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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024; 41:977-989. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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2
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Han EJ, Seyedsayamdost M. Genome mining for new enediyne antibiotics. Curr Opin Chem Biol 2024; 81:102481. [PMID: 38917732 DOI: 10.1016/j.cbpa.2024.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Enediyne antibiotics epitomize nature's chemical creativity. They contain intricate molecular architectures that are coupled with potent biological activities involving double-stranded DNA scission. The recent explosion in microbial genome sequences has revealed a large reservoir of novel enediynes. However, while hundreds of enediyne biosynthetic gene clusters (BGCs) can be detected, less than two dozen natural products have been characterized to date as many clusters remain silent or sparingly expressed under standard laboratory growth conditions. This review focuses on four distinct strategies, which have recently enabled discoveries of novel enediynes: phenotypic screening from rare sources, biosynthetic manipulation, genomic signature-based PCR screening, and DNA-cleavage assays coupled with activation of silent BGCs via high-throughput elicitor screening. With an abundance of enediyne BGCs and emerging approaches for accessing them, new enediyne natural products and further insights into their biogenesis are imminent.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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3
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, 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
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4
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Han EJ, Lee SR, Townsend CA, Seyedsayamdost MR. Targeted Discovery of Cryptic Enediyne Natural Products via FRET-Coupled High-Throughput Elicitor Screening. ACS Chem Biol 2023; 18:1854-1862. [PMID: 37463302 PMCID: PMC11062413 DOI: 10.1021/acschembio.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences, which have recently accumulated, point to an untapped trove of "cryptic" enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled with high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized 10 cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities, with one of these congeners matching the recently reported jejucarboside. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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5
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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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6
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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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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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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9
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Cheemalamarri C, Batchu UR, Thallamapuram NP, Katragadda SB, Reddy Shetty P. A review on hydroxy anthraquinones from bacteria: crosstalk's of structures and biological activities. Nat Prod Res 2022; 36:6186-6205. [PMID: 35175877 DOI: 10.1080/14786419.2022.2039920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Anthraquinones (AQ), unveiling large structural diversity, among polyketides demonstrate a wide range of applications. The hydroxy anthraquinones (HAQ), a group of anthraquinone derivatives, are secondary metabolites produced by bacteria and eukaryotes. Plant-based HAQ are well-studied unlike bacterial HAQ and applied as herbal medicine for centuries. Bacteria are known to synthesize a wide variety of structurally diversified HAQ through polyketide pathways using polyketide synthases (I, II & III) principally through polyketide synthase-II. The actinobacteria especially the genus Streptomyces and Micromonospora represent a rich source of HAQ, however novel HAQ are reported from the rare actinobacteria genera (Salinospora, Actinoplanes, Amycoloptosis, Verrucosispora, Xenorhabdus, and Photorhabdus. Though several reviews are available on AQ produced by plants and fungi, however none on bacterial AQ. The current review focused on sources of bacterial HAQ and their structural diversity and biological activities along with toxicity and side effects.
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Affiliation(s)
- Chandrasekhar Cheemalamarri
- Medicinal Chemistry and Biotechnology Lab- Organic Synthesis and Process Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, India.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India
| | - Uma Rajeswari Batchu
- Medicinal Chemistry and Biotechnology Lab- Organic Synthesis and Process Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, India
| | - Nagendra Prasad Thallamapuram
- Medicinal Chemistry and Biotechnology Lab- Organic Synthesis and Process Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, India
| | - Suresh Babu Katragadda
- Centre for natural products and traditional knowledge, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, India
| | - Prakasham Reddy Shetty
- Medicinal Chemistry and Biotechnology Lab- Organic Synthesis and Process Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, India
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10
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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: 47] [Impact Index Per Article: 15.7] [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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11
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Abstract
Covering: up to the end of July, 2021Anthraquinone-fused enediynes (AFEs) are a subfamily of enediyne natural products. Dynemicin A (DYN A), the first member of the AFE family, was discovered more than thirty years ago. Subsequently, extensive studies have been reported on the mode of action and the interactions of AFEs with DNA using DYN A as a model. However, progress in the discovery, biosynthesis and clinical development of AFEs has been limited for a long time. In the past five years, four new AFEs have been discovered and significant progress has been made in the biosynthesis of AFEs, especially on the biogenesis of the anthraquinone moiety and their tailoring steps. Moreover, the streamlined total synthesis of AFEs and their analogues boosts the preparation of AFE-based linker-drugs, thus enabling the development of AFE-based antibody-drug conjugates (ADCs). This review summarizes the discovery, mechanism of action, biosynthesis, total synthesis and preclinical studies of AFEs.
