1
|
Liuu S, Damont A, Perret A, Firmesse O, Becher F, Lavison-Bompard G, Hueber A, Woods AS, Darii E, Fenaille F, Tabet JC. Origin and characterization of cyclodepsipeptides: Comprehensive structural approaches with focus on mass spectrometry analysis of alkali-cationized molecular species. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39166474 DOI: 10.1002/mas.21904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024]
Abstract
Cyclodepsipeptides (CDPs) represent a huge family of chemically and structurally diverse molecules with a wide ability for molecular interactions. CDPs are cyclic peptide-related natural products made up of both proteinogenic and nonproteinogenic amino acids linked by amide and ester bonds. The combined use of different analytical methods is required to accurately determine their integral structures including stereochemistry, thus allowing deeper insights into their often-intriguing bioactivities and their possible usefulness. Our goal is to present the various methods developed to accurately characterize CDPs. Presently, Marfey's method and NMR (nuclear magnetic resonance) are still considered the best for characterizing CDP configuration. Nevertheless, electrospray-high resolution tandem mass spectrometry (ESI-HRMS/MS) is of great value for efficiently resolving CDP's composition and sequences. For instance, recent data shows that the fragmentation of cationized CDPs (e.g., [M + Li]+ and [M + Na]+) leads to selective cleavage of ester bonds and specific cationized product ions (b series) useful to get unprecedented sequence information. Thus, after a brief presentation of their structure, biological functions, and biosynthesis, we also provide a historic overview of these various analytical approaches as well as their advantages and limitations with a special emphasis on the emergence of methods based on HRMS/MS through recent fundamental works and applications.
Collapse
Affiliation(s)
- Sophie Liuu
- Staphylococcus, Bacillus & Clostridium (SBCL) unit, Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA-INRAE, Laboratoire Innovations en Spectrométrie de Masse pour la Santé (LI-MS), DRF/Institut Joliot/DMTS/SPI, MetaboHUB, CEA Saclay, Gif sur Yvette, France
| | - Alain Perret
- Génomique métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Olivier Firmesse
- Staphylococcus, Bacillus & Clostridium (SBCL) unit, Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - François Becher
- Université Paris-Saclay, CEA-INRAE, Laboratoire Innovations en Spectrométrie de Masse pour la Santé (LI-MS), DRF/Institut Joliot/DMTS/SPI, MetaboHUB, CEA Saclay, Gif sur Yvette, France
| | - Gwenaëlle Lavison-Bompard
- Pesticides and Marine Biotoxins (PBM) unit, Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Amandine Hueber
- Staphylococcus, Bacillus & Clostridium (SBCL) unit, Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Amina S Woods
- National Institute on Drug Abuse Intramural Research Program (NIDA IRP), National Institute of Health (NIH), Baltimore, Maryland, USA
- Johns Hopkins School of Medicine, Pharmacology and Molecular Sciences, Baltimore, Maryland, USA
| | - Ekaterina Darii
- Génomique métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - François Fenaille
- Université Paris-Saclay, CEA-INRAE, Laboratoire Innovations en Spectrométrie de Masse pour la Santé (LI-MS), DRF/Institut Joliot/DMTS/SPI, MetaboHUB, CEA Saclay, Gif sur Yvette, France
| | - Jean-Claude Tabet
- Université Paris-Saclay, CEA-INRAE, Laboratoire Innovations en Spectrométrie de Masse pour la Santé (LI-MS), DRF/Institut Joliot/DMTS/SPI, MetaboHUB, CEA Saclay, Gif sur Yvette, France
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, France
| |
Collapse
|
2
|
Grabski M, Gawor J, Cegłowska M, Gromadka R, Mazur-Marzec H, Węgrzyn G. Genome Mining of Pseudanabaena galeata CCNP1313 Indicates a New Scope in the Search for Antiproliferative and Antiviral Agents. Microorganisms 2024; 12:1628. [PMID: 39203471 PMCID: PMC11356792 DOI: 10.3390/microorganisms12081628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
Compounds derived from natural sources pave the way for novel drug development. Cyanobacteria is an ubiquitous phylum found in various habitats. The fitness of those microorganisms, within different biotopes, is partially dependent on secondary metabolite production. Their enhanced production under biotic/abiotic stress factors accounts for better survival rates of cells, and thereby cyanobacteria are as an enticing source of bioactive compounds. Previous studies have shown the potent activity of extracts and fractions from Pseudanabaena galeata (Böcher 1949) strain CCNP1313 against cancer cells and viruses. However, active agents remain unknown, as the selected peptides had no effect on the tested cell lines. Here, we present a bottom-up approach, pinpointing key structures involved in secondary metabolite production. Consisting of six replicons, a complete genome sequence of P. galeata strain CCNP1313 was found to carry genes for non-ribosomal peptide/polyketide synthetases embedded within chromosome spans (4.9 Mbp) and for a ribosomally synthesized peptide located on one of the plasmids (0.2 Mbp). Elucidation of metabolite synthesis pathways led to prediction of their structure. While none of the synthesis-predicted products were found in mass spectrometry analysis, unexplored synthetases are characterized by structural similarities to those producing potent bioactive compounds.
Collapse
Affiliation(s)
- Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland;
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822 Gdańsk, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland;
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Hanna Mazur-Marzec
- Department of Marine Biology and Biotechnology, University of Gdansk, Piłsudskiego 46, 81-378 Gdynia, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| |
Collapse
|
3
|
Chen J, Jiang Y, Yan J, Xu C, Ye T. Total Syntheses of Colletopeptide A and Colletotrichamide A. Molecules 2023; 28:7194. [PMID: 37894673 PMCID: PMC10608858 DOI: 10.3390/molecules28207194] [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: 08/31/2023] [Revised: 09/27/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The first total syntheses of cyclic depsipeptides colletopeptide A and colletotrichamide A, have been accomplished. The key advanced intermediate, a cyclic tridepsipeptide derivative, was constructed using a sequence of transformations that features asymmetric Brown crotylation, cross metathesis, Yamaguchi esterification, ozonolysis, and macrolactamization. A late-stage incorporation of the mannose fragment completed the synthesis of colletotrichamide A, and the desilylation of the common intermediate gave rise to colletopeptide A, which led to unambiguous confirmation of the absolute stereochemistry of the aforementioned natural products.
Collapse
Affiliation(s)
- Jing Chen
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (J.C.); (Y.J.)
| | - Yangyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (J.C.); (Y.J.)
| | - Jialei Yan
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China;
| | - Chao Xu
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China;
- QianYan (Shenzhen) Pharmatech. Ltd., Building-3, Longcheng Industrial Park, Qinglin Road West, Longgang District, Shenzhen 518172, China
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (J.C.); (Y.J.)
- QianYan (Shenzhen) Pharmatech. Ltd., Building-3, Longcheng Industrial Park, Qinglin Road West, Longgang District, Shenzhen 518172, China
| |
Collapse
|
4
|
Liu SX, Ou-Yang SY, Lu YF, Guo CL, Dai SY, Li C, Yu TY, Pei YH. Recent advances on cyclodepsipeptides: biologically active compounds for drug research. Front Microbiol 2023; 14:1276928. [PMID: 37849925 PMCID: PMC10577210 DOI: 10.3389/fmicb.2023.1276928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Cyclodepsipeptides are a large family of peptide-related natural products consisting of hydroxy and amino acids linked by amide and ester bonds. A number of cyclodepsipeptides have been isolated and characterized from fungi and bacteria. Most of them showed antitumor, antifungal, antiviral, antimalarial, and antitrypanosomal properties. Herein, this review summarizes the recent literatures (2010-2022) on the progress of cyclodepsipeptides from fungi and bacteria except for those of marine origin, in order to enrich our knowledge about their structural features and biological sources.
