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Lin J, Xiao Y, Liu H, Gao D, Duan Y, Zhu X. Combined transcriptomic and pangenomic analyses guide metabolic amelioration to enhance tiancimycins production. Appl Microbiol Biotechnol 2024; 108:18. [PMID: 38170317 DOI: 10.1007/s00253-023-12937-y] [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: 08/03/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 01/05/2024]
Abstract
Exploration of high-yield mechanism is important for further titer improvement of valuable antibiotics, but how to achieve this goal is challenging. Tiancimycins (TNMs) are anthraquinone-fused enediynes with promising drug development potentials, but their prospective applications are limited by low titers. This work aimed to explore the intrinsic high-yield mechanism in previously obtained TNMs high-producing strain Streptomyces sp. CB03234-S for the further titer amelioration of TNMs. First, the typical ribosomal RpsL(K43N) mutation in CB03234-S was validated to be merely responsible for the streptomycin resistance but not the titer improvement of TNMs. Subsequently, the combined transcriptomic, pan-genomic and KEGG analyses revealed that the significant changes in the carbon and amino acid metabolisms could reinforce the metabolic fluxes of key CoA precursors, and thus prompted the overproduction of TNMs in CB03234-S. Moreover, fatty acid metabolism was considered to exert adverse effects on the biosynthesis of TNMs by shunting and reducing the accumulation of CoA precursors. Therefore, different combinations of relevant genes were respectively overexpressed in CB03234-S to strengthen fatty acid degradation. The resulting mutants all showed the enhanced production of TNMs. Among them, the overexpression of fadD, a key gene responsible for the first step of fatty acid degradation, achieved the highest 21.7 ± 1.1 mg/L TNMs with a 63.2% titer improvement. Our studies suggested that comprehensive bioinformatic analyses are effective to explore metabolic changes and guide rational metabolic reconstitution for further titer improvement of target products. KEY POINTS: • Comprehensive bioinformatic analyses effectively reveal primary metabolic changes. • Primary metabolic changes cause precursor enrichment to enhance TNMs production. • Strengthening of fatty acid degradation further improves the titer of TNMs.
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Affiliation(s)
- Jing Lin
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yu Xiao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Huiming Liu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Die Gao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
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2
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Li W, Ricker R, Lok Chan K, Fung Lau P, Buchbinder NW, Krebs J, Friedrich A, Lin Z, Santos WL, Radius U, Marder TB. Phosphine-catalyzed 1,2-cis-diboration of 1,3-butadiynes. Chemistry 2024:e202401235. [PMID: 38593362 DOI: 10.1002/chem.202401235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024]
Abstract
Trialkyl phosphines PMe3 and PEt3 catalyze the 1,2-cis-diboration of 1,3-butadiynes to give 1,2-diboryl enynes. The products were utilized to synthesize 1,1,2,4-tetraaryl enynes using a Suzuki-Miyaura protocol and can readily undergo proto-deborylation.
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Affiliation(s)
- Weipeng Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Würzburg, 97074, Germany
| | - Robert Ricker
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Würzburg, 97074, Germany
| | - Ka Lok Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Pak Fung Lau
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | | | - Johannes Krebs
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Würzburg, 97074, Germany
| | - Alexandra Friedrich
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Würzburg, 97074, Germany
| | - Zhenyang Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Webster L Santos
- Department of Chemistry Virginia Tech, Blacksburg, VA, 24061, USA
| | - Udo Radius
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Würzburg, 97074, Germany
| | - Todd B Marder
- Institute of Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Würzburg, 97074, Germany
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3
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Im JH, Shin YH, Bae ES, Lee SK, Oh DC. Jejucarbosides B-E, Chlorinated Cycloaromatized Enediynes, from a Marine Streptomyces sp. Mar Drugs 2023; 21:405. [PMID: 37504936 PMCID: PMC10381858 DOI: 10.3390/md21070405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
Four new chlorinated cycloaromatized enediyne compounds, jejucarbosides B-E (1-4), were discovered together with previously-identified jejucarboside A from a marine actinomycete strain. Compounds 1-4 were identified as new chlorinated cyclopenta[a]indene glycosides based on 1D and 2D nuclear magnetic resonance, high-resolution mass spectrometry, and circular dichroism (CD) spectra. Jejucarbosides B and E bear a carbonate functional group whereas jejucarbosides C and D are variants possessing 1,2-diol by losing the carbonate functionality. It is proposed that the production of 1-4 occurs via Bergman cycloaromatization capturing Cl- and H+ in the alternative positions of a p-benzyne intermediate derived from a 9-membered enediyne core. Jejucarboside E (4) displayed significant cytotoxicity against human cancer cell lines including SNU-638, SK-HEP-1, A549, HCT116, and MDA-MB-231, with IC50 values of 0.31, 0.40, 0.25, 0.29, and 0.48 μM, respectively, while jejucarbosides B-D (1-3) showed moderate or no cytotoxic effects.
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Affiliation(s)
- Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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4
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Yancey CE, Yu F, Tripathi A, Sherman DH, Dick GJ. Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie. Appl Environ Microbiol 2023; 89:e0209222. [PMID: 37070981 PMCID: PMC10231183 DOI: 10.1128/aem.02092-22] [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: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/19/2023] Open
Abstract
Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCE Microcystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.
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Affiliation(s)
- Colleen E. Yancey
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Natural Products Discovery Core, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, Michigan, USA
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5
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Iqbal S, Begum F, Rabaan AA, Aljeldah M, Al Shammari BR, Alawfi A, Alshengeti A, Sulaiman T, Khan A. Classification and Multifaceted Potential of Secondary Metabolites Produced by Bacillus subtilis Group: A Comprehensive Review. Molecules 2023; 28:molecules28030927. [PMID: 36770594 PMCID: PMC9919246 DOI: 10.3390/molecules28030927] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Despite their remarkable biosynthetic potential, Bacillus subtilis have been widely overlooked. However, their capability to withstand harsh conditions (extreme temperature, Ultraviolet (UV) and γ-radiation, and dehydration) and the promiscuous metabolites they synthesize have created increased commercial interest in them as a therapeutic agent, a food preservative, and a plant-pathogen control agent. Nevertheless, the commercial-scale availability of these metabolites is constrained due to challenges in their accessibility via synthesis and low fermentation yields. In the context of this rising in interest, we comprehensively visualized the antimicrobial peptides produced by B. subtilis and highlighted their prospective applications in various industries. Moreover, we proposed and classified these metabolites produced by the B. subtilis group based on their biosynthetic pathways and chemical structures. The biosynthetic pathway, bioactivity, and chemical structure are discussed in detail for each class. We believe that this review will spark a renewed interest in the often disregarded B. subtilis and its remarkable biosynthetic capabilities.
