51
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Acedo JZ, Bothwell IR, An L, Trouth A, Frazier C, van der Donk WA. O-Methyltransferase-Mediated Incorporation of a β-Amino Acid in Lanthipeptides. J Am Chem Soc 2019; 141:16790-16801. [PMID: 31568727 DOI: 10.1021/jacs.9b07396] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lanthipeptides represent a large class of cyclic natural products defined by the presence of lanthionine (Lan) and methyllanthionine (MeLan) cross-links. With the advances in DNA sequencing technologies and genome mining tools, new biosynthetic enzymes capable of installing unusual structural features are continuously being discovered. In this study, we investigated an O-methyltransferase that is a member of the most prominent auxiliary enzyme family associated with class I lanthipeptide biosynthetic gene clusters. Despite the prevalence of these enzymes, their function has not been established. Herein, we demonstrate that the O-methyltransferase OlvSA encoded in the olv gene cluster from Streptomyces olivaceus NRRL B-3009 catalyzes the rearrangement of a highly conserved aspartate residue to a β-amino acid, isoaspartate, in the lanthipeptide OlvA(BCSA). We elucidated the NMR solution structure of the GluC-digested peptide, OlvA(BCSA)GluC, which revealed a unique ring topology comprising four interlocking rings and positions the isoaspartate residue in a solvent exposed loop that is stabilized by a MeLan ring. Gas chromatography-mass spectrometry analysis further indicated that OlvA(BCSA) contains two dl-MeLan rings and two Lan rings with an unusual ll-stereochemistry. Lastly, in vitro reconstitution of OlvSA activity showed that it is a leader peptide-independent and S-adenosyl methionine-dependent O-methyltransferase that mediates the conversion of a highly conserved aspartate residue in a cyclic substrate into a succinimide, which is hydrolyzed to generate an Asp or isoAsp containing peptide. This overall transformation converts an α-amino acid into a β-amino acid in a ribosomally synthesized peptide, via an electrophilic intermediate that may be the intended product.
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Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ian R Bothwell
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Linna An
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Abby Trouth
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Clara Frazier
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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52
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Bhushan A, Egli PJ, Peters EE, Freeman MF, Piel J. Genome mining- and synthetic biology-enabled production of hypermodified peptides. Nat Chem 2019; 11:931-939. [PMID: 31501509 PMCID: PMC6763334 DOI: 10.1038/s41557-019-0323-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/01/2019] [Indexed: 12/12/2022]
Abstract
The polytheonamides are among the most complex and biosynthetically distinctive natural products known to date. These potent peptide cytotoxins are derived from a ribosomal precursor processed by 49 mostly non-canonical posttranslational modifications. As the producer is a 'microbial dark matter' bacterium only distantly related to any cultivated organism, >70-step chemical syntheses have been developed to access these unique compounds. Here, we mined prokaryotic diversity to establish a synthetic platform based on the new host Microvirgula aerodenitrificans that produces hypermodified peptides within two days. Using this system, we generated the aeronamides, new polytheonamide-type compounds with near-picomolar cytotoxicity. Aeronamides, as well as the polygeonamides produced from deep-rock biosphere DNA, contain the highest numbers of D-amino acids in known biomolecules. With increasing bacterial genomes being sequenced, similar host mining strategies might become feasible to access further elusive natural products from uncultivated life.