Collapse
Affiliation(s)
- Si-Xuan Liu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Si-Yi Ou-Yang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yong-Fu Lu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chun-Lin Guo
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Si-Yang Dai
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
- Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Tian-Yi Yu
- The Third Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Yue-Hu Pei
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| |
Collapse
|
5
|
Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
Collapse
Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| |
Collapse
|
6
|
Ahmed S, Alam W, Aschner M, Filosa R, Cheang WS, Jeandet P, Saso L, Khan H. Marine Cyanobacterial Peptides in Neuroblastoma: Search for Better Therapeutic Options. Cancers (Basel) 2023; 15:cancers15092515. [PMID: 37173981 PMCID: PMC10177606 DOI: 10.3390/cancers15092515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/03/2023] [Accepted: 03/12/2023] [Indexed: 05/15/2023] Open
Abstract
Neuroblastoma is the most prevalent extracranial solid tumor in pediatric patients, originating from sympathetic nervous system cells. Metastasis can be observed in approximately 70% of individuals after diagnosis, and the prognosis is poor. The current care methods used, which include surgical removal as well as radio and chemotherapy, are largely unsuccessful, with high mortality and relapse rates. Therefore, attempts have been made to incorporate natural compounds as new alternative treatments. Marine cyanobacteria are a key source of physiologically active metabolites, which have recently received attention owing to their anticancer potential. This review addresses cyanobacterial peptides' anticancer efficacy against neuroblastoma. Numerous prospective studies have been carried out with marine peptides for pharmaceutical development including in research for anticancer potential. Marine peptides possess several advantages over proteins or antibodies, including small size, simple manufacturing, cell membrane crossing capabilities, minimal drug-drug interactions, minimal changes in blood-brain barrier (BBB) integrity, selective targeting, chemical and biological diversities, and effects on liver and kidney functions. We discussed the significance of cyanobacterial peptides in generating cytotoxic effects and their potential to prevent cancer cell proliferation via apoptosis, the activation of caspases, cell cycle arrest, sodium channel blocking, autophagy, and anti-metastasis behavior.
Collapse
Affiliation(s)
- Salman Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Waqas Alam
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine Forchheimer, 209 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Rosanna Filosa
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Wai San Cheang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Philippe Jeandet
- Faculty of Sciences, RIBP-USC INRAe 1488, University of Reims, 51100 Reims, France
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University, 00185 Rome, Italy
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| |
Collapse
|
7
|
Wang YJ, Liu CY, Wang YL, Zhang FX, Lu YF, Dai SY, Li C, Sun Y, Pei YH. Cytotoxic Cyclodepsipeptides and Cyclopentane Derivatives from a Plant-Associated Fungus Fusarium sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:2592-2602. [PMID: 36288556 DOI: 10.1021/acs.jnatprod.2c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this work, four new cyclodepsipeptides, fusarihexins C-E (1-3) and enniatin Q (4), four new cyclopentane derivatives, fusarilins A-D (5-8), together with eight known compounds (9-16), were isolated from cultures of the endophytic fungus Fusarium sp. The structures of the isolated compounds were elucidated by analysis of HRMS and NMR spectroscopic data. The absolute configurations were determined using Marfey's method, a modified Mosher's method, single-crystal X-ray diffraction analysis, and ECD analysis. The antitumor activities of the isolated compounds in vitro were evaluated. Cyclodepsipeptides displayed cytotoxicities against the Huh-7, MRMT-1, and HepG-2 cell lines. Compounds 4, 9, 10, and 12 with IC50 values of 1.0-9.1 μM exhibited the most potent cytotoxicities against the three cell lines as compared to the positive control-5-fluorouracil. Compounds 1-3 and 11 exhibited moderate cytotoxic activities (IC50 values of 10.7-20.1 μM).
Collapse
Affiliation(s)
- Ya-Jing Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Chun-Yue Liu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yan-Lei Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Feng-Xiang Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, People's Republic of China
| | - Yong-Fu Lu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Si-Yang Dai
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yi Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Yue-Hu Pei
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| |
Collapse
|
8
|
Lu H, Batey RA. Total synthesis of chaiyaphumines A-D: A case study comparing macrolactonization and macrolactamization approaches. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
9
|
Phaeosphamides A and B, Cytotoxic Cyclodecadepsipeptides from the Mangrove-Derived Fungus Phaeosphaeriopsis sp. S296. Mar Drugs 2022; 20:md20100591. [PMID: 36286415 PMCID: PMC9604837 DOI: 10.3390/md20100591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 12/02/2022] Open
Abstract
Chemical examination of the fermented broth of the mangrove-derived fungus Phaeosphaeriopsis sp. S296 resulted in the isolation of two new cyclodecadepsipeptides, namely phaeosphamides A (1) and B (2), as well as one known congener Sch 217048 (3). The structures of new metabolites, including absolute configurations, were established on the basis of extensive spectroscopic data analyses, chemical conversion, and Marfey’s method. The 2-hydroxy-3-methylpentanoic acid (Hmp) moiety and pipecolic acid (Pip) unit in structures were rarely discovered in nature. Interestingly, compounds 1–3 are examples of peptides discovered from the fungal genus Phaeosphaeriopsis for the first time. All identified compounds were evaluated for their cytotoxicity against five tumor cell lines of AGS, BEL-7402, HepG2, B16, and BIU87. Among them, compound 1 showed inhibitory activities against these tumor cell lines with IC50 values ranging from 5.14 to 66.38 μM. A further mechanistic investigation found that 1 arrested AGS cells in the G2 phase and induced their apoptosis in a dose-dependent manner.
Collapse
|
10
|
Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753. Appl Environ Microbiol 2022; 88:e0110522. [PMID: 36000852 PMCID: PMC9469707 DOI: 10.1128/aem.01105-22] [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: 11/20/2022] Open
Abstract
The marine bacterium Photobacterium galatheae S2753 produces a group of cyclodepsipeptides, called solonamides, which impede the virulence but not the survival of Staphylococcus aureus. In addition to their invaluable antivirulence activity, little is known about the biosynthesis and physiological function of solonamides in the native producer. This study generated a solonamide-deficient (Δsol) mutant by in-frame deletion of the sol gene, thereby identifying the core gene for solonamide biosynthesis. By annotation from antiSMASH, the biosynthetic pathway of solonamides in S2753 was also proposed. Mass spectrometry analysis of cell extracts found that deficiency of solonamide production influenced the production of a group of unknown compounds but otherwise did not alter the overall secondary metabolite profile. Physiological comparison between Δsol and wild-type S2753 demonstrated that growth dynamics and biofilm formation of both strains were similar; however, the Δsol mutant displayed reduced motility rings compared to the wild type. Reintroduction of sol restored solonamide production and motility to the mutant, indicating that solonamides influence the motility behavior of P. galatheae S2753. Proteomic analysis of the Δsol and wild-type strains found that eliminating solonamides influenced many cellular processes, including swimming-related proteins and proteins adjusting the cellular cyclic di-GMP concentration. In conclusion, our results revealed the biosynthetic pathway of solonamides and their ecological benefits to P. galatheae S2753 by enhancing motility, likely by altering the motile physiology. IMPORTANCE The broad range of bioactive potentials of cyclodepsipeptides makes these compounds invaluable in the pharmaceutical industry. Recently, a few novel cyclodepsipeptides have been discovered in marine Proteobacteria; however, their biosynthetic pathways remain to be revealed. Here, we demonstrated the biosynthetic genetic basis and pathway of the antivirulence compounds known as solonamides in P. galatheae S2753. This can pave the way for the biological overproduction of solonamides on an industrial scale. Moreover, the comparison of a solonamide-deficient mutant and wild-type S2753 demonstrated that solonamides stimulate the swimming behavior of S2753 and also influence a few key physiological processes of the native producers. These results evidenced that, in addition to their importance as novel drug candidates, these compounds play a pivotal role in the physiology of the producing microorganisms and potentially provide the native producer competitive benefits for their survival in nature.
Collapse
|
11
|
Merlin TS, Umar M, Puthiyedathu ST. Genomic insights into symbiosis and host adaptation of an ascidian-associated bacterium Bacillus aryabhattai MCCB 387. Symbiosis 2022. [DOI: 10.1007/s13199-022-00860-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
12
|
Sequeira P, Rothkegel M, Domingos P, Martins I, Leclercq CC, Renaut J, Goldman GH, Silva Pereira C. Untargeted Metabolomics Sheds Light on the Secondary Metabolism of Fungi Triggered by Choline-Based Ionic Liquids. Front Microbiol 2022; 13:946286. [PMID: 35958129 PMCID: PMC9361774 DOI: 10.3389/fmicb.2022.946286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Fungal secondary metabolites constitute a rich source of yet undiscovered bioactive compounds. Their production is often silent under standard laboratory conditions, but the production of some compounds can be triggered simply by altering the cultivation conditions. The usage of an organic salt – ionic liquid – as growth medium supplement can greatly impact the biosynthesis of secondary metabolites, leading to higher diversity of compounds accumulating extracellularly. This study examines if such supplements, specifically cholinium-based ionic liquids, can support the discovery of bioactive secondary metabolites across three model species: Neurospora crassa, Aspergillus nidulans, and Aspergillus fumigatus. Enriched organic extracts obtained from medium supernatant revealed high diversity in metabolites. The supplementation led apparently to increased levels of either 1-aminocyclopropane-1-carboxylate or α-aminoisobutyric acid. The extracts where bioactive against two major foodborne bacterial strains: Staphylococcus aureus and Escherichia coli. In particular, those retrieved from N. crassa cultures showed greater bactericidal potential compared to control extracts derived from non-supplemented cultures. An untargeted mass spectrometry analysis using the Global Natural Product Social Molecular Networking tool enabled to capture the chemical diversity driven by the ionic liquid stimuli. Diverse macrolides, among other compounds, were putatively associated with A. fumigatus; whereas an unexpected richness of cyclic (depsi)peptides with N. crassa. Further studies are required to understand if the identified peptides are the major players of the bioactivity of N. crassa extracts, and to decode their biosynthesis pathways as well.