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Affiliation(s)
- Sajid Iqbal
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: or
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Pakistan
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Tarek Sulaiman
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Alam Khan
- Department of Life Sciences, Abasyn University Islamabad Campus, Islamabad 44000, Pakistan
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6
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Singh HW, Creamer KE, Chase AB, Klau LJ, Podell S, Jensen PR. Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523365. [PMID: 36711755 PMCID: PMC9882069 DOI: 10.1101/2023.01.09.523365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically important natural products, yet only a small fraction of nature's polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be delineated into different classes and subclasses based on domain organization and structural features of the compounds encoded. Notably, phylogenetic relationships among PKS ketosynthase (KS) domains provide a method to classify the larger and more complex genes in which they occur. Increased access to large metagenomic datasets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through the analysis of KS domain sequences. Here, we used the webtool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse biomes. We found biome-specific separation with soils enriched in modular cis -AT and hybrid cis -AT KSs relative to other biomes and marine sediments enriched in KSs associated with PUFA and enediyne biosynthesis. By extracting full-length KS domains, we linked the phylum Actinobacteria to soil-specific enediyne and cis -AT clades and identified enediyne and monomodular KSs in phyla from which the associated compound classes have not been reported. These sequences were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting novel structures or enzyme functions remain to be discovered. Lastly, we employed our metagenome-extracted KS domains to evaluate commonly used type I KS PCR primers and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries. Importance Polyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis coupled with the accumulation of metagenomic sequence data provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the webtool NaPDoS2 to assess type I PKS diversity and distributions by detecting and classifying KS domains across 137 metagenomes. We show that biomes are differentially enriched in KS domain classes, providing a roadmap for future biodiscovery strategies. Further, KS phylogenies reveal both biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS dataset allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across earth's major biomes.
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7
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Pan J, Tan Q, Zhu S, Yan X, Li Y, Zhuang Z, Zhu X, Duan Y, Huang Y. Discovery of pentaene polyols by the activation of an enediyne gene cluster: biosynthetic implications for 9-membered enediyne core structures. Chem Sci 2022; 13:13475-13481. [PMID: 36507168 PMCID: PMC9682884 DOI: 10.1039/d2sc04379c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022] Open
Abstract
The identification and characterization of enediyne polyketide synthases (PKSEs) revealed that PKSE-bound polyene is a common intermediate, while its subsequent tailoring steps to enediyne cores remain obscure. Herein, we report pentaene polyols 5-7 and cinnamic acid derivatives 8 and 9 biosynthesized from an activated enediyne biosynthetic gene cluster in Streptomyces sp. CB02130. The C-1027 pksE could partially complement production of these polyene polyols in a CB02130 mutant where the native pksE is inactivated. The yields of 5-7 were improved by increasing the cellular pool of l-Phe through either gene inactivation of a prephenate dehydrogenase WlsPDH or supplementation of l-Phe. A flexible ammonia lyase WlsC4 is responsible for biosynthesis of 8 and 9 from l-Phe. The co-localization of wlsPDH and PKSE gene cassette supports their close evolutionary relationships and an enediyne genome mining strategy using WlsPDH. These findings not only provide a facile approach to activate silent enediyne BGCs, but suggest that a polyene epoxide intermediate may be formed for construction of 9-membered enediyne macrocycles.
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Affiliation(s)
- Jian Pan
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Qingwen Tan
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Saibin Zhu
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Xiaohui Yan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China, State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese MedicineTianjinChina
| | - Yu Li
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China,National Engineering Research Center of Combinatorial Biosynthesis for Drug DiscoveryChangshaHunan 410205China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug DiscoveryChangshaHunan 410205China,National Engineering Research Center of Combinatorial Biosynthesis for Drug DiscoveryChangshaHunan 410205China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug DiscoveryChangshaHunan 410205China
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8
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Jos S, Szwetkowski C, Slebodnick C, Ricker R, Chan KL, Chan WC, Radius U, Lin Z, Marder TB, Santos WL. Transition Metal-Free Regio- and Stereo-Selective trans Hydroboration of 1,3-Diynes: A Phosphine-Catalyzed Access to (E)-1-Boryl-1,3-Enynes. Chemistry 2022; 28:e202202349. [PMID: 35917135 PMCID: PMC9804376 DOI: 10.1002/chem.202202349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 01/05/2023]
Abstract
We report a transition metal-free, regio- and stereo-selective, phosphine-catalyzed method for the trans hydroboration of 1,3-diynes with pinacolborane that affords (E)-1-boryl-1,3-enynes. The reaction proceeds with excellent selectivity for boron addition to the external carbon of the 1,3-diyne framework as unambiguously established by NMR and X-ray crystallographic studies. The reaction displays a broad substrate scope including unsymmetrical diynes to generate products in high yield (up to 95 %). Experimental and theoretical studies suggest that phosphine attack on the alkyne is a key process in the catalytic cycle.
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Affiliation(s)
- Swetha Jos
- Department of ChemistryVirginia TechBlacksburgVirginiaUnited States
| | | | - Carla Slebodnick
- Department of ChemistryVirginia TechBlacksburgVirginiaUnited States
| | - Robert Ricker
- Institute of Inorganic ChemistryInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgGermany
| | - Ka Lok Chan
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong SARChina
| | - Wing Chun Chan
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong SARChina
| | - Udo Radius
- Institute of Inorganic ChemistryInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgGermany
| | - Zhenyang Lin
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong SARChina
| | - Todd B. Marder
- Institute of Inorganic ChemistryInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgGermany
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9
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Im JH, Shin D, Ban YH, Byun WS, Bae ES, Lee D, Du YE, Cui J, Kwon Y, Nam SJ, Cha S, Lee SK, Yoon YJ, Oh DC. Targeted Discovery of an Enediyne-Derived Cycloaromatized Compound, Jejucarboside A, from a Marine Actinomycete. Org Lett 2022; 24:7188-7193. [PMID: 36165456 DOI: 10.1021/acs.orglett.2c02934] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A genomic and spectroscopic signature-based search revealed a cycloaromatized enediyne, jejucarboside A (1), from a marine actinomycete strain. The structure of 1 was determined as a new cyclopenta[a]indene glycoside bearing carbonate functionality by nuclear magnetic resonance, high-resolution mass spectrometry (MS), MS/MS, infrared spectroscopy, and a modified Mosher's method. An iterative enediyne synthase pathway has been proposed for the putative biosynthesis of 1 by genomic analysis. Jejucarboside A exhibited cytotoxicity against the HCT116 colon carcinoma cells.
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Affiliation(s)
- Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Donghoon Lee
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yun Kwon
- Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sangwon Cha
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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10
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Gambushe SM, Zishiri OT, El Zowalaty ME. Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective. Infect Drug Resist 2022; 15:4645-4673. [PMID: 36039321 PMCID: PMC9420067 DOI: 10.2147/idr.s365269] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.
