1
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Malit JJL, Leung HYC, Qian PY. Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery. Mar Drugs 2022; 20:398. [PMID: 35736201 PMCID: PMC9231227 DOI: 10.3390/md20060398] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022] Open
Abstract
Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.
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Affiliation(s)
- Jessie James Limlingan Malit
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hiu Yu Cherie Leung
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
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2
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Zhang JN, Xia YX, Zhang HJ. Natural Cyclopeptides as Anticancer Agents in the Last 20 Years. Int J Mol Sci 2021; 22:3973. [PMID: 33921480 PMCID: PMC8068844 DOI: 10.3390/ijms22083973] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/24/2022] Open
Abstract
Cyclopeptides or cyclic peptides are polypeptides formed by ring closing of terminal amino acids. A large number of natural cyclopeptides have been reported to be highly effective against different cancer cells, some of which are renowned for their clinical uses. Compared to linear peptides, cyclopeptides have absolute advantages of structural rigidity, biochemical stability, binding affinity as well as membrane permeability, which contribute greatly to their anticancer potency. Therefore, the discovery and development of natural cyclopeptides as anticancer agents remains attractive to academic researchers and pharmaceutical companies. Herein, we provide an overview of anticancer cyclopeptides that were discovered in the past 20 years. The present review mainly focuses on the anticancer efficacies, mechanisms of action and chemical structures of cyclopeptides with natural origins. Additionally, studies of the structure-activity relationship, total synthetic strategies as well as bioactivities of natural cyclopeptides are also included in this article. In conclusion, due to their characteristic structural features, natural cyclopeptides have great potential to be developed as anticancer agents. Indeed, they can also serve as excellent scaffolds for the synthesis of novel derivatives for combating cancerous pathologies.
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Affiliation(s)
| | | | - Hong-Jie Zhang
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (J.-N.Z.); (Y.-X.X.)
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3
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De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst 2019; 10:99-108.e5. [PMID: 31864964 DOI: 10.1016/j.cels.2019.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/18/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
Abstract
Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS). https://github.com/bbehsaz/cyclonovo.
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4
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Sinha R, Sharma B, Dangi AK, Shukla P. Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development. World J Microbiol Biotechnol 2019; 35:166. [DOI: 10.1007/s11274-019-2746-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/13/2019] [Indexed: 02/08/2023]
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5
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Fisher MF, Mylne JS. Sequencing Orbitides by Acid-Mediated Ring Cleavage Followed by Tandem Mass Spectrometry. J Proteome Res 2019; 18:4065-4071. [DOI: 10.1021/acs.jproteome.9b00516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark F. Fisher
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology (M310), The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology (M310), The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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6
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CycLS: Accurate, whole-library sequencing of cyclic peptides using tandem mass spectrometry. Bioorg Med Chem 2018; 26:1232-1238. [DOI: 10.1016/j.bmc.2018.01.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 01/20/2023]
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7
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Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol 2018; 3:319-327. [PMID: 29358742 DOI: 10.1038/s41564-017-0094-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/08/2017] [Indexed: 11/09/2022]
Abstract
Peptidic natural products (PNPs) include many antibiotics and other bioactive compounds. While the recent launch of the Global Natural Products Social (GNPS) molecular networking infrastructure is transforming PNP discovery into a high-throughput technology, PNP identification algorithms are needed to realize the potential of the GNPS project. GNPS relies on the assumption that each connected component of a molecular network (representing related metabolites) illuminates the 'dark matter of metabolomics' as long as it contains a known metabolite present in a database. We reveal a surprising diversity of PNPs produced by related bacteria and show that, contrary to the 'comparative metabolomics' assumption, two related bacteria are unlikely to produce identical PNPs (even though they are likely to produce similar PNPs). Since this observation undermines the utility of GNPS, we developed a PNP identification tool, VarQuest, that illuminates the connected components in a molecular network even if they do not contain known PNPs and only contain their variants. VarQuest reveals an order of magnitude more PNP variants than all previous PNP discovery efforts and demonstrates that GNPS already contains spectra from 41% of the currently known PNP families. The enormous diversity of PNPs suggests that biosynthetic gene clusters in various microorganisms constantly evolve to generate a unique spectrum of PNP variants that differ from PNPs in other species.