Collapse
Affiliation(s)
- Patrícia Sequeira
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Maika Rothkegel
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Patrícia Domingos
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Isabel Martins
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Céline C. Leclercq
- Integrative Biology Platform, Environmental Research and Technology Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Jenny Renaut
- Integrative Biology Platform, Environmental Research and Technology Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Gustavo H. Goldman
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Cristina Silva Pereira
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
- *Correspondence: Cristina Silva Pereira,
| |
Collapse
|
13
|
Brinkmann S, Spohn MS, Schäberle TF. Bioactive natural products from Bacteroidetes. Nat Prod Rep 2022; 39:1045-1065. [PMID: 35315462 DOI: 10.1039/d1np00072a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Covering: up to end of January 2022Bacteria representing the phylum Bacteroidetes produce a diverse range of natural products, including polyketides, peptides and lactams. Here, we discuss unique aspects of the bioactive compounds discovered thus far, and the corresponding biosynthetic pathways if known, providing a comprehensive overview of the Bacteroidetes as a natural product reservoir.
Collapse
Affiliation(s)
- Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany.
| | - Marius S Spohn
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany.
| | - Till F Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany. .,Institute for Insect Biotechnology, Justus Liebig University of Giessen, 35392 Giessen, Germany.,German Centre for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| |
Collapse
|
14
|
Bellotto O, Semeraro S, Bandiera A, Tramer F, Pavan N, Marchesan S. Polymer Conjugates of Antimicrobial Peptides (AMPs) with d-Amino Acids (d-aa): State of the Art and Future Opportunities. Pharmaceutics 2022; 14:pharmaceutics14020446. [PMID: 35214178 PMCID: PMC8879212 DOI: 10.3390/pharmaceutics14020446] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
In recent years, antimicrobial peptides (AMPs) have enjoyed a renaissance, as the world is currently facing an emergency in terms of severe infections that evade antibiotics’ treatment. This is due to the increasing emergence and spread of resistance mechanisms. Covalent conjugation with polymers is an interesting strategy to modulate the pharmacokinetic profile of AMPs and enhance their biocompatibility profile. It can also be an effective approach to develop active coatings for medical implants and devices, and to avoid biofilm formation on their surface. In this concise review, we focus on the last 5 years’ progress in this area, pertaining in particular to AMPs that contain d-amino acids, as well as their role, and the advantages that may arise from their introduction into AMPs.
Collapse
Affiliation(s)
- Ottavia Bellotto
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (S.S.)
| | - Sabrina Semeraro
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (S.S.)
| | - Antonella Bandiera
- Life Sciences Department, University of Trieste, 34127 Trieste, Italy; (A.B.); (F.T.)
| | - Federica Tramer
- Life Sciences Department, University of Trieste, 34127 Trieste, Italy; (A.B.); (F.T.)
| | - Nicola Pavan
- Medical, Surgical and Health Sciences Department, University of Trieste, 34127 Trieste, Italy;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (S.S.)
- Correspondence:
| |
Collapse
|
15
|
Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 501] [Impact Index Per Article: 250.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
Collapse
|
16
|
Araújo IF, Marinho VHDS, Sena IDS, Curti JM, Ramos RDS, Ferreira RMA, Souto RNP, Ferreira IM. Larvicidal activity against Aedes aegypti and molecular docking studies of compounds extracted from the endophytic fungus Aspergillus sp. isolated from Bertholletia excelsa Humn. & Bonpl. Biotechnol Lett 2022; 44:439-459. [PMID: 35147845 DOI: 10.1007/s10529-022-03220-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/01/2022] [Indexed: 12/27/2022]
Abstract
Endophytic fungi are microorganisms capable of colonizing the interior of plant tissues without causing damage to them. The study of the secondary metabolites produced by their vast biodiversity fungal is relevant for the discovery of new products for biotechnological and agrochemical applications. In addition, extract of the endophytic fungus Aspergillus sp., isolated from the almonds of Bertholletia excelsa Humn & Bonlp collected in the Brazilian Amazon, oviposition deterrent, and larvicidal activity of against Aedes aegypti. In the oviposition deterrence test was observed that females able to lay eggs preferred the control oviposition sites (46.6%). Furthermore, the extract showed larvicidal activity with LC50 26.86 µg/mL at 24 h and 18.75 µg/mL at 48 h. Molecular docking studies showed the compound Aspergillol B a potent larvicide by to inhibit the acetylcholinesterase enzyme (- 7.74 kcal/mol). These results indicate that compounds from secondary metabolites of Aspergillus sp., isolated from almonds of B. excelsa, are useful biological potential against vectors A. aegypti.
Collapse
Affiliation(s)
- Inana F Araújo
- Biocatalysis and Applied Organic Synthesis Laboratory, Collegiate of Chemistry, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil
| | - Victor Hugo de S Marinho
- Biocatalysis and Applied Organic Synthesis Laboratory, Collegiate of Chemistry, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil
| | - Iracirema da S Sena
- Biocatalysis and Applied Organic Synthesis Laboratory, Collegiate of Chemistry, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil
| | - Jhone M Curti
- Biocatalysis and Applied Organic Synthesis Laboratory, Collegiate of Chemistry, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil
| | - Ryan da S Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, AP, 68902-280, Brazil
| | - Ricardo M A Ferreira
- Arthropod Laboratory, Collegiate of Biology, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil
| | - Raimundo N P Souto
- Arthropod Laboratory, Collegiate of Biology, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil
| | - Irlon M Ferreira
- Biocatalysis and Applied Organic Synthesis Laboratory, Collegiate of Chemistry, Federal University of Amapá, Rod. JK, KM 02, Macapá, Amapá, 68902-280, Brazil.
| |
Collapse
|
17
|
Yue H, Miller AL, Khetrapal V, Jayaseker V, Wright S, Du L. Biosynthesis, regulation, and engineering of natural products from Lysobacter. Nat Prod Rep 2022; 39:842-874. [PMID: 35067688 DOI: 10.1039/d1np00063b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.
Collapse
Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Amanda Lynn Miller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vimmy Khetrapal
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vishakha Jayaseker
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| |
Collapse
|
18
|
Flores-Holguín N, Ortega-Castro J, Frau J, Glossman-Mitnik D. Conceptual DFT-Based Computational Peptidology, Pharmacokinetics Study and ADMET Report of the Veraguamides A–G Family of Marine Natural Drugs. Mar Drugs 2022; 20:md20020097. [PMID: 35200627 PMCID: PMC8874632 DOI: 10.3390/md20020097] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 12/17/2022] Open
Abstract
As a continuation of our research on the chemical reactivity, pharmacokinetics and ADMET properties of cyclopeptides of marine origin with potential therapeutic abilities, in this work our already presented integrated molecular modeling protocol has been used for the study of the chemical reactivity and bioactivity properties of the Veraguamides A–G family of marine natural drugs. This protocol results from the estimation of the conceptual density functional theory (CDFT) chemical reactivity descriptors together with several chemoinformatics tools commonly considered within the process of development of new therapeutic drugs. CP-CDFT is a branch of computational chemistry and molecular modeling dedicated to the study of peptides, and it is a protocol that allows the estimation with great accuracy of the CDFT-based reactivity descriptors and the associated physical and chemical properties, which can aid in determining the ability of the studied peptides to behave as potential useful drugs. Moreover, the superiority of the MN12SX density functional over other long-range corrected density functionals for the prediction of chemical and physical properties in the presence of water as the solvent is clearly demonstrated. The research was supplemented with an investigation of the bioactivity of the molecular systems and their ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, as is customary in medicinal chemistry. Some instances of the CDFT-based chemical reactivity descriptors’ capacity to predict the pKas of peptides as well as their potential as AGE inhibitors are also shown.