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Affiliation(s)
- Xiaohui Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, China.
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12
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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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13
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Ma GL, Tran HT, Low ZJ, Candra H, Pang LM, Cheang QW, Fang M, Liang ZX. Pathway Retrofitting Yields Insights into the Biosynthesis of Anthraquinone-Fused Enediynes. J Am Chem Soc 2021; 143:11500-11509. [PMID: 34293863 DOI: 10.1021/jacs.1c03911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Anthraquinone-fused enediynes (AQEs) are renowned for their distinctive molecular architecture, reactive enediyne warhead, and potent anticancer activity. Although the first members of AQEs, i.e., dynemicins, were discovered three decades ago, how their nitrogen-containing carbon skeleton is synthesized by microbial producers remains largely a mystery. In this study, we showed that the recently discovered sungeidine pathway is a "degenerative" AQE pathway that contains upstream enzymes for AQE biosynthesis. Retrofitting the sungeidine pathway with genes from the dynemicin pathway not only restored the biosynthesis of the AQE skeleton but also produced a series of novel compounds likely as the cycloaromatized derivatives of chemically unstable biosynthetic intermediates. The results suggest a cascade of highly surprising biosynthetic steps leading to the formation of the anthraquinone moiety, the hallmark C8-C9 linkage via alkyl-aryl cross-coupling, and the characteristic epoxide functionality. The findings provide unprecedented insights into the biosynthesis of AQEs and pave the way for examining these intriguing biosynthetic enzymes.
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Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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14
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Discovery of a Dual Function Cytochrome P450 that Catalyzes Enyne Formation in Cyclohexanoid Terpenoid Biosynthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Chen Y, Naresh A, Liang S, Lin C, Chein R, Lin H. Discovery of a Dual Function Cytochrome P450 that Catalyzes Enyne Formation in Cyclohexanoid Terpenoid Biosynthesis. Angew Chem Int Ed Engl 2020; 59:13537-13541. [DOI: 10.1002/anie.202004435] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Yu‐Rong Chen
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | | | - Suh‐Yuen Liang
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | - Chun‐Hung Lin
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | - Rong‐Jie Chein
- Institute of Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | - Hsiao‐Ching Lin
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
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16
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Low ZJ, Ma GL, Tran HT, Zou Y, Xiong J, Pang L, Nuryyeva S, Ye H, Hu JF, Houk KN, Liang ZX. Sungeidines from a Non-canonical Enediyne Biosynthetic Pathway. J Am Chem Soc 2020; 142:1673-1679. [PMID: 31922407 DOI: 10.1021/jacs.9b10086] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the genome-guided discovery of sungeidines, a class of microbial secondary metabolites with unique structural features. Despite evolutionary relationships with dynemicin-type enediynes, the sungeidines are produced by a biosynthetic gene cluster (BGC) that exhibits distinct differences from known enediyne BGCs. Our studies suggest that the sungeidines are assembled from two octaketide chains that are processed differently than those of the dynemicin-type enediynes. The biosynthesis also involves a unique activating sulfotransferase that promotes a dehydration reaction. The loss of genes, including a putative epoxidase gene, is likely to be the main cause of the divergence of the sungeidine pathway from other canonical enediyne pathways. The findings disclose the surprising evolvability of enediyne pathways and set the stage for characterizing the intriguing enzymatic steps in sungeidine biosynthesis.
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Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Guang-Lei Ma
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Hoa Thi Tran
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Yike Zou
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Juan Xiong
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore.,School of Pharmacy , Fudan University , Shanghai 200433 , China
| | - Limei Pang
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Selbi Nuryyeva
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Hong Ye
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Jin-Feng Hu
- School of Pharmacy , Fudan University , Shanghai 200433 , China
| | - K N Houk
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Zhao-Xun Liang
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
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17
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Teijaro CN, Adhikari A, Shen B. Challenges and opportunities for natural product discovery, production, and engineering in native producers versus heterologous hosts. J Ind Microbiol Biotechnol 2019; 46:433-444. [PMID: 30426283 PMCID: PMC6405299 DOI: 10.1007/s10295-018-2094-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/19/2018] [Indexed: 10/27/2022]
Abstract
Recent advances and emerging technologies for metabolic pathway engineering and synthetic biology have transformed the field of natural product discovery, production, and engineering. Despite these advancements, there remain many challenges in understanding how biosynthetic gene clusters are silenced or activated, including changes in the transcription of key biosynthetic and regulatory genes. This knowledge gap is highlighted by the success and failed attempts of manipulating regulatory genes within biosynthetic gene clusters in both native producers and heterologous hosts. These complexities make the choice of native producers versus heterologous hosts, fermentation medium, and supply of precursors crucial factors in achieving the production of the target natural products and engineering designer analogs. Nature continues to serve as inspiration for filling the knowledge gaps and developing new research strategies. By exploiting the evolutionary power of nature, alternative producers, with the desired genetic amenability and higher titers of the target natural products, and new strains, harboring gene clusters that encode evolutionary optimized congeners of the targeted natural product scaffolds, can be discovered. These newly identified strains can serve as an outstanding biotechnology platform for the engineered production of sufficient quantities of the target natural products and their analogs, enabling biosynthetic studies and potential therapeutic applications. These challenges and opportunities are showcased herein using fredericamycin, iso-migrastatin, platencin and platensimycin, the enediynes of C-1027, tiancimycin, and yangpumicin, and the leinamycin family of natural products.
