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Wahi A, Jain P, Sinhari A, Jadhav HR. Progress in discovery and development of natural inhibitors of histone deacetylases (HDACs) as anti-cancer agents. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:675-702. [PMID: 37615708 DOI: 10.1007/s00210-023-02674-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
The study of epigenetic translational modifications had drawn great interest for the last few decades. These processes play a vital role in many diseases and cancer is one of them. Histone acetyltransferase (HAT) and histone deacetylases (HDACs) are key enzymes involved in the acetylation and deacetylation of histones and ultimately in post-translational modifications. Cancer frequently exhibits epigenetic changes, particularly disruption in the expression and activity of HDACs. It includes the capacity to regulate proliferative signalling, circumvent growth inhibitors, escape cell death, enable replicative immortality, promote angiogenesis, stimulate invasion and metastasis, prevent immunological destruction, and genomic instability. The majority of tumours develop and spread as a result of HDAC dysregulation. As a result, HDAC inhibitors (HDACis) were developed, and they today stand as a very promising therapeutic approach. One of the most well-known and efficient therapies for practically all cancer types is chemotherapy. However, the efficiency and safety of treatment are constrained by higher toxicity. The same has been observed with the synthetic HDACi. Natural products, owing to many advantages over synthetic compounds for cancer treatment have always been a choice for therapy. Hence, naturally available molecules are of particular interest for HDAC inhibition and HDAC has drawn the attention of the research fraternity due to their potential to offer a diverse array of chemical structures and bioactive compounds. This diversity opens up new avenues for exploring less toxic HDAC inhibitors to reduce side effects associated with conventional synthetic inhibitors. The review presents comprehensive details on natural product HDACi, their mechanism of action and their biological effects. Moreover, this review provides a brief discussion on the structure activity relationship of selected natural HDAC inhibitors and their analogues which can guide future research to discover selective, more potent HDACi with minimal toxicity.
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Affiliation(s)
- Abhishek Wahi
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, DPSRU, New Delhi, 110017, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, DPSRU, New Delhi, 110017, India.
| | - Apurba Sinhari
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333031, India
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333031, India
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Bai X, Chen H, Ren X, Zhong L, Wang X, Ji X, Zhang Y, Wang Y, Bian X. Heterologous Biosynthesis of Complex Bacterial Natural Products in Burkholderia gladioli. ACS Synth Biol 2023; 12:3072-3081. [PMID: 37708405 DOI: 10.1021/acssynbio.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Bacterial natural products (NPs) are an indispensable source of drugs and biopesticides. Heterologous expression is an essential method for discovering bacterial NPs and the efficient biosynthesis of valuable NPs, but the chassis for Gram-negative bacterial NPs remains inadequate. In this study, we built a Burkholderiales mutant Burkholderia gladioli Δgbn::attB by introducing an integrated site (attB) to inactivate the native gladiolin (gbn) biosynthetic gene cluster, which stabilizes large foreign gene clusters and reduces the native metabolite profile. The growth and successful heterologous production of high-value NPs such as phylogenetically close Burkholderiales-derived antitumor polyketides (PKs) rhizoxins, phylogenetically distant Gammaproteobacteria-derived anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotics WAP-8294As, and Deltaproteobacteria-derived antitumor PKs disorazols demonstrate that this strain is a potential chassis for Gram-negative bacterial NPs. We further improved the yields of WAP-8294As through promoter insertions and precursor pathway overexpression based on heterologous expression in this strain. This study provides a robust bacterial chassis for genome mining, efficient production, and molecular engineering of bacterial NPs.
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Affiliation(s)
- Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiangmei Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoqi Ji
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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3
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Gong K, Wang M, Duan Q, Li G, Yong D, Ren C, Li Y, Zhang Q, Wang Z, Sun T, Zhang H, Tu Q, Wu C, Fu J, Li A, Song C, Zhang Y, Li R. High-yield production of FK228 and new derivatives in a Burkholderia chassis. Metab Eng 2023; 75:131-142. [PMID: 36528227 DOI: 10.1016/j.ymben.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
FK228 (romidepsin) is the only natural histone deacetylases (HDACs) inhibitor approved by FDA to treat cutaneous and peripheral T-cell lymphoma. However, the limited supply and severe cardiotoxicity of FK228 underscore the importance to develop an effective synthetic biology platform for the manufacturing and fine-tuning of this drug lead. In this work, we constructed a Burkholderia chassis for the high-yield production of FK228-family (unnatural) natural products. By virtue of the optimized Burkholderia-specific recombineering system, the biosynthetic gene cluster (BGC) encoding the FK228-like skeleton thailandepsins (tdp) in Burkholderia thailandensis E264 was replaced with an attB integration site to afford the basal chassis KOGC1. The tdp BGC directly captured from E264 was hybridized with the FK228-encoding BGC (dep) using the versatile Red/ET technology. The hybrid BGC (tdp-dep) was integrated into the attB site of KOGC1, resulting in the heterologous expression of FK228. Remarkably, the titer reached 581 mg/L, which is 30-fold higher than that of native producer Chromobacterium violaceum No. 968. This success encouraged us to further engineer the NRPS modules 4 or 6 of hybrid tdp-dep BGC by domain units swapping strategy, and eight new FK228 derivatives (1-8) varying in the composition of amino acids were generated. Especially, the titers of 2 and 3 in KOGC1 were up to 985 mg/L and 453 mg/L, respectively. 2 and 3 displayed stronger cytotoxic activity than FK228. All in all, this work established a robust platform to produce FK228 and its new derivatives in sufficient quantities for anticancer drug development.