Collapse
Affiliation(s)
- Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Joaquín Ortega-Castro
- Departament de Química, Facultat de Ciènces, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain; (J.O.-C.); (J.F.)
| | - Juan Frau
- Departament de Química, Facultat de Ciènces, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain; (J.O.-C.); (J.F.)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
- Correspondence: ; Tel.: +52-614-439-1151
| |
Collapse
|
19
|
Flores-Holguín N, Frau J, Glossman-Mitnik D. Computational peptidology approach to the study of the chemical reactivity and bioactivity properties of Aspergillipeptide D, a cyclopentapeptide of marine origin. Sci Rep 2022; 12:506. [PMID: 35017576 PMCID: PMC8752680 DOI: 10.1038/s41598-021-04513-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/24/2021] [Indexed: 12/19/2022] Open
Abstract
Aspergillipeptide D is a cyclic pentapeptide isolated from the marine gorgonian Melitodes squamata-derived fungus Aspergillus sp. SCSIO 41501 that it has been shown to present moderate activity against herpes virus simplex type 1 (HSV-1). Thus, this paper presents the results of a computational study of this cyclopentapeptide's chemical reactivity and bioactivity properties using a CDFT-based computational peptidology (CDFT-CP) methodology, which is derived from combining chemical reactivity descriptors derived from Conceptual Density Functional Theory (CDFT) and some Cheminformatics tools which may be used. This results in an improvement of the virtual screening procedure by a similarity search allowing the identification and validation of the known ability of the peptide to act as a possible useful drug. This was followed by an examination of the drug's bioactivity and pharmacokinetics indices in relation to the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) characteristics. The findings provide further evidence of the MN12SX density functional's superiority in proving the Janak and Ionization Energy theorems using the proposed KID approach. This has proven to be beneficial in accurately predicting CDFT reactivity characteristics, which aid in the understanding of chemical reactivity. The Computational Pharmacokinetics study revealed the potential ability of Aspergillipeptide D as a therapeutic drug through the interaction with different target receptors. The ADMET indices confirm this assertion through the absence of toxicity and good absorption and distribution properties.
Collapse
Affiliation(s)
- Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, 31136, Chihuahua, CHIH, Mexico
| | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, Palma de Mallorca, 07122, Spain
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, 31136, Chihuahua, CHIH, Mexico.
| |
Collapse
|
20
|
Farah HI, Supratman U, Hidayat AT, Maharani R. An Overview of the Synthesis of Biologically Active Cyclodepsipeptides. ChemistrySelect 2022. [DOI: 10.1002/slct.202103470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Harra Ismi Farah
- Department of Chemistry Faculty of Mathematics and Natural Sciences Laboratorium Sentral Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
- Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
- Pharmaceutical Research and Development Laboratory of Farmaka Tropis Pharmacy Faculty Universitas Mulawarman Jalan Penajam No.1 Samarinda 75119 East Kalimantan Indonesia
| | - Unang Supratman
- Department of Chemistry Faculty of Mathematics and Natural Sciences Laboratorium Sentral Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
- Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
| | - Ace Tatang Hidayat
- Department of Chemistry Faculty of Mathematics and Natural Sciences Laboratorium Sentral Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
- Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
| | - Rani Maharani
- Department of Chemistry Faculty of Mathematics and Natural Sciences Laboratorium Sentral Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
- Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Padjadjaran Jalan Raya Bandung-Sumedang Km 21 Jatinangor 45363 West Java Indonesia
| |
Collapse
|
21
|
Smith AN, Blackwell DJ, Knollmann BC, Johnston JN. Ring Size as an Independent Variable in Cyclooligomeric Depsipeptide Antiarrhythmic Activity. ACS Med Chem Lett 2021; 12:1942-1947. [PMID: 34917258 DOI: 10.1021/acsmedchemlett.1c00508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
Hit-to-lead studies employ a variety of strategies to optimize binding to a target of interest. When a structure for the target is available, hypothesis-driven structure-activity relationships (SAR) are a powerful strategy for refining the pharmacophore to achieve robust binding and selectivity characteristics necessary to identify a lead compound. Recrafting the three-dimensional space occupied by a small molecule, optimization of hydrogen bond contacts, and enhancing local attractive interactions are traditional approaches in medicinal chemistry. Ring size, however, is rarely able to be leveraged as an independent variable because most hits lack the symmetry required for such a study. Our discovery that the cyclic oligomeric depsipeptide ent-verticilide inhibits mammalian cardiac ryanodine receptor calcium release channels with submicromolar potency provided an opportunity to explore ring size as a variable, independent of other structural or functional group changes. We report here that ring size can be a critical independent variable, suggesting that modest conformational changes alone can dramatically affect potency.
Collapse
Affiliation(s)
- Abigail N. Smith
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
| | - Bjorn C. Knollmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
| | - Jeffrey N. Johnston
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
22
|
Klöppel S, Richarz R, Wirtz DA, Vasenda N, König GM, Crüsemann M. A Specialized Dehydrogenase Provides l-Phenyllactate for FR900359 Biosynthesis. Chembiochem 2021; 23:e202100569. [PMID: 34846772 PMCID: PMC9299796 DOI: 10.1002/cbic.202100569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Indexed: 11/30/2022]
Abstract
d‐Phenyllactate (PLA) is a component of the selective Gq protein inhibitor and nonribosomal cyclic depsipeptide FR900359 (FR). Here we report a detailed biochemical investigation of pla biosynthesis and its incorporation into the natural product FR. The enzyme FrsC, member of the lactate/malate dehydrogenase superfamily, was shown to catalyze the formation of l‐PLA from phenylpyruvate. FrsC was kinetically characterized and its substrate specificity determined. Incorporation of l‐PLA was probed by assaying the adenylation domain FrsE‐A3 and feeding studies with a Chromobacterium vaccinii ΔfrsC mutant, confirming preferred activation of l‐PLA followed by on‐line epimerization to d‐pla. Finally, detailed bioinformatic analyses of FrsC revealed its close relation to malate dehydrogenases from primary metabolism and suggest extensions in the substrate binding loop to be responsible for its adaptation to accepting larger aromatic substrates with high specificity.
Collapse
Affiliation(s)
- Sophie Klöppel
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - René Richarz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Daniel A Wirtz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Natalia Vasenda
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| |
Collapse
|
23
|
Souto JA, Román D, Domínguez M, Lera ÁR. Synthetic Studies on Alotamide A: Construction of
N
‐Demethylalotamide A. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- José A. Souto
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| | - David Román
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| | - Marta Domínguez
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| | - Ángel R. Lera
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| |
Collapse
|
24
|
Flores‐Holguín N, Frau J, Glossman‐Mitnik D. Computational Pharmacokinetics Report, ADMET Study and Conceptual DFT-Based Estimation of the Chemical Reactivity Properties of Marine Cyclopeptides. ChemistryOpen 2021; 10:1142-1149. [PMID: 34806828 PMCID: PMC8607802 DOI: 10.1002/open.202100178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Homophymines A-E and A1-E1 are bioactive natural cyclodepsipeptides with a complex molecular architecture. These molecules could have a potential use as antimicrobial, antiviral, and anticancer substances. We have carried out a computational study of the properties of this family of marine peptides using a CDFT-based Computational Peptidology (CDFT-CP) methodology that results from the combination of the chemical reactivity descriptors that arise from conceptual Density Functional Theory (CDFT) together with cheminformatics tools. The latter can be used to estimate the associated physicochemical parameters and to improve the process of virtual screening through a similarity search. Using this approach, the ability of the peptides to behave as a potentially useful drugs can be investigated. An analysis of their bioactivity and pharmacokinetics indices related to the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) features has also been carried out.
Collapse
Affiliation(s)
- Norma Flores‐Holguín
- Laboratorio Virtual NANOCOSMOSDepartamento de Medio Ambiente y EnergíaCentro de Investigación en Materiales AvanzadosMiguel de Cervantes 120, Complejo Industrial Chihuahua31136Chihuahua, ChihMexico
| | - Juan Frau
- Departament de QuímicaFacultat de CiencesUniversitat de les Illes Balears07122Pama de MallorcaSpain
| | - Daniel Glossman‐Mitnik
- Laboratorio Virtual NANOCOSMOSDepartamento de Medio Ambiente y EnergíaCentro de Investigación en Materiales AvanzadosMiguel de Cervantes 120, Complejo Industrial Chihuahua31136Chihuahua, ChihMexico
| |
Collapse
|
25
|
An integrated molecular modeling protocol for drug screening based on conceptual density functional theory and chemoinformatics for the study of marine cyclopeptides. J Mol Model 2021; 27:314. [PMID: 34623510 DOI: 10.1007/s00894-021-04901-2] [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: 07/28/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
An integrated molecular modeling protocol resulting from the combination of conceptual density functional theory (CDFT) chemical reactivity descriptors with several chemoinformatics tools has been used for the study of the chemical reactivity and bioactivity properties of a group of marine cyclic peptides. CP-CDFT is a branch of computational chemistry and molecular modeling dedicated to the study of peptides. The protocol allowed the estimation of the CDFT-based reactivity indices together with the associated physicochemical parameters that can help to identify the ability of the studied peptides to behave as potential useful drugs. This was complemented with an analysis of the bioactivity and pharmacokinetics parameters related to the ADMET (absorption, distribution, metabolism, excretion, and toxicity) features. Some examples related to the ability of the CDFT-based chemical reactivity descriptors for the prediction of the pKas of the peptides as well as their potential as AGE inhibitors are also presented.