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Affiliation(s)
- Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | | | - Eike E Peters
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
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53
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Pilié PG, Gay CM, Byers LA, O'Connor MJ, Yap TA. PARP Inhibitors: Extending Benefit Beyond BRCA-Mutant Cancers. Clin Cancer Res 2019; 25:3759-3771. [PMID: 30760478 DOI: 10.1158/1078-0432.ccr-18-0968] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/04/2019] [Accepted: 02/08/2019] [Indexed: 02/03/2023]
Abstract
A mounting body of evidence now indicates that PARP inhibitors have the potential to be used as a foundation for both monotherapy and combination strategies across a wide spectrum of molecular backgrounds and tumor types. Although PARP inhibitors as a class display many similarities, critical differences in structure can translate into differences in tolerability and antitumor activity that have important implications for the clinic. Furthermore, while PARP inhibitors have demonstrated a clear role in treating tumors with underlying homologous recombination deficiencies, there is now biological and early clinical evidence to support their use in other molecular subsets of cancer, including tumors associated with high levels of replication stress such as small-cell lung cancer. In this article, we highlight the key similarities and differences between individual PARP inhibitors and their implications for the clinic. We discuss data that currently support clinical strategies for extending the benefit of PARP inhibitors beyond BRCA-mutant cancers, toward broader populations of patients through the use of novel biomarkers of homologous recombination repair deficiency (HRD), as well as predictive biomarkers rooted in mechanisms of sensitivity outside of HRD. We also explore the potential application of PARP inhibitors in earlier treatment settings, including neoadjuvant, adjuvant, and even chemoprevention approaches. Finally, we focus on promising combination therapeutic strategies, such as those with other DNA damage response (DDR) inhibitors such as ATR inhibitors, immune checkpoint inhibitors, and non-DDR-targeted agents that induce "chemical BRCAness."
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Affiliation(s)
- Patrick G Pilié
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J O'Connor
- Oncology Innovative Medicines and Early Clinical Development, AstraZeneca, Cambridge, United Kingdom
| | - Timothy A Yap
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
- The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
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54
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Wu Q, Nay B, Yang M, Ni Y, Wang H, Yao L, Li X. Marine sponges of the genus Stelletta as promising drug sources: chemical and biological aspects. Acta Pharm Sin B 2019; 9:237-257. [PMID: 30972275 PMCID: PMC6437601 DOI: 10.1016/j.apsb.2018.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/20/2018] [Accepted: 10/03/2018] [Indexed: 12/18/2022] Open
Abstract
Marine sponges of the genus Stelletta are well known as rich sources of diverse and complex biologically relevant natural products, including alkaloids, terpenoids, peptides, lipids, and steroids. Some of these metabolites, with novel structures and promising biological activities, have attracted a lot of attention from chemists seeking to perform their total synthesis in parallel to intensive biological studies towards new drug leads. In this review, we summarized the distribution of the chemically investigated Stelletta sponges, the isolation, synthesis and biological activities of their secondary metabolites, covering the literature from 1982 to early 2018.
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55
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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56
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019; 36:1412-1436. [DOI: 10.1039/c8np00091c] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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57
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Are Microbial Endophytes the ‘Actual’ Producers of Bioactive Antitumor Agents? Trends Cancer 2018; 4:662-670. [DOI: 10.1016/j.trecan.2018.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 11/22/2022]
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58
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Xie CL, Xia JM, Wang JS, Lin DH, Yang XW. Metabolomic Investigations on Nesterenkonia flava Revealed Significant Differences between Marine and Terrestrial Actinomycetes. Mar Drugs 2018; 16:E356. [PMID: 30274334 PMCID: PMC6213030 DOI: 10.3390/md16100356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 12/25/2022] Open
Abstract
Marine microorganisms are an important source of natural products with potent bioactivities. Unlike the land, the ocean, especially the deep-sea, is characterized by high pressure, high salinity, low nutrition, and no light among others. Therefore, the biodiversity of marine microorganisms is supposed to be very different from that of the terrestrial ones. Yet, many marine microorganisms can find their counterparts in terrestrial environments. To evaluate their differences, a comparative metabolomics investigation was performed on four strains of Nesterenkonia flava isolated from terrestrial and marine environments. As a result, marine strains were clearly distinguished from terrestrial ones on the principal components analysis (PCA) score plot. Furthermore, by partial least squares discrimination analysis (PLS-DA) and univariate analysis, the characteristic metabolites were figured out and found to be involved in osmotic regulation, redox balancing, and energy metabolism. Our results demonstrated that marine actinomycetes could produce novel secondary metabolites different from their terrestrial relatives because they have special metabolic patterns closely related to the unique features of their living environment.