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Affiliation(s)
- Kai Gong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Maoqin Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiong Duan
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy, Qingdao University, Qingdao, Shandong, China
| | - Daojing Yong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Cailing Ren
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Yue Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qijun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Zongjie Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Tao Sun
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Huanyun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiang Tu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Changsheng Wu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
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Narita K. [Synthetic Study on Bicyclic Depsipeptides Containing an Intramolecular Disulfide Bond]. YAKUGAKU ZASSHI 2022; 142:917-926. [PMID: 36047217 DOI: 10.1248/yakushi.22-00091] [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: 11/22/2022]
Abstract
Bicyclic depsipeptide natural products containing an intramolecular disulfide bond are potent histone deacetylase (HDAC) inhibitors. Among them, FK228 (romidepsin) is approved for treating cutaneous T-cell lymphoma and peripheral T-cell lymphoma. This study focused on developing a new synthesis method for producing this class of natural products for use as HDAC inhibitors with high efficacy and low toxicity. In this paper, the total syntheses of FK228 as well as spiruchostatins A and B are described. The synthesis routes include a convergent way to assemble seco-acids via the amide condensation of amine segments with carboxylic acid segments. The syntheses of C4- and C7-modified FK228 analogs (FK-A1 to FK-A8) are also described. The evaluation of HDAC and cell growth inhibitory activities of the synthesized analogs revealed novel aspects of their structure-activity relationship. Potent and highly isoform-selective HDAC1 inhibitors were identified. Furthermore, the analogs showed phosphatidylinositol 3-kinase (PI3K) inhibitory activity. Structural optimization of the analogs as HDAC/PI3K dual inhibitors led to the identification of FK-A11 as the most potent analog.
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Affiliation(s)
- Koichi Narita
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University
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5
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Aiosa N, Sinha A, Jaiyesimi OA, da Silva RR, Branda SS, Garg N. Metabolomics Analysis of Bacterial Pathogen Burkholderia thailandensis and Mammalian Host Cells in Co-culture. ACS Infect Dis 2022; 8:1646-1662. [PMID: 35767828 DOI: 10.1021/acsinfecdis.2c00233] [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: 11/28/2022]
Abstract
The Tier 1 HHS/USDA Select Agent Burkholderia pseudomallei is a bacterial pathogen that is highly virulent when introduced into the respiratory tract and intrinsically resistant to many antibiotics. Transcriptomic- and proteomic-based methodologies have been used to investigate mechanisms of virulence employed by B. pseudomallei and Burkholderia thailandensis, a convenient surrogate; however, analysis of the pathogen and host metabolomes during infection is lacking. Changes in the metabolites produced can be a result of altered gene expression and/or post-transcriptional processes. Thus, metabolomics complements transcriptomics and proteomics by providing a chemical readout of a biological phenotype, which serves as a snapshot of an organism's physiological state. However, the poor signal from bacterial metabolites in the context of infection poses a challenge in their detection and robust annotation. In this study, we coupled mammalian cell culture-based metabolomics with feature-based molecular networking of mono- and co-cultures to annotate the pathogen's secondary metabolome during infection of mammalian cells. These methods enabled us to identify several key secondary metabolites produced by B. thailandensis during infection of airway epithelial and macrophage cell lines. Additionally, the use of in silico approaches provided insights into shifts in host biochemical pathways relevant to defense against infection. Using chemical class enrichment analysis, for example, we identified changes in a number of host-derived compounds including immune lipids such as prostaglandins, which were detected exclusively upon pathogen challenge. Taken together, our findings indicate that co-culture of B. thailandensis with mammalian cells alters the metabolome of both pathogen and host and provides a new dimension of information for in-depth analysis of the host-pathogen interactions underlying Burkholderia infection.
