOURNAL OF NATURAL PRODUCTS 2019; 82:221-231. [PMID: 30702286 DOI: 10.1021/acs.jnatprod.8b00589] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ten new prenylated indole diterpene alkaloids, tolypocladin A-J (1-10), including four chlorinated metabolites, have been isolated from a culture of a mine-soil-derived fungus, Tolypocladium sp. XL115. The structures and absolute configurations of 1-10 were determined by spectroscopic analysis, ECD calculations, and comparison with known compounds. Compounds 1 and 8 displayed significant antimicrobial activities. In addition, compound 1 also showed weak cytotoxic activity against all tested human cancer cell lines and suppressed the growth and viability of the patient-derived HCC cells T1224.
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Affiliation(s)
- Lu-Lin Xu
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences , Chongqing University , Chongqing 401331 , People's Republic of China
| | - Ping Hai
- Department of Chemical Engineering , Yibin University , Yibin 644000 , People's Republic of China
| | - Shuai-Bing Zhang
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
| | - Jing-Fang Xiao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital and Key Laboratory of Tumor Immunopathology of the Ministry of Education of China , Third Military Medical University , Chongqing 400038 , People's Republic of China
| | - Yuan Gao
- Department of Chemical Engineering , Yibin University , Yibin 644000 , People's Republic of China
| | - Bing-Ji Ma
- Department of Traditional Chinese Medicine , Henan Agricultural University , Wenhua Road 12 , Zhengzhou 450002 , People's Republic of China
| | - Hai-Yan Fu
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
| | - Ye-Miao Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital and Key Laboratory of Tumor Immunopathology of the Ministry of Education of China , Third Military Medical University , Chongqing 400038 , People's Republic of China
| | - Xiao-Long Yang
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences , Chongqing University , Chongqing 401331 , People's Republic of China
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12
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Chen HY, Liu TK, Yang J, Yang XL. Emerones A–C: three novel merosesquiterpenoids with unprecedented skeletons from Emericella sp. XL029. Org Biomol Chem 2019; 17:8450-8455. [DOI: 10.1039/c9ob01788g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Three novel merosesquiterpenoids (1–3) from Emericella sp. XL029.
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Affiliation(s)
- Heng-Ye Chen
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- China
| | - Ting-Kai Liu
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- China
| | - Jian Yang
- National Resource Center for Chinese Materia Medica
- China Academy of Chinese Medical Sciences
- Beijing 100700
- China
| | - Xiao-Long Yang
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan 430074
- China
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13
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Della Sala G, Agriesti F, Mazzoccoli C, Tataranni T, Costantino V, Piccoli C. Clogging the Ubiquitin-Proteasome Machinery with Marine Natural Products: Last Decade Update. Mar Drugs 2018; 16:E467. [PMID: 30486251 PMCID: PMC6316072 DOI: 10.3390/md16120467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/11/2018] [Accepted: 11/22/2018] [Indexed: 01/08/2023] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the central protein degradation system in eukaryotic cells, playing a key role in homeostasis maintenance, through proteolysis of regulatory and misfolded (potentially harmful) proteins. As cancer cells produce proteins inducing cell proliferation and inhibiting cell death pathways, UPP inhibition has been exploited as an anticancer strategy to shift the balance between protein synthesis and degradation towards cell death. Over the last few years, marine invertebrates and microorganisms have shown to be an unexhaustive factory of secondary metabolites targeting the UPP. These chemically intriguing compounds can inspire clinical development of novel antitumor drugs to cope with the incessant outbreak of side effects and resistance mechanisms induced by currently approved proteasome inhibitors (e.g., bortezomib). In this review, we report about (a) the role of the UPP in anticancer therapy, (b) chemical and biological properties of UPP inhibitors from marine sources discovered in the last decade, (c) high-throughput screening techniques for mining natural UPP inhibitors in organic extracts. Moreover, we will tell about the fascinating story of salinosporamide A, the first marine natural product to access clinical trials as a proteasome inhibitor for cancer treatment.