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Affiliation(s)
- Sydney M Gambushe
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Oliver T Zishiri
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Mohamed E El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE 75 123, Sweden
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11
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Pasternak A, Bechthold A, Zechel DL. Identification of genes essential for sulfamate and fluorine incorporation during nucleocidin biosynthesis. Chembiochem 2022; 23:e202200140. [PMID: 35544615 DOI: 10.1002/cbic.202200140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/05/2022] [Indexed: 11/07/2022]
Abstract
Nucleocidin is an adenosine derivative containing 4'-fluoro and 5'-O-sulfamoyl substituents. In this study, nucleocidin biosynthesis is examined in two newly discovered producers, Streptomyces virens B-24331 and Streptomyces aureorectus B-24301, which produce nucleocidin and related derivatives at titres 30-fold greater than S. calvus . This enabled the identification of two new O -acetylated nucleocidin derivatives, and a potential glycosyl- O-acetyltransferase. Disruption of nucJ , nucG , and nucI , within S. virens B-24331, specifying a radical SAM / Fe-S dependent enzyme, sulfatase, and arylsulfatase, respectively, led to loss of 5'-O-sulfamoyl biosynthesis, but not fluoronucleoside production. Disruption of nucN , nucK , and nucO specifying an amidinotransferase, and two sulfotransferases respectively, led to loss of fluoronucleoside production. Identification of S. virens B-24331 as a genetically tractable and high producing strain sets the stage for understanding nucleocidin biosynthesis and highlights the utility of using 16S-RNA sequences to identify alternative producers of valuable compounds in the absence of genome sequence data.
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Affiliation(s)
- Aleksandra Pasternak
- Queen's University Faculty of Arts and Science, Chemistry, 90 Bader Lane, Chernoff Hall, K7L 3N6, Kingston, CANADA
| | - Andreas Bechthold
- Albert-Ludwigs-Universität Freiburg Fakultät für Chemie Pharmazie und Geowissenschaften: Albert-Ludwigs-Universitat Freiburg Fakultat fur Chemie und Pharmazie, Pharmaceutical Biology and Biotechnology, Stefan-Meier-Str. 19, 79104, Freiburg i. Br., GERMANY
| | - David L Zechel
- Queen's University, Department of Chemsitry, Chernoff Hall, K7L 3N6, Kingston, CANADA
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12
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Feng X, Liu H, Pan J, Xiong Y, Zhu X, Yan X, Duan Y, Huang Y. Liposome-Encapsulated Tiancimycin A Is Active against Melanoma and Metastatic Breast Tumors: The Effect of cRGD Modification of the Liposomal Carrier and Tiancimycin A Dose on Drug Activity and Toxicity. Mol Pharm 2022; 19:1078-1090. [PMID: 35290067 DOI: 10.1021/acs.molpharmaceut.1c00753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enediyne natural products, including neocarzinostatin and calicheamicin γ1, are used in the form of a copolymer or antibody-drug conjugate to treat hepatomas and leukemia. Tiancimycin (TNM) A is a novel anthraquinone-fused enediyne that can rapidly and completely kill tumor cells. Herein, we encapsulated TNM A in liposomes (Lip-TNM A) and cyclic arginine-glycine-aspartate (cRGD)-functionalized liposomes (cRGD-Lip-TNM A) and demonstrated its antitumor activity using mouse xenografts. Because TNM A causes rapid DNA damage, cell cycle arrest, and apoptosis, these nanoparticles exhibited potent cytotoxicity against multiple tumor cells for 8 h. In B16-F10 and KPL-4 xenografts, both nanoparticles showed superior potency over doxorubicin and trastuzumab. However, cRGD-Lip-TNM A reduced the tumor weight more significantly than Lip-TNM A in B16-F10 xenografts, in which the αvβ3-integrin receptors are significantly overexpressed in this melanoma. Lip-TNM A was slightly more active than cRGD-Lip-TNM A against KPL-4 xenografts, which probably reflected the difference of their in vivo fate in this mouse model. In a highly metastatic 4T1 tumor model, cRGD-Lip-TNM A reduced tumor metastasis induced by losartan, a tumor microenvironment-remodeling agent. These findings suggest that targeted delivery of enediynes with unique modes of action may enable more effective translation of anticancer nanomedicines.
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Affiliation(s)
- Xueqiong Feng
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
| | - Huiming Liu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
| | - Jian Pan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
| | - Yi Xiong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discover, Changsha, Hunan 410011, China
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China.,State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discover, Changsha, Hunan 410011, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
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13
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Chevrette MG, Handelsman J. Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites. Nat Prod Rep 2021; 38:2083-2099. [PMID: 34693961 DOI: 10.1039/d1np00044f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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14
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Bauman KD, Butler KS, Moore BS, Chekan JR. Genome mining methods to discover bioactive natural products. Nat Prod Rep 2021; 38:2100-2129. [PMID: 34734626 PMCID: PMC8597713 DOI: 10.1039/d1np00032b] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/22/2022]
Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
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15
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Abstract
Enediynes are widely studied to understand their cycloaromatization and the trapping of the resulting p-dehydrobenzene diradical. However, few model substrates are known, and they are hard to synthesize and difficult to handle. Herein we report cyclohexeno[3,4]cyclodec-1,5-diyne-3-ene as a convenient model for studying the reactivity of enediynes. It can be easily synthesized from 1,2-diethynylcyclohexene and 1,4-diiodobutane. It is a solid that is stable at room temperature. In solution the p-dehydrobenzene diradical derived from its cycloaromatization can be trapped by nucleophiles. The rate-limiting step is the cyclization, which is slightly slower than that of the parent cyclodec-1,5-diyne-3-ene but faster than that of its benzo analogue, consistent with the distances between the reacting carbon atoms.
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Affiliation(s)
- Annadka Shrinidhi
- Department of Chemistry, University of California-San Diego, La Jolla, California 92093-0358, United States
| | - Charles L Perrin
- Department of Chemistry, University of California-San Diego, La Jolla, California 92093-0358, United States
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16
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Wang Z, Sun R, Li M, Liu L, Duan Y, Huang Y. Yield improvement of enediyne yangpumicins in Micromonospora yangpuensis through ribosome engineering and fermentation optimization. Biotechnol J 2021; 16:e2100250. [PMID: 34473904 DOI: 10.1002/biot.202100250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Abstract
Yangpumicins (YPMs), for example, YPM A, F, and G, are newly discovered enediynes from Micromonospora yangpuensis DSM 45577, which could be exploited as promising payloads of antibody-drug conjugates. However, the low yield of YPMs in the wild-type strain (∼1 mg L-1 ) significantly hampers their further drug development. In this study, a combined ribosome engineering and fermentation optimization strategy has been used for yield improvement of YPMs. One gentamicin-resistant M. yangpuensis DSM 45577 strain (MY-G-1) showed higher YPMs production (7.4 ± 1.0 mg L-1 ), while it exhibits delayed sporulation and slender mycelium under scanning electron microscopy. Whole genome re-sequencing of MY-G-1 reveals several deletion and single nucleotide polymorphism mutations, which were confirmed by PCR and DNA sequencing. Further Box-Behnken experiment and regression analysis determined that the optimal medium concentrations of soluble starch, D-mannitol, and pharmamedia for YPMs production in shaking flasks (10.0 ± 0.8 mg L-1 ). Finally, the total titer of YPM A/F/G in MY-G-1 reached to 15.0 ± 2.5 mg L-1 in 3 L fermenters, which was about 11-fold higher than the original titer of 1.3 ± 0.3 mg L-1 in wild-type strain. Our study may be instrumental to develop YPMs into a clinical anticancer drug, and inspire the use of these multifaceted strategies for yield improvement in Micromonospora species. GRAPHICAL ABSTRACT LAY SUMMARY: ???
