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Nelson S, Parkinson EI. Synthetic-bioinformatic natural product-inspired peptides. Nat Prod Rep 2025; 42:50-66. [PMID: 39479929 PMCID: PMC11525955 DOI: 10.1039/d4np00043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Indexed: 11/02/2024]
Abstract
Covering: 2016 to 2024Natural products, particularly cyclic peptides, are a promising source of bioactive compounds. Nonribosomal peptide synthetases (NRPSs) play a key role in biosynthesizing these compounds, which include antibiotic and anticancer agents, immunosuppressants, and others. Traditional methods of discovering natural products have limitations including cryptic biosynthetic gene clusters (BGCs), low titers, and currently unculturable organisms. This has prompted the exploration of alternative approaches. Synthetic-bioinformatic natural products (syn-BNPs) are one such alternative that utilizes bioinformatics techniques to predict nonribosomal peptides (NRPs) followed by chemical synthesis of the predicted peptides. This approach has shown promise, resulting in the discovery of a variety of bioactive compounds including peptides with antibacterial, antifungal, anticancer, and proteasome-stimulating activities. Despite the success of this approach, challenges remain especially in the accurate prediction of fatty acid incorporation, tailoring enzyme modifications, and peptide release mechanisms. Further work in these areas will enable the discovery of many bioactive peptides that are currently inaccessible.
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Affiliation(s)
- Samantha Nelson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
| | - Elizabeth I Parkinson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
- James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, USA
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2
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Delawská K, Hájek J, Voráčová K, Kuzma M, Mareš J, Vicková K, Kádek A, Tučková D, Gallob F, Divoká P, Moos M, Opekar S, Koch L, Saurav K, Sedlák D, Novák P, Urajová P, Dean J, Gažák R, Niedermeyer TJH, Kameník Z, Šimek P, Villunger A, Hrouzek P. Discovery of nostatin A, an azole-containing proteusin with prominent cytostatic and pro-apoptotic activity. Org Biomol Chem 2025; 23:449-460. [PMID: 39576263 PMCID: PMC11583998 DOI: 10.1039/d4ob01395f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Accepted: 11/04/2024] [Indexed: 11/24/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are intriguing compounds with potential pharmacological applications. While many RiPPs are known as antimicrobial agents, a limited number of RiPPs with anti-proliferative effects in cancer cells are available. Here we report the discovery of nostatin A (NosA), a highly modified RiPP belonging among nitrile hydratase-like leader peptide RiPPs (proteusins), isolated from a terrestrial cyanobacterium Nostoc sp. Its structure was established based on the core peptide sequence encoded in the biosynthetic gene cluster recovered from the producing strain and subsequent detailed nuclear magnetic resonance and high-resolution mass spectrometry analyses. NosA, composed of a 30 amino-acid peptide core, features a unique combination of moieties previously not reported in RiPPs: the simultaneous presence of oxazole/thiazole heterocycles, dehydrobutyrine/dehydroalanine residues, and a sactionine bond. NosA includes an isobutyl-modified proline residue, highly unusual in natural products. NosA inhibits proliferation of multiple cancer cell lines at low nanomolar concentration while showing no hemolysis. It induces cell cycle arrest in S-phase followed by mitochondrial apoptosis employing a mechanism different from known tubulin binding and DNA damaging compounds. NosA also inhibits Staphylococcus strains while it exhibits no effect in other tested bacteria or yeasts. Due to its novel structure and selective bioactivity, NosA represents an excellent candidate for combinatorial chemistry approaches leading to development of novel NosA-based lead compounds.
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Affiliation(s)
- Kateřina Delawská
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Jan Hájek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
| | - Kateřina Voráčová
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
| | - Marek Kuzma
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Praha 4, Czech Republic
| | - Jan Mareš
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
| | - Kateřina Vicková
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
| | - Alan Kádek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Praha 4, Czech Republic
| | - Dominika Tučková
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Filip Gallob
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Lazarettgasse 14, 1090 Wien, Austria
| | - Petra Divoká
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Martin Moos
- Institute of Entomology, Laboratory of Analytical Biochemistry and Metabolomics, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05, České Budějovice, Czech Republic
| | - Stanislav Opekar
- Institute of Entomology, Laboratory of Analytical Biochemistry and Metabolomics, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05, České Budějovice, Czech Republic
| | - Lukas Koch
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, (Saale), Germany
| | - Kumar Saurav
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
| | - David Sedlák
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Praha 4, Czech Republic
| | - Petra Urajová
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
| | - Jason Dean
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
| | - Radek Gažák
- Laboratory of Antibiotic Resistance and Microbial Metabolomics, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Praha 4, Czech Republic
| | - Timo J H Niedermeyer
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, (Saale), Germany
| | - Zdeněk Kameník
- Laboratory of Antibiotic Resistance and Microbial Metabolomics, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Praha 4, Czech Republic
| | - Petr Šimek
- Institute of Entomology, Laboratory of Analytical Biochemistry and Metabolomics, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05, České Budějovice, Czech Republic
| | - Andreas Villunger
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Lazarettgasse 14, 1090 Wien, Austria
- Institute for Developmental Immunology, Medical University of Innsbruck, Biocenter, Innsbruck, Austria
| | - Pavel Hrouzek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradká 237, Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 01 Třeboň, Czech Republic.