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Affiliation(s)
- Gerardo Della Sala
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Francesca Agriesti
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Carmela Mazzoccoli
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Tiziana Tataranni
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Valeria Costantino
- The NeaNat Group, Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy.
| | - Claudia Piccoli
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
- Department of Clinical and Experimental Medicine, University of Foggia, via L. Pinto c/o OO.RR., 71100 Foggia, Italy.
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14
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A one-pot chemoenzymatic synthesis of (2S, 4R)-4-methylproline enables the first total synthesis of antiviral lipopeptide cavinafungin B. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Zhao W, Xu LL, Zhang X, Gong XW, Zhu DL, Xu XH, Wang F, Yang XL. Three new phenanthrenes with antimicrobial activities from the aerial parts of Juncus effusus. Fitoterapia 2018; 130:247-250. [DOI: 10.1016/j.fitote.2018.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 11/29/2022]
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16
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Chen PY, Hsieh CY, Shih CJ, Lin YJ, Tsao CW, Yang YL. Exploration of Fungal Metabolic Interactions Using Imaging Mass Spectrometry on Nanostructured Silicon. JOURNAL OF NATURAL PRODUCTS 2018; 81:1527-1533. [PMID: 29916245 DOI: 10.1021/acs.jnatprod.7b00866] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Application of matrix-assisted laser desorption/ionization imaging mass spectrometry to microbiology and natural product research has opened the door to the exploration of microbial interactions and the consequent discovery of new natural products and their functions in the interactions. However, several drawbacks of matrix-assisted laser desorption/ionization imaging mass spectrometry have limited its application especially to complicated and uneven microbial samples. Here, we applied nanostructured silicon as a substrate for surface-assisted laser desorption/ionization mass spectrometry for microbial imaging mass spectrometry to explore fungal metabolic interactions. We chose Phellinus noxius and Aspergillus strains to evaluate the potential of microbial imaging mass spectrometry on nanostructured silicon because both fungi produce a dense mass of aerial mycelia, which is known to complicate the collection of high-quality imaging mass spectrometry data. Our simple and straightforward sample imprinting method and low background interference resulted in an efficient analysis of small metabolites from the complex microbial interaction samples.
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Affiliation(s)
- Pi-Yu Chen
- Agricultural Biotechnology Research Center , Academia Sinica , 11529 Taipei , Taiwan
| | - Chi-Ying Hsieh
- Agricultural Biotechnology Research Center , Academia Sinica , 11529 Taipei , Taiwan
| | - Chao-Jen Shih
- Agricultural Biotechnology Research Center , Academia Sinica , 11529 Taipei , Taiwan
- Bioresource Collection and Research Center , Food Industry Research and Development Institute , 30062 Hsinchu , Taiwan
| | - Yuan-Jing Lin
- Department of Mechanical Engineering , National Central University , 32001 Taoyuan , Taiwan
| | - Chia-Wen Tsao
- Department of Mechanical Engineering , National Central University , 32001 Taoyuan , Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center , Academia Sinica , 11529 Taipei , Taiwan
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17
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Gogineni V, Hamann MT. Marine natural product peptides with therapeutic potential: Chemistry, biosynthesis, and pharmacology. Biochim Biophys Acta Gen Subj 2018; 1862:81-196. [PMID: 28844981 PMCID: PMC5918664 DOI: 10.1016/j.bbagen.2017.08.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022]
Abstract
The oceans are a uniquely rich source of bioactive metabolites, of which sponges have been shown to be among the most prolific producers of diverse bioactive secondary metabolites with valuable therapeutic potential. Much attention has been focused on marine bioactive peptides due to their novel chemistry and diverse biological properties. As summarized in this review, marine peptides are known to exhibit various biological activities such as antiviral, anti-proliferative, antioxidant, anti-coagulant, anti-hypertensive, anti-cancer, antidiabetic, antiobesity, and calcium-binding activities. This review focuses on the chemistry and biology of peptides isolated from sponges, bacteria, cyanobacteria, fungi, ascidians, and other marine sources. The role of marine invertebrate microbiomes in natural products biosynthesis is discussed in this review along with the biosynthesis of modified peptides from different marine sources. The status of peptides in various phases of clinical trials is presented, as well as the development of modified peptides including optimization of PK and bioavailability.