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Affiliation(s)
- Zilong Wang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Runze Sun
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Miao Li
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Ling Liu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, China
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17
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18
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Adhikari A, Shen B, Rader C. Challenges and Opportunities to Develop Enediyne Natural Products as Payloads for Antibody-Drug Conjugates. Antib Ther 2021; 4:1-15. [PMID: 33554043 PMCID: PMC7850032 DOI: 10.1093/abt/tbab001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Calicheamicin, the payload of the antibody-drug-conjugates (ADCs) gemtuzumab ozogamicin (Mylotarg®) and inotuzumab ozogamicin (Besponsa®), belongs to the class of enediyne natural products. Since the isolation and structural determination of the neocarzinostatin chromophore in 1985, the enediynes have attracted considerable attention for their value as DNA damaging agents in cancer chemotherapy. Due to their non-discriminatory cytotoxicity towards both cancer and healthy cells, the clinical utilization of enediyne natural products relies on conjugation to an appropriate delivery system, such as an antibody. Here we review the current landscape of enediynes as payloads of first-generation and next-generation ADCs.
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Affiliation(s)
- Ajeeth Adhikari
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA.,Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, FL, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
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19
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Youssef DTA, Almagthali H, Shaala LA, Schmidt EW. Secondary Metabolites of the Genus Didemnum: A Comprehensive Review of Chemical Diversity and Pharmacological Properties. Mar Drugs 2020; 18:E307. [PMID: 32545321 PMCID: PMC7344992 DOI: 10.3390/md18060307] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
Tunicates (ascidians) are common marine invertebrates that are an exceptionally important source of natural products with biomedical and pharmaceutical applications, including compounds that are used clinically in cancers. Among tunicates, the genus Didemnum is important because it includes the most species, and it belongs to the most speciose family (Didemnidae). The genus Didemnum includes the species D. molle, D. chartaceum, D. albopunctatum, and D. obscurum, as well as others, which are well known for their chemically diverse secondary metabolites. To date, investigators have reported secondary metabolites, usually including bioactivity data, for at least 69 members of the genus Didemnum, leading to isolation of 212 compounds. Many of these compounds exhibit valuable biological activities in assays targeting cancers, bacteria, fungi, viruses, protozoans, and the central nervous system. This review highlights compounds isolated from genus Didemnum through December 2019. Chemical diversity, pharmacological activities, geographical locations, and applied chemical methods are described.
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Affiliation(s)
- Diaa T. A. Youssef
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Hadeel Almagthali
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Pharmacognosy, College of Pharmacy, Taif University, Al-Haweiah 21974, Saudi Arabia
| | - Lamiaa A. Shaala
- Natural Products Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Suez Canal University Hospital, Suez Canal University, Ismailia 41522, Egypt
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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20
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Lv J, Gao Y, Zhao H, Awakawa T, Liu L, Chen G, Yao X, Hu D, Abe I, Gao H. Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian‐Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan University Guangzhou 510632 P. R. China
| | - Yao‐Hui Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Huan Zhao
- College of Traditional Chinese Medicine Jinan University Guangzhou 510632 P. R. China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ling Liu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 P. R. China
| | - Guo‐Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Xin‐Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
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21
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Lv J, Gao Y, Zhao H, Awakawa T, Liu L, Chen G, Yao X, Hu D, Abe I, Gao H. Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation. Angew Chem Int Ed Engl 2020; 59:13531-13536. [DOI: 10.1002/anie.202004364] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Jian‐Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan University Guangzhou 510632 P. R. China
| | - Yao‐Hui Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Huan Zhao
- College of Traditional Chinese Medicine Jinan University Guangzhou 510632 P. R. China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ling Liu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 P. R. China
| | - Guo‐Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Xin‐Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
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22
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Genome shuffling based on different types of ribosome engineering mutants for enhanced production of 10-membered enediyne tiancimycin-A. Appl Microbiol Biotechnol 2020; 104:4359-4369. [PMID: 32236679 DOI: 10.1007/s00253-020-10583-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/21/2022]
Abstract
Tiancimycin-A (TNM-A) is an anthraquinone-fused ten-membered enediyne produced by Streptomyces sp. CB03234, which is very promising for the development of anticancer antibody-drug conjugates (ADCs). To improve the titer of TNM-A, we have generated high-producing mutants CB03234-S and CB03234-R through ribosome engineering, but still not sufficient for pilot production of TNM-A. As the follow-up work, gentamycin-induced ribosome engineering was further adopted here to generate the mutant CB03234-G, which produced similar level of TNM-A as in CB03234-S and CB03234-R. Benefiting from the distinct antibiotic resistances of three ribosome engineering mutants, genome shuffling between any two of them was respectively carried out, and finally obtained the recombinant CB03234-GS26. Under optimal conditions, CB03234-GS26 produced 40.6 ± 1.0 mg/L TNM-A in shaking flasks and 20.8 ± 0.4 mg/L in a scaled-up 30-L fermentor. Comparing with the parental high-producing mutants, the over 1.6-fold titer improvement of CB03234-GS26 in fermentor was more promising for pilot production of TNM-A. Besides the distinctive morphological features, genetic characterization revealed that CB03234-GS26 possessed 1.8 kb rsmG related deletion just the same as CB03234-S, but no mutation was found in rpsL. Subsequent knockouts proved that rsmG was unrelated to titer improvement of TNM-A, which implied other genomic variations and mechanisms rather than ribosome engineering to enhance the biosynthesis of TNM-A. Therefore, CB03234-GS26 provided a basis to locate potential novel genetic targets, and explore the interactions between complex metabolic network and TNM biosynthetic pathway, which shall promote future construction of high-yielding systems for TNM-A and other anthraquinone-fused enediynes.Key Points •United genome shuffling and ribosome engineering help further strain improvement. •CB03234-GS26 with improved titer is practical for the pilot production of TNM-A. •Enhanced TNM-A production should attribute to novel genetic features/mechanisms.