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de Oliveira Chagas MB, Mendonca da Costa VDC, Montenegro C, de Lima MDCA, da Rosa MM, Pereira MC, de Melo Rego MJB, da Rocha Pitta MG. The Imidazacridine Derivative LPSF/AC-05 Induces Apoptosis, Cell Cycle Arrest, and Topoisomerase II Inhibition in Breast Cancer, Leukemia, and Lymphoma. Curr Cancer Drug Targets 2025; 25:431-444. [PMID: 38982694 DOI: 10.2174/0115680096290753240613114122] [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: 01/03/2024] [Revised: 04/11/2024] [Accepted: 05/14/2024] [Indexed: 07/11/2024]
Abstract
INTRODUCTION Cancer is one of the major causes of morbidity and mortality worldwide. Current treatments for both solid and hematological tumors are associated with severe adverse effects and drug resistance, necessitating the development of novel selective antineoplastic drugs. METHODS The present study describes the antitumor activity of the imidazacridine derivative 5- acridin-9-ylmethylidene-2-thioxoimidazolidin-4-one (LPSF/AC05) in breast cancer, leukemia, and lymphoma cells. Cytotoxicity assays were performed in PBMC and in breast cancer, leukemia, and lymphoma cell lines using the MTT method. Changes in cell cycle progression and apoptosis were assessed using flow cytometry. Moreover, topoisomerase II inhibition assays were performed. LPSF/AC05 exhibited cytotoxicity in six of the nine cell lines tested. RESULTS The best results for leukemia and lymphoma were observed in the Toledo, Jurkat, and Raji cell lines (IC50 = 27.18, 31.04, and 33.36 µM, respectively). For breast cancer, the best results were observed in the triple-negative cell line MDA-MB-231 (IC50 = 27.54 μM). The compound showed good selectivity, with no toxicity to normal human cells (IC50 > 100µM; selectivity index > 3). Cell death was primarily induced by apoptosis in all cell lines. Furthermore, LPSF/AC05 treatment induced cell cycle arrest at the G0/G1 phase in leukemia/lymphoma and at the G2/M phase in breast cancer. Finally, topoisomerase II was inhibited. CONCLUSION These results indicate the potential application of LPSF/AC05 in cancer therapy.
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Affiliation(s)
- Mardonny Bruno de Oliveira Chagas
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Valecia de Cassia Mendonca da Costa
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Claudio Montenegro
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Maria do Carmo Alves de Lima
- Laboratory of chemistry and Therapeutic Innovation (LQIT), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Michelle Melgarejo da Rosa
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Michelly Cristiny Pereira
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Moacyr Jesus Barreto de Melo Rego
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
| | - Maira Galdino da Rocha Pitta
- Laboratory for Immunomodulation and New Therapeutic Approaches, Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Brazil
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Ma T, Chu J. Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond. Beilstein J Org Chem 2024; 20:3050-3060. [PMID: 39600953 PMCID: PMC11590018 DOI: 10.3762/bjoc.20.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 11/05/2024] [Indexed: 11/29/2024] Open
Abstract
Bioactivity-guided fractionation (BGF) has historically been a fruitful natural product discovery workflow. However, it is plagued by increasing rediscovery rates in recent years and new methods capable of exploring the natural product chemical space more broadly and more efficiently is in urgent need. Chemical structure metagenomics as one such method is the theme of this Perspective. It emphasizes a chemical-structure-centered viewpoint toward natural product research. Key to chemical structure metagenomics is the ability to predict the structure of a natural product based on its biosynthetic gene sequences, which facilitated the discovery of numerous new bioactive molecules and helped uncover oversampled/underexplored niches of decades of BGF based discovery. While microbial nonribosomal peptides have been the focus of chemical structure metagenomics efforts thus far, it is in principle applicable to other natural product families. The future outlook of this new approach will also be discussed.