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Affiliation(s)
- Vedanjali Gogineni
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, The University of Mississippi, University, MS, United States.
| | - Mark T Hamann
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy and Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States.
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18
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19
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Liao L, Bae SY, Won TH, You M, Kim SH, Oh DC, Lee SK, Oh KB, Shin J. Asperphenins A and B, Lipopeptidyl Benzophenones from a Marine-Derived Aspergillus sp. Fungus. Org Lett 2017; 19:2066-2069. [DOI: 10.1021/acs.orglett.7b00661] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lijuan Liao
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Song Yi Bae
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Tae Hyung Won
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Minjung You
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Seong-Hwan Kim
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Dong-Chan Oh
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Sang Kook Lee
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Science, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-921, Korea
| | - Jongheon Shin
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
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20
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Abstract
ABSTRACT
Invasive fungal infections are becoming an increasingly important cause of human mortality and morbidity, particularly for immunocompromised populations. The fungal pathogens
Candida albicans
,
Cryptococcus neoformans
, and
Aspergillus fumigatus
collectively contribute to over 1 million human deaths annually. Hence, the importance of safe and effective antifungal therapeutics for the practice of modern medicine has never been greater. Given that fungi are eukaryotes like their human host, the number of unique molecular targets that can be exploited for drug development remains limited. Only three classes of molecules are currently approved for the treatment of invasive mycoses. The efficacy of these agents is compromised by host toxicity, fungistatic activity, or the emergence of drug resistance in pathogen populations. Here we describe our current arsenal of antifungals and highlight current strategies that are being employed to improve the therapeutic safety and efficacy of these drugs. We discuss state-of-the-art approaches to discover novel chemical matter with antifungal activity and highlight some of the most promising new targets for antifungal drug development. We feature the benefits of combination therapy as a strategy to expand our current repertoire of antifungals and discuss the antifungal combinations that have shown the greatest potential for clinical development. Despite the paucity of new classes of antifungals that have come to market in recent years, it is clear that by leveraging innovative approaches to drug discovery and cultivating collaborations between academia and industry, there is great potential to bolster the antifungal armamentarium.
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21
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Pirrung MC, Zhang F, Ambadi S, Gangadhara Rao Y. Total synthesis of fellutamides, lipopeptide proteasome inhibitors. More sustainable peptide bond formation. Org Biomol Chem 2016; 14:8367-75. [PMID: 27533920 DOI: 10.1039/c6ob01233g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solution-phase syntheses of three bioactive natural products of mixed polypeptide-polyketide biogenesis, fellutamides A, B, and C, have been achieved. Three peptide bonds are generated without the use of coupling reagents in each synthesis of the fellutamides, which act against proteasomes.
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Affiliation(s)
- Michael C Pirrung
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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22
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Application of chemical biology in target identification and drug discovery. Arch Pharm Res 2015; 38:1642-50. [PMID: 26242900 DOI: 10.1007/s12272-015-0643-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/29/2015] [Indexed: 10/23/2022]
Abstract
Drug discovery and development is vital to the well-being of mankind and sustainability of the pharmaceutical industry. Using chemical biology approaches to discover drug leads has become a widely accepted path partially because of the completion of the Human Genome Project. Chemical biology mainly solves biological problems through searching previously unknown targets for pharmacologically active small molecules or finding ligands for well-defined drug targets. It is a powerful tool to study how these small molecules interact with their respective targets, as well as their roles in signal transduction, molecular recognition and cell functions. There have been an increasing number of new therapeutic targets being identified and subsequently validated as a result of advances in functional genomics, which in turn led to the discovery of numerous active small molecules via a variety of high-throughput screening initiatives. In this review, we highlight some applications of chemical biology in the context of drug discovery.