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8
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Koehbach J, Clark RJ. Unveiling the diversity of cyclotides by combining peptidome and transcriptome analysis. Biopolymers 2016; 106:774-783. [DOI: 10.1002/bip.22858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Johannes Koehbach
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
| | - Richard J. Clark
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
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9
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Truman AW. Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides. Beilstein J Org Chem 2016; 12:1250-68. [PMID: 27559376 PMCID: PMC4979651 DOI: 10.3762/bjoc.12.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/02/2016] [Indexed: 12/15/2022] Open
Abstract
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.
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Affiliation(s)
- Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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10
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Informatic search strategies to discover analogues and variants of natural product archetypes. ACTA ACUST UNITED AC 2016; 43:293-8. [DOI: 10.1007/s10295-015-1675-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/13/2015] [Indexed: 01/05/2023]
Abstract
Abstract
Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts. Using our specialised software packages, we could elaborate specific branches of chemical space, uncovering new variants of trichopolyn and demonstrating a way forward in mining natural products as a valuable source of potential pharmaceutical agents.
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11
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Weber T, Kim HU. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol 2016; 1:69-79. [PMID: 29062930 PMCID: PMC5640684 DOI: 10.1016/j.synbio.2015.12.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/10/2015] [Accepted: 12/26/2015] [Indexed: 01/02/2023] Open
Abstract
Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.
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Key Words
- A, adenylation domain
- Antibiotics
- BGC, biosynthetic gene cluster
- Bioinformatics
- Biosynthesis
- C, condensation domain
- GPR, gene-protein-reaction
- HMM, hidden Markov model
- LC, liquid chromatography
- MS, mass spectrometry
- NMR, nuclear magnetic resonance
- NRP, non-ribosomally synthesized peptide
- NRPS
- NRPS, non-ribosomal peptide synthetase
- Natural product
- PCP, peptidyl carrier protein
- PK, polyketide
- PKS
- PKS, polyketide synthase
- RiPP, ribosomally and post-translationally modified peptide
- SVM, support vector machine
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Affiliation(s)
- Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
| | - Hyun Uk Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark.,BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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12
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Mohimani H, Pevzner PA. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Nat Prod Rep 2016; 33:73-86. [PMID: 26497201 PMCID: PMC5590107 DOI: 10.1039/c5np00050e] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Covering: 2000 to 2015. While recent breakthroughs in the discovery of peptide antibiotics and other Peptidic Natural Products (PNPs) raise a challenge for developing new algorithms for their analyses, the computational technologies for high-throughput PNP discovery are still lacking. We discuss the computational bottlenecks in analyzing PNPs and review recent advances in genome mining, peptidogenomics, and spectral networks that are now enabling the discovery of new PNPs via mass spectrometry. We further describe the connections between these advances and the new generation of software tools for PNP dereplication, de novo sequencing, and identification.
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Affiliation(s)
- Hosein Mohimani
- Department of Computer Science and Engineering, University of California, San Diego, USA.
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, USA.
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13
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Knolhoff AM, Zheng J, McFarland MA, Luo Y, Callahan JH, Brown EW, Croley TR. Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1768-1779. [PMID: 26250559 DOI: 10.1007/s13361-015-1190-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/24/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to exhibit antimicrobial activity against a number of pathogens, such as E. coli, Salmonella, and methicillin-resistant Staphylococcus aureus (MRSA). The responsible antimicrobial compounds were isolated from these Paenibacillus strains and a combination of low and high resolution mass spectrometry with multiple-stage tandem mass spectrometry was used for identification. A group of closely related cyclic lipopeptides was identified, differing primarily by fatty acid chain length and one of two possible amino acid substitutions. Variation in the fatty acid length resulted in mass differences of 14 Da and yielded groups of related MS(n) spectra. Despite the inherent complexity of MS/MS spectra of cyclic compounds, straightforward analysis of these spectra was accomplished by determining differences in complementary product ion series between compounds that differ in molecular weight by 14 Da. The primary peptide sequence assignment was confirmed through genome mining; the combination of these analytical tools represents a workflow that can be used for the identification of complex antibiotics. The compounds also share amino acid sequence similarity to a previously identified broad-spectrum antibiotic isolated from Paenibacillus. The presence of such a wide distribution of related compounds produced by the same organism represents a novel class of broad-spectrum antibiotic compounds.