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Affiliation(s)
- Thomas Ma
- Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
| | - John Chu
- Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
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5
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MacIntyre LW, Koirala B, Rosenzweig A, Morales-Amador A, Brady SF. Cinnamosyn, a Cinnamoylated Synthetic-Bioinformatic Natural Product with Cytotoxic Activity. Org Lett 2024; 26:4433-4437. [PMID: 38767867 PMCID: PMC11948286 DOI: 10.1021/acs.orglett.4c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Most biosynthetic gene clusters (BGCs) are functionally inaccessible by using fermentation methods. Bioinformatic-coupled total synthesis provides an alternative approach for accessing BGC-encoded bioactivities. To date, synthetic bioinformatic natural product (synBNP) methods have focused on lipopeptides containing simple lipids. Here we increase the bioinformatic and synthetic complexity of the synBNP approach by targeting BGCs that encode N-cinnamoyl lipids. This led to our synthesis of cinnamosyn, a 10-mer N-cinnamoyl-containing peptide that is cytotoxic to human cells.
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Affiliation(s)
- Logan W MacIntyre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Adam Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Adrián Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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6
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Wang Z, Kasper A, Takahashi M, Amador AM, Bhattacharjee A, Kan J, Hernandez Y, Ternei M, Brady SF. Tapcin, an In Vivo Active Dual Topoisomerase I/II Inhibitor Discovered by Synthetic Bioinformatic Natural Product (Syn-BNP)-Coupled Metagenomics. Angew Chem Int Ed Engl 2024; 63:e202317187. [PMID: 38231130 PMCID: PMC11018531 DOI: 10.1002/anie.202317187] [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: 11/12/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
DNA topoisomerases are attractive targets for anticancer agents. Dual topoisomerase I/II inhibitors are particularly appealing due to their reduced rates of resistance. A number of therapeutically relevant topoisomerase inhibitors are bacterial natural products. Mining the untapped chemical diversity encoded by soil microbiomes presents an opportunity to identify additional natural topoisomerase inhibitors. Here we couple metagenome mining, bioinformatic structure prediction algorithms, and chemical synthesis to produce the dual topoisomerase inhibitor tapcin. Tapcin is a mixed p-aminobenzoic acid (PABA)-thiazole with a rare tri-thiazole substructure and picomolar antiproliferative activity. Tapcin reduced colorectal adenocarcinoma HT-29 cell proliferation and tumor volume in mouse hollow fiber and xenograft models, respectively. In both studies it showed similar activity to the clinically used topoisomerase I inhibitor irinotecan. The study suggests that the interrogation of soil microbiomes using synthetic bioinformatic natural product methods has the potential to be a rewarding strategy for identifying potent, biomedically relevant, antiproliferative agents.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Mai Takahashi
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Adrian Morales Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Abir Bhattacharjee
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Jingbo Kan
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
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Shen Y, Liu N, Wang Z. Recent advances in the culture-independent discovery of natural products using metagenomic approaches. Chin J Nat Med 2024; 22:100-111. [PMID: 38342563 DOI: 10.1016/s1875-5364(24)60585-6] [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: 08/24/2023] [Indexed: 02/13/2024]
Abstract
Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads. However, the cultivation of only about 1% of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria. Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods. This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening, sequence tag-based homology screening, and bioinformatic-assisted chemical synthesis. Through this process, numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories. This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.
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Affiliation(s)
- Yiping Shen
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
| | - Nan Liu
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
| | - Zongqiang Wang
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China.
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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Tang X. Synthetic biology to revive microbial natural product discovery. MLIFE 2023; 2:123-125. [PMID: 38817621 PMCID: PMC10989979 DOI: 10.1002/mlf2.12071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Affiliation(s)
- Xiaoyu Tang
- Shenzhen Bay LaboratoryInstitute of Chemical BiologyShenzhenChina
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10
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Li L. Accessing hidden microbial biosynthetic potential from underexplored sources for novel drug discovery. Biotechnol Adv 2023:108176. [PMID: 37211187 DOI: 10.1016/j.biotechadv.2023.108176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Microbial natural products and their structural analogues have widely used as pharmaceutical agents, especially for infectious diseases and cancer. Despite this success, new structural classes with innovative chemistry and modes of action are urgently needed to be developed to combat the growing antimicrobial resistance and other public health problems. The advances in next-generation sequencing technologies and powerful computational tools open up new opportunities to explore microbial biosynthetic potential from underexplored sources, with millions of secondary metabolites awaiting discovery. The review highlights challenges associated with discovery of new chemical entities, rich reservoirs provided by untapped taxa, ecological niches or host microbiomes, emerging synthetic biotechnologies to unearth the hidden microbial biosynthetic potential for novel drug discovery at scale and speed.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.