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23
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Ortíz-López FJ, Monteiro MC, González-Menéndez V, Tormo JR, Genilloud O, Bills GF, Vicente F, Zhang C, Roemer T, Singh SB, Reyes F. Cyclic colisporifungin and linear cavinafungins, antifungal lipopeptides isolated from Colispora cavincola. JOURNAL OF NATURAL PRODUCTS 2015; 78:468-475. [PMID: 25636062 DOI: 10.1021/np500854j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Colisporifungin (1), a cyclic depsilipopeptide structurally related to the aselacins, and cavinafungins A and B, two linear peptides, were isolated from liquid culture broths of the hitherto unstudied fungus Colispora cavincola using a Candida albicans whole-cell assay as well as a bioassay to detect compounds potentiating the antifungal activity of caspofungin. The structural elucidation, including the absolute configuration of the new molecules, was accomplished using a combination of spectroscopic and chemical techniques, including 1D and 2D NMR, HRMS, and Marfey's analysis. The cyclic peptide colisporifungin displayed a strong potentiation of the growth inhibitory effect of caspofungin against Aspergillus fumigatus and, to a lesser extent, against Candida albicans. The linear peptides displayed broad-spectrum antifungal activities inhibiting growth of Candida species (MIC values 0.5-4 μg/mL) as well as A. fumigatus with a prominent inhibition of 8 μg/mL.
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Affiliation(s)
- Francisco Javier Ortíz-López
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Maria Cândida Monteiro
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Víctor González-Menéndez
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - José R Tormo
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Olga Genilloud
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Gerald F Bills
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Francisca Vicente
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Chaowei Zhang
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Terry Roemer
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Sheo B Singh
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Fernando Reyes
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
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24
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Mann PA, McLellan CA, Koseoglu S, Si Q, Kuzmin E, Flattery A, Harris G, Sher X, Murgolo N, Wang H, Devito K, de Pedro N, Genilloud O, Kahn JN, Jiang B, Costanzo M, Boone C, Garlisi CG, Lindquist S, Roemer T. Chemical Genomics-Based Antifungal Drug Discovery: Targeting Glycosylphosphatidylinositol (GPI) Precursor Biosynthesis. ACS Infect Dis 2015; 1:59-72. [PMID: 26878058 PMCID: PMC4739577 DOI: 10.1021/id5000212] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Steadily increasing antifungal drug resistance and persistent high rates of fungal-associated mortality highlight the dire need for the development of novel antifungals. Characterization of inhibitors of one enzyme in the GPI anchor pathway, Gwt1, has generated interest in the exploration of targets in this pathway for further study. Utilizing a chemical genomics-based screening platform referred to as the Candida albicans fitness test (CaFT), we have identified novel inhibitors of Gwt1 and a second enzyme in the glycosylphosphatidylinositol (GPI) cell wall anchor pathway, Mcd4. We further validate these targets using the model fungal organism Saccharomyces cerevisiae and demonstrate the utility of using the facile toolbox that has been compiled in this species to further explore target specific biology. Using these compounds as probes, we demonstrate that inhibition of Mcd4 as well as Gwt1 blocks the growth of a broad spectrum of fungal pathogens and exposes key elicitors of pathogen recognition. Interestingly, a strong chemical synergy is also observed by combining Gwt1 and Mcd4 inhibitors, mirroring the demonstrated synthetic lethality of combining conditional mutants of GWT1 and MCD4. We further demonstrate that the Mcd4 inhibitor M720 is efficacious in a murine infection model of systemic candidiasis. Our results establish Mcd4 as a promising antifungal target and confirm the GPI cell wall anchor synthesis pathway as a promising antifungal target area by demonstrating that effects of inhibiting it are more general than previously recognized.