Collapse
|
26
|
Barthélemy M, Elie N, Genta-Jouve G, Stien D, Touboul D, Eparvier V. Identification of Antagonistic Compounds between the Palm Tree Xylariale Endophytic Fungi and the Phytopathogen Fusarium oxysporum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10893-10906. [PMID: 34516124 DOI: 10.1021/acs.jafc.1c03141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To discover microorganisms that naturally possess chemical weapons against the phytopathogen Fusarium oxysporum, the biological and chemical diversity of plant leaf endophytes was investigated. Endophytes were isolated from the palm tree Astrocaryum sciophyllum collected in pristine forests of French Guiana. Several Xylariaceae inhibited the growth of F. oxysporum and were further explored. Antifungal specialized metabolites were isolated from the Xylariaceae BSNB-0294 strain in confrontation with the phytopathogen and led to the identification of undescribed compounds, i.e., two depsipeptides named xylariaceins, two metabolites containing a 3-imidazolinone moiety, and four new compounds including a nitro-phenylpropanamide and three phenylalanine analogues named xylariains A-D. In parallel, the chemical investigation of the phytopathogen during the coculture led to the identification of an unknown compound, which we named focicin. The production of focicin was exacerbated during the competition. Matrix-assisted laser desorption/ionization coupled to time-of-flight mass spectometry (MALDI-TOF MS) imaging of the competition between BSNB-0294 (endophytic strain) and F. oxysporum f.sp. ciceris (phytopathogen) highlighted time-dependent chemical interactions between the two microorganisms.
Collapse
Affiliation(s)
- Morgane Barthélemy
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Nicolas Elie
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Grégory Genta-Jouve
- Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens (LEEISA), USR 3456, Université De Guyane, CNRS Guyane, 97300 Cayenne, French Guiana, France
| | - Didier Stien
- Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Sorbonne Universités, UPMC Université Paris 06, CNRS, 66650 Banyuls-sur-Mer, France
| | - David Touboul
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Véronique Eparvier
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| |
Collapse
|
27
|
A CDFT-Based Computational Peptidology (CDFT-CP) Study of the Chemical Reactivity and Bioactivity of the Marine-Derived Alternaramide Cyclopentadepsipeptide. J CHEM-NY 2021. [DOI: 10.1155/2021/2989611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Alternaramide is a cyclic pentadepsipeptide isolated from marine sources that has been shown to present weak antibiotic activity against Bacillus subtilis and Staphylococcus aureus as well as inhibitory effects on inflammatory mediator expressions. Thus, this work reports the results of a computational study of the chemical reactivity and bioactivity properties of this cyclopentadepsipeptide considering a CDFT-based computational peptidology (CDFT-CP) methodology that results from the combination of the chemical reactivity descriptors that arise from conceptual density functional theory (CDFT) together with some cheminformatics tools that can be used to estimate the associated physicochemical parameters, to improve the process of virtual screening through a similarity search, and to identify the ability of the peptide to behave as a potential useful drug, complemented with an analysis of its bioactivity and pharmacokinetics indices related to the ADMET (absorption, distribution, metabolism, excretion, and toxicity) features. The results represent a new confirmation of the superiority of the MN12SX density functional in the fulfilment of the Janak and ionization energy theorems through the proposed KID procedure. This has been useful for the accurate prediction of the CDFT reactivity descriptors that help in understanding the chemical reactivity. The computational pharmacokinetics study revealed the potential ability of alternaramide as a therapeutic drug by interacting with GPCR ligands and protease inhibitors. The ADMET indices confirm this assertion through the absence of toxicity and good absorption and distribution properties.
Collapse
|
28
|
Patel KD, Gulick AM. Anti-Zika candidates from a marine fungus with a remarkable biosynthetic repertoire. J Biol Chem 2021; 297:101047. [PMID: 34358564 PMCID: PMC8384895 DOI: 10.1016/j.jbc.2021.101047] [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] [Indexed: 11/02/2022] Open
Abstract
The study of natural products provides exciting opportunities for the discovery of novel biologically active molecules and biosynthetic pathways. Recently, Yuan and colleagues described 30 cyclic depsipeptides that are biosynthesized by proteins encoded by three distinct gene clusters in the marine fungus, Beauveria felina. Genetic and biochemical studies confirmed the involvement of nonribosomal peptide synthetases in the production of multiple compounds, some of which inhibit Zika virus replication.
Collapse
Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, New York, USA.
| |
Collapse
|
29
|
The Nonribosomal Peptide Valinomycin: From Discovery to Bioactivity and Biosynthesis. Microorganisms 2021; 9:microorganisms9040780. [PMID: 33917912 PMCID: PMC8068249 DOI: 10.3390/microorganisms9040780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Valinomycin is a nonribosomal peptide that was discovered from Streptomyces in 1955. Over the past more than six decades, it has received continuous attention due to its special chemical structure and broad biological activities. Although many research papers have been published on valinomycin, there has not yet been a comprehensive review that summarizes the diverse studies ranging from structural characterization, biogenesis, and bioactivity to the identification of biosynthetic gene clusters and heterologous biosynthesis. In this review, we aim to provide an overview of valinomycin to address this gap, covering from 1955 to 2020. First, we introduce the chemical structure of valinomycin together with its chemical properties. Then, we summarize the broad spectrum of bioactivities of valinomycin. Finally, we describe the valinomycin biosynthetic gene cluster and reconstituted biosynthesis of valinomycin. With that, we discuss possible opportunities for the future research and development of valinomycin.
Collapse
|
30
|
A Novel Cyclic Pentadepsipeptide, N-Methylsansalvamide, Suppresses Angiogenic Responses and Exhibits Antitumor Efficacy against Bladder Cancer. Cancers (Basel) 2021; 13:cancers13020191. [PMID: 33430488 PMCID: PMC7827157 DOI: 10.3390/cancers13020191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary We found a novel cyclic pentadepsipeptide, N-methylsansalvamide (MSSV), and evaluated its anti-tumor action against bladder cancer using in vitro and in vivo model systems. Additionally, we report its anti-angiogenic responses both in vitro and in vivo. Moreover, acute toxicity test and tissue staining for liver function revealed that orally administered MSSV (2000 mg/kg for 14 days) exerted no harmful effects as it did not cause animal death, undesirable weigh alteration, adverse clinical symptoms, and abnormal biochemical marker levels (AST, ALT). Abstract Here, we explored the anti-tumor efficacy of a cyclic pentadepsipeptide, N-methylsansalvamide (MSSV), in bladder cancer. MSSV inhibited the proliferation of both bladder cancer 5637 and T24 cells, which was attributed to the G1-phase cell cycle arrest, apoptosis induction, and alteration of mitogen-activated protein kinases (MAPKs) and protein kinase b (AKT) signaling pathways. Additionally, the treatment of bladder cancer cells with MSSV suppressed migratory and invasive potential via the transcription factor-mediated expression of matrix metalloproteinase 9 (MMP-9). MSSV abrogated vascular endothelial growth factor (VEGF)-induced angiogenic responses in vitro and in vivo. Furthermore, our result showed the potent anti-tumor efficacy of MSSV in a xenograft mouse model implanted with bladder cancer 5637 cells. Finally, acute toxicity test data obtained from blood biochemical test and liver staining indicated that the oral administration of MSSV at 2000 mg/kg caused no adverse cytotoxic effects. Our preclinical data described the potent anti-angiogenic and anti-tumor efficacy of MSSV and showed no signs of acute toxicity, thereby suggesting the putative potential of oral MSSV as a novel anti-tumor agent in bladder cancer treatment.
Collapse
|
31
|
Urbaniak M, Waśkiewicz A, Stępień Ł. Fusarium Cyclodepsipeptide Mycotoxins: Chemistry, Biosynthesis, and Occurrence. Toxins (Basel) 2020; 12:toxins12120765. [PMID: 33287253 PMCID: PMC7761704 DOI: 10.3390/toxins12120765] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
Most of the fungi from the Fusarium genus are pathogenic to cereals, vegetables, and fruits and the products of their secondary metabolism mycotoxins may accumulate in foods and feeds. Non-ribosomal cyclodepsipeptides are one of the main mycotoxin groups and include beauvericins (BEAs), enniatins (ENNs), and beauvenniatins (BEAEs). When ingested, even small amounts of these metabolites significantly affect human and animal health. On the other hand, in view of their antimicrobial activities and cytotoxicity, they may be used as components in drug discovery and processing and are considered as suitable candidates for anti-cancer drugs. Therefore, it is crucial to expand the existing knowledge about cyclodepsipeptides and to search for new analogues of these compounds. The present manuscript aimed to highlight the extensive variability of cyclodepsipeptides by describing chemistry, biosynthesis, and occurrence of BEAs, ENNs, and BEAEs in foods and feeds. Moreover, the co-occurrence of Fusarium species was compared to the amounts of toxins in crops, vegetables, and fruits from different regions of the world.
