1
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Xu Y, Zhang Y, Zhang Q, Li JC, Zhou ZH, Yang Z, Xiu J, Chen X, Huang J, Ge HM, Shi J. Genome Mining of Cinnamoyl-Containing Nonribosomal Peptide Gene Clusters Directs the Production of Malacinnamycin. Org Lett 2024; 26:971-976. [PMID: 38265233 DOI: 10.1021/acs.orglett.4c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Cinnamoyl-containing nonribosomal peptides (CCNPs) constitute a unique family of actinobacterial secondary metabolites that display a broad spectrum of biological activities. Here, we present a genome mining approach targeting cyclase and is isomerase to discover new CCNPs, which led to the identification of 207 putative CCNP gene clusters from public bacterial genome databases. After strain prioritization, a novel class of CCNP-type glycopeptides named malacinnamycin was identified. A plausible biosynthetic pathway for malacinnamycin was deduced by bioinformatics analysis.
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Affiliation(s)
- Ying Xu
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Yi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Qun Zhang
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Jian Cheng Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhao Hui Zhou
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Zhengming Yang
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Jianlong Xiu
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Xinglong Chen
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Jia Huang
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration and Development, Beijing 100083, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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2
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Yan JX, Wu Q, Maity M, Braun DR, Alas I, Wang X, Yin X, Zhu Y, Bell BA, Rajski SR, Ge Y, Richardson DD, Zhong W, Bugni TS. Rapid Unambiguous Structure Elucidation of Streptnatamide A, a New Cyclic Peptide Isolated from A Marine-derived Streptomyces sp. Chemistry 2023; 29:e202301813. [PMID: 37452377 PMCID: PMC10592287 DOI: 10.1002/chem.202301813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Cyclic peptides have been excellent source of drug leads. With the advances in discovery platforms, the pharmaceutical industry has a growing interest in cyclic peptides and has pushed several into clinical trials. However, structural complexity of cyclic peptides brings extreme challenges for structure elucidation efforts. Isotopic fine structure analysis, Nuclear magnetic resonance (NMR), and detailed tandem mass spectrometry rapidly provided peptide sequence for streptnatamide A, a cyclic peptide isolated from a marine-derived Streptomyces sp. Marfey's analysis determined the stereochemistry of all amino acids, enabling the unambiguous structure determination of this compound. A non-ribosomal peptide synthetase biosynthetic gene cluster (stp) was tentatively identified and annotated for streptnatamide A based on the in silico analysis of whole genome sequencing data. These analytical tools will be powerful tools to overcome the challenges for cyclic peptide structure elucidation and accelerate the development of bioactive cyclic peptides.
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Affiliation(s)
- Jia-Xuan Yan
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Qihao Wu
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Current address: Department of Chemistry, Institute of Biomolecular Design & Discovery, Yale University, 06516, West Haven, CT, USA
| | - Mitasree Maity
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Imraan Alas
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Xiao Wang
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Xing Yin
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
| | - Bailey A Bell
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, 53706, Madison, WI, USA
| | | | - Wendy Zhong
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Lachman Institute for Pharmaceutical Development, University of Wisconsin-Madison, 600 Highland Ave, 53792, Madison, WI, USA
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3
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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4
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Khire SS, Gattadahalli N, Gurav ND, Kumar A, Gadre SR. Constructing Potential Energy Surface with Correlated Theory for Dipeptides Using Molecular Tailoring Approach. Chemphyschem 2023; 24:e202200784. [PMID: 36735449 DOI: 10.1002/cphc.202200784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023]
Abstract
We demonstrate a cost-effective alternative employing the fragment-based molecular tailoring approach (MTA) for building the potential energy surface (PES) for two dipeptides viz. alanine-alanine and alanine-proline employing correlated theory, with augmented Dunning basis sets. About 1369 geometries are generated for each test dipeptide by systematically varying the dihedral angles Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . These conformational geometries are partially optimized by relaxing all the other Z-matrix parameters, fixing the values of Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . The MP2 level PES is constructed from the MTA-energies of chemically intact geometries using minimal hardware. The fidelity of MP2/aug-cc-pVDZ level PES is brought out by comparing it with its full calculation counterpart. Further, we bring out the power of the method by reporting the MTA-based CCSD/aug-cc-pVDZ level PES for these two dipeptides containing 498 and 562 basis functions respectively.