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Affiliation(s)
- Paul A. Mann
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Catherine A. McLellan
- Whitehead Institute
for Biomedical Research, 9 Cambridge
Center, Cambridge, Massachusetts 02142, United States
- Howard
Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sandra Koseoglu
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qian Si
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Elena Kuzmin
- Banting and
Best Department of Medical Research, Terrance Donnally Centre of Cellular
and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Amy Flattery
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Guy Harris
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xinwei Sher
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Nicholas Murgolo
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hao Wang
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kristine Devito
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Nuria de Pedro
- Fundación
Centro de Excelencia en Investigación de Medicamentos Innovadores
en Andalucı́a, Medina, Parque Tecnológico de Ciencias de la Salud , Avenida Conocimiento 34, 18016 Grenada, Spain
| | - Olga Genilloud
- Fundación
Centro de Excelencia en Investigación de Medicamentos Innovadores
en Andalucı́a, Medina, Parque Tecnológico de Ciencias de la Salud , Avenida Conocimiento 34, 18016 Grenada, Spain
| | - Jennifer Nielsen Kahn
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Bo Jiang
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Michael Costanzo
- Banting and
Best Department of Medical Research, Terrance Donnally Centre of Cellular
and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Charlie Boone
- Banting and
Best Department of Medical Research, Terrance Donnally Centre of Cellular
and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Charles G. Garlisi
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Susan Lindquist
- Whitehead Institute
for Biomedical Research, 9 Cambridge
Center, Cambridge, Massachusetts 02142, United States
- Howard
Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Terry Roemer
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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25
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 2014; 31:1348-75. [PMID: 25156669 DOI: 10.1039/c4np00046c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are a primary modality for fungal peptidic natural product assembly and are responsible for some of the best known, most useful, and most destructive fungal metabolites. Through genome sequencing and computer-assisted recognition of modular motifs of catalytic domains, one can now confidently identify most NRPS biosynthetic genes of a fungal strain. The biosynthetic gene clusters responsible for two of the most important classes of NRP fungal derived drugs, cyclosporine and the echinocandins, have been recently characterized by genomic sequencing and annotation. Complete biosynthetic gene clusters for the pneumocandins and echinocandins have been mapped at the genetic level and functionally characterized to some extent. Genomic sequencing of representative strains of most of the variants in the echinocandin family, including the wild-type of the three fungal strains employed for industrial-scale production of caspofungin, micafungin and anidulofungin, has enabled characterization of the basic architecture of the echinocandin NRPS pathways. A comparative analysis of how pathway genes cause variations in lipoinitiation, biosynthesis of the non-proteinogenic amino acids, amino acid substitutions, and hydroxylations and sulfonations of the core peptide and contribute to the molecular diversity of the family is presented. We also review new information on the natural functions of NRPs, the differences between fungal and bacterial NRPSs, and functional characterization of selected NRPS gene clusters. Continuing discovery of the new fungal nonribosomal peptides has contributed new structural diversity and potential insights into their biological functions among other natural peptides and peptaibiotics. We therefore provide an update on new peptides, depsipeptides and peptaibols discovered in the Fungi since 2009.
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Affiliation(s)
- Gerald Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Centre at Houston, Houston, Texas 77054, USA.
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26
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Martín J, Crespo G, González-Menéndez V, Pérez-Moreno G, Sánchez-Carrasco P, Pérez-Victoria I, Ruiz-Pérez LM, González-Pacanowska D, Vicente F, Genilloud O, Bills GF, Reyes F. MDN-0104, an antiplasmodial betaine lipid from Heterospora chenopodii. JOURNAL OF NATURAL PRODUCTS 2014; 77:2118-2123. [PMID: 25215605 DOI: 10.1021/np500577v] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bioassay-guided fractionation of the crude fermentation extract of Heterospora chenopodii led to the isolation of a novel monoacylglyceryltrimethylhomoserine (1). The structure of this new betaine lipid was elucidated by detailed spectroscopic analysis using one- and two-dimensional NMR experiments and high-resolution mass spectrometry. Compound 1 displayed moderate in vitro antimalarial activity against Plasmodium falciparum, with an IC50 value of 7 μM. This betaine lipid is the first monoacylglyceryltrimethylhomoserine ever reported in the Fungi, and its acyl moiety also represents a novel natural 3-keto fatty acid. The new compound was isolated during a drug discovery program aimed at the identification of new antimalarial leads from a natural product library of microbial extracts. Interestingly, the related fungus Heterospora dimorphospora was also found to produce compound 1, suggesting that species of this genus may be a promising source of monoacylglyceryltrimethylhomoserines.