Collapse
Affiliation(s)
- Monika Urbaniak
- Plant-Pathogen Interaction Team, Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
- Correspondence: (M.U.); (Ł.S.); Tel.: +48-616-55-02-34 (M.U.)
| | - Agnieszka Waśkiewicz
- Department of Chemistry, Poznan University of Life Sciences, Wojska Polskiego 75, 60-625 Poznań, Poland;
| | - Łukasz Stępień
- Plant-Pathogen Interaction Team, Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
- Correspondence: (M.U.); (Ł.S.); Tel.: +48-616-55-02-34 (M.U.)
| |
Collapse
|
32
|
Urbaniak M, Waśkiewicz A, Koczyk G, Błaszczyk L, Stępień Ł. Divergence of Beauvericin Synthase Gene among Fusarium and Trichoderma Species. J Fungi (Basel) 2020; 6:E288. [PMID: 33203083 PMCID: PMC7712144 DOI: 10.3390/jof6040288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Beauvericin (BEA) is a cyclodepsipeptide mycotoxin, showing insecticidal, antibiotic and antimicrobial activities, as well as inducing apoptosis of cancer cell lines. BEA can be produced by multiple fungal species, including saprotrophs, plant, insect and human pathogens, particularly belonging to Fusarium, Beauveria and Isaria genera. The ability of Trichoderma species to produce BEA was until now uncertain. Biosynthesis of BEA is governed by a non-ribosomal peptide synthase (NRPS), known as beauvericin synthase (BEAS), which appears to present considerable divergence among different fungal species. In the present study we compared the production of beauvericin among Fusarium and Trichoderma strains using UPLC methods. BEAS fragments were sequenced and analyzed to examine the level of the gene's divergence between these two genera and confirm the presence of active BEAS copy in Trichoderma. Seventeen strains of twelve species were studied and phylogenetic analysis showed distinctive grouping of Fusarium and Trichoderma strains. The highest producers of beauvericin were F. proliferatum and F. nygamai. Trichoderma strains of three species (T. atroviride, T. viride, T. koningiopsis) were minor BEA producers. The study showed beauvericin production by Fusarium and Trichoderma species and high variance of the non-ribosomal peptide synthase gene among fungal species from the Hypocreales order.
Collapse
Affiliation(s)
- Monika Urbaniak
- Plant-Pathogen Interaction Team, Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Agnieszka Waśkiewicz
- Department of Chemistry, Poznan University of Life Sciences, Wojska Polskiego 75, 60-625 Poznań, Poland;
| | - Grzegorz Koczyk
- Functional Evolution of Biological Systems Team, Department of Biometrics and Bioinformatics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Lidia Błaszczyk
- Plant Microbiome Structure and Function Team, Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Łukasz Stępień
- Plant-Pathogen Interaction Team, Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| |
Collapse
|
33
|
Alonzo DA, Schmeing TM. Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations. Protein Sci 2020; 29:2316-2347. [PMID: 33073901 DOI: 10.1002/pro.3979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
Depsipeptides are compounds that contain both ester bonds and amide bonds. Important natural product depsipeptides include the piscicide antimycin, the K+ ionophores cereulide and valinomycin, the anticancer agent cryptophycin, and the antimicrobial kutzneride. Furthermore, database searches return hundreds of uncharacterized systems likely to produce novel depsipeptides. These compounds are made by specialized nonribosomal peptide synthetases (NRPSs). NRPSs are biosynthetic megaenzymes that use a module architecture and multi-step catalytic cycle to assemble monomer substrates into peptides, or in the case of specialized depsipeptide synthetases, depsipeptides. Two NRPS domains, the condensation domain and the thioesterase domain, catalyze ester bond formation, and ester bonds are introduced into depsipeptides in several different ways. The two most common occur during cyclization, in a reaction between a hydroxy-containing side chain and the C-terminal amino acid residue in a peptide intermediate, and during incorporation into the growing peptide chain of an α-hydroxy acyl moiety, recruited either by direct selection of an α-hydroxy acid substrate or by selection of an α-keto acid substrate that is reduced in situ. In this article, we discuss how and when these esters are introduced during depsipeptide synthesis, survey notable depsipeptide synthetases, and review insight into bacterial depsipeptide synthetases recently gained from structural studies.
Collapse
Affiliation(s)
- Diego A Alonzo
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| |
Collapse
|
34
|
Stadelmann T, Subramanian G, Menon S, Townsend CE, Lokey RS, Ebert MO, Riniker S. Connecting the conformational behavior of cyclic octadepsipeptides with their ionophoric property and membrane permeability. Org Biomol Chem 2020; 18:7110-7126. [PMID: 32902550 PMCID: PMC7796559 DOI: 10.1039/d0ob01447h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cyclic octadepsipeptides such as PF1022A and its synthetic derivative emodepside exhibit anthelmintic activity with the latter sold as a commercial drug treatment against gastrointestinal nematodes for animal health use. The structure-permeability relationship of these cyclic depsipeptides that could ultimately provide insights into the compound bioavailability is not yet well understood. The fully N-methylated amide backbone and apolar sidechain residues do not allow for the formation of intramolecular hydrogen bonds, normally observed in the membrane-permeable conformations of cyclic peptides. Hence, any understanding gained on these depsipeptides would serve as a prototype for future design strategies. In previous nuclear magnetic resonance (NMR) studies, two macrocyclic core conformers of emodepside were detected, one with all backbone amides in trans-configuration (hereon referred as the symmetric conformer) and the other with one amide in cis-configuration (hereon referred as the asymmetric conformer). In addition, these depsipeptides were also reported to be ionophores with a preference of potassium over sodium. In this study, we relate the conformational behavior of PF1022A, emodepside, and closely related analogs with their ionophoric characteristic probed using NMR and molecular dynamics (MD) simulations and finally evaluated their passive membrane permeability using PAMPA. We find that the equilibrium between the two core conformers shifts more towards the symmetric conformer upon addition of monovalent cations with selectivity for potassium over sodium. Both the NMR experiments and the theoretical Markov state models based on extensive MD simulations indicate a more rigid backbone for the asymmetric conformation, whereas the symmetric conformation shows greater flexibility. The experimental results further advocate for the symmetric conformation binding the cation. The PAMPA results suggest that the investigated depsipeptides are retained in the membrane, which may be advantageous for the likely target, a membrane-bound potassium channel.
Collapse
Affiliation(s)
- Thomas Stadelmann
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland.
| | - Govindan Subramanian
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, Michigan 49007, USA
| | - Sanjay Menon
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, Michigan 49007, USA
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 93064, USA
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 93064, USA
| | - Marc-Olivier Ebert
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland.
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland.
| |
Collapse
|
35
|
Production of Diverse Beauveriolide Analogs in Closely Related Fungi: a Rare Case of Fungal Chemodiversity. mSphere 2020; 5:5/5/e00667-20. [PMID: 32878933 PMCID: PMC7471007 DOI: 10.1128/msphere.00667-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Fungal chemodiversity is well known in part due to the production of diverse analogous compounds by a single biosynthetic gene cluster (BGC). Usually, similar or the same metabolites are produced by closely related fungal species under a given condition, the foundation of fungal chemotaxonomy. Here, we report a rare case of the production of the cyclodepsipeptide beauveriolides (BVDs) in three insect-pathogenic fungi. We found that the more closely related fungi Beauveria bassiana and Beauveria brongniartii produced structurally distinct analogs of BVDs, whereas the less-close relatives B. brongniartii and Cordyceps militaris biosynthesized structurally similar congeners under the same growth condition. It was verified that a conserved BGC containing four genes is responsible for BVD biosynthesis in three fungi, including a polyketide synthase (PKS) for the production of 3-hydroxy fatty acids (FAs) with chain length variations. In contrast to BVD production patterns, phylogenetic analysis of the BGC enzymes or enzyme domains largely resulted in the congruence relationship with fungal speciation. Feeding assays demonstrated that an FA with a chain length of eight carbon atoms was preferentially utilized, whereas an FA with a chain longer than 10 carbon atoms could not be used as a substrate for BVD biosynthesis. Insect survival assays suggested that the contribution of BVDs to fungal virulence might be associated with the susceptibility of insect species. The results of this study enrich the knowledge of fungal secondary metabolic diversity that can question the reliability of fungal chemotaxonomy.IMPORTANCE Fungal chemotaxonomy is an approach to classify fungi based on the fungal production profile of metabolites, especially the secondary metabolites. We found an atypical example that could question the reliability of fungal chemical classifications in this study, i.e., the more closely related entomopathogenic species Beauveria bassiana and Beauveria brongniartii produced structurally different congeners of the cyclodepsipeptide beauveriolides, whereas the rather divergent species B. brongniartii and Cordyceps militaris biosynthesized similar analogs under the same growth condition. The conserved biosynthetic gene cluster (BGC) containing four genes present in each species is responsible for beauveriolide production. In contrast to the compound formation profiles, the phylogenies of biosynthetic enzymes or enzymatic domains show associations with fungal speciation. Dependent on the insect species, production of beauveriolides may contribute to fungal virulence against the susceptible insect hosts. The findings in this study augment the diversity of fungal secondary metabolisms.