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11
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Li L. Next-generation synthetic biology approaches for the accelerated discovery of microbial natural products. ENGINEERING MICROBIOLOGY 2023; 3:100060. [PMID: 39628520 PMCID: PMC11610963 DOI: 10.1016/j.engmic.2022.100060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/06/2024]
Abstract
Microbial natural products (NPs) and their derivates have been widely used in health care and agriculture during the past few decades. Although large-scale bacterial or fungal (meta)genomic mining has revealed the tremendous biosynthetic potentials to produce novel small molecules, there remains a lack of universal approaches to link NP biosynthetic gene clusters (BGCs) to their associated products at a large scale and speed. In the last ten years, a series of emerging technologies have been established alongside the developments in synthetic biology to engineer cryptic metabolite BGCs and edit host genomes. Diverse computational tools, such as antiSMASH and PRISM, have also been simultaneously developed to rapidly identify BGCs and predict the chemical structures of their products. This review discusses the recent developments and trends pertaining to the accelerated discovery of microbial NPs driven by a wide variety of next-generation synthetic biology approaches, with an emphasis on the in situ activation of silent BGCs at scale, the direct cloning or refactoring of BGCs of interest for heterologous expression, and the synthetic-bioinformatic natural products (syn-BNP) approach for the guided rapid access of bioactive non-ribosomal peptides.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
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Li D, Chen X, Yan R, Jiang Z, Zhou B, Lv B. G-quadruplex-containing oligodeoxynucleotides as DNA topoisomerase I inhibitors. Int J Biol Macromol 2022; 223:281-289. [PMID: 36356864 DOI: 10.1016/j.ijbiomac.2022.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
DNA topoisomerase I was found to be highly abundant in fast-proliferating tumor cells and is a potential target for anticancer therapy. A series of G-quadruplex-containing oligodeoxynucleotides (ODNs) were designed and used as inhibitors of DNA topoisomerase I. It was demonstrated that ODNs with G-quadruplexes can efficiently inhibit the supercoiled DNA relaxation reaction catalyzed by DNA topoisomerase I. Compared with the other conformations, the parallel propeller-type G-quadruplex was the most efficient DNA topoisomerase I inhibitor. Further studies revealed that integrating G-quadruplexes with duplexes to form quadruplex-duplex hybrids could significantly improve the inhibition efficiency. In addition, a circular ODN that consists of a G-quadruplex motif and DNA topoisomerase I binding site was synthesized and used as a DNA topoisomerase I inhibitor. The results showed that the particularly designed circular ODN displayed high inhibitory efficiency on the activity of DNA topoisomerase I with an IC50 value of 54.8 nM. Moreover, the circular ODN exhibited excellent thermal stability and nuclease resistance. Considering the low cytotoxicity of DNA-based biopharmaceuticals, the design strategy and results reported in this study may shed new light on nucleic acid-based DNA topoisomerase I inhibitor construction for potential anticancer drugs.
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Affiliation(s)
- Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Xiyu Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Rumeng Yan
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing 210013, China
| | - Zeshan Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Bing Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Bei Lv
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing 210013, China.
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13
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Regulated Expression of an Environmental DNA-Derived Type II Polyketide Gene Cluster in Streptomyces Hosts Identified a New Tetracenomycin Derivative TCM Y. Curr Microbiol 2022; 79:336. [PMID: 36201117 DOI: 10.1007/s00284-022-03039-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022]
Abstract
As bacterial natural products have been proved to be the most important source of many therapeutic medicines, the need to discover novel natural products becomes extremely urgent. Despite the fact that the majority of bacterial species are yet to be cultured in a laboratory setting, and that most of the bacterial natural product biosynthetic genes are silent, "metagenomics technology" offers a solution to help clone natural product biosynthetic genes from environmental samples, and genetic engineering enables the silent biosynthetic genes to be activated. In this work, a type II polyketide biosynthetic gene cluster was identified from a soil metagenomic library and was activated by over-expression of a SARP regulator gene in the gene cluster in Streptomyces hosts. A new tetracenomycin type compound tetracenomycin Y was identified from the fermentation broth. This study shows that metagenomics and genetic engineering could be combined to provide access to new natural metabolites.
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