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Affiliation(s)
- Christiana N Teijaro
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ajeeth Adhikari
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
- Department of Molecular Medicine, 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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18
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Yan X, Chen JJ, Adhikari A, Teijaro CN, Ge H, Crnovcic I, Chang CY, Annaval T, Yang D, Rader C, Shen B. Comparative Studies of the Biosynthetic Gene Clusters for Anthraquinone-Fused Enediynes Shedding Light into the Tailoring Steps of Tiancimycin Biosynthesis. Org Lett 2018; 20:5918-5921. [PMID: 30212211 DOI: 10.1021/acs.orglett.8b02584] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Comparative analyses of the four known anthraquinone-fused enediynes biosynthetic gene clusters identified four genes, tnmE6, tnmH, tnmL, and tnmQ, unique to the tnm gene cluster. Larger scale fermentation of both the S. sp. CB03234 wild-type and the Δ tnmH and Δ tnmL mutant strains resulted in the characterization of 20 new tiancimycin (TNM) congeners, including five enediynes. These findings enabled a proposal for the late stage of TNM biosynthesis featuring an intermediate possibly common for all anthraquinone-fused enediynes.
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19
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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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20
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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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21
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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22
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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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23
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Lee JTD, Zhao Y. Access to Acyclic Z
-Enediynes by Alkyne Trimerization: Cooperative Bimetallic Catalysis Using Air as the Oxidant. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jin Tu Danence Lee
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Yu Zhao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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24
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Access to Acyclic Z
-Enediynes by Alkyne Trimerization: Cooperative Bimetallic Catalysis Using Air as the Oxidant. Angew Chem Int Ed Engl 2016; 55:13872-13876. [DOI: 10.1002/anie.201608192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 12/16/2022]
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25
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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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26
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Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:034702. [PMID: 27191010 PMCID: PMC4851618 DOI: 10.1063/1.4948539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.
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Affiliation(s)
- Hongnan Cao
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Lance Bigelow
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | | | - Robert Jedrzejczak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Gyorgy Babnigg
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA
| | - Andrzej Joachimiak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Madan K Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Shanteri Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - George N Phillips
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
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27
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Li W, Li X, Huang T, Teng Q, Crnovcic I, Rader C, Shen B. Engineered production of cancer targeting peptide (CTP)-containing C-1027 in Streptomyces globisporus and biological evaluation. Bioorg Med Chem 2016; 24:3887-3892. [PMID: 27094150 DOI: 10.1016/j.bmc.2016.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/25/2022]
Abstract
Conjugation of cancer targeting peptides (CTPs) with small molecular therapeutics has emerged as a promising strategy to deliver potent (but typically nonspecific) cytotoxic agents selectively to cancer cells. Here we report the engineered production of a CTP (NGR)-containing C-1027 and evaluation of its activity against selected cancer cell lines. C-1027 is an enediyne chromoprotein produced by Streptomyces globisporus, consisting of an apo-protein (CagA) and an enediyne chromophore (C-1027). NGR is a CTP that targets CD13 in tumor vasculature. S. globisporus SB1026, a recombinant strain engineered to encode CagA with the NGR sequence fused at its C-terminus, directly produces the NGR-containing C-1027 that is equally active as the native C-1027. Our results demonstrate the feasibility to produce CTP-containing enediyne chromoproteins by metabolic pathway engineering and microbial fermentation and will inspire efforts to engineer other CTP-containing drug binding proteins for targeted delivery.