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Affiliation(s)
- Subodh S Khire
- RIKEN Center for Computational Science, Kobe, 650-0047, Japan.,Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
| | - Nandini Gattadahalli
- Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
| | - Nalini D Gurav
- Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India.,Organisch-Chemisches Institut and Center for Multiscale Theory and Computation (CMTC), Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Anmol Kumar
- School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, HSFII, Baltimore, Maryland, 21201, U.S.A
| | - Shridhar R Gadre
- Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
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5
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Kang S, Han J, Jang SC, An JS, Kang I, Kwon Y, Nam SJ, Shim SH, Cho JC, Lee SK, Oh DC. Epoxinnamide: An Epoxy Cinnamoyl-Containing Nonribosomal Peptide from an Intertidal Mudflat-Derived Streptomyces sp. Mar Drugs 2022; 20:md20070455. [PMID: 35877748 PMCID: PMC9321520 DOI: 10.3390/md20070455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/09/2022] [Accepted: 07/09/2022] [Indexed: 12/03/2022] Open
Abstract
Cinnamoyl-containing nonribosomal peptides (CCNPs) form a unique family of actinobacterial secondary metabolites and display various biological activities. A new CCNP named epoxinnamide (1) was discovered from intertidal mudflat-derived Streptomyces sp. OID44. The structure of 1 was determined by the analysis of one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) data along with a mass spectrum. The absolute configuration of 1 was assigned by the combination of advanced Marfey’s method, 3JHH and rotating-frame overhauser effect spectroscopy (ROESY) analysis, DP4 calculation, and genomic analysis. The putative biosynthetic pathway of epoxinnamide (1) was identified through the whole-genome sequencing of Streptomyces sp. OID44. In particular, the thioesterase domain in the nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster was proposed as a bifunctional enzyme, which catalyzes both epimerization and macrocyclization. Epoxinnamide (1) induced quinone reductase (QR) activity in murine Hepa-1c1c7 cells by 1.6-fold at 5 μM. It also exhibited effective antiangiogenesis activity in human umbilical vein endothelial cells (IC50 = 13.4 μM).
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Affiliation(s)
- Sangwook Kang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (J.-C.C.)
| | - Yun Kwon
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea;
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea;
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (J.-C.C.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
- Correspondence: ; Tel.: +82-880-2491; Fax: +82-762-8322
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6
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Karim MRU, In Y, Zhou T, Harunari E, Oku N, Igarashi Y. Nyuzenamides A and B: Bicyclic Peptides with Antifungal and Cytotoxic Activity from a Marine-Derived Streptomyces sp. Org Lett 2021; 23:2109-2113. [PMID: 33661652 DOI: 10.1021/acs.orglett.1c00210] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two bicyclic peptides, nyuzenamides A (1) and B (2), were discovered from Streptomyces isolated from suspended matter in deep sea water collected in the Sea of Japan. Their structures were determined through nuclear magnetic resonance and mass spectrometry analyses in combination with X-ray crystallography and the chiral-phase gas chromatography-mass spectrometry method to comprise ten amino acid residues containing four unusual amino acids along with aromatic acyl units. Both compounds displayed antifungal activity against pathogenic fungi and cytotoxicity against P388 murine leukemia cells.
