1
|
Wu Y, Wang M, Liu L. Advances on structure, bioactivity, and biosynthesis of amino acid-containing trans-AT polyketides. Eur J Med Chem 2023; 262:115890. [PMID: 37907023 DOI: 10.1016/j.ejmech.2023.115890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Trans-AT polyketides represent a class of natural compounds utilizing independent acyltransferase during their biosynthesis. They are well known for their diverse chemical structures and potent bioactivities. Trans-AT polyketides are synthesized through biosynthetic gene clusters predominantly composed of polyketide synthases (PKS), but often found in hybrid with non-ribosomal peptide synthetases (NRPS). This genetic hybridization results in the incorporation of amino acid residues into polyketide structures, significantly enhancing their structural diversity. Numerous amino acid-containing trans-AT polyketides have been identified, drawing significant attention to the mechanisms underlying amino acid incorporation and their impact on the biological activity of polyketides. Here, we discussed their origins, structures, biological activities, and the specific roles of amino acids in modulating both the bioactivity and biosynthesis of 38 trans-AT polyketides containing amino acids for the first time. This comprehensive analysis will serve as a crucial reference for the exploration of novel compounds and the improvement of structures and activities.
Collapse
Affiliation(s)
- Yunqiang Wu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Liwei Liu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
| |
Collapse
|
2
|
Chen H, Bai X, Sun T, Wang X, Zhang Y, Bian X, Zhou H. The Genomic-Driven Discovery of Glutarimide-Containing Derivatives from Burkholderia gladioli. Molecules 2023; 28:6937. [PMID: 37836780 PMCID: PMC10574677 DOI: 10.3390/molecules28196937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Glutarimide-containing polyketides exhibiting potent antitumor and antimicrobial activities were encoded via conserved module blocks in various strains that favor the genomic mining of these family compounds. The bioinformatic analysis of the genome of Burkholderia gladioli ATCC 10248 showed a silent trans-AT PKS biosynthetic gene cluster (BGC) on chromosome 2 (Chr2C8), which was predicted to produce new glutarimide-containing derivatives. Then, the silent polyketide synthase gene cluster was successfully activated via in situ promoter insertion and heterologous expression. As a result, seven glutarimide-containing analogs, including five new ones, gladiofungins D-H (3-7), and two known gladiofungin A/gladiostatin (1) and 2 (named gladiofungin C), were isolated from the fermentation of the activated mutant. Their structures were elucidated through the analysis of HR-ESI-MS and NMR spectroscopy. The structural diversities of gladiofungins may be due to the degradation of the butenolide group in gladiofungin A (1) during the fermentation and extraction process. Bioactivity screening showed that 2 and 4 had moderate anti-inflammatory activities. Thus, genome mining combined with promoter engineering and heterologous expression were proved to be effective strategies for the pathway-specific activation of the silent BGCs for the directional discovery of new natural products.
Collapse
Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
- School of Medicine, Linyi University, Shuangling Road, Linyi 276000, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Tao Sun
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| |
Collapse
|
3
|
Hussain A, Bourguet-Kondracki ML, Majeed M, Ibrahim M, Imran M, Yang XW, Ahmed I, Altaf AA, Khalil AA, Rauf A, Wilairatana P, Hemeg HA, Ullah R, Green IR, Ali I, Shah STA, Hussain H. Marine life as a source for breast cancer treatment: A comprehensive review. Biomed Pharmacother 2023; 159:114165. [PMID: 36634590 DOI: 10.1016/j.biopha.2022.114165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
Breast cancer, one of the most significant tumors among all cancer cells, still has deficiencies for effective treatment. Moreover, substitute treatments employing natural products as bioactive metabolites has been seriously considered. The source of bioactive metabolites are not only the most numerous but also represent the richest source. A unique source is from the oceans or marine species which demonstrated intriguing chemical and biological diversity which represents an astonishing reserve for discovering novel anticancer drugs. Notably, marine sponges produce the largest amount of diverse bioactive peptides, alkaloids, terpenoids, polyketides along with many secondary metabolites whose potential is mostly therapeutic. In this review, our main focus is on the marine derived secondary metabolites which demonstrated cytotoxic effects towards numerous breast cancer cells and have been isolated from the marine sources such as marine sponges, cyanobacteria, fungi, algae, tunicates, actinomycetes, ascidians, and other sources of marine organisms.
Collapse
Affiliation(s)
- Amjad Hussain
- Department of Chemistry University of Okara, Okara, Pakistan; Laboratoire Molécules de Communication et Adaptation des Micro-organismes, UMR 7245 MNHN-CNRS, Muséum National d'Histoire Naturelle, 57 rue Cuvier (C.P. 54), 75005 Paris, France.
| | - Marie-Lise Bourguet-Kondracki
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, UMR 7245 MNHN-CNRS, Muséum National d'Histoire Naturelle, 57 rue Cuvier (C.P. 54), 75005 Paris, France
| | - Maryam Majeed
- Department of Applied Chemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Ibrahim
- Department of Applied Chemistry, Government College University, Faisalabad, Pakistan
| | - Muhammad Imran
- Department of chemistry, Faculty of Science, Research center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Xian-Wen Yang
- Key Laboratory of Marine Biogentic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Ishtiaq Ahmed
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Ataf Ali Altaf
- Department of Chemistry University of Okara, Okara, Pakistan
| | - Anees Ahmed Khalil
- University Institute of Diet and Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Abdur Rauf
- Department of Chemistry, University of Swabi Khyber Pukhtanukha, Pakistan
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
| | - Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Al-Medinah Al-Monawara, Saudi Arabia
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ivan R Green
- Department of Chemistry and Polymer Science, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch 7600, South Africa
| | - Iftikhar Ali
- Department of Chemistry, Karakoram International University, Gilgit 15100, Pakistan
| | | | - Hidayat Hussain
- Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, D-06120 Halle (Saale), Germany.