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Affiliation(s)
- Wenli Li
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, WI 53705, USA
| | - Xiuling Li
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Qihui Teng
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, WI 53705, USA; 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 at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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28
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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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29
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Williams DE, Bottriell H, Davies J, Tietjen I, Brockman MA, Andersen RJ. Unciaphenol, an Oxygenated Analogue of the Bergman Cyclization Product of Uncialamycin Exhibits Anti-HIV Activity. Org Lett 2015; 17:5304-7. [DOI: 10.1021/acs.orglett.5b02664] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David E. Williams
- Departments of Chemistry and Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Helen Bottriell
- Departments of Chemistry and Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Julian Davies
- Life
Sciences Institute, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Ian Tietjen
- Faculty
of Health Sciences and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Mark A. Brockman
- Faculty
of Health Sciences and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
- British
Columbia Centre for Excellence in HIV/AIDS, St. Paul’s Hospital, Vancouver, BC, Canada V6Z 1Y6
| | - Raymond J. Andersen
- Departments of Chemistry and Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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30
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Shen B, Hindra, Yan X, Huang T, Ge H, Yang D, Teng Q, Rudolf JD, Lohman JR. Enediynes: Exploration of microbial genomics to discover new anticancer drug leads. Bioorg Med Chem Lett 2015; 25:9-15. [PMID: 25434000 PMCID: PMC4480864 DOI: 10.1016/j.bmcl.2014.11.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022]
Abstract
The enediyne natural products have been explored for their phenomenal cytotoxicity. The development of enediynes into anticancer drugs has been successfully achieved through the utilization of polymer- and antibody-drug conjugates (ADCs) as drug delivery systems. An increasing inventory of enediynes would benefit current application of ADCs in many oncology programs. Innovations in expanding the enediyne inventory should take advantage of the current knowledge of enediyne biosynthesis and post-genomics technologies. Bioinformatics analysis of microbial genomes reveals that enediynes are underexplored, in particular from Actinomycetales. This digest highlights the emerging opportunities to explore microbial genomics for the discovery of novel enediyne natural products.
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Affiliation(s)
- 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.
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Huiming Ge
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Qihui Teng
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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31
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Cinar ME, Morbach G, Schmittel M. Thermal reactivity of neutral and oxidized ferrocenyl-substituted enediynes. Molecules 2014; 19:18399-413. [PMID: 25397734 PMCID: PMC6271431 DOI: 10.3390/molecules191118399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 11/16/2022] Open
Abstract
The coupling of two equivalents of ethynylferrocene (2) with one equivalent of 1,2-diiodocyclohexene (1) and 1,2-diiodobenzene (4) using Sonogashira cross-coupling conditions led to 1,2-bis(ferrocenylethynyl)cyclohexene (3) and 1,2-bis(ferrocenylethy-nyl)benzene (5), respectively. At high temperatures enediynes 3 and 5 showed exothermic signals in differential scanning calorimetry (DSC) measurements, suggestive of intramolecular diradicaloid ring formation (Bergman (C1-C6) or Schreiner-Pascal (C1-C5) cyclizations). The oxidation of 3 and 5 to the mono-oxidized enediynes 3+ and 5+ decreased the onset temperatures drastically. Equally, 1-ferrocenylethynyl-2-(p-nitro-phenyl)ethynylbenzene (8) displayed a significant decrease in the onset temperature after oxidation to 8+. Because the insoluble nature of the polymeric material formed in the thermolysis of the oxidized enediynes prevented characterization, the origin of this drastic effect was studied by DFT. Contrary to expectations, one-electron oxidation does not lower the barrier for intramolecular cyclization. Rather, the computations suggest that the polymerization is initiated by a bimolecular process.
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Affiliation(s)
- Mehmet Emin Cinar
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str., Siegen D-57068, Germany
| | - Guido Morbach
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str., Siegen D-57068, Germany
| | - Michael Schmittel
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str., Siegen D-57068, Germany.