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Affiliation(s)
- Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Granada, Spain
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27
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Dey G, Bharti R, Sen R, Mandal M. Microbial amphiphiles: a class of promising new-generation anticancer agents. Drug Discov Today 2014; 20:136-46. [PMID: 25241656 DOI: 10.1016/j.drudis.2014.09.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/14/2014] [Accepted: 09/10/2014] [Indexed: 12/15/2022]
Abstract
Developing new classes of anticancer molecules has always been a major scientific challenge owing to multidrug resistance of cancer cells to conventional chemotherapeutic agents. Microbial amphiphiles, particularly lipopeptides and glycolipids, have recently emerged as potential new-generation anticancer agents, owing to low toxicity, high efficacy and easy biodegradability. They exhibit anticancer activities by retarding cell cycle progression, inhibiting crucial signaling pathways such as Akt, extracellular signal-regulated kinase/c-Jun N-terminal kinase (ERK/JNK) and Janus kinase/signal transducer and activator of transcription (JAK/STAT), reducing angiogenesis, activating natural killer T (NKT) cells and inducing apoptosis through death receptors in cancer cells. It has been well established that the oncogenic signals of cancer cells are amplified by the overexpression of various membrane-bound receptors such as epidermal growth factor receptor (EGFR), vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor (PDGFR) and insulin-like growth factor receptor (IGFR). Microbial amphiphiles, upon interaction with the cell membrane, are believed to suppress the activities of these cell surface receptors by fatty acid chain mediated membrane destabilization. This review analyzes the modes and mechanisms of action of these green molecules for application as potential anticancer agents.
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Affiliation(s)
- Goutam Dey
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Rashmi Bharti
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Ramkrishna Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India.
| | - Mahitosh Mandal
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India.
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Roemer T, Krysan DJ. Antifungal drug development: challenges, unmet clinical needs, and new approaches. Cold Spring Harb Perspect Med 2014; 4:a019703. [PMID: 24789878 PMCID: PMC3996373 DOI: 10.1101/cshperspect.a019703] [Citation(s) in RCA: 326] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Invasive, life-threatening fungal infections are an important cause of morbidity and mortality, particularly for patients with compromised immune function. The number of therapeutic options for the treatment of invasive fungal infections is quite limited when compared with those available to treat bacterial infections. Indeed, only three classes of molecules are currently used in clinical practice and only one new class of antifungal drugs has been developed in the last 30 years. Here we summarize the unmet clinical needs of current antifungal therapy, discuss challenges inherent to antifungal drug discovery and development, and review recent developments aimed at addressing some of these challenges.
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Affiliation(s)
- Terry Roemer
- Infectious Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033
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Seven new and two known lipopeptides as well as five known polyketides: the activated production of silent metabolites in a marine-derived fungus by chemical mutagenesis strategy using diethyl sulphate. Mar Drugs 2014; 12:1815-38. [PMID: 24686557 PMCID: PMC4012460 DOI: 10.3390/md12041815] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 11/17/2022] Open
Abstract
AD-2-1 is an antitumor fungal mutant obtained by diethyl sulfate mutagenesis of a marine-derived Penicillium purpurogenum G59. The G59 strain originally did not produce any metabolites with antitumor activities in MTT assays using K562 cells. Tracing newly produced metabolites under guidance of MTT assay and TLC analysis by direct comparison with control G59 extract, seven new (1–7) and two known (8–9) lipopeptides were isolated together with five known polyketides 10–14 from the extract of mutant AD-2-1. Structures of the seven new compounds including their absolute configurations were determined by spectroscopic and chemical evidences and named as penicimutalides A–G (1–7). Seven known compounds were identified as fellutamide B (8), fellutamide C (9), 1′-O-methylaverantin (10), averantin (11), averufin (12), nidurufin (13), and sterigmatocystin (14). In the MTT assay, 1–14 inhibited several human cancer cell lines to varying extents. All the bioassays and HPLC-photodiode array detector (PDAD)-UV and HPLC-electron spray ionization (ESI)-MS analyses demonstrated that the production of 1–14 in the mutant AD-2-1 was caused by the activated production of silent metabolites in the original G59 fungal strain. Present results provided additional examples for effectiveness of the chemical mutagenesis strategy using diethyl sulphate mutagenesis to discover new compounds by activating silent metabolites in fungal isolates.