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Affiliation(s)
- Chun-Lan Xie
- State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
- College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, 422 Siming South Road, Xiamen 361005, China.
| | - Jin-Mei Xia
- State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
| | - Jun-Song Wang
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Dong-Hai Lin
- College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, 422 Siming South Road, Xiamen 361005, China.
| | - Xian-Wen Yang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
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59
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Substrate-assisted enzymatic formation of lysinoalanine in duramycin. Nat Chem Biol 2018; 14:928-933. [PMID: 30177849 PMCID: PMC6372306 DOI: 10.1038/s41589-018-0122-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023]
Abstract
Duramycin is a heavily post-translationally modified peptide that binds phosphatidylethanolamine. It has been investigated as an antibiotic, inhibitor of viral entry, therapeutic for cystic fibrosis, and tumor and vasculature imaging agent. Duramycin contains a β-hydroxylated Asp (Hya) and four macrocycles, including an essential lysinoalanine (Lal) crosslink. The mechanism of Lal formation is not known. We here show that Lal is installed stereospecifically by DurN via addition of Lys19 to a dehydroalanine. The structure of DurN reveals an unusual dimer with a new fold. Surprisingly, in the structure of duramycin bound to DurN, no residues of the enzyme are near the Lal crosslink. Instead, Hya15 of the substrate makes interactions with Lal, suggesting it acts as a base to deprotonate Lys19 during catalysis. Biochemical data suggest that DurN preorganizes the reactive conformation of the substrate, such that the Hya15 of the substrate can serve as the catalytic base for Lal formation.
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60
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Zhang Y, Chen M, Bruner SD, Ding Y. Heterologous Production of Microbial Ribosomally Synthesized and Post-translationally Modified Peptides. Front Microbiol 2018; 9:1801. [PMID: 30135682 PMCID: PMC6092494 DOI: 10.3389/fmicb.2018.01801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides, or RiPPs, which have mainly isolated from microbes as well as plants and animals, are an ever-expanding group of peptidic natural products with diverse chemical structures and biological activities. They have emerged as a major category of secondary metabolites partly due to a myriad of microbial genome sequencing endeavors and the availability of genome mining software in the past two decades. Heterologous expression of RiPP gene clusters mined from microbial genomes, which are often silent in native producers, in surrogate hosts such as Escherichia coli and Streptomyces strains can be an effective way to elucidate encoded peptides and produce novel derivatives. Emerging strategies have been developed to facilitate the success of the heterologous expression by targeting multiple synthetic biology levels, including individual proteins, pathways, metabolic flux and hosts. This review describes recent advances in heterologous production of RiPPs, mainly from microbes, with a focus on E. coli and Streptomyces strains as the surrogate hosts.
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Affiliation(s)
- Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
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61
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Alves C, Silva J, Pinteus S, Gaspar H, Alpoim MC, Botana LM, Pedrosa R. From Marine Origin to Therapeutics: The Antitumor Potential of Marine Algae-Derived Compounds. Front Pharmacol 2018; 9:777. [PMID: 30127738 PMCID: PMC6089330 DOI: 10.3389/fphar.2018.00777] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/26/2018] [Indexed: 11/13/2022] Open
Abstract
Marine environment has demonstrated to be an interesting source of compounds with uncommon and unique chemical features on which the molecular modeling and chemical synthesis of new drugs can be based with greater efficacy and specificity for the therapeutics. Cancer is a growing public health threat, and despite the advances in biomedical research and technology, there is an urgent need for the development of new anticancer drugs. In this field, it is estimated that more than 60% of commercially available anticancer drugs are natural biomimetic inspired. Among the marine organisms, algae have revealed to be one of the major sources of new compounds of marine origin, including those exhibiting antitumor and cytotoxic potential. These compounds demonstrated ability to mediate specific inhibitory activities on a number of key cellular processes, including apoptosis pathways, angiogenesis, migration and invasion, in both in vitro and in vivo models, revealing their potential to be used as anticancer drugs. This review will focus on the bioactive molecules from algae with antitumor potential, from their origin to their potential uses, with special emphasis to the alga Sphaerococcus coronopifolius as a producer of cytotoxic compounds.