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32
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Elshahawi SI, Ramelot TA, Seetharaman J, Chen J, Singh S, Yang Y, Pederson K, Kharel MK, Xiao R, Lew S, Yennamalli RM, Miller MD, Wang F, Tong L, Montelione GT, Kennedy MA, Bingman CA, Zhu H, Phillips GN, Thorson JS. Structure-guided functional characterization of enediyne self-sacrifice resistance proteins, CalU16 and CalU19. ACS Chem Biol 2014; 9:2347-58. [PMID: 25079510 PMCID: PMC4201346 DOI: 10.1021/cb500327m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Calicheamicin γ1I (1)
is an enediyne antitumor compound produced by Micromonospora
echinospora spp. calichensis, and its biosynthetic gene cluster
has been previously reported. Despite extensive analysis and biochemical
study, several genes in the biosynthetic gene cluster of 1 remain functionally unassigned. Using a structural genomics approach
and biochemical characterization, two proteins encoded by genes from
the 1 biosynthetic gene cluster assigned as “unknowns”,
CalU16 and CalU19, were characterized. Structure analysis revealed
that they possess the STeroidogenic Acute Regulatory protein related
lipid Transfer (START) domain known mainly to bind and transport lipids
and previously identified as the structural signature of the enediyne
self-resistance protein CalC. Subsequent study revealed calU16 and calU19 to confer resistance to 1, and reminiscent of the prototype CalC, both CalU16 and CalU19 were
cleaved by 1in vitro. Through site-directed
mutagenesis and mass spectrometry, we identified the site of cleavage
in each protein and characterized their function in conferring resistance
against 1. This report emphasizes the importance of structural
genomics as a powerful tool for the functional annotation of unknown
proteins.
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Affiliation(s)
- Sherif I. Elshahawi
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Theresa A. Ramelot
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Jayaraman Seetharaman
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry & Center for Structural Biology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Shanteri Singh
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yunhuang Yang
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Kari Pederson
- Complex Carbohydrate
Research Center, Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602, United States
| | - Madan K. Kharel
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Rong Xiao
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology
and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Scott Lew
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Ragothaman M. Yennamalli
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Mitchell D. Miller
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Fengbin Wang
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Liang Tong
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Gaetano T. Montelione
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology
and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Michael A. Kennedy
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Craig A. Bingman
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry & Center for Structural Biology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - George N. Phillips
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Jon S. Thorson
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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33
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Chen X, Ji R, Jiang X, Yang R, Liu F, Xin Y. Iterative type I polyketide synthases involved in enediyne natural product biosynthesis. IUBMB Life 2014; 66:587-95. [PMID: 25278375 DOI: 10.1002/iub.1316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/14/2014] [Indexed: 12/12/2022]
Abstract
Enediyne natural products are potent antibiotics structurally characterized by an enediyne core containing two acetylenic groups conjugated to a double bond in a 9- or 10-membered carbocycle. The biosynthetic gene clusters for enediynes encode a novel iterative type I polyketide synthase (PKSE), which is generally believed to initiate the biosynthetic process of enediyne cores. This review article will cover research efforts made since its discovery to elucidate the role of the PKSE in enediyne core biosynthesis. Topics covered include the unique domain architecture, identification, and characterization of turnover products, and interaction with partner thioesterase protein.
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Affiliation(s)
- Xiaolei Chen
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
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34
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Danilkina NA, Kulyashova AE, Khlebnikov AF, Bräse S, Balova IA. Electrophilic Cyclization of Aryldiacetylenes in the Synthesis of Functionalized Enediynes Fused to a Heterocyclic Core. J Org Chem 2014; 79:9018-45. [DOI: 10.1021/jo501396s] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- N. A. Danilkina
- Institute
of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, 198504 Saint Petersburg, Russia
| | - A. E. Kulyashova
- Institute
of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, 198504 Saint Petersburg, Russia
| | - A. F. Khlebnikov
- Institute
of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, 198504 Saint Petersburg, Russia
| | - S. Bräse
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology, Campus South, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - I. A. Balova
- Institute
of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, 198504 Saint Petersburg, Russia
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35
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Ge HM, Huang T, Rudolf JD, Lohman JR, Huang SX, Guo X, Shen B. Enediyne polyketide synthases stereoselectively reduce the β-ketoacyl intermediates to β-D-hydroxyacyl intermediates in enediyne core biosynthesis. Org Lett 2014; 16:3958-61. [PMID: 25019332 PMCID: PMC4144755 DOI: 10.1021/ol501767v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
PKSE
biosynthesizes an enediyne core precursor from decarboxylative
condensation of eight malonyl-CoAs. The KR domain of PKSE is responsible
for iterative β-ketoreduction in each round of polyketide chain
elongation. KRs from selected PKSEs were investigated in vitro with
β-ketoacyl-SNACs as substrate mimics. Each of the KRs reduced
the β-ketoacyl-SNACs stereoselectively, all affording the corresponding
β-d-hydroxyacyl-SNACs, and the catalytic efficiencies
(kcat/KM)
of the KRs increased significantly as the chain length of the β-ketoacyl-SNAC
substrate increases.