| |
Collapse
|
4
|
Cytotoxic and chemomodulatory effects of Phyllanthus niruri in MCF-7 and MCF-7 ADR breast cancer cells. Sci Rep 2023; 13:2683. [PMID: 36792619 PMCID: PMC9932073 DOI: 10.1038/s41598-023-29566-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
The members of the genus Phyllanthus have long been used in the treatment of a broad spectrum of diseases. They exhibited antiproliferative activity against various human cancer cell lines. Breast cancer is the most diagnosed cancer and a leading cause of cancer death among women. Doxorubicin (DOX) is an anticancer agent used to treat breast cancer despite its significant cardiotoxicity along with resistance development. Therefore, this study was designed to assess the potential cytotoxicity of P. niruri extracts (and fractions) alone and in combination with DOX against naïve (MCF-7) and doxorubicin-resistant breast cancer cell lines (MCF-7ADR). The methylene chloride fraction (CH2Cl2) showed the most cytotoxic activity among all tested fractions. Interestingly, the CH2Cl2-fraction was more cytotoxic against MCF-7ADR than MCF-7 at 100 µg/mL. At sub-cytotoxic concentrations, this fraction enhanced the cytotoxic effect of DOX against the both cell lines under investigation (IC50 values of 0.054 µg/mL and 0.14 µg/mL vs. 0.2 µg/mL for DOX alone against MCF-7) and (1.2 µg/mL and 0.23 µg/mL vs. 9.9 µg/mL for DOX alone against MCF-7ADR), respectively. Further, TLC fractionation showed that B2 subfraction in equitoxic combination with DOX exerted a powerful synergism (IC50 values of 0.03 µg/mL vs. 9.9 µg/mL for DOX alone) within MCF-7ADR. Untargeted metabolite profiling of the crude methanolic extract (MeOH) and CH2Cl2 fraction exhibiting potential cytotoxicity was conducted using liquid chromatography diode array detector-quadrupole time-of-flight mass spectrometry (LC-DAD-QTOF). Further studies are needed to separate the active compounds from the CH2Cl2 fraction and elucidate their mechanism(s) of action.
Collapse
|
5
|
Abstract
Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.
Collapse
|
6
|
Chevrette MG, Handelsman J. Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites. Nat Prod Rep 2021; 38:2083-2099. [PMID: 34693961 DOI: 10.1039/d1np00044f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.
Collapse
Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
7
|
Biermann F, Helfrich EJN. Hidden Treasures: Microbial Natural Product Biosynthesis off the Beaten Path. mSystems 2021; 6:e0084621. [PMID: 34463578 DOI: 10.1128/msystems.00846-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microbes produce structurally diverse natural products to interact with their environment. Many of the biosynthetic products involved in this "metabolic small talk" have been exploited for the treatment of various diseases. As an alternative to the traditional bioactivity-guided workflow, genome mining has been introduced for targeted natural product discovery based on genome sequence information. In this commentary, we will discuss the evolution of genome mining, as well as its current limitations. The Helfrich laboratory aims to play a leading role in overcoming these limitations with the development of computational strategies to identify noncanonical biosynthetic pathways and to decipher the principles that govern the production of the associated metabolites. We will use these insights to develop algorithms for the prediction of natural product scaffolds. These studies will pave the way toward a more comprehensive understanding of the full biosynthetic repertoire encoded in microbial genomes and provide access to novel metabolites.
Collapse
Affiliation(s)
- Friederike Biermann
- Institute for Molecular Bio Science, Goethe University Frankfurtgrid.7839.5, Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Eric J N Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurtgrid.7839.5, Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| |
Collapse
|
8
|
Sesbanimide R, a Novel Cytotoxic Polyketide Produced by Magnetotactic Bacteria. mBio 2021; 12:mBio.00591-21. [PMID: 34006654 PMCID: PMC8262917 DOI: 10.1128/mbio.00591-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genomic information from various magnetotactic bacteria suggested that besides their common ability to form magnetosomes, they potentially also represent a source of bioactive natural products. By using targeted deletion and transcriptional activation, we connected a large biosynthetic gene cluster (BGC) of the trans-acyltransferase polyketide synthase (trans-AT PKS) type to the biosynthesis of a novel polyketide in the alphaproteobacterium Magnetospirillum gryphiswaldense Structure elucidation by mass spectrometry and nuclear magnetic resonance spectroscopy (NMR) revealed that this secondary metabolite resembles sesbanimides, which were very recently reported from other taxa. However, sesbanimide R exhibits an additional arginine moiety the presence of which reconciles inconsistencies in the previously proposed sesbanimide biosynthesis pathway observed when comparing the chemical structure and the potential biochemistry encoded in the BGC. In contrast to the case with sesbanimides D, E, and F, we were able to assign the stereocenter of the arginine moiety experimentally and two of the remaining three stereocenters by predictive biosynthetic tools. Sesbanimide R displayed strong cytotoxic activity against several carcinoma cell lines.IMPORTANCE The findings of this study contribute a new secondary metabolite member to the glutarimide-containing polyketides. The determined structure of sesbanimide R correlates with its cytotoxic bioactivity, characteristic for members of this family. Sesbanimide R represents the first natural product isolated from magnetotactic bacteria and identifies this highly diverse group as a so-far-untapped source for the future discovery of novel secondary metabolites.
Collapse
|