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Giltrap AM, Cergol KM, Pang A, Britton WJ, Payne RJ. Total synthesis of fellutamide B and deoxy-fellutamides B, C, and D. Mar Drugs 2013; 11:2382-97. [PMID: 23880930 PMCID: PMC3736429 DOI: 10.3390/md11072382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/21/2013] [Accepted: 05/27/2013] [Indexed: 11/21/2022] Open
Abstract
The total syntheses of the marine-derived lipopeptide natural product fellutamide B and deoxy-fellutamides B, C, and D are reported. These compounds were accessed through a novel solid-phase synthetic strategy using Weinreb amide-derived resin. As part of the synthesis, a new enantioselective route to (3R)-hydroxy lauric acid was developed utilizing a Brown allylation reaction followed by an oxidative cleavage-oxidation sequence as the key steps. The activity of these natural products, and natural product analogues was also assessed against Mycobacterium tuberculosisin vitro.
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Affiliation(s)
- Andrew M Giltrap
- School of Chemistry, The University of Sydney, NSW 2006, Australia.
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31
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Singh SB, Ondeyka J, Harris G, Herath K, Zink D, Vicente F, Bills G, Collado J, Platas G, González del Val A, Martin J, Reyes F, Wang H, Kahn JN, Galuska S, Giacobbe R, Abruzzo G, Roemer T, Xu D. Isolation, structure, and biological activity of Phaeofungin, a cyclic lipodepsipeptide from a Phaeosphaeria sp. Using the Genome-Wide Candida albicans Fitness Test. JOURNAL OF NATURAL PRODUCTS 2013; 76:334-345. [PMID: 23259972 DOI: 10.1021/np300704s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phaeofungin (1), a new cyclic depsipeptide isolated from Phaeosphaeria sp., was discovered by application of reverse genetics technology, using the Candida albicans fitness test (CaFT). Phaeofungin is comprised of seven amino acids and a β,γ-dihydroxy-γ-methylhexadecanoic acid arranged in a 25-membered cyclic depsipeptide. Five of the amino acids were assigned with d-configurations. The structure was elucidated by 2D-NMR and HRMS-MS analysis of the natural product and its hydrolyzed linear peptide. The absolute configuration of the amino acids was determined by Marfey's method by complete and partial hydrolysis of 1. The CaFT profile of the phaeofungin-containing extract overlapped with that of phomafungin (3), another structurally different cyclic lipodepsipeptide isolated from a Phoma sp. using the same approach. Comparative biological characterization further demonstrated that these two fungal lipodepsipeptides are functionally distinct. While phomafungin was potentiated by cyclosporin A (an inhibitor of the calcineurin pathway), phaeofungin was synergized with aureobasidin A (2) (an inhibitor of the sphingolipid biosynthesis) and to some extent caspofungin (an inhibitor of glucan synthase). Furthermore, phaeofungin caused ATP release in wild-type C. albicans strains but phomafungin did not. It showed modest antifungal activity against C. albicans (MIC 16-32 μg/mL) and better activity against Aspergillus fumigatus (MIC 8-16 μg/mL) and Trichophyton mentagrophytes (MIC 4 μg/mL). The linear peptide was inactive, suggesting that the macrocyclic depsipeptide ring is essential for target engagement and antifungal activity.
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Affiliation(s)
- Sheo B Singh
- Department of Medicinal Chemistry, Merck Research Laboratories , PO Box 2000, Rahway, New Jersey 07065, USA.