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Affiliation(s)
- Hui-Ming Ge
- Department of Chemistry, ‡Department of Molecular Therapeutics, and §Natural Products Library Initiatives, The Scripps Research Institute , Jupiter, Florida 33458, United States
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36
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Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014; 53:5423-6. [DOI: 10.1002/anie.201402623] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 02/06/2023]
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38
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Increasing appendage diversity on 3,4-dihydro-3-oxo-2H-1,4-benzoxazines via Aphos–Pd(OAc)2-catalyzed Suzuki–Miyaura cross-coupling of aryl chlorides. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.09.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Kraka E, Cremer D. Enediynes, enyne-allenes, their reactions, and beyond. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1174] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry; Southern Methodist University; Dallas TX USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group, Department of Chemistry; Southern Methodist University; Dallas TX USA
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40
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Belecki K, Townsend CA. Biochemical determination of enzyme-bound metabolites: preferential accumulation of a programmed octaketide on the enediyne polyketide synthase CalE8. J Am Chem Soc 2013; 135:14339-48. [PMID: 24041368 DOI: 10.1021/ja406697t] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite considerable interest in the enediyne family of antitumor antibiotics, assembly of their polyketide core structures in nature remains poorly understood. Discriminating methods to access enzyme-bound intermediates are critical for elucidating unresolved polyketide and nonribosomal peptide biosynthetic pathways. Here, we describe the development of broadly applicable techniques for the mild chemical release and analysis of intermediates bound to carrier proteins (CPs), providing access to these species even in sensitive systems. These techniques were applied to CalE8, the polyketide synthase (PKS) involved in calicheamicin biosynthesis, facilitating the unambiguous identification of enzyme-bound polyketides on an enediyne PKS. Moreover, these methods enabled the preparation of fully unloaded CalE8, providing a "clean slate" for reconstituted activity and allowing us to demonstrate the preferential accumulation of a PKS-bound octaketide with evidence of programmed processing control by CalE8. This intermediate, which has the expected chain length for enediyne core construction, could previously only be indirectly inferred. These studies prove that this polyketide is an authentic product of CalE8 and may be a key precursor to the enediyne core of calicheamicin, as it is the only programmed, enzyme-bound species observed for any enediyne system to date. Our experimental advances into a generally inaccessible system illustrate the utility of these techniques for investigating CP-based biosynthetic pathways.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University , Remsen 252, 3400 North Charles St., Baltimore, Maryland 21218, United States
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41
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Horsman GP, Lechner A, Ohnishi Y, Moore BS, Shen B. Predictive model for epoxide hydrolase-generated stereochemistry in the biosynthesis of nine-membered enediyne antitumor antibiotics. Biochemistry 2013; 52:5217-24. [PMID: 23844627 DOI: 10.1021/bi400572a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nine-membered enediyne antitumor antibiotics C-1027, neocarzinostatin (NCS), and kedarcidin (KED) possess enediyne cores to which activity-modulating peripheral moieties are attached via (R)- or (S)-vicinal diols. We have previously shown that this stereochemical difference arises from hydrolysis of epoxide precursors by epoxide hydrolases (EHs) with different regioselectivities. The inverting EHs, such as SgcF, hydrolyze an (S)-epoxide substrate to yield an (R)-diol in C-1027 biosynthesis, whereas the retaining EHs, such as NcsF2 and KedF, hydrolyze an (S)-epoxide substrate to yield an (S)-diol in NCS and KED biosynthesis. We now report the characterization of a series of EH mutants and provide a predictive model for EH regioselectivity in the biosynthesis of the nine-membered enediyne antitumor antibiotics. A W236Y mutation in SgcF increased the retaining activity toward (S)-styrene oxide by 3-fold, and a W236Y/Q237M double mutation in SgcF, mimicking NcsF2 and KedF, resulted in a 20-fold increase in the retaining activity. To test the predictive utility of these mutations, two putative enediyne biosynthesis-associated EHs were identified by genome mining and confirmed as inverting enzymes, SpoF from Salinospora tropica CNB-440 and SgrF (SGR_625) from Streptomyces griseus IFO 13350. Finally, phylogenetic analysis of EHs revealed a familial classification according to inverting versus retaining activity. Taken together, these results provide a predictive model for vicinal diol stereochemistry in enediyne biosynthesis and set the stage for further elucidating the origins of EH regioselectivity.