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23
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Sarker SD, Nahar L, Miron A, Guo M. Anticancer natural products. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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24
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Kalkreuter E, Pan G, Cepeda AJ, Shen B. Targeting Bacterial Genomes for Natural Product Discovery. Trends Pharmacol Sci 2019; 41:13-26. [PMID: 31822352 DOI: 10.1016/j.tips.2019.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/19/2022]
Abstract
Bacterial natural products (NPs) and their analogs constitute more than half of the new small molecule drugs developed over the past few decades. Despite this success, interest in natural products from major pharmaceutical companies has decreased even as genomics has uncovered the large number of biosynthetic gene clusters (BGCs) that encode for novel natural products. To date, there is still a lack of universal strategies and enabling technologies to discover natural products at scale and speed. This review highlights several of the opportunities provided by genome sequencing and bioinformatics, challenges associated with translating genomes into natural products, and examples of successful strain prioritization and BGC activation strategies that have been used in the genomic era for natural product discovery from cultivatable bacteria.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Alexis J Cepeda
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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25
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Li B, Zhang M, Lu H, Ma H, Wang Y, Chen H, Ding Y, Hu A. Coordination‐Accelerated Radical Formation from Acyclic Enediynes for Tumor Cell Suppression. Chem Asian J 2019; 14:4352-4357. [DOI: 10.1002/asia.201901182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/21/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Baojun Li
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Mengsi Zhang
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Haotian Lu
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Hailong Ma
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Yue Wang
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Huimin Chen
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Yun Ding
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
| | - Aiguo Hu
- Shanghai Key Laboratory of Advanced Polymeric MaterialsSchool of Materials Science and EngineeringEast China University of Science and Technology Shanghai 200237 China
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26
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Martins TP, Rouger C, Glasser NR, Freitas S, de Fraissinette NB, Balskus EP, Tasdemir D, Leão PN. Chemistry, bioactivity and biosynthesis of cyanobacterial alkylresorcinols. Nat Prod Rep 2019; 36:1437-1461. [PMID: 30702733 PMCID: PMC6836626 DOI: 10.1039/c8np00080h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/18/2022]
Abstract
Covering: up to 2019 Alkylresorcinols are amphiphilic metabolites, well-known for their diverse biological activities, produced by both prokaryotes and eukaryotes. A few classes of alkylresorcinol scaffolds have been reported from the photoautotrophic cyanobacteria, ranging from the relatively simple hierridins to the more intricate cylindrocyclophanes. Recently, it has emerged that cyanobacteria employ two different biosynthetic pathways to produce unique alkylresorcinol scaffolds. However, these convergent pathways intersect by sharing biosynthetic elements which lead to common structural motifs. To obtain a broader view of the biochemical diversity of these compounds in cyanobacteria, we comprehensively cover the isolation, structure, biological activity and biosynthesis of their mono- and dialkylresorcinols. Moreover, we provide an overview of the diversity and distribution of alkylresorcinol-generating biosynthetic gene clusters in this phylum and highlight opportunities for discovery of novel alkylresorcinol scaffolds. Because some of these molecules have inspired notable syntheses, different approaches used to build these molecules in the laboratory are showcased.
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Affiliation(s)
- Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)
, University of Porto
,
Matosinhos
, Portugal
.
| | - Caroline Rouger
- Research Unit Marine Natural Products Chemistry
, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech)
, GEOMAR Helmholtz Centre for Ocean Research Kiel
,
Germany
| | - Nathaniel R. Glasser
- Department of Chemistry & Chemical Biology
, Harvard University
,
Cambridge
, MA
, USA
| | - Sara Freitas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)
, University of Porto
,
Matosinhos
, Portugal
.
| | - Nelly B. de Fraissinette
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)
, University of Porto
,
Matosinhos
, Portugal
.
| | - Emily P. Balskus
- Department of Chemistry & Chemical Biology
, Harvard University
,
Cambridge
, MA
, USA
| | - Deniz Tasdemir
- Research Unit Marine Natural Products Chemistry
, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech)
, GEOMAR Helmholtz Centre for Ocean Research Kiel
,
Germany
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)
, University of Porto
,
Matosinhos
, Portugal
.
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27
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Wang Z, Wen Z, Liu L, Zhu X, Shen B, Yan X, Duan Y, Huang Y. Yangpumicins F and G, Enediyne Congeners from Micromonospora yangpuensis DSM 45577. JOURNAL OF NATURAL PRODUCTS 2019; 82:2483-2488. [PMID: 31490685 PMCID: PMC7170010 DOI: 10.1021/acs.jnatprod.9b00229] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enediyne natural products are among the most cytotoxic small molecules and thus excellent payload candidates for the development of antibody-drug conjugates (ADCs). Here we report the isolation and structural elucidation of two new 10-membered anthraquinone-fused enediynes, yangpumicins (YPM) F (6) and G (7), together with five known congeners, YPM A-E (1-5), from Micromonospora yangpuensis DSM 45577. YPM F (6) and G (7) showed strong cytotoxicity against the tested human cancer cell lines, as well as activity against several Gram-positive and Gram-negative pathogens. The 1,2-diols in 6 and 7 promise to enable new linker chemistry for the development of YPM-based ADCs.
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Affiliation(s)
- Zilong Wang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Zhongqing Wen
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Ling Liu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410011, China
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Department of Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, China
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28
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Porter MR, Walker JM, Zaleski JM. The Outliers: Metal-Mediated Radical Reagents for Biological Substrate Degradation. Acc Chem Res 2019; 52:1957-1967. [PMID: 31243967 DOI: 10.1021/acs.accounts.9b00185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The predictable and controllable interaction of small organic or peptidic molecules with biological substrates is the primary reason most pharmaceuticals are narrowly decorated carbon frameworks. The inhibition or activation binding models are measurable and without side reactions that can cause pathological angst. Yet many diseases, especially those involving rapid proliferation of cells (i.e., cancer) or aggregation of peptides (e.g., heart disease, Alzheimer's disease) have not yet been cured by inhibition therapeutics. Additionally, interventional medicine is often required to alleviate such maladies by physical removal first, followed by molecular-level therapy as a second stage. Thus, there appears to be a niche for more aggressive therapeutics that may employ harsher chemical processes to realize clinical efficacy, albeit without causing catastrophic side effects. Molecules that may be considered for this challenge are not typically biomimetic, nor do they fit the traditional pharmaceutical paradigm. They may have unusual modes of action or undesired reactivity that can be lethal if not controlled. These are the outliers; potential pharmacophores that biology does not know how to manage or adapt to. This is why they may be an intriguing class of agents that needs continuous development. In this Account, we connect the under-developed enediyne family of compounds and our metalloenediyne derivatives to existing radical-based therapeutics such as bleomycin and doxorubicin to illustrate that controlled diradical reactivity, although an outlier mechanism, has a place in the therapeutic portfolio. This is self-evident in that of the 11 natural product enediynes known, 2 have clinical impact, a strong ratio. We expand on the chemical diversity of potential enediyne constructs and focus on the accessible trigger mechanisms to activate diradical formation as a method to control toxicity. Moreover, we further illustrate how electromagnetic fields can be employed to activate both molecular and larger nanomaterial constructs that carry highly concentrated payloads of reactive reagent. Finally, we describe how controlled diradical reactivity can reach beyond traditional therapeutic targets such as DNA, to peptide aggregates found in blood clots, neural fibrils, and membrane scaffolds. It is our belief that cleverly constructed frameworks with well-designed and controlled activation/reaction schemes can lead to novel therapeutics that can challenge evolving viral and bacterial invaders. From this evangelical perspective, our hope is that the conceptual framework, if not the specific designs in this Account, stimulate the readership to develop out-of-the-box therapeutic designs that may combat resistant disease targets.
