1
|
Muangkaew P, Prasad D, De Roo V, Verleysen Y, Zhou L, De Mot R, Höfte M, Madder A, Geudens N, Martins JC. Breaking Cycles: Saponification-Enhanced NMR Fingerprint Matching for the Identification and Stereochemical Evaluation of Cyclic Lipodepsipeptides from Natural Sources. Chemistry 2024:e202400667. [PMID: 38647356 DOI: 10.1002/chem.202400667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 04/25/2024]
Abstract
We previously described NMR based fingerprint matching with peptide backbone resonances as a fast and reliable structural dereplication approach for Pseudomonas cyclic lipodepsipeptides (CLiPs). In combination with total synthesis of a small library of configurational CLiP congeners this also allows unambiguous determination of stereochemistry, facilitating structure-activity relationship studies and enabling three-dimensional structure determination. However, the on-resin macrocycle formation in the synthetic workflow brings considerable burden and limits universal applicability. This drawback is here removed altogether by also transforming the native CLiP into a linearized analogue by controlled saponification of the ester bond. This eliminates the need for macrocycle formation, limiting the synthesis effort to linear peptide analogues. NMR fingerprints of such linear peptide analogues display a sufficiently distinctive chemical shift fingerprint to act as effective discriminators. The approach is developed using viscosin group CLiPs and subsequently demonstrated on putisolvin, leading to a structural revision, and tanniamide from Pseudomonas ekonensis COR58, a newly isolated lipododecapeptide that defines a new group characterized by a ten-residue large macrocycle, the largest to date in the Pseudomonas CLiP portfolio. These examples demonstrate the effectiveness of the saponification- enhanced approach that broadens applicability of NMR fingerprint matching for the determination of the stereochemistry of CLiPs.
Collapse
Affiliation(s)
- Penthip Muangkaew
- Organic Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Durga Prasad
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Vic De Roo
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Yentl Verleysen
- Organic Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - René De Mot
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Annemieke Madder
- Organic Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| |
Collapse
|
2
|
Faleye OO, Faleye OS, Lee JH, Lee J. Antibacterial and antibiofilm activities of iodinated hydrocarbons against Vibrio parahaemolyticus and Staphylococcus aureus. Sci Rep 2024; 14:9160. [PMID: 38644387 PMCID: PMC11033260 DOI: 10.1038/s41598-024-55479-7] [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: 08/29/2023] [Accepted: 02/23/2024] [Indexed: 04/23/2024] Open
Abstract
Food-related illnesses have become a growing public concern due to their considerable socioeconomic and medical impacts. Vibrio parahaemolyticus and Staphylococcus aureus have been implicated as causative organisms of food-related infections and poisoning, and both can form biofilms which confer antibiotic resistance. Hence, the need for continuous search for compounds with antibiofilm and antivirulence properties. In this study, 22 iodinated hydrocarbons were screened for their antibiofilm activity, and of these, iodopropynyl butylcarbamate (IPBC) was found to effectively control biofilm formation of both pathogens with a MIC of 50 µg/mL which was bactericidal to V. parahaemolyticus and S. aureus. Microscopic studies confirmed IPBC inhibits biofilm formation of both bacteria and also disrupted their mixed biofilm formation. Furthermore, IPBC suppressed virulence activities such as motility and hemolytic activity of V. parahaemolyticus and the cell surface hydrophobicity of S. aureus. It exhibited a preservative potential against both pathogens in a shrimp model. IPBC disrupted the cell membrane of S. aureus and V. parahaemolyticus and differentially affected gene expressions related to biofilm formation and virulence. Additionally, it displayed broad-spectrum antibiofilm activities against other clinically relevant pathogens. These findings indicate IPBC offers a potential means of controlling infections mediated by Vibrio and Staphylococcus biofilms.
Collapse
Affiliation(s)
| | - Olajide Sunday Faleye
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Republic of Korea
| | - Jin-Hyung Lee
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Republic of Korea.
| |
Collapse
|
3
|
Mishra S, Gupta A, Jain S, Vaidya A. Anticancer mechanisms of β-carbolines. Chem Biol Drug Des 2024; 103:e14521. [PMID: 38653576 DOI: 10.1111/cbdd.14521] [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: 01/12/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
β-Carboline nucleus is therapeutically valuable in medicinal chemistry for the treatment of varied number of diseases, most importantly cancer. The potent and wide-ranging activity of β-carboline has established them as imperative pharmacological scaffolds especially in the cancer treatment. Numerous derivatives such as Tetrahydro β-carbolines, metal complexed β-carbolines, mono, di and tri substituted β-carbolines have been reported to possess dynamic anticancer activity. These different substituted β-carboline derivatives had shown different mechanism of action and plays important role in anticancer drug discovery and development. The review is an update of the chemistry of β-carbolines, both synthetic and natural origin acting through various targets against cancerous cells. In addition to this, studies of multitarget molecules designed by coupling β-carbolines along with other mechanisms for treatment of neoplasm are also summarized.