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Affiliation(s)
- Geoffrey P Horsman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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42
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Gerber HP, Koehn FE, Abraham RT. The antibody-drug conjugate: an enabling modality for natural product-based cancer therapeutics. Nat Prod Rep 2013; 30:625-39. [PMID: 23525375 DOI: 10.1039/c3np20113a] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Antibody Drug Conjugate (ADC) is a therapeutic modality consisting of a monoclonal antibody attached to a cytotoxic, small-molecule payload. The antibody portion of the ADC serves as a transport vehicle that recognizes and binds to a protein antigen expressed in tumor tissues. The localized delivery and release of the payload within or near malignant cells allows for targeted delivery of a potent cytotoxic agent to diseased tissue, while reducing damage to antigen-negative, normal tissues. Recent years have witnessed an explosive increase in ADC-based therapies, due mainly to clinical reports of activity in both hematologic and epithelial cancers. Accompanying this upsurge in ADC development is a renewed interest in natural product cytotoxins, which are typically highly potent cell-killing agents, but suffer from poor drug-like properties and narrow safety margins when systemically administered as conventional chemotherapeutics. In this review, we discuss recent advances related to the construction of ADCs, the optimization of ADC safety and efficacy, and the increasingly pivotal roles of natural product payloads in the current and future landscape of ADC therapy.
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Affiliation(s)
- Hans-Peter Gerber
- Pfizer Worldwide Research and Development, Oncology Research Unit, 401 Middletown Road, Pearl River, NY, USA.
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43
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Zhang Q, Pang B, Ding W, Liu W. Aromatic Polyketides Produced by Bacterial Iterative Type I Polyketide Synthases. ACS Catal 2013. [DOI: 10.1021/cs400211x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qi Zhang
- State Key
Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Bo Pang
- State Key
Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wei Ding
- State Key
Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key
Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy
of Sciences, 345 Lingling Road, Shanghai 200032, China
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44
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Kersten RD, Lane AL, Nett M, Richter TKS, Duggan BM, Dorrestein PC, Moore BS. Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica. Chembiochem 2013; 14:955-62. [PMID: 23649992 DOI: 10.1002/cbic.201300147] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 12/27/2022]
Abstract
The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.
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Affiliation(s)
- Roland D Kersten
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA
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Lane AL, Nam SJ, Fukuda T, Yamanaka K, Kauffman CA, Jensen PR, Fenical W, Moore BS. Structures and comparative characterization of biosynthetic gene clusters for cyanosporasides, enediyne-derived natural products from marine actinomycetes. J Am Chem Soc 2013; 135:4171-4. [PMID: 23458364 PMCID: PMC3611589 DOI: 10.1021/ja311065v] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyanosporasides are marine bacterial natural products containing a chlorinated cyclopenta[a]indene core of suspected enediyne polyketide biosynthetic origin. Herein, we report the isolation and characterization of novel cyanosporasides C-F (3-6) from the marine actinomycetes Salinispora pacifica CNS-143 and Streptomyces sp. CNT-179, highlighted by the unprecedented C-2' N-acetylcysteamine functionalized hexose group of 6. Cloning, sequencing, and mutagenesis of homologous ~50 kb cyanosporaside biosynthetic gene clusters from both bacteria afforded the first genetic evidence supporting cyanosporaside's enediyne, and thereby p-benzyne biradical, biosynthetic origin and revealed the molecular basis for nitrile and glycosyl functionalization. This study provides new opportunities for bioengineering of enediyne derivatives and expands the structural diversity afforded by enediyne gene clusters.
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Affiliation(s)
- Amy L. Lane
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Sang Jip Nam
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Takashi Fukuda
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Kazuya Yamanaka
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Christopher A. Kauffman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
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Lohman JR, Huang SX, Horsman GP, Dilfer PE, Huang T, Chen Y, Wendt-Pienkowski E, Shen B. Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics. MOLECULAR BIOSYSTEMS 2013; 9:478-91. [PMID: 23360970 DOI: 10.1039/c3mb25523a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enediyne natural product biosynthesis is characterized by a convergence of multiple pathways, generating unique peripheral moieties that are appended onto the distinctive enediyne core. Kedarcidin (KED) possesses two unique peripheral moieties, a (R)-2-aza-3-chloro-β-tyrosine and an iso-propoxy-bearing 2-naphthonate moiety, as well as two deoxysugars. The appendage pattern of these peripheral moieties to the enediyne core in KED differs from the other enediynes studied to date with respect to stereochemical configuration. To investigate the biosynthesis of these moieties and expand our understanding of enediyne core formation, the biosynthetic gene cluster for KED was cloned from Streptoalloteichus sp. ATCC 53650 and sequenced. Bioinformatics analysis of the ked cluster revealed the presence of the conserved genes encoding for enediyne core biosynthesis, type I and type II polyketide synthase loci likely responsible for 2-aza-l-tyrosine and 3,6,8-trihydroxy-2-naphthonate formation, and enzymes known for deoxysugar biosynthesis. Genes homologous to those responsible for the biosynthesis, activation, and coupling of the l-tyrosine-derived moieties from C-1027 and maduropeptin and of the naphthonate moiety from neocarzinostatin are present in the ked cluster, supporting 2-aza-l-tyrosine and 3,6,8-trihydroxy-2-naphthoic acid as precursors, respectively, for the (R)-2-aza-3-chloro-β-tyrosine and the 2-naphthonate moieties in KED biosynthesis.