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Affiliation(s)
- Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Anupama Sinha
- Biotechnology & Bioengineering, Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Olakunle A Jaiyesimi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Ricardo R da Silva
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Av. do Café─Vila Monte Alegre, 14040-903 Ribeirão Preto-SP, Brazil
| | - Steven S Branda
- Systems Biology, Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, ES&T, Atlanta, Georgia 30332, United States
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6
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Frühauf A, Meyer-Almes FJ. Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases. Molecules 2021; 26:5151. [PMID: 34500583 PMCID: PMC8434074 DOI: 10.3390/molecules26175151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Histone deacetylases (HDACs) remove acetyl groups from acetylated lysine residues and have a large variety of substrates and interaction partners. Therefore, it is not surprising that HDACs are involved in many diseases. Most inhibitors of zinc-dependent HDACs (HDACis) including approved drugs contain a hydroxamate as a zinc-binding group (ZBG), which is by far the biggest contributor to affinity, while chemical variation of the residual molecule is exploited to create more or less selectivity against HDAC isozymes or other metalloproteins. Hydroxamates have a propensity for nonspecificity and have recently come under considerable suspicion because of potential mutagenicity. Therefore, there are significant concerns when applying hydroxamate-containing compounds as therapeutics in chronic diseases beyond oncology due to unwanted toxic side effects. In the last years, several alternative ZBGs have been developed, which can replace the critical hydroxamate group in HDACis, while preserving high potency. Moreover, these compounds can be developed into highly selective inhibitors. This review aims at providing an overview of the progress in the field of non-hydroxamic HDACis in the time period from 2015 to present. Formally, ZBGs are clustered according to their binding mode and structural similarity to provide qualitative assessments and predictions based on available structural information.
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Affiliation(s)
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany;
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Brosowsky J, Lutterbeck M, Liebich A, Keller M, Herp D, Vogelmann A, Jung M, Breit B. Syntheses of Thailandepsin B Pseudo-Natural Products: Access to New Highly Potent HDAC Inhibitors via Late-Stage Modification. Chemistry 2020; 26:16241-16245. [PMID: 32725698 PMCID: PMC7756392 DOI: 10.1002/chem.202002449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Indexed: 01/08/2023]
Abstract
New Thailandepsin B pseudo‐natural products have been prepared. Our synthetic strategy offers the possibility to introduce varying warheads via late stage modification. Additionally, it gives access to the asymmetric branched allylic ester moiety of the natural product in a highly diastereoselective manner applying rhodium‐catalyzed hydrooxycarbonylation. The newly developed pseudo‐natural products are extremely potent and selective HDAC inhibitors. The non‐proteinogenic amino acid d‐norleucine was obtained enantioselectively by a recently developed method of rhodium‐catalyzed hydroamination.
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Affiliation(s)
- Jana Brosowsky
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Monika Lutterbeck
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Amelie Liebich
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Manfred Keller
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Daniel Herp
- Institut für Pharmazeutische WissenschaftenAlbert-Ludwigs-Universität FreiburgAlbertstr. 2579104FreiburgGermany
| | - Anja Vogelmann
- Institut für Pharmazeutische WissenschaftenAlbert-Ludwigs-Universität FreiburgAlbertstr. 2579104FreiburgGermany
| | - Manfred Jung
- Institut für Pharmazeutische WissenschaftenAlbert-Ludwigs-Universität FreiburgAlbertstr. 2579104FreiburgGermany
| | - Bernhard Breit
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
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Custom Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometric Database for Identification of Environmental Isolates of the Genus Burkholderia and Related Genera. Appl Environ Microbiol 2020; 86:AEM.00354-20. [PMID: 32245762 DOI: 10.1128/aem.00354-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/13/2020] [Indexed: 11/20/2022] Open
Abstract
Success of discovery programs for microbial natural products is dependent on quick and concise discrimination between isolates from diverse environments. However, laboratory isolation and identification of priority genera using current 16S rRNA PCR-based methods are both challenging and time-consuming. An emerging strategy for rapid isolate discrimination is protein fingerprinting via matrix-assisted laser desorption ionization (MALDI) mass spectrometry. Using our in-house environmental isolate repository, we have created a main spectral (MSP) library for the Bruker Biotyper MALDI mass spectrometer that contains 95 entries, including Burkholderia, Caballeronia, Paraburkholderia, and other environmentally related genera. The library creation required the acquisition of over 2,250 mass spectra, which were manually reviewed for quality control and consolidated into a single reference library using a commercial software platform. We tested the effectiveness of the reference library by analyzing 49 environmental isolate strains using two different sample preparation methods. Overall, this approach correctly identified all strains to the genus level provided that suitable reference spectra were present in the MSP library. In this study, we present a fast, accurate method for taxonomic assignment of environmentally derived bacteria from the order Burkholderiales, providing a valuable alternative to traditional PCR-based methods. The MSP library described in the manuscript is available for use.IMPORTANCE The Gram-negative proteobacterial order Burkholderiales has emerged as a promising source of novel natural products in recent years. This order includes the genus Burkholderia and the newly defined genera Caballeronia and Paraburkholderia However, development of this resource has been hampered by difficulties with rapid and selective isolation of Burkholderiales strains from the environment. Environmental metagenome sequencing has revealed that the potential for natural products is not evenly distributed throughout the microbial world. Thus, large but targeted microbial isolate libraries are needed to effectively explore the chemical potential of natural products. To study these organisms efficiently, methods to quickly identify isolates to the genus level are required. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is already used in clinical settings to reliably identify unknown bacterial pathogens. We have adapted similar methodology using the MALDI Biotyper instrument to rapidly identify environmental isolates of Burkholderia, Caballeronia, and Paraburkholderia for downstream natural product discovery.