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Affiliation(s)
- Ann M Knolhoff
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA.
| | - Jie Zheng
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Melinda A McFarland
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Yan Luo
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - John H Callahan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Eric W Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Timothy R Croley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
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14
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Yang L, Ibrahim A, Johnston CW, Skinnider MA, Ma B, Magarvey NA. Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm. ACTA ACUST UNITED AC 2015; 22:1259-69. [PMID: 26364933 DOI: 10.1016/j.chembiol.2015.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023]
Abstract
Microbial natural products are some of the most important pharmaceutical agents and possess unparalleled chemical diversity. Here we present an untargeted metabolomics algorithm that builds on our validated iSNAP platform to rapidly identify families of peptide natural products. By utilizing known or in silico-dereplicated seed structures, this algorithm screens tandem mass spectrometry data to elaborate extensive molecular families within crude microbial culture extracts with high confidence and statistical significance. Analysis of peptide natural product producers revealed an abundance of unreported congeners, revealing one of the largest families of natural products described to date, as well as a novel variant with greater potency. These findings demonstrate the effectiveness of the iSNAP platform as an accurate tool for rapidly profiling large families of nonribosomal peptides.
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Affiliation(s)
- Lian Yang
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Ashraf Ibrahim
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Chad W Johnston
- The Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Michael A Skinnider
- The Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Bin Ma
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Nathan A Magarvey
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8N 3Z5, Canada; The Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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15
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Medema MH, Fischbach MA. Computational approaches to natural product discovery. Nat Chem Biol 2015; 11:639-48. [PMID: 26284671 PMCID: PMC5024737 DOI: 10.1038/nchembio.1884] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/07/2015] [Indexed: 01/13/2023]
Abstract
Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.
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Affiliation(s)
- Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Michael A. Fischbach
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158
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16
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Abstract
Cyclic peptides are found in a diverse range of organisms and are characterized by their stability and role in defense. Why is only one class of cyclic peptides found in mammals? Possibly we have not looked hard enough for them, or the technologies needed to identify them are not fully developed. We also do not yet understand their intriguing biosynthesis from two separate gene products. Addressing these challenges will require the application of chemical tools and insights from other classes of cyclic peptides. Herein, we highlight recent developments in the characterization of theta defensins and describe the important role that chemistry has played in delineating their modes of action. Furthermore, we emphasize the potential of theta defensins as antimicrobial agents and scaffolds for peptide drug design.
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Affiliation(s)
- Anne C. Conibear
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD (Australia) http://www.imb.uq.edu.au/index.html?page=11695
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD (Australia) http://www.imb.uq.edu.au/index.html?page=11695
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17
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Mohimani H, Liu WT, Kersten R, Moore BS, Dorrestein PC, Pevzner PA. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. JOURNAL OF NATURAL PRODUCTS 2014; 77:1902-9. [PMID: 25116163 PMCID: PMC4143176 DOI: 10.1021/np500370c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 05/31/2023]
Abstract
Nonribosomal peptides (NRPs) such as vancomycin and daptomycin are among the most effective antibiotics. While NRPs are biomedically important, the computational techniques for sequencing these peptides are still in their infancy. The recent emergence of mass spectrometry techniques for NRP analysis (capable of sequencing an NRP from small amounts of nonpurified material) revealed an enormous diversity of NRPs. However, as many NRPs have nonlinear structure (e.g., cyclic or branched-cyclic peptides), the standard de novo sequencing tools (developed for linear peptides) are not applicable to NRP analysis. Here, we introduce the first NRP identification algorithm, NRPquest, that performs mutation-tolerant and modification-tolerant searches of spectral data sets against a database of putative NRPs. In contrast to previous studies aimed at NRP discovery (that usually report very few NRPs), NRPquest revealed nearly a hundred NRPs (including unknown variants of previously known peptides) in a single study. This result indicates that NRPquest can potentially make MS-based NRP identification as robust as the identification of linear peptides in traditional proteomics.