Collapse
Affiliation(s)
- Shivam Mishra
- Pharmacy College Saifai, Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh, India
| | - Aditi Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shweta Jain
- Sir Madan Lal Institute of Pharmacy, Etawah, Uttar Pradesh, India
| | - Ankur Vaidya
- Pharmacy College Saifai, Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh, India
| |
Collapse
|
4
|
Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [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: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
Collapse
Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
| |
Collapse
|
5
|
Corbett MK, Gifford A, Fimognari N, Watkin ELJ. Analysis of element yield, bacterial community structure and the impact of carbon sources for bioleaching rare earth elements from high grade monazite. Res Microbiol 2024; 175:104133. [PMID: 37683878 DOI: 10.1016/j.resmic.2023.104133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Rare earth element (REE) recovery from waste streams, mine tailings or recyclable components using bioleaching is gaining traction due to the shortage and security of REE supply as well as the environmental problems that occur from processing and refining. Four heterotrophic microbial species with known phosphate solubilizing capabilities were evaluated for their ability to leach REE from a high-grade monazite when provided with either galactose, fructose or maltose. Supplying fructose resulted in the greatest amount of REE leached from the ore due to the largest amount of organic acid produced. Gluconic acid was the dominant organic acid identified produced by the cultures, followed by acetic acid. The monazite proved difficult to leach with the different carbon sources, with preferential release of Ce over La, Nd and Pr.
Collapse
Affiliation(s)
- Melissa K Corbett
- Curtin Medical School, Curtin University GPO Box U1987, Perth, Australia.
| | - April Gifford
- Curtin Medical School, Curtin University GPO Box U1987, Perth, Australia.
| | - Nick Fimognari
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, Australia.
| | - Elizabeth L J Watkin
- Curtin Medical School, Curtin University GPO Box U1987, Perth, Australia; School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, Australia.
| |
Collapse
|
6
|
Chen X, Zhang M, Tang L, Huang S, Guo T, Li Q. Screening and characterization of biocontrol bacteria isolated from Ageratum conyzoides against Collectotrichum fructicola causing Chinese plum ( Prunus salicina Lindl.) anthracnose. Front Microbiol 2023; 14:1296755. [PMID: 38130944 PMCID: PMC10734640 DOI: 10.3389/fmicb.2023.1296755] [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: 09/19/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Chinese plum (Prunus salicina Lindl.) is a nutritionally and economically important stone fruit widely grown around the world. Anthracnose, caused by Collectotrichum spp., is one of the primary biotic stress factors limiting plum production. Medicinal plants may harbor rhizospheric or endophytic microorganisms that produce bioactive metabolites that can be used as anthracnose biocontrol agents. Here, 27 bacterial isolates from the medicinal plant A. conyzoides with diverse antagonistic activities against C. fructicola were screened. Based on morphological, physiological, biochemical, and molecular characterization, 25 of these isolates belong to different species of genus Bacillus, one to Pseudomonas monsensis, and one more to Microbacterium phyllosphaerae. Eight representative strains showed high biocontrol efficacy against plum anthracnose in a pot experiment. In addition, several Bacillus isolates showed a broad spectrum of inhibitory activity against a variety of fungal phytopathogens. Analysis of the volatile organic compound profile of these eight representative strains revealed a total of 47 compounds, most of which were ketones, while the others included alkanes, alkenes, alcohols, pyrazines, and phenols. Overall, this study confirmed the potential value of eight bacterial isolates for development as anthracnose biocontrol agents.
Collapse
Affiliation(s)
| | | | | | | | | | - Qili Li
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| |
Collapse
|
7
|
Buroni S, Samy RP. Editorial: Burkholderia spp.-transmission, pathogenesis, host-pathogen interaction, prevention and treatment. Front Microbiol 2023; 14:1226865. [PMID: 37346750 PMCID: PMC10280153 DOI: 10.3389/fmicb.2023.1226865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Silvia Buroni
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
| | - Ramar Perumal Samy
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|