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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Chen H, Bian Z, Ravichandran V, Li R, Sun Y, Huo L, Fu J, Bian X, Xia L, Tu Q, Zhang Y. Biosynthesis of polyketides by trans-AT polyketide synthases in Burkholderiales. Crit Rev Microbiol 2019; 45:162-181. [PMID: 31218924 DOI: 10.1080/1040841x.2018.1514365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Widely used as drugs and agrochemicals, polyketides are a family of bioactive natural products, with diverse structures and functions. Polyketides are produced by megaenzymes termed as polyketide synthases (PKSs). PKS biosynthetic pathways are divided into the cis-AT PKSs and trans-AT PKSs; a division based mainly on the absence of an acyltransferase (AT) domain in the trans-AT PKS modules. In trans-AT biosynthesis, the AT activity is contributed via one or several independent proteins, and there are few other characteristics that distinguish trans-AT PKSs from cis-AT PKSs, especially in the formation of the β-branch. The trans-AT PKSs constitute a major PKS pathway, and many are found in Burkholderia species, which are prevalent in the environment and prolific sources of polyketides. This review summarizes studies from 1973 to 2017 on the biosynthesis of natural products by trans-AT PKSs from Burkholderia species.
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Affiliation(s)
- Hanna Chen
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China.,b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| | - Zhilong Bian
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Vinothkannan Ravichandran
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Ruijuan Li
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Yi Sun
- c Institute of Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , People's Republic of China
| | - Liujie Huo
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Jun Fu
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Xiaoying Bian
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Liqiu Xia
- b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| | - Qiang Tu
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Youming Zhang
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China.,b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
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11
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Liu X, Currens GC, Xue L, Cheng YQ. Origin and bioactivities of thiosulfinated FK228. MEDCHEMCOMM 2019; 10:538-542. [PMID: 31057733 DOI: 10.1039/c9md00060g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/14/2019] [Indexed: 11/21/2022]
Abstract
During a large laboratory-scale purification of FK228 from the fermentation broth of Burkholderia thailandensis MSMB43, a small amount of thiosulfinated FK228 (TS-FK228) was unexpectedly purified only after the broth was mixed with silica gel. Evidence supports the postulations that TS-FK228 was derived from FK228 through spontaneous chemical reaction with silica gel, and TS-FK228 existed as two isomers 1 and 2. TS-FK228 demonstrated similar inhibitory activity and profile against human class I histone deacetylases but exhibited a much higher antiproliferative activity against representative human cancer cell lines when compared to FK228.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Blvd , Fort Worth , TX 76107 , USA . ; ; Tel: +817 735 0165
| | - Grant C Currens
- UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Blvd , Fort Worth , TX 76107 , USA . ; ; Tel: +817 735 0165
| | - Liang Xue
- Alcon NMR laboratory at Novartis , 6201 South Fwy , Fort Worth , TX 76134 , USA
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Blvd , Fort Worth , TX 76107 , USA . ; ; Tel: +817 735 0165
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12
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A selective genome-guided method for environmental Burkholderia isolation. J Ind Microbiol Biotechnol 2019; 46:345-362. [PMID: 30680473 DOI: 10.1007/s10295-018-02121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMART protocol, we have developed a two-stage isolation protocol for strains from the genus Burkholderia. This method uses a combination of selective agar isolation media and multiplexed PCR profiling to derive Burkholderia strains from environmental samples with 95% efficiency. Creation of this new method paves the way for the systematic exploration of natural products chemistry from this important genus and offers new insight into potential methods for selective isolation method development for other priority genera.
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13
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Lascano S, Lopez M, Arimondo PB. Natural Products and Chemical Biology Tools: Alternatives to Target Epigenetic Mechanisms in Cancers. CHEM REC 2018; 18:1854-1876. [PMID: 30537358 DOI: 10.1002/tcr.201800133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
Abstract
DNA methylation and histone acetylation are widely studied epigenetic modifications. They are involved in numerous pathologies such as cancer, neurological disease, inflammation, obesity, etc. Since the discovery of the epigenome, numerous compounds have been developed to reverse DNA methylation and histone acetylation aberrant profile in diseases. Among them several were inspired by Nature and have a great interest as therapeutic molecules. In the quest of finding new ways to target epigenetic mechanisms, the use of chemical tools is a powerful strategy to better understand epigenetic mechanisms in biological systems. In this review we will present natural products reported as DNMT or HDAC inhibitors for anticancer treatments. We will then discuss the use of chemical tools that have been used in order to explore the epigenome.