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Affiliation(s)
- Hosein Mohimani
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Wei-Ting Liu
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Roland
D. Kersten
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Bradley S. Moore
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Pavel A. Pevzner
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
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18
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19
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20
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Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol 2014; 9:1545-51. [PMID: 24802639 PMCID: PMC4215869 DOI: 10.1021/cb500199h] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Ribosomally synthesized and posttranslationally
modified peptides
(RiPPs), especially from microbial sources, are a large group of bioactive
natural products that are a promising source of new (bio)chemistry
and bioactivity.1 In light of exponentially
increasing microbial genome databases and improved mass spectrometry
(MS)-based metabolomic platforms, there is a need for computational
tools that connect natural product genotypes predicted from microbial
genome sequences with their corresponding chemotypes from metabolomic
data sets. Here, we introduce RiPPquest, a tandem mass spectrometry
database search tool for identification of microbial RiPPs, and apply
it to lanthipeptide discovery. RiPPquest uses genomics to limit search
space to the vicinity of RiPP biosynthetic genes and proteomics to
analyze extensive peptide modifications and compute p-values of peptide-spectrum
matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs
from extracts of Streptomyces to their gene clusters
and by the discovery of a new class III lanthipeptide, informatipeptin,
from Streptomyces viridochromogenes DSM 40736 to
reflect that it is a natural product that was discovered by mass spectrometry
based genome mining using algorithmic tools rather than manual inspection
of mass spectrometry data and genetic information. The presented tool
is available at cyclo.ucsd.edu.
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Affiliation(s)
- Hosein Mohimani
- Department
of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Roland D. Kersten
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Wei-Ting Liu
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Mingxun Wang
- Department
of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Samuel O. Purvine
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Si Wu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Heather M. Brewer
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Pasa-Tolic
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Nuno Bandeira
- Department
of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Bradley S. Moore
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Pavel A. Pevzner
- Department
of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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21
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Bouslimani A, Sanchez LM, Garg N, Dorrestein PC. Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 2014; 31:718-29. [PMID: 24801551 PMCID: PMC4161218 DOI: 10.1039/c4np00044g] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex biological systems. In this Highlight, we feature emerging mass spectrometric methods and tools used by the natural product community and give a perspective of future directions where the mass spectrometry field is migrating towards over the next decade.
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Affiliation(s)
- Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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22
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Hufsky F, Scheubert K, Böcker S. New kids on the block: novel informatics methods for natural product discovery. Nat Prod Rep 2014; 31:807-17. [DOI: 10.1039/c3np70101h] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Kavan D, Kuzma M, Lemr K, Schug KA, Havlicek V. CYCLONE--a utility for de novo sequencing of microbial cyclic peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1177-1184. [PMID: 23702710 DOI: 10.1007/s13361-013-0652-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 04/19/2013] [Accepted: 04/19/2013] [Indexed: 06/02/2023]
Abstract
We have developed a de novo sequencing software tool (CYCLONE) and applied it for determination of cyclic peptides. The program uses a non-redundant database of 312 nonribosomal building blocks identified to date in bacteria and fungi (more than 230 additional residues in the database list were isobaric). The software was used to fully characterize the tandem mass spectrum of several cyclic peptides and provide sequence tags. The general strategy of the script was based on fragment ion pre-characterization to accomplish unambiguous b-ion series assignments. Showcase examples were a cyclic tetradepsipeptide beauverolide, a cyclic hexadepsipeptide roseotoxin A, a lasso-like hexapeptide pseudacyclin A, and a cyclic undecapeptide cyclosporin A. The extent of ion scrambling in smaller peptides was as low as 5 % of total ion current; this demonstrated the feasibility of CYCLONE de novo sequencing. The robustness of the script was also tested against database sets of various sizes and isotope-containing data. It can be downloaded from the http://ms.biomed.cas.cz/MSTools/ website. ᅟ
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Affiliation(s)
- Daniel Kavan
- Institute of Microbiology, v.v.i., Videnska 1083, CZ 14220, Prague 4, Czech Republic