Collapse
|
36
|
Grab HA, Kirsch VC, Sieber SA, Bach T. Total Synthesis of the Cyclic Depsipeptide Vioprolide D via its (Z)-Diastereoisomer. Angew Chem Int Ed Engl 2020; 59:12357-12361. [PMID: 32126146 PMCID: PMC7383572 DOI: 10.1002/anie.202002328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Indexed: 12/15/2022]
Abstract
The first total synthesis of vioprolide D was accomplished in an overall yield of 2.0 % starting from methyl (2S)-3-benzyloxy-2-hydroxypropanoate (16 steps in the longest linear sequence). The cyclic depsipeptide was assembled from two building blocks of similar size and complexity in a modular, highly convergent approach. Peptide bond formation at the C-terminal dehydrobutyrine amino acid of the northern fragment was possible via its (Z)-diastereoisomer. After macrolactamization and formation of the thiazoline ring, the (Z)-double bond of the dehydrobutyrine unit was isomerized to the (E)-double bond of the natural product. The cytotoxicity of vioprolide D is significantly higher than that of its (Z)-diastereoisomer.
Collapse
Affiliation(s)
- Hanusch A. Grab
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| | - Volker C. Kirsch
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| | - Stephan A. Sieber
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| | - Thorsten Bach
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485747GarchingGermany
| |
Collapse
|
37
|
Czernek J, Brus J. Polymorphic Forms of Valinomycin Investigated by NMR Crystallography. Int J Mol Sci 2020; 21:E4907. [PMID: 32664570 PMCID: PMC7404035 DOI: 10.3390/ijms21144907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.
Collapse
Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square #2, 16206 Prague, Czech Republic;
| | | |
Collapse
|
38
|
Cyclodepsipeptide Biosynthesis in Hypocreales Fungi and Sequence Divergence of The Non-Ribosomal Peptide Synthase Genes. Pathogens 2020; 9:pathogens9070552. [PMID: 32660015 PMCID: PMC7400199 DOI: 10.3390/pathogens9070552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
Fungi from the Hypocreales order synthesize a range of toxic non-ribosomal cyclic peptides with antimicrobial, insecticidal and cytotoxic activities. Entomopathogenic Beauveria, Isaria and Cordyceps as well as phytopathogenic Fusarium spp. are known producers of beauvericins (BEAs), beauvenniatins (BEAEs) or enniatins (ENNs). The compounds are synthesized by beauvericin/enniatin synthase (BEAS/ESYN1), which shows significant sequence divergence among Hypocreales members. We investigated ENN, BEA and BEAE production among entomopathogenic (Beauveria, Cordyceps, Isaria) and phytopathogenic (Fusarium) fungi; BEA and ENNs were quantified using an LC-MS/MS method. Phylogenetic analysis of partial sequences of putative BEAS/ESYN1 amplicons was also made. Nineteen fungal strains were identified based on sequence analysis of amplified ITS and tef-1α regions. BEA was produced by all investigated fungi, with F. proliferatum and F. concentricum being the most efficient producers. ENNs were synthesized mostly by F. acuminatum, F. avenaceum and C. confragosa. The phylogeny reconstruction suggests that ancestral BEA biosynthesis independently diverged into biosynthesis of other compounds. The divergent positioning of three Fusarium isolates raises the possibility of parallel acquisition of cyclic depsipeptide synthases in ancient complexes within Fusarium genus. Different fungi have independently evolved NRPS genes involved in depsipeptide biosynthesis, with functional adaptation towards biosynthesis of overlapping yet diversified metabolite profiles.
Collapse
|
39
|
Cytotoxic Activities and Molecular Mechanisms of the Beauvericin and Beauvericin G 1 Microbial Products against Melanoma Cells. Molecules 2020; 25:molecules25081974. [PMID: 32340351 PMCID: PMC7221855 DOI: 10.3390/molecules25081974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Melanoma is the most serious type of skin cancer and remains highly drug-resistant. Therefore, the discovery of novel effective agents against melanoma is in high demand. Herein, we investigated the cytotoxic activities in melanoma cells and underlying molecular mechanisms of beauvericin (BEA) and its analogue beauvericin G1 (BEA G1), which are cyclohexadepsipeptides isolated from fungi. BEA and BEA G1 significantly suppressed the growth, clonogenicity, migration, and invasion of A375SM human melanoma cells and promoted caspase-dependent apoptosis through upregulation of death receptors, as well as modulation of pro- and anti-apoptotic Bcl-2 family members. Furthermore, the effects of BEA and BEA G1 were associated with the suppression of multiple molecular targets that play crucial roles in melanoma oncogenesis, including ERK, JNK, p38, NF-κB, STAT3, and MITF. Notably, the cytotoxic efficacy of BEA G1 against A375SM cells was stronger than that of BEA. These findings suggest that BEA and BEA G1 can be further investigated as potent cytotoxic natural compounds for the suppression of melanoma progression.
Collapse
|
40
|
Grab HA, Kirsch VC, Sieber SA, Bach T. Totalsynthese des cyclischen Depsipeptids Vioprolid D über sein (
Z
)‐Diastereomer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hanusch A. Grab
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| | - Volker C. Kirsch
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| | - Thorsten Bach
- Department Chemie Technische Universität München Lichtenbergstrasse 4 85747 Garching Deutschland
| |
Collapse
|
41
|
Gao YQ, Du ST, Xiao J, Wang DC, Han WB, Zhang Q, Gao JM. Isolation and Characterization of Antifungal Metabolites from the Melia azedarach-Associated Fungus Diaporthe eucalyptorum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2418-2425. [PMID: 32011876 DOI: 10.1021/acs.jafc.9b07825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Two biosynthetically related new metabolites, eucalyptacid A (1) and eucalactam B (2), along with six known compounds (3-8), eugenitol (3), cytosporone C (4), 4-hydroxyphenethyl alcohol (5), 1-(4-hydroxyphenyl)ethane-1,2-diol (6), N-(2-hydroxy-2-phenylethyl)acetamide (7), and phomopene (8), were isolated from the solid rice cultures of the endophytic fungus Diaporthe eucalyptorum KY-9 that had been isolated from Melia azedarach. Also, two further new derivatives (2a, 2b) were prepared from 2. The structures were elucidated by exhaustive analysis of NMR and ESIMS data and chemical methods such as Marfey's protocol. Compound 1 was identified as a rare polyketide fatty acid, (8E)-3,5,11-trihydroxy-2,10,12-trimethyltetradecenoic acid, and 2 was determined to be the first cyclic depsipeptide containing the same fatty acid unit as 1 and a Gly-Gly-Thr tripeptide chain. Its N-terminal end is N-acylated by an 11-hydroxy fatty acid with a branch alkyl chain of 14:1. The 11-hydroxyl group connects to the carboxylic group of the C-terminal amino acid to form a 22-membered lactone ring. A hypothetical biosynthetic pathway for the new polyketides is proposed. The isolated compounds were assayed for their inhibition against four plant pathogenic fungi, Alternaria solani, Botrytis cinerea, Fusarium solani, and Gibberella saubinettii. Compounds 1, 4, 6, and 7 exhibited antifungal activities against Alternaria solani, with minimal inhibitory concentration (MIC) values from 6.25 to 50 μM. Thus, strain KY-9 represents an untapped source for the development of biological control agents to prevent the infection of pathogenic fungus A. solani.