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Affiliation(s)
- Celso Alves
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal.,Biology Department, DoMar Doctoral Programme on Marine Science, Technology and Management, University of Aveiro, Aveiro, Portugal
| | - Joana Silva
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal
| | - Susete Pinteus
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal
| | - Helena Gaspar
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal.,Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Maria C Alpoim
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal.,Center of Investigation in Environment, Genetics and Oncobiology, University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Luis M Botana
- Departament of Pharmacology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Rui Pedrosa
- MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Peniche, Portugal
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62
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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63
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Rivera GSM, Beamish CR, Wencewicz TA. Immobilized FhuD2 Siderophore-Binding Protein Enables Purification of Salmycin Sideromycins from Streptomyces violaceus DSM 8286. ACS Infect Dis 2018; 4:845-859. [PMID: 29460625 DOI: 10.1021/acsinfecdis.8b00015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Siderophores are a structurally diverse class of natural products common to most bacteria and fungi as iron(III)-chelating ligands. Siderophores, including trihydroxamate ferrioxamines, are used clinically to treat iron overload diseases and show promising activity against many other iron-related human diseases. Here, we present a new method for the isolation of ferrioxamine siderophores from complex mixtures using affinity chromatography based on resin-immobilized FhuD2, a siderophore-binding protein (SBP) from Staphylococcus aureus. The SBP-resin enabled purification of charge positive, charge negative, and neutral ferrioxamine siderophores. Treatment of culture supernatants from Streptomyces violaceus DSM 8286 with SBP-resin provided an analytically pure sample of the salmycins, a mixture of structurally complex glycosylated sideromycins (siderophore-antibiotic conjugates) with potent antibacterial activity toward human pathogenic Staphylococcus aureus (minimum inhibitory concentration (MIC) = 7 nM). Siderophore affinity chromatography could enable the rapid discovery of new siderophore and sideromycin natural products from complex mixtures to aid drug discovery and metabolite identification efforts in a broad range of therapeutic areas.
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Affiliation(s)
- Gerry Sann M. Rivera
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Catherine R. Beamish
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
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64
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Hegemann JD, van der Donk WA. Investigation of Substrate Recognition and Biosynthesis in Class IV Lanthipeptide Systems. J Am Chem Soc 2018; 140:5743-5754. [PMID: 29633842 PMCID: PMC5932250 DOI: 10.1021/jacs.8b01323] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are subdivided into four classes. The first two classes have been heavily studied, but less is known about classes III and IV. The lanthipeptide synthetases of classes III and IV share a similar organization of protein domains: A lyase domain at the N-terminus, a central kinase domain, and a C-terminal cyclase domain. Here, we provide deeper insight into class IV enzymes (LanLs). A series of putative producer strains was screened to identify production conditions of four new venezuelin-like lanthipeptides, and an Escherichia coli based heterologous production system was established for a fifth. The latter not only allowed production of fully modified core peptide but was also employed as the basis for mutational analysis of the precursor peptide to identify regions important for enzyme recognition. These experiments were complemented by in vitro binding studies aimed at identifying the region of the leader peptide recognized by the LanL enzymes as well as determining which domain of the enzyme is recognizing the substrate peptide. Combined, these studies revealed that the kinase domain is mediating the interaction with the precursor peptide and that a putatively α-helical stretch of residues at the center to N-terminal region of the leader peptide is important for enzyme recognition. In addition, a combination of in vitro assays and tandem mass spectrometry was used to elucidate the order of dehydration events in these systems.
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Affiliation(s)
- Julian D Hegemann
- Howard Hughes Medical Institute and Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana, Illinois 61801 , United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana, Illinois 61801 , United States
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Altering form for function. Nat Chem Biol 2018; 14:187. [DOI: 10.1038/nchembio.2582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bauermeister A, Branco PC, Furtado LC, Jimenez PC, Costa-Lotufo LV, da Cruz Lotufo TM. Tunicates: A model organism to investigate the effects of associated-microbiota on the production of pharmaceuticals. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ddmod.2019.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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