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Affiliation(s)
- Meghan R. Porter
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Joan M. Walker
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jeffrey M. Zaleski
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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29
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Zhuang Z, Jiang C, Zhang F, Huang R, Yi L, Huang Y, Yan X, Duan Y, Zhu X. Streptomycin-induced ribosome engineering complemented with fermentation optimization for enhanced production of 10-membered enediynes tiancimycin-A and tiancimycin-D. Biotechnol Bioeng 2019; 116:1304-1314. [PMID: 30712262 DOI: 10.1002/bit.26944] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 01/01/2023]
Abstract
Tiancimycins (TNMs) are a group of 10-membered anthraquinone-fused enediynes, newly discovered from Streptomyces sp. CB03234. Among them, TNM-A and TNM-D have exhibited excellent antitumor performances and could be exploited as very promising warheads for the development of anticancer antibody-drug conjugates (ADCs). However, their low titers, especially TNM-D, have severely limited following progress. Therefore, the streptomycin-induced ribosome engineering was adopted in this work for strain improvement of CB03234, and a TNMs high producer S. sp. CB03234-S with the K43N mutation at 30S ribosomal protein S12 was successfully screened out. Subsequent media optimization revealed the essential effects of iodide and copper ion on the production of TNMs, while the substitution of nitrogen source could evidently promote the accumulation of TNM-D, and the ratio of produced TNM-A and TNM-D was responsive to the change of carbon and nitrogen ratio in the medium. Further amelioration of the pH control in scaled up 25 L fermentation increased the average titers of TNM-A and TNM-D up to 13.7 ± 0.3 and 19.2 ± 0.4 mg/L, respectively. The achieved over 45-fold titer improvement of TNM-A, and 109-fold total titer improvement of TNM-A and TNM-D enabled the efficient purification of over 200 mg of each target molecule from 25 L fermentation. Our efforts have demonstrated a practical strategy for titer improvement of anthraquinone-fused enediynes and set up a solid base for the pilot scale production and preclinical studies of TNMs to expedite the future development of anticancer ADC drugs.
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Affiliation(s)
- Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Chengzhou Jiang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Fan Zhang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Rong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, China
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30
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Braesel J, Crnkovic CM, Kunstman KJ, Green SJ, Maienschein-Cline M, Orjala J, Murphy BT, Eustáquio AS. Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete. JOURNAL OF NATURAL PRODUCTS 2018; 81:2057-2068. [PMID: 30110167 PMCID: PMC6174880 DOI: 10.1021/acs.jnatprod.8b00394] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Actinomycete bacteria isolated from freshwater environments are an unexplored source of natural products. Here we report the complete genome of the Great Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to close remaining gaps. All identified biosynthetic gene clusters (BGCs) were manually curated. Five known BGCs were identified encoding desferrioxamine, alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and diazepinomicin, which is currently in phase II clinical trials to treat Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006 is indeed a producer of diazepinomicin and at yields higher than previously reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were transcriptionally active under the culture condition tested. Orphan BGCs include an enediyne polyketide synthase and an uncharacteristically large, 36-module polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in the future. This study is one of the few attempts to report the biosynthetic capacity of a freshwater-derived actinomycete and highlights this resource as a potential reservoir for new natural products.
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Affiliation(s)
- Jana Braesel
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Camila M. Crnkovic
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
| | - Kevin J. Kunstman
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, IL 60615, USA
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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31
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Chang CY, Yan X, Crnovcic I, Annaval T, Chang C, Nocek B, Rudolf JD, Yang D, Hindra, Babnigg G, Joachimiak A, Phillips GN, Shen B. Resistance to Enediyne Antitumor Antibiotics by Sequestration. Cell Chem Biol 2018; 25:1075-1085.e4. [PMID: 29937405 DOI: 10.1016/j.chembiol.2018.05.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/04/2018] [Accepted: 05/16/2018] [Indexed: 10/28/2022]
Abstract
The enediynes, microbial natural products with extraordinary cytotoxicities, have been translated into clinical drugs. Two self-resistance mechanisms are known in the enediyne producers-apoproteins for the nine-membered enediynes and self-sacrifice proteins for the ten-membered enediyne calicheamicin. Here we show that: (1) tnmS1, tnmS2, and tnmS3 encode tiancimycin (TNM) resistance in its producer Streptomyces sp. CB03234, (2) tnmS1, tnmS2, and tnmS3 homologs are found in all anthraquinone-fused enediyne producers, (3) TnmS1, TnmS2, and TnmS3 share a similar β barrel-like structure, bind TNMs with nanomolar KD values, and confer resistance by sequestration, and (4) TnmS1, TnmS2, and TnmS3 homologs are widespread in nature, including in the human microbiome. These findings unveil an unprecedented resistance mechanism for the enediynes. Mechanisms of self-resistance in producers serve as models to predict and combat future drug resistance in clinical settings. Enediyne-based chemotherapies should now consider the fact that the human microbiome harbors genes encoding enediyne resistance.
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Affiliation(s)
- Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Thibault Annaval
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Changsoo Chang
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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32
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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33
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Liu L, Pan J, Wang Z, Yan X, Yang D, Zhu X, Shen B, Duan Y, Huang Y. Ribosome engineering and fermentation optimization leads to overproduction of tiancimycin A, a new enediyne natural product from Streptomyces sp. CB03234. J Ind Microbiol Biotechnol 2018; 45:141-151. [PMID: 29396746 DOI: 10.1007/s10295-018-2014-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
Tiancimycin (TNM) A, a recently discovered enediyne natural product from Streptomyces sp. CB03234, showed rapid and complete killing of cancer cells and could be used as a payload in antibody drug conjugates. The low yield of TNM A in the wild-type strain promoted us to use ribosome engineering and fermentation optimization for its yield improvement. The Streptomyces sp. CB03234-R-16 mutant strain with a L422P mutation in RpoB, the RNA polymerase β-subunit, was obtained from the rifamycin-resistant screening. After fermentation optimization, the titers of TNM A in Streptomyces sp. CB03234-R-16 reached to 22.5 ± 3.1 mg L-1 in shaking flasks, and 13 ± 1 mg L-1 in 15 L fermentors, which were at least 40-fold higher than that in the wild-type strain (~ 0.3 mg L-1). Quantitative real-time RT-PCR revealed markedly enhanced expression of key genes encoding TNM A biosynthetic enzymes and regulators in Streptomyces sp. CB03234-R-16. Our study should greatly facilitate the future efforts to develop TNM A into a clinical anticancer drug.