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Affiliation(s)
- Md Rokon Ul Karim
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuko In
- Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1041, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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7
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Zhang C, Seyedsayamdost MR. Corrigendum: Discovery of a Cryptic Depsipeptide from
Streptomyces ghanaensis
via MALDI‐MS‐Guided High‐Throughput Elicitor Screening. Angew Chem Int Ed Engl 2020; 59:22824. [DOI: 10.1002/anie.202014201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Zhang C, Seyedsayamdost MR. Berichtigung: Discovery of a Cryptic Depsipeptide from
Streptomyces ghanaensis
via MALDI‐MS‐Guided High‐Throughput Elicitor Screening. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202014201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Berlinck RGS, Bernardi DI, Fill T, Fernandes AAG, Jurberg ID. The chemistry and biology of guanidine secondary metabolites. Nat Prod Rep 2020; 38:586-667. [PMID: 33021301 DOI: 10.1039/d0np00051e] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2017-2019Guanidine natural products isolated from microorganisms, marine invertebrates and terrestrial plants, amphibians and spiders, represented by non-ribosomal peptides, guanidine-bearing polyketides, alkaloids, terpenoids and shikimic acid derived, are the subject of this review. The topics include the discovery of new metabolites, total synthesis of natural guanidine compounds, biological activity and mechanism-of-action, biosynthesis and ecological functions.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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10
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Yang C, Qian R, Xu Y, Yi J, Gu Y, Liu X, Yu H, Jiao B, Lu X, Zhang W. Marine Actinomycetes-derived Natural Products. Curr Top Med Chem 2020; 19:2868-2918. [PMID: 31724505 DOI: 10.2174/1568026619666191114102359] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/02/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022]
Abstract
Actinomycetes is an abundant resource for discovering a large number of lead compounds, which play an important role in microbial drug discovery. Compared to terrestrial microorganisms, marine actinomycetes have unique metabolic pathways because of their special living environment, which has the potential to produce a variety of bioactive substances. In this paper, secondary metabolites isolated from marine actinomycetes are reviewed (2013-2018), most of which exhibited cytotoxic, antibacterial, and antiviral biological activities.
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Affiliation(s)
- Chengfang Yang
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Rui Qian
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Yao Xu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Junxi Yi
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Yiwen Gu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Xiaoyu Liu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Haobing Yu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Binghua Jiao
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Xiaoling Lu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, Australia.,Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, Australia
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11
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Götze S, Stallforth P. Structure elucidation of bacterial nonribosomal lipopeptides. Org Biomol Chem 2020; 18:1710-1727. [DOI: 10.1039/c9ob02539a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
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Affiliation(s)
- Sebastian Götze
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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12
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Jayanetti DR, Braun DR, Barns KJ, Rajski SR, Bugni TS. Bulbiferates A and B: Antibacterial Acetamidohydroxybenzoates from a Marine Proteobacterium, Microbulbifer sp. JOURNAL OF NATURAL PRODUCTS 2019; 82:1930-1934. [PMID: 31181927 PMCID: PMC6660402 DOI: 10.1021/acs.jnatprod.9b00312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Here we report the discovery of two new 3-acetamido-4-hydroxybenzoate esters, bulbiferates A (1) and B (2), isolated from Microbulbifer sp. cultivated from the marine tunicate Ecteinascidia turbinata. The structures of 1 and 2 were determined by analysis of 2D NMR and MS data. Additionally, three synthetic analogues (3-5), differing in ester sizes/lengths, were prepared for the purposes of evaluating potential structure-activity relationships; no clear correlations tying ester lengths to activity were evident. Bulbiferates A (1) and B (2) demonstrated antibacterial activity against both Escherichia coli (E. coli) and methicillin-sensitive Staphylococcus aureus (MSSA), whereas the synthetic analogues 3 and 4 displayed activity only against MSSA.