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Affiliation(s)
- Santiago Lascano
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier-ENSCM, 240 avenue du Prof. E. Jeanbrau, 34296, Montpellier cedex 5, France
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier-ENSCM, 240 avenue du Prof. E. Jeanbrau, 34296, Montpellier cedex 5, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, 28 rue du Docteur Roux, 75724, Paris cedex 15, France
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14
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Liu X, Xie F, Doughty LB, Wang Q, Zhang L, Liu X, Cheng YQ. Genomics-guided discovery of a new and significantly better source of anticancer natural drug FK228. Synth Syst Biotechnol 2018; 3:268-274. [PMID: 30417143 PMCID: PMC6222137 DOI: 10.1016/j.synbio.2018.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 11/28/2022] Open
Abstract
FK228 is an FDA-approved anticancer drug naturally produced by Chromobacterium violaceum No. 968 up to 19 mg/L in a pilot industry-scale batch fermentation. Here we report a genomics-guided discovery of Burkholderia thailandensis MSMB43 as a new and significantly better source of FK228. The genome of B. thailandensis MSMB43 was found to contain a functional biosynthetic gene cluster highly homologous to that of FK228 in C. violaceum No. 968, and the bacterium indeed produces authentic FK228. By simple fermentation in shaking flasks in a preferred M8 medium, B. thailandensis MSMB43 produced FK228 up to 67.7 mg/L; by fed-batch fermentation in a 20-L fermentor in M8 medium, B. thailandensis MSMB43 produced FK228 up to 115.9 mg/L, which is 95 fold higher than that of C. violaceum No. 968 under the same laboratory fermentation conditions. RT-PCR analysis indicated that the high FK228 yield of B. thailandensis MSMB43 was due to high expression of biosynthetic genes, represented by Bth_depA, during the fermentation process. Further genetic manipulation resulted in a recombinant strain, B. thailandensis MSMB43/pBMTL3-tdpR, which harbors a broad host-range vector expressing the thailandepsin biosynthetic pathway regulatory gene tdpR. This engineered strain produced up to 168.5 mg/L of FK228 in fed-batch fermentation in a 20-L fermentor in M8 medium. Therefore, the wild-type B. thailandensis MSMB43 or its engineered derivative could potentially be a good starting point for an industrial process to improve FK228 production for its expanding use in therapy.
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Affiliation(s)
- Xiangyang Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.,UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Feng Xie
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Leah B Doughty
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Qi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.,Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
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15
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Zagni C, Floresta G, Monciino G, Rescifina A. The Search for Potent, Small-Molecule HDACIs in Cancer Treatment: A Decade After Vorinostat. Med Res Rev 2017; 37:1373-1428. [PMID: 28181261 DOI: 10.1002/med.21437] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022]
Abstract
Histone deacetylases (HDACs) play a crucial role in the remodeling of chromatin, and are involved in the epigenetic regulation of gene expression. In the last decade, inhibition of HDACs came out as a target for specific epigenetic changes associated with cancer and other diseases. Until now, more than 20 HDAC inhibitors (HDACIs) have entered clinical studies, and some of them (e.g., vorinostat, romidepsin) have been approved for the treatment of cutaneous T-cell lymphoma. This review provides an overview of current knowledge, progress, and molecular mechanisms of HDACIs, covering a period from 2011 until 2015.
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Affiliation(s)
- Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Giuseppe Floresta
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy.,Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Giulia Monciino
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
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16
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Maolanon AR, Kristensen HME, Leman LJ, Ghadiri MR, Olsen CA. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes. Chembiochem 2016; 18:5-49. [DOI: 10.1002/cbic.201600519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alex R. Maolanon
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Helle M. E. Kristensen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Luke J. Leman
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - M. Reza Ghadiri
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Christian A. Olsen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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17
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Narita K, Matsuhara K, Itoh J, Akiyama Y, Dan S, Yamori T, Ito A, Yoshida M, Katoh T. Synthesis and biological evaluation of novel FK228 analogues as potential isoform selective HDAC inhibitors. Eur J Med Chem 2016; 121:592-609. [DOI: 10.1016/j.ejmech.2016.05.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 11/25/2022]
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18
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Target engagement and drug residence time can be observed in living cells with BRET. Nat Commun 2015; 6:10091. [PMID: 26631872 PMCID: PMC4686764 DOI: 10.1038/ncomms10091] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/30/2015] [Indexed: 12/18/2022] Open
Abstract
The therapeutic action of drugs is predicated on their physical engagement with cellular targets. Here we describe a broadly applicable method using bioluminescence resonance energy transfer (BRET) to reveal the binding characteristics of a drug with selected targets within intact cells. Cell-permeable fluorescent tracers are used in a competitive binding format to quantify drug engagement with the target proteins fused to Nanoluc luciferase. The approach enabled us to profile isozyme-specific engagement and binding kinetics for a panel of histone deacetylase (HDAC) inhibitors. Our analysis was directed particularly to the clinically approved prodrug FK228 (Istodax/Romidepsin) because of its unique and largely unexplained mechanism of sustained intracellular action. Analysis of the binding kinetics by BRET revealed remarkably long intracellular residence times for FK228 at HDAC1, explaining the protracted intracellular behaviour of this prodrug. Our results demonstrate a novel application of BRET for assessing target engagement within the complex milieu of the intracellular environment.