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Affiliation(s)
- Ling Liu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Jian Pan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Zilong Wang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China.,Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China. .,Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China. .,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China.
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China. .,Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China.
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34
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Tracanna V, de Jong A, Medema MH, Kuipers OP. Mining prokaryotes for antimicrobial compounds: from diversity to function. FEMS Microbiol Rev 2018; 41:417-429. [PMID: 28402441 DOI: 10.1093/femsre/fux014] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023] Open
Abstract
The bacterial kingdom provides a major source of antimicrobials that can either be directly applied or used as scaffolds to further improve their functionality in the host. The rapidly increasing amount of bacterial genomic, metabolomic and transcriptomic data offers unique opportunities to apply a variety of approaches to mine for existing and novel antimicrobials. Here, we discuss several powerful mining approaches to identify novel molecules with antimicrobial activity across structurally diverse natural products, including ribosomally synthesized and posttranslationally modified peptides, nonribosomal peptides and polyketides. We not only discuss the direct mining of genomes based on identification of biosynthetic gene clusters, but also describe more advanced and integrative approaches in ecology-based mining, functionality-based mining and mode-of-action-based mining. These efforts are likely to accelerate the discovery and development of novel antimicrobial drugs.
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Affiliation(s)
- Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB Wageningen, The Netherlands
| | - Anne de Jong
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9726AG Groningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB Wageningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9726AG Groningen, The Netherlands
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Ma SY, Xiao YS, Zhang B, Shao FL, Guo ZK, Zhang JJ, Jiao RH, Sun Y, Xu Q, Tan RX, Ge HM. Amycolamycins A and B, Two Enediyne-Derived Compounds from a Locust-Associated Actinomycete. Org Lett 2017; 19:6208-6211. [PMID: 29090939 DOI: 10.1021/acs.orglett.7b03113] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two novel enediyne-derived natural products, amycolamycins A and B (1 and 2), were characterized from a locust-associated actinomycete Amycolatopsis sp. HCa4. Amycolamycins A and B contain a unique 2-(cyclopenta[a]inden-5-yl)oxirane core with suspected enediyne polyketide biosynthetic origin. Sequencing and analysis of the acm biosynthetic gene cluster allowed us to propose the biosynthetic pathway of 1 and 2. Moreover, amycolamycin A (1) was selectively cytotoxic to the M231 breast cancer cell line.
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Affiliation(s)
- Shi Ying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Yong Sheng Xiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Fen Li Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , Hainan 571101, China
| | - Juan Juan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China.,State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine , Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
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Yan X, Chen JJ, Adhikari A, Yang D, Crnovcic I, Wang N, Chang CY, Rader C, Shen B. Genome Mining of Micromonospora yangpuensis DSM 45577 as a Producer of an Anthraquinone-Fused Enediyne. Org Lett 2017; 19:6192-6195. [PMID: 29086572 DOI: 10.1021/acs.orglett.7b03120] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new anthraquinone-fused enediyne, yangpumicin A (YPM A, 1), along with four Bergman cyclization congeners (YPM B-E, 2-5), was isolated from Micromonospora yangpuensis DSM 45577 after mining enediyne biosynthetic gene clusters from public actinobacterial genome databases and prioritizing the hits by an enediyne genome neighborhood network analysis for discovery. YPM A is potent against a broad spectrum of human cancer cell lines. The discovery of 1 provides new opportunities for the functionalization of enediynes to develop new conjugation chemistries for antibody-drug conjugates.
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Affiliation(s)
- Xiaohui Yan
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Jian-Jun Chen
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ajeeth Adhikari
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ivana Crnovcic
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Nan Wang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Chin-Yuan Chang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Christoph Rader
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ben Shen
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
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Annaval T, Rudolf JD, Chang CY, Lohman JR, Kim Y, Bigelow L, Jedrzejczak R, Babnigg G, Joachimiak A, Phillips GN, Shen B. Crystal Structure of Thioesterase SgcE10 Supporting Common Polyene Intermediates in 9- and 10-Membered Enediyne Core Biosynthesis. ACS OMEGA 2017; 2:5159-5169. [PMID: 28884166 PMCID: PMC5579567 DOI: 10.1021/acsomega.7b00933] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/16/2017] [Indexed: 05/04/2023]
Abstract
Enediynes are potent natural product anticancer antibiotics, and are classified as 9- or 10-membered according to the size of their enediyne core carbon skeleton. Both 9- and 10-membered enediyne cores are biosynthesized by the enediyne polyketide synthase (PKSE), thioesterase (TE), and PKSE-associated enzymes. Although the divergence between 9- and 10-membered enediyne core biosynthesis remains unclear, it has been observed that nascent polyketide intermediates, tethered to the acyl carrier protein (ACP) domain of PKSE, could be released by TE in the absence of the PKSE-associated enzymes. In this study, we determined the crystal structure of SgcE10, the TE that participates in the biosynthesis of the 9-membered enediyne C-1027. Structural comparison of SgcE10 with CalE7 and DynE7, two TEs that participate in the biosynthesis of the 10-membered enediynes calicheamicin and dynemicin, respectively, revealed that they share a common α/β hot-dog fold. The amino acids involved in both substrate binding and catalysis are conserved among SgcE10, CalE7, and DynE7. The volume and the shape of the substrate-binding channel and active site in SgcE10, CalE7, and DynE7 confirm that TEs from both 9- and 10-membered enediyne biosynthetic machineries bind the linear form of similar ACP-tethered polyene intermediates. Taken together, these findings further support the proposal that the divergence between 9- and 10-membered enediyne core biosynthesis occurs beyond PKSE and TE catalysis.