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Affiliation(s)
- Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
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Belecki K, Townsend CA. Environmental Control of the Calicheamicin Polyketide Synthase Leads to Detection of a Programmed Octaketide and a Proposal for Enediyne Biosynthesis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Belecki K, Townsend CA. Environmental control of the calicheamicin polyketide synthase leads to detection of a programmed octaketide and a proposal for enediyne biosynthesis. Angew Chem Int Ed Engl 2012; 51:11316-9. [PMID: 23042574 DOI: 10.1002/anie.201206462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Indexed: 11/09/2022]
Abstract
A light in the dark: the fermentation products of the polyketide synthase CalE8 (without its cognate thioesterase) were identified and gave some insight into the elusive early steps of calicheamicin biosynthesis. Fermentation in either the light or dark resulted in different proportions of a new octaketide and led to an updated mechanistic proposal.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
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Liew CW, Nilsson M, Chen MW, Sun H, Cornvik T, Liang ZX, Lescar J. Crystal structure of the acyltransferase domain of the iterative polyketide synthase in enediyne biosynthesis. J Biol Chem 2012; 287:23203-15. [PMID: 22589546 DOI: 10.1074/jbc.m112.362210] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biosynthesis of the enediyne natural product dynemicin in Micromonospora chersina is initiated by DynE8, a highly reducing iterative type I polyketide synthase that assembles polyketide intermediates from the acetate units derived solely from malonyl-CoA. To understand the substrate specificity and the evolutionary relationship between the acyltransferase (AT) domains of DynE8, fatty acid synthase, and modular polyketide synthases, we overexpressed a 44-kDa fragment of DynE8 (hereafter named AT(DYN10)) encompassing its entire AT domain and the adjacent linker domain. The crystal structure at 1.4 Å resolution unveils a α/β hydrolase and a ferredoxin-like subdomain with the Ser-His catalytic dyad located in the cleft between the two subdomains. The linker domain also adopts a α/β fold abutting the AT catalytic domain. Co-crystallization with malonyl-CoA yielded a malonyl-enzyme covalent complex that most likely represents the acyl-enzyme intermediate. The structure explains the preference for malonyl-CoA with a conserved arginine orienting the carboxylate group of malonate and several nonpolar residues that preclude α-alkyl malonyl-CoA binding. Co-crystallization with acetyl-CoA revealed two noncovalently bound acetates generated by the enzymatic hydrolysis of acetyl-CoA that acts as an inhibitor for DynE8. This suggests that the AT domain can upload the acyl groups from either malonyl-CoA or acetyl-CoA onto the catalytic Ser(651) residue. However, although the malonyl group can be transferred to the acyl carrier protein domain, transfer of the acetyl group to the acyl carrier protein domain is suppressed. Local structural differences may account for the different stability of the acyl-enzyme intermediates.
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Affiliation(s)
- Chong Wai Liew
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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Piel J. Approaches to capturing and designing biologically active small molecules produced by uncultured microbes. Annu Rev Microbiol 2012; 65:431-53. [PMID: 21682647 DOI: 10.1146/annurev-micro-090110-102805] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria are one of the most important sources of bioactive natural products for drug discovery. Yet, in most habitats only a small percentage of all existing prokaryotes is amenable to cultivation and chemical study. There is strong evidence that the uncultivated diversity represents an enormous resource of novel biosynthetic enzymes and secondary metabolites. In addition, many animal-derived drug candidates that are structurally characterized but difficult to access seem to be produced by uncultivated, symbiotic bacteria. This review provides an overview about established and emerging techniques for the investigation and exploitation of the environmental metabolome. These include metagenomic library construction and screening, heterologous expression, community sequencing, and single-cell methods. Such tools, the advantages and shortcomings of which are discussed, have just begun to reveal the full metabolic potential of free-living and symbiotic bacteria, providing exciting new avenues for natural product research and environmental microbiology.
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Affiliation(s)
- Jörn Piel
- Kekulé Insitute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany.
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