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24
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Mohimani H, Kim S, Pevzner PA. A new approach to evaluating statistical significance of spectral identifications. J Proteome Res 2013; 12:1560-8. [PMID: 23343606 DOI: 10.1021/pr300453t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While nonlinear peptide natural products such as Vancomycin and Daptomycin are among the most effective antibiotics, the computational techniques for sequencing such peptides are still in their infancy. Previous methods for sequencing peptide natural products are based on Nuclear Magnetic Resonance spectroscopy and require large amounts (milligrams) of purified materials. Recently, development of mass spectrometry-based methods has enabled accurate sequencing of nonlinear peptide natural products using picograms of material, but the question of evaluating statistical significance of Peptide Spectrum Matches (PSM) for these peptides remains open. Moreover, it is unclear how to decide whether a given spectrum is produced by a linear, cyclic, or branch-cyclic peptide. Surprisingly, all previous mass spectrometry studies overlooked the fact that a very similar problem has been successfully addressed in particle physics in 1951. In this work, we develop a method for estimating statistical significance of PSMs defined by any peptide (including linear and nonlinear). This method enables us to identify whether a peptide is linear, cyclic, or branch-cyclic, an important step toward identification of peptide natural products.
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Affiliation(s)
- Hosein Mohimani
- Department of Electrical and Computer Engineering and ‡Department of Computer Science and Engineering, University of California-San Diego , San Diego, California 92093
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25
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Göransson U, Burman R, Gunasekera S, Strömstedt AA, Rosengren KJ. Circular proteins from plants and fungi. J Biol Chem 2012; 287:27001-6. [PMID: 22700984 DOI: 10.1074/jbc.r111.300129] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Circular proteins, defined as head-to-tail cyclized polypeptides originating from ribosomal synthesis, represent a novel class of natural products attracting increasing interest. From a scientific point of view, these compounds raise questions of where and why they occur in nature and how they are formed. From a rational point of view, these proteins and their structural concept may be exploited for crop protection and novel pharmaceuticals. Here, we review the current knowledge of three protein families: cyclotides and circular sunflower trypsin inhibitors from the kingdom of plants and the Amanita toxins from fungi. A particular emphasis is placed on their biological origin, structure, and activity. In addition, the opportunity for discovery of novel circular proteins and recent insights into their mechanism of action are discussed.
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Affiliation(s)
- Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden.
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26
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Gerwick WH, Moore BS. Lessons from the past and charting the future of marine natural products drug discovery and chemical biology. ACTA ACUST UNITED AC 2012; 19:85-98. [PMID: 22284357 DOI: 10.1016/j.chembiol.2011.12.014] [Citation(s) in RCA: 405] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 12/31/2022]
Abstract
Marine life forms are an important source of structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents. These success stories have had to overcome difficulties inherent to natural products-derived drugs, such as adequate sourcing of the agent and issues related to structural complexity. Nevertheless, several marine-derived agents are now approved, most as "first-in-class" drugs, with five of seven appearing in the past few years. Additionally, there is a rich pipeline of clinical and preclinical marine compounds to suggest their continued application in human medicine. Understanding of how these agents are biosynthetically assembled has accelerated in recent years, especially through interdisciplinary approaches, and innovative manipulations and re-engineering of some of these gene clusters are yielding novel agents of enhanced pharmaceutical properties compared with the natural product.
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Affiliation(s)
- William H Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92037, USA.
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27
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Johnston C, Ibrahim A, Magarvey N. Informatic strategies for the discovery of polyketides and nonribosomal peptides. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20120h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A modern challenge and opportunity exists for in the ability to link genomic and metabolomic data, using novel informatic methods to find new bioactive natural products.
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Affiliation(s)
- Chad Johnston
- Department of Biochemistry and Biomedical Sciences
- Department of Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
| | - Ashraf Ibrahim
- Department of Biochemistry and Biomedical Sciences
- Department of Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
| | - Nathan Magarvey
- Department of Biochemistry and Biomedical Sciences
- Department of Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
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