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Affiliation(s)
- Thibault Annaval
- Department
of Chemistry, Department of Molecular Medicine, and Natural Products Library Initiative
at The Scripps Research Institute, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Jeffrey D. Rudolf
- Department
of Chemistry, Department of Molecular Medicine, and Natural Products Library Initiative
at The Scripps Research Institute, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Chin-Yuan Chang
- Department
of Chemistry, Department of Molecular Medicine, and Natural Products Library Initiative
at The Scripps Research Institute, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Jeremy R. Lohman
- Department
of Chemistry, Department of Molecular Medicine, and Natural Products Library Initiative
at The Scripps Research Institute, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Youngchang Kim
- Midwest Center for Structural Genomics and Structural Biology
Center, Biosciences
Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Lance Bigelow
- Midwest Center for Structural Genomics and Structural Biology
Center, Biosciences
Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics and Structural Biology
Center, Biosciences
Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics and Structural Biology
Center, Biosciences
Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology
Center, Biosciences
Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
- Department
of Biochemistry and Molecular Biology, University
of Chicago, 929 E. 57th
Street, W225, Chicago, Illinois 60637, United States
| | - George N. Phillips
- BioSciences
at Rice and Department of Chemistry, Rice
University, 6100 Main
Street, Houston, Texas 77251, United States
| | - Ben Shen
- Department
of Chemistry, Department of Molecular Medicine, and Natural Products Library Initiative
at The Scripps Research Institute, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
- E-mail: . Tel: (561) 228-2456. Fax: (561) 228-2472
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Abstract
The enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 enediynes have been structurally characterized to date. Here we report a genome survey of 3,400 actinomycetes, identifying 81 strains that harbor genes encoding the enediyne polyketide synthase cassettes that could be grouped into 28 distinct clades based on phylogenetic analysis. Genome sequencing of 31 representative strains confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster. A genome neighborhood network allows prediction of new structural features and biosynthetic insights that could be exploited for enediyne discovery. We confirmed one clade as new C-1027 producers, with a significantly higher C-1027 titer than the original producer, and discovered a new family of enediyne natural products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a broad spectrum of cancer cell lines. Our results demonstrate the feasibility of rapid discovery of new enediynes from a large strain collection. Recent advances in microbial genomics clearly revealed that the biosynthetic potential of soil actinomycetes to produce enediynes is underappreciated. A great challenge is to develop innovative methods to discover new enediynes and produce them in sufficient quantities for chemical, biological, and clinical investigations. This work demonstrated the feasibility of rapid discovery of new enediynes from a large strain collection. The new C-1027 producers, with a significantly higher C-1027 titer than the original producer, will impact the practical supply of this important drug lead. The TNMs, with their extremely potent cytotoxicity against various cancer cells and their rapid and complete cancer cell killing characteristics, in comparison with the payloads used in FDA-approved antibody-drug conjugates (ADCs), are poised to be exploited as payload candidates for the next generation of anticancer ADCs. Follow-up studies on the other identified hits promise the discovery of new enediynes, radically expanding the chemical space for the enediyne family.
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39
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40
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Huang T, Chang CY, Lohman JR, Rudolf JD, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN, Shen B. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. J Antibiot (Tokyo) 2016; 69:731-740. [PMID: 27406907 PMCID: PMC5083130 DOI: 10.1038/ja.2016.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/30/2016] [Accepted: 06/15/2016] [Indexed: 12/28/2022]
Abstract
Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.
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Affiliation(s)
- Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Changsoo Chang
- Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Shonda Clancy
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA
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41
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Cruz-Morales P, Kopp JF, Martínez-Guerrero C, Yáñez-Guerra LA, Selem-Mojica N, Ramos-Aboites H, Feldmann J, Barona-Gómez F. Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes. Genome Biol Evol 2016; 8:1906-16. [PMID: 27289100 PMCID: PMC4943196 DOI: 10.1093/gbe/evw125] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Natural products from microbes have provided humans with beneficial antibiotics for millennia. However, a decline in the pace of antibiotic discovery exerts pressure on human health as antibiotic resistance spreads, a challenge that may better faced by unveiling chemical diversity produced by microbes. Current microbial genome mining approaches have revitalized research into antibiotics, but the empirical nature of these methods limits the chemical space that is explored. Here, we address the problem of finding novel pathways by incorporating evolutionary principles into genome mining. We recapitulated the evolutionary history of twenty-three enzyme families previously uninvestigated in the context of natural product biosynthesis in Actinobacteria, the most proficient producers of natural products. Our genome evolutionary analyses where based on the assumption that expanded—repurposed enzyme families—from central metabolism, occur frequently and thus have the potential to catalyze new conversions in the context of natural products biosynthesis. Our analyses led to the discovery of biosynthetic gene clusters coding for hidden chemical diversity, as validated by comparing our predictions with those from state-of-the-art genome mining tools; as well as experimentally demonstrating the existence of a biosynthetic pathway for arseno-organic metabolites in Streptomyces coelicolor and Streptomyces lividans, Using a gene knockout and metabolite profile combined strategy. As our approach does not rely solely on sequence similarity searches of previously identified biosynthetic enzymes, these results establish the basis for the development of an evolutionary-driven genome mining tool termed EvoMining that complements current platforms. We anticipate that by doing so real ‘chemical dark matter’ will be unveiled.
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Affiliation(s)
- Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Johannes Florian Kopp
- Trace Element Speciation Laboratory (TESLA) College of Physical Sciences, Aberdeen, Scotland, UK
| | | | | | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Hilda Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Jörg Feldmann
- Trace Element Speciation Laboratory (TESLA) College of Physical Sciences, Aberdeen, Scotland, UK
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, Guanajuato, México
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Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 404] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
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Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
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43
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44
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Rudolf JD, Yan X, Shen B. Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery. J Ind Microbiol Biotechnol 2016; 43:261-76. [PMID: 26318027 PMCID: PMC4753101 DOI: 10.1007/s10295-015-1671-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/09/2015] [Indexed: 01/24/2023]
Abstract
The enediynes are one of the most fascinating families of bacterial natural products given their unprecedented molecular architecture and extraordinary cytotoxicity. Enediynes are rare with only 11 structurally characterized members and four additional members isolated in their cycloaromatized form. Recent advances in DNA sequencing have resulted in an explosion of microbial genomes. A virtual survey of the GenBank and JGI genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains, implying that enediynes are more common than previously thought. Here we report the construction and analysis of an enediyne genome neighborhood network (GNN) as a high-throughput approach to analyze secondary metabolite gene clusters. Analysis of the enediyne GNN facilitated rapid gene cluster annotation, revealed genetic trends in enediyne biosynthetic gene clusters resulting in a simple prediction scheme to determine 9- versus 10-membered enediyne gene clusters, and supported a genomic-based strain prioritization method for enediyne discovery.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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45
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Tianqin G, Chunlei C, Jingjing W. Synergistic Anti-glioma Effects in Vitro and in Vivo of Enediyne Antibiotic Neocarzinostatin and Paclitaxel via Enhanced Growth Delay and Apoptosis-Induction. Biol Pharm Bull 2016; 39:1623-1630. [DOI: 10.1248/bpb.b16-00285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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47
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Shen B, Hindra H, Yan X, Huang T, Ge H, Yang D, Teng Q, Rudolf JD, Lohman JR. ChemInform Abstract: Enediynes: Exploration of Microbial Genomics to Discover New Anticancer Drug Leads. ACTA ACUST UNITED AC 2015. [DOI: 10.1002/chin.201506306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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