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19
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Kim B, Hong J. An overview of naturally occurring histone deacetylase inhibitors. Curr Top Med Chem 2015; 14:2759-82. [PMID: 25487010 DOI: 10.2174/1568026615666141208105614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 11/26/2014] [Accepted: 11/29/2014] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) have recently emerged as key elements in epigenetic control of gene expression. Due to the implication of HDACs in a variety of diseases ranging from cancer to neurodegenerative disorder, HDAC inhibitors have received increased attention in recent years. Over the last few decades, a myriad of HDAC inhibitors containing a wide variety of structural features have been identified from natural sources. Here, we review the discovery, synthesis, biological properties, and modes of action of these naturally occurring HDAC inhibitors and consider their implications for future research.
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Affiliation(s)
| | - Jiyong Hong
- Duke University, Department of Chemistry, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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20
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Zhou J, Li M, Chen N, Wang S, Luo HB, Zhang Y, Wu R. Computational design of a time-dependent histone deacetylase 2 selective inhibitor. ACS Chem Biol 2015; 10:687-92. [PMID: 25546141 PMCID: PMC4372102 DOI: 10.1021/cb500767c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Development of isoform-selective
histone deacetylase (HDAC) inhibitors is of great biological and medical
interest. Among 11 zinc-dependent HDAC isoforms, it is particularly
challenging to achieve isoform inhibition selectivity between HDAC1
and HDAC2 due to their very high structural similarities. In this
work, by developing and applying a novel de novo reaction-mechanism-based
inhibitor design strategy to exploit the reactivity difference, we
have discovered the first HDAC2-selective inhibitor, β-hydroxymethyl
chalcone. Our bioassay experiments show that this new compound has
a unique time-dependent selective inhibition on HDAC2, leading to
about 20-fold isoform-selectivity against HDAC1. Furthermore, our
ab initio QM/MM molecular dynamics simulations, a state-of-the-art
approach to study reactions in biological systems, have elucidated
how the β-hydroxymethyl chalcone can achieve the distinct time-dependent
inhibition toward HDAC2.
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Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Min Li
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Nanhao Chen
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Shenglong Wang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Hai-Bin Luo
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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21
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Abstract
Background: Thailandepsin B (TDP-B) is a potent histone deacetylase inhibitor under development. A reliable bioanalytical method for the quantification of TDP-B in plasma samples is required. Results: The stabilizer mixture containing hydrochloric acid, formic acid and dichlorvos was applied to stabilize TDP-B in matrix samples. The method validation was conducted over the curve range of 1.00 to 1000 ng/ml. The intrabatch and interbatch precision and accuracy of the quality control samples showed ≤10.9% relative standard deviation and -6.7% to 15.0% relative error. Moreover, a possible metabolite M of TDP-B was tentatively characterized. Conclusion: A reliable LC–MS/MS method was developed and validated for the quantification of TDP-B and was successfully applied to a rat pharmacokinetic study.
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22
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Abstract
This review highlights known disulfide-bridged peptide bicycles and the studies on their unique structural and biological features.
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Affiliation(s)
| | - Andrei K. Yudin
- Lash Miller Chemical Laboratories
- University of Toronto
- Toronto
- Canada M5S 3H6
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23
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Zhou J, Xie H, Liu Z, Luo HB, Wu R. Structure–Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. J Chem Inf Model 2014; 54:3162-71. [DOI: 10.1021/ci500513n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Hujun Xie
- School
of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035 Zhejiang, P.R. China
| | - Zhihong Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
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24
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Identification and characterization of the spiruchostatin biosynthetic gene cluster enable yield improvement by overexpressing a transcriptional activator. J Ind Microbiol Biotechnol 2014; 41:1457-65. [PMID: 24973954 DOI: 10.1007/s10295-014-1474-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/10/2014] [Indexed: 01/05/2023]
Abstract
Spiruchostatins A and B are members of the FK228-family of natural products with potent histone deacetylase inhibitory activities and antineoplastic activities. However, their production in the wild-type strain of Pseudomonas sp. Q71576 is low. To improve the yield, the spiruchostatin biosynthetic gene cluster (spi) was first identified by rapid genome sequencing and characterized by genetic mutations. This spi gene cluster encodes a hybrid biosynthetic pathway similar to that encoded by the FK228 biosynthetic gene cluster (dep) in Chromobacterium violaceum No. 968. Each gene cluster contains a pathway regulatory gene (spiR vs. depR), but these two genes encode transcriptional activators of different classes. Overexpression of native spiR or heterologous depR in the wild-type strain of Pseudomonas sp. Q71576 resulted in 268 or 1,285 % increase of the combined titer of spiruchostatins A and B, respectively. RT-PCR analysis indicates that overexpression of heterologous depR upregulates the expression of native spiR.