Collapse
Affiliation(s)
- Yu-Qi Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| | - Shuang-Tian Du
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| | - Jian Xiao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| | - Da-Cheng Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| | - Wen-Bo Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy , Northwest A&F University , Yangling 712100 , People's Republic of China
| |
Collapse
|
42
|
Lobo-Ruiz A, Tulla-Puche J. General Fmoc-Based Solid-Phase Synthesis of Complex Depsipeptides Circumventing Problematic Fmoc Removal. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ariadna Lobo-Ruiz
- Department of Inorganic and Organic Chemistry - Organic Chemistry Section; University of Barcelona; Martí i Franquès 1-11 08028 Barcelona Catalonia Spain
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry - Organic Chemistry Section; University of Barcelona; Martí i Franquès 1-11 08028 Barcelona Catalonia Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB); Martí i Franquès 1-11 08028 Barcelona Catalonia Spain
| |
Collapse
|
43
|
Fusarium Secondary Metabolism Biosynthetic Pathways: So Close but So Far Away. REFERENCE SERIES IN PHYTOCHEMISTRY 2020. [DOI: 10.1007/978-3-319-96397-6_28] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
44
|
Linden A, Magirius JEF, Heimgartner H. Solid-state conformations of linear depsipeptide amides with an alternating sequence of α,α-disubstituted α-amino acid and α-hydroxy acid. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:1-9. [PMID: 31919301 DOI: 10.1107/s2053229619016073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 11/28/2019] [Indexed: 11/10/2022]
Abstract
Depsipeptides and cyclodepsipeptides are analogues of the corresponding peptides in which one or more amide groups are replaced by ester functions. Reports of crystal structures of linear depsipeptides are rare. The crystal structures and conformational analyses of four depsipeptides with an alternating sequence of an α,α-disubstituted α-amino acid and an α-hydroxy acid are reported. The molecules in the linear hexadepsipeptide amide in (S)-Pms-Acp-(S)-Pms-Acp-(S)-Pms-Acp-NMe2 acetonitrile solvate, C47H58N4O9·C2H3N, (3b), as well as in the related linear tetradepsipeptide amide (S)-Pms-Aib-(S)-Pms-Aib-NMe2, C28H37N3O6, (5a), the diastereoisomeric mixture (S,R)-Pms-Acp-(R,S)-Pms-Acp-NMe2/(R,S)-Pms-Acp-(R,S)-Pms-Acp-NMe2 (1:1), C32H41N3O6, (5b), and (R,S)-Mns-Acp-(S,R)-Mns-Acp-NMe2, C30H37N3O6, (5c) (Pms is phenyllactic acid, Acp is 1-aminocyclopentanecarboxylic acid and Mns is mandelic acid), generally adopt a β-turn conformation in the solid state, which is stabilized by intramolecular N-H...O hydrogen bonds. Whereas β-turns of type I (or I') are formed in the cases of (3b), (5a) and (5b), which contain phenyllactic acid, the torsion angles for (5c), which incorporates mandelic acid, indicate a β-turn in between type I and type III. Intermolecular N-H...O and O-H...O hydrogen bonds link the molecules of (3a) and (5b) into extended chains, and those of (5a) and (5c) into two-dimensional networks.
Collapse
Affiliation(s)
- Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - J E Florian Magirius
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Heinz Heimgartner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| |
Collapse
|
45
|
On-resin multicomponent 1,3-dipolar cycloaddition of cyclopentanone-proline enamines and sulfonylazides as an efficient tool for the synthesis of amidino depsipeptide mimics. Amino Acids 2019; 52:15-24. [PMID: 31781906 DOI: 10.1007/s00726-019-02805-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023]
Abstract
Depsipeptides are biologically active peptide derivatives that possess a high therapeutic interest. The development of depsipeptide mimics characterized by a chemical diversity could lead to compounds with enhanced features and activity. In this work, an on-resin multicomponent procedure for the synthesis of amidino depsipeptide mimics is described. This approach exploits a metal-free 1,3-dipolar cycloaddition of cyclopentanone-proline enamines and sulfonylazides. In this reaction, the obtained primary cycloadduct undergoes a ring opening and molecular rearrangement giving access to a linear sulfonyl amidine functionalized with both a peptide chain and a diazoalkane. The so-obtained diazo function "one pot" reacts with the carboxylic group of N-Fmoc-protected amino acids leading to amidino depsipeptide mimics possessing a C4 aliphatic chain. An important advantage of this procedure is the possibility to easily obtain amidino-functionalized derivatives that are proteolytically stable peptide bond bioisosteres. Moreover, the conformational freedom given by the alkyl chain could promote the obtainment of cyclic depsipeptide with a stabilized secondary structure as demonstrated with both in silico calculations and experimental conformational studies. Finally, labeled depsipeptide mimics can be also synthesized using a fluorescent sulfonylazide in the multicomponent reaction.
Collapse
|
46
|
Brango-Vanegas J, Martinho LA, Bessa LJ, Vasconcelos AG, Plácido A, Pereira AL, Leite JRSA, Machado AHL. Synthesis of novel sulfide-based cyclic peptidomimetic analogues to solonamides. Beilstein J Org Chem 2019; 15:2544-2551. [PMID: 31728168 PMCID: PMC6839570 DOI: 10.3762/bjoc.15.247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 10/09/2019] [Indexed: 11/23/2022] Open
Abstract
Eight new sulfide-based cyclic peptidomimetic analogues of solonamides A and B have been synthesized via solid-phase peptide synthesis and SN2’ reaction on a Morita–Baylis–Hillman (MBH) residue introduced at the N-terminal of a tetrapeptide. This last step takes advantage of the electrophilic feature of the MBH residue and represents a new cyclization strategy occurring. The analogues were prepared in moderate overall yields and did not show toxic effects on Staphylococcus aureus growth and were not toxic to human fibroblasts. Two of them inhibited the hemolytic activity of S. aureus, suggesting an interfering action in the bacterial quorum sensing similar to the one already reported for solonamides.
Collapse
Affiliation(s)
- José Brango-Vanegas
- Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Asa Norte, Brasília DF, Brasil
| | - Luan A Martinho
- Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Asa Norte, Brasília DF, Brasil
| | - Lucinda J Bessa
- LAQV/REQUIMTE, Departamento de Química e Bíoquímica, Faculdade de Ciências da Universidade do Porto, 4169007, Porto, Portugal
| | - Andreanne G Vasconcelos
- Área de Morfologia, Faculdade de Medicina, Universidade de Brasília, 70910-900, Brasília, DF, Brasil
| | - Alexandra Plácido
- Glial Cell Biology Lab, Instituto de Investigação e Inovação em Saúde, i3S, Universidade do Porto, 420013, Porto, Portugal.,Bioprospectum, Lda, UPTEC, 4200135, Porto, Portugal
| | - Alex L Pereira
- Campus de Ceilândia, Universidade de Brasília, Centro Metropolitano, 72220-275, Ceilândia Sul, Ceilândia, DF, Brazil
| | - José R S A Leite
- Área de Morfologia, Faculdade de Medicina, Universidade de Brasília, 70910-900, Brasília, DF, Brasil
| | - Angelo H L Machado
- Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, 70910-900, Asa Norte, Brasília DF, Brasil
| |
Collapse
|
47
|
Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
Collapse
Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
| |
Collapse
|
48
|
Kyne GM, Curtis MP, Keiser J, Woods DJ. Soil‐transmitted Helminthiasis – Challenges with Discovery of Novel Anthelmintics. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527808656.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
49
|
Blanc A, Perrin DM. Synthesis of 3a-hydroxyhexahydropyrrolo[2,3-B]Indole-2-carboxamide, an oxidation product of tryptophan present in natural products. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Antoine Blanc
- Department of Chemistry; University of British Columbia; Vancouver V6T 1Z1 Canada
| | - David M. Perrin
- Department of Chemistry; University of British Columbia; Vancouver V6T 1Z1 Canada
| |
Collapse
|
50
|
D'Amato A, Della Sala G, Izzo I, Costabile C, Masuda Y, De Riccardis F. Cyclic Octamer Peptoids: Simplified Isosters of Bioactive Fungal Cyclodepsipeptides. Molecules 2018; 23:molecules23071779. [PMID: 30029532 PMCID: PMC6100324 DOI: 10.3390/molecules23071779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/17/2022] Open
Abstract
Cyclic peptoids have recently emerged as an important class of bioactive scaffolds with unique conformational properties and excellent metabolic stabilities. In this paper, we describe the design and synthesis of novel cyclic octamer peptoids as simplified isosters of mycotoxin depsipeptides bassianolide, verticilide A1, PF1022A and PF1022B. We also examine their complexing abilities in the presence of sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (TFPB) salt and explore their general insecticidal activity. Finally, we discuss the possible relationship between structural features of free and Na⁺-complexed cyclic octamer peptoids and bioactivities in light of conformational isomerism, a crucial factor affecting cyclic peptoids' biomimetic potentials.
Collapse
Affiliation(s)
- Assunta D'Amato
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Giorgio Della Sala
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Chiara Costabile
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Yuichi Masuda
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu 514-8507, Japan.
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| |
Collapse
|