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Dang HT, Xiao B, Lee YM, Hong JK, Lee CO, Choi JS, Jung JH. Synthesis of Fellutamide C and its Diastereomer. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.8.2777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pérez-Victoria I, Martín J, González-Menéndez V, de Pedro N, El Aouad N, Ortiz-López FJ, Tormo JR, Platas G, Vicente F, Bills GF, Genilloud O, Goetz MA, Reyes F. Isolation and structural elucidation of cyclic tetrapeptides from Onychocola sclerotica. JOURNAL OF NATURAL PRODUCTS 2012; 75:1210-1214. [PMID: 22694270 DOI: 10.1021/np3000987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Three new cyclic tetrapeptides (1-3) have been isolated from the crude fermentation extract of Onychocola sclerotica. The planar structures of 1-3 were elucidated by detailed spectroscopic analyses using one- and two-dimensional NMR experiments and high-resolution mass spectrometry. The absolute configuration of the amino acid residues in each cyclotetrapeptide was established by Marfey's method. Compounds 1-3 displayed activity as cardiac calcium channel blockers (Cav1.2) but did not inhibit the hERG potassium channel and were not cytotoxic. These peptides are the first secondary metabolites ever reported from fungi of the order Arachnomycetales.
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Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, E-18100 Armilla, Granada, Spain.
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Herath K, Jayasuriya H, Zink DL, Sigmund J, Vicente F, de la Cruz M, Basilio A, Bills GF, Polishook JD, Donald R, Phillips J, Goetz M, Singh SB. Isolation, structure elucidation, and antibacterial activity of methiosetin, a tetramic acid from a tropical sooty mold (Capnodium sp.). JOURNAL OF NATURAL PRODUCTS 2012; 75:420-424. [PMID: 22288374 DOI: 10.1021/np200857y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Drug-resistant bacteria continue to make many existing antibiotic classes ineffective. In order to avoid a future epidemic from drug-resistant bacterial infections, new antibiotics with new modes of action are needed. In an antibiotic screening program for new drug leads with new modes of action using antisense Staphylococcus aureus Fitness Test screening, we discovered a new tetramic acid, methiosetin, from a tropical sooty mold, Capnodium sp. The fungus also produced epicorazine A, a known antibiotic. The structure and relative configuration of methiosetin was elucidated by 2D NMR and ESIMS techniques. Methiosetin and epicorazine A showed weak to modest antibacterial activity against S. aureus and Haemophilus influenzae. The isolation, structure elucidation, and antibacterial activity of both compounds are described.
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Affiliation(s)
- Kithsiri Herath
- Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, New Jersey 07065, United States
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Tormo JR, Asensio FJ, Bills GF. Manipulating filamentous fungus chemical phenotypes by growth on nutritional arrays. Methods Mol Biol 2012; 944:59-78. [PMID: 23065608 DOI: 10.1007/978-1-62703-122-6_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methods for manipulating and fermenting microorganisms in multi-well plates offer unlimited possibilities for high-throughput parallel experimentation. Furthermore, bar-coded data tracking and downstream processing with modern liquid handling equipment reduce handling errors and are able to format microbial products for autosampler-equipped analytical instruments, e.g., HPLCs, mass spectrometers, and plate readers. An integrated system for high-throughput culturing of filamentous fungi replicating strains across many fermentation parameters, called nutritional arrays, was developed. It takes advantage of this equipment while addressing the age-old dilemma of how to manipulate fungal phenotypes to express a more complete spectrum of their secondary metabolites. Growth of any given strain in a well-designed nutritional array increases the chances of detecting a biologically active metabolite while reducing the manpower and materials needed for preparing individual fermentations and extracts. Fungi fermented in nutritional arrays are directly processed in a semi-automated fashion and the extracts prepared for bioassays and analytical chemistry. The necessary equipment, custom tools, and protocols to grow fungi in nutritional arrays are described along with examples of bioactive secondary metabolites discovered using this system.
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Affiliation(s)
- José R Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Armilla, Granada, Spain.
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