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25
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The structural basis of an NADP⁺-independent dithiol oxidase in FK228 biosynthesis. Sci Rep 2014; 4:4145. [PMID: 24553401 PMCID: PMC4894451 DOI: 10.1038/srep04145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 02/05/2014] [Indexed: 01/06/2023] Open
Abstract
The disulfide bond is unusual in natural products and critical for thermal stability, cell permeability and bioactivity. DepH from Chromobacterium violaceum No. 968 is an FAD-dependent enzyme responsible for catalyzing the disulfide bond formation of FK228, an anticancer prodrug approved for the treatment of cutaneous T-cell lymphoma. Here we report the crystal structures of DepH and DepH complexed with a substrate analogue S,S'-dimethyl FK228 at 1.82 Å and 2.00 Å, respectively. Structural and biochemical analyses revealed that DepH, in contrast to the well characterized low molecular weight thioredoxin reductases (LMW TrxRs), is an NADP+-independent dithiol oxidase. DepH not only lacks a conserved GGGDXAXE motif necessary for NADP+ binding in the canonical LMW TrxRs, but also contains a 11-residue sequence which physically impedes the binding of NADP+. These observations explain the difference between NADP+-independent small molecule dithiol oxidases and NADP+-dependent thioredoxin reductases and provide insights for understanding the catalytic mechanism of dithiol oxidases involved in natural product biosynthesis.
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26
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Liu X, Cheng YQ. Genome-guided discovery of diverse natural products from Burkholderia sp. J Ind Microbiol Biotechnol 2013; 41:275-84. [PMID: 24212473 DOI: 10.1007/s10295-013-1376-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/24/2013] [Indexed: 01/09/2023]
Abstract
Burkholderia species have emerged as a new source of diverse natural products. This mini-review covers all of the natural products discovered in recent years from Burkholderia sp. by genome-guided approaches--these refer to the use of bacterial genome sequence as an entry point for in silico structural prediction, wet lab experimental design, and execution. While reliable structural prediction based on cryptic biosynthetic gene cluster sequence was not always possible due to noncanonical domains and/or module organization of a deduced biosynthetic pathway, a molecular genetic method was often employed to detect or alter the expression level of the gene cluster to achieve an observable phenotype, which facilitated downstream natural product purification and identification. Those examples of natural product discovery from Burkholderia sp. provide practical guidance for future exploration of Gram-negative bacteria as a new source of natural products.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, 76107, USA
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27
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Walsh CT, O'Brien RV, Khosla C. Nonproteinogenic amino acid building blocks for nonribosomal peptide and hybrid polyketide scaffolds. Angew Chem Int Ed Engl 2013; 52:7098-124. [PMID: 23729217 PMCID: PMC4634941 DOI: 10.1002/anie.201208344] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 12/24/2022]
Abstract
Freestanding nonproteinogenic amino acids have long been recognized for their antimetabolite properties and tendency to be uncovered to reactive functionalities by the catalytic action of target enzymes. By installing them regiospecifically into biogenic peptides and proteins, it may be possible to usher a new era at the interface between small molecule and large molecule medicinal chemistry. Site-selective protein functionalization offers uniquely attractive strategies for posttranslational modification of proteins. Last, but not least, many of the amino acids not selected by nature for protein incorporation offer rich architectural possibilities in the context of ribosomally derived polypeptides. This Review summarizes the biosynthetic routes to and metabolic logic for the major classes of the noncanonical amino acid building blocks that end up in both nonribosomal peptide frameworks and in hybrid nonribosomal peptide-polyketide scaffolds.