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Affiliation(s)
- Dinith R. Jayanetti
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Kenneth J. Barns
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Scott Raymond Rajski
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
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13
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Zhao P, Xue Y, Gao W, Li J, Zu X, Fu D, Feng S, Bai X, Zuo Y, Li P. Actinobacteria-Derived peptide antibiotics since 2000. Peptides 2018; 103:48-59. [PMID: 29567053 DOI: 10.1016/j.peptides.2018.03.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 11/23/2022]
Abstract
Members of the Actinobacteria, including Streptomyces spp., Kutzneria sp. Actinoplanes spp., Actinomycete sp., Nocardia sp., Brevibacteriumsp.,Actinomadura spp., Micromonospora sp., Amycolatopsis spp., Nonomuraea spp., Nocardiopsis spp., Marinactinospora sp., Rhodococcus sp., Lentzea sp., Actinokineospora sp., Planomonospora sp., Streptomonospora sp., and Microbacterium sp., are an important source of structurally diverse classes of short peptides of ∼30 residues or fewer that will likely play an important role in new antibiotic development and discovery. Additionally, many have unique structures that make them recalcitrant to traditional modes of drug resistance via novel mechanisms, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic is urgent, and this review summarizes 199 Actinobacteria compounds published since 2000, including 35 cyclic lipopeptides containing piperazic or pipecolic acids, eight aromatic peptides, five glycopeptides, 21 bicyclic peptides, 44 other cyclic lipopeptides, five linear lipopeptides, six 2,5-diketopiperazines, one dimeric peptide, four nucleosidyl peptides, two thioamide-containing peptides, 25 thiopeptides, nine lasso peptides, and 34 typical cyclic peptides. The current and potential therapeutic applications of these peptides, including their structure, antituberculotic, antibacterial, antifungal, antiviral, anti-brugia, anti-plasmodial, and anti-trypanosomal activities, are discussed.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Dongliao Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shuxiao Feng
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yanjun Zuo
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ping Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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14
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Zhang F, Barns K, Hoffmann FM, Braun DR, Andes DR, Bugni TS. Thalassosamide, a Siderophore Discovered from the Marine-Derived Bacterium Thalassospira profundimaris. JOURNAL OF NATURAL PRODUCTS 2017; 80:2551-2555. [PMID: 28840714 PMCID: PMC5740872 DOI: 10.1021/acs.jnatprod.7b00328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Here we describe the rapid identification and prioritization of novel active marine natural products using an improved dereplication strategy. During the course of our screening of marine natural product libraries, a new cyclic trihydroxamate compound, thalassosamide, was discovered from the α-proteobacterium Thalassospira profundimaris. Its structure was determined by 2D NMR and MS/MS experiments, and the absolute configuration of the lysine-derived units was established by Marfey's analysis, whereas that of C-9, 9', and 9″ was determined via the circular dichroism data of the [Rh2(OCOCF3)4] complex and DFT NMR calculations. Thalassosamide showed moderate in vivo efficacy against Pseudomonas aeruginosa.
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Affiliation(s)
- Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, Wisconsin 53705, United States
| | - Kenneth Barns
- Small Molecule Screening & Synthesis Facility, UW Carbone Cancer Center, Madison, Wisconsin 53792, United States
| | - F. Michael Hoffmann
- Small Molecule Screening & Synthesis Facility, UW Carbone Cancer Center, Madison, Wisconsin 53792, United States
| | - Doug R. Braun
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, Wisconsin 53705, United States
| | - David R. Andes
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, Wisconsin 53705, United States
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15
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Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules. ACS Chem Biol 2017; 12:2157-2163. [PMID: 28617580 DOI: 10.1021/acschembio.7b00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.
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Affiliation(s)
| | - René F. Ramos Alvarenga
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Thomas P. Wyche
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biological
Chemistry and Molecular Pharmacology Department, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | | | | | | | - Charles D. Schwieters
- Center for
Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, United States
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16
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Abstract
Covering: 2015. Previous review: Nat. Prod. Rep., 2016, 33, 382-431This review covers the literature published in 2015 for marine natural products (MNPs), with 1220 citations (792 for the period January to December 2015) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1340 in 429 papers for 2015), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Murray H G Munro
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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