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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28
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Walsh CT, O'Brien RV, Khosla C. Nichtproteinogene Aminosäurebausteine für Peptidgerüste aus nichtribosomalen Peptiden und hybriden Polyketiden. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208344] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Liu X, Biswas S, Berg MG, Antapli CM, Xie F, Wang Q, Tang MC, Tang GL, Zhang L, Dreyfuss G, Cheng YQ. Genomics-guided discovery of thailanstatins A, B, and C As pre-mRNA splicing inhibitors and antiproliferative agents from Burkholderia thailandensis MSMB43. JOURNAL OF NATURAL PRODUCTS 2013; 76:685-93. [PMID: 23517093 PMCID: PMC3696399 DOI: 10.1021/np300913h] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mining the genome sequence of Burkholderia thailandensis MSMB43 revealed a cryptic biosynthetic gene cluster resembling that of FR901464 (4), a prototype spliceosome inhibitor produced by Pseudomonas sp. No. 2663. Transcriptional analysis revealed a cultivation condition in which a regulatory gene of the cryptic gene cluster is adequately expressed. Consequently, three new compounds, named thailanstatins A (1), B (2), and C (3), were isolated from the fermentation broth of B. thailandensis MSMB43. Thailanstatins are proposed to be biosynthesized by a hybrid polyketide synthase-nonribosomal peptide synthetase pathway. They differ from 4 by lacking an unstable hydroxyl group and by having an extra carboxyl moiety; those differences endow thailanstatins with a significantly greater stability than 4 as tested in phosphate buffer at pH 7.4. In vitro assays showed that thailanstatins inhibit pre-mRNA splicing as potently as 4, with half-maximal inhibitory concentrations in the single to sub-μM range. Cell culture assays indicated that thailanstatins also possess potent antiproliferative activities in representative human cancer cell lines, with half-maximal growth inhibitory concentrations in the single nM range. This work provides new chemical entities for research and development and new structure-activity information for chemical optimization of related spliceosome inhibitors.
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Affiliation(s)
- Xiangyang Liu
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Sreya Biswas
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Michael G. Berg
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Christopher M. Antapli
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Feng Xie
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Qi Wang
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Man-Cheng Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lixin Zhang
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Gideon Dreyfuss
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Yi-Qiang Cheng
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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30
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Liu XY, Wang C, Cheng YQ. Cyclo-(-l-prolyl-l-valinyl-) from Burkholderia thailandensis MSMB43. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o3182-3. [PMID: 23284494 PMCID: PMC3515274 DOI: 10.1107/s1600536812043000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 10/15/2012] [Indexed: 11/10/2022]
Abstract
THE TITLE COMPOUND [SYSTEMATIC NAME: (3S,8aS)-3-isopropyl-hexa-hydro-pyrrolo-[1,2-a]pyrazine-1,4-dione], C(10)H(16)N(2)O(2),, is a newly isolated cyclic dipeptide from Burkholderia thailandensis MSMB43. There are two independent mol-ecules in the asymmetric unit. Two C atoms and their attached H atoms in the five-membered ring of one of the mol-ecules are disordered over two sets of sites in a 0.715 (5):0.285 (5) ratio. The two independent mol-ecules have the same configuration and the absolute configurations of the chiral centers were determined based on the observation of anomalous dispersion. In the crystal, two types of N-H⋯O hydrogen bonds link pairs of independent mol-ecules.
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Affiliation(s)
- Xiang-Yang Liu
- Department of Biological Sciences, Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
| | - Cheng Wang
- Department of Biological Sciences, Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
| | - Yi-Qiang Cheng
- Department of Biological Sciences, Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
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Revised genome sequence of Burkholderia thailandensis MSMB43 with improved annotation. J Bacteriol 2012; 194:4749-50. [PMID: 22887659 DOI: 10.1128/jb.00931-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is growing interest in discovery of novel bioactive natural products from Burkholderia thailandensis. Here we report a significantly improved genome sequence and reannotation of Burkholderia thailandensis MSMB43, which will facilitate the discovery of new natural products through genome mining and studies of the metabolic versatility of this bacterium.
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Liu XY, Wang C, Cheng YQ. FK228 from Burkholderia thailandensis MSMB43. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2757-8. [PMID: 22969639 PMCID: PMC3435793 DOI: 10.1107/s160053681203601x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 08/16/2012] [Indexed: 11/10/2022]
Abstract
FK228 [systematic name: (1S,4S,7Z,10S,16E,21R)-7-ethyl-idene-4,21-di(propan-2-yl)-2-oxa-12,13-dithia-5,8,20,23-tetra-za--bicyclo[8.7.6]tricos-16-ene-3,6,9,19,22-pentone], C(24)H(36)N(4)O(6)S(2), also known as FR901228, depsipeptide, NSC 630176, romidepsin, and marketed as Istodax by Celgene Corporation, is crystallized from ethyl acetate in P2(1) as compared to the absolute configuration of FK228, first crystallized from methanol in P2(1)2(1)2(1) [Shigematsu et al. (1994 ▶). J. Anti-biot.47, 311-314]. A slight difference is observed between the absolute configuration of FK228 and the present structure. The molecular structure is stabilized by intramolecular N-H⋯O hydrogen bonds. In the crystal, molecules are linked via N-H⋯O hydrogen bonds.
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Affiliation(s)
- Xiang-Yang Liu
- Department of Biological Sciences, Department of Chemistry and Biochemistry, Univeristy of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
| | - Cheng Wang
- Department of Biological Sciences, Department of Chemistry and Biochemistry, Univeristy of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
| | - Yi-Qiang Cheng
- Department of Biological Sciences, Department of Chemistry and Biochemistry, Univeristy of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
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