UPLC-MS chemical profiling and isolation of bioactive secondary metabolites from Ammi visnaga-derived endophyte Alternaria destruens assessed by in silico studies
9 affiliations
- 1Faculty of Pharmacy, Department of Pharmacognosy, Ain Shams University, Cairo, 11566, Egypt
- 2Department of Microbial Genetic Resources, National Gene Bank (NGB), Agricultural Research Center (ARC), Giza, 12619, Egypt
- 3School of Biotechnology, Nile University, Giza, 12677, Egypt
- 4Faculty of Science, Botany and Microbiology Department, Cairo University, Giza, Egypt
- 5Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, Egypt
- 6Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
- 7Biotechnology and Valorization of Natural Resources Laboratory, Faculty of Sciences, Université Ibn Zohr, Agadir, Morocco
- 8Imbewu Metabolomics Research, Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- 9Research Centre for Plant Metabolomics, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
Abstract
Microbial endophytes have emerged as a potential source of bioactive secondary metabolites and provide an excellent resource to overcome the challenges resulting from over-consumption of medicinal plants. Ammi visnaga is an Egyptian medicinal plant widely recognized for its medicinal value. The roots of A. visnaga are considered as waste products; the aim of this study is to explore the fungal endophytes associated with A.visnaga roots. Fungal isolate was identified using PCR; large-scale fermentation was performed on solid rice media followed by extraction with Ethyl acetate. The fungal extract was subjected to chromatographic purification utilizing VLC and HPLC. Isolated compounds were identified using HRESIMS and NMR techniques. UPLC-ESI-Q-Tof was utilized to perform the chemical profiling of the fungal extract. Disc diffusion and MIC experiments were performed to evaluate the antimicrobial activity. In silico assessment was performed using AutoDock Vina against ten bacterial proteins incorporated in DNA replication, antibiotic resistance, and virulence. Biovia Discovery Studio was utilized to assess the pharmacokinetic properties of the compounds applying ADMET protocol. Four compounds were isolated and identified from Alternaria destruens NGB-AvF1 including one previously undescribed perylene quinone epoxide ( 1) and three known polyketides ( 2–3 , 4). Metabolic profiling of the extract using UPLC-Q-Tof in the negative mode resulted in the tentative identification of 18 secondary metabolites belonging to different chemical classes with high percentages of polyketides, perylene quinones and isocoumarins. Antimicrobial evaluation revealed strong and selective antimicrobial activities for compounds 2 and 3 against Staphylococcus aureus , with inhibition zones of 28 mm and 30 mm, respectively. In silico assessment revealed favourable binding affinities for 2 and 3 with several key enzymes. Compound 2 exhibited the strongest binding with DNA ligase, β-lactamase, and Clumping factor A, while compound 3 showed high affinity for ClfA, DNA ligase and β-lactamase. Both compounds also interacted moderately with Sortase A, PBP2a, and BlaR1. These results suggest that compounds 2 and 3 possess multitarget antibacterial activity. A. destruens extract revealed wide chemical diversity and displayed a potent antimicrobial activity; in silico studies revealed the potential bacterial targets for the antimicrobial compounds. Compounds 2–3 displayed selective and potent antibacterial activity reinforcing their candidacy as lead compounds for further drug development.
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BibTeX
@article{singab2026uplcms,
title = {{UPLC-MS chemical profiling and isolation of bioactive secondary metabolites from Ammi visnaga-derived endophyte Alternaria destruens assessed by in silico studies}},
author = {Abdel Nasser B. Singab and Fadia Salah Youssef and Fayrouz H. Abd El-Megeed and Akram H. Mohamed and Sameh H. Youseif and Mohamed S. Mahmoud and Heba A. Dahdooh and Naziha Hassanein and Mohamed Ben-El-Caid and Msizi Innocent Mhlongo and Anathi Msobo and Ahmed M. Elissawy},
journal = {Beni-Suef University Journal of Basic and Applied Sciences},
year = {2026},
month = jul,
doi = {10.1186/s43088-026-00793-4},
url = {https://doi.org/10.1186/s43088-026-00793-4},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - UPLC-MS chemical profiling and isolation of bioactive secondary metabolites from Ammi visnaga-derived endophyte Alternaria destruens assessed by in silico studies
AU - Abdel Nasser B. Singab
AU - Fadia Salah Youssef
AU - Fayrouz H. Abd El-Megeed
AU - Akram H. Mohamed
AU - Sameh H. Youseif
AU - Mohamed S. Mahmoud
AU - Heba A. Dahdooh
AU - Naziha Hassanein
AU - Mohamed Ben-El-Caid
AU - Msizi Innocent Mhlongo
AU - Anathi Msobo
AU - Ahmed M. Elissawy
PY - 2026
DA - 2026/07/21
JO - Beni-Suef University Journal of Basic and Applied Sciences
DO - 10.1186/s43088-026-00793-4
UR - https://doi.org/10.1186/s43088-026-00793-4
AB - Microbial endophytes have emerged as a potential source of bioactive secondary metabolites and provide an excellent resource to overcome the challenges resulting from over-consumption of medicinal plants. Ammi visnaga is an Egyptian medicinal plant widely recognized for its medicinal value. The roots of A. visnaga are considered as waste products; the aim of this study is to explore the fungal endophytes associated with A.visnaga roots. Fungal isolate was identified using PCR; large-scale fermentation was performed on solid rice media followed by extraction with Ethyl acetate. The fungal extract was subjected to chromatographic purification utilizing VLC and HPLC. Isolated compounds were identified using HRESIMS and NMR techniques. UPLC-ESI-Q-Tof was utilized to perform the chemical profiling of the fungal extract. Disc diffusion and MIC experiments were performed to evaluate the antimicrobial activity. In silico assessment was performed using AutoDock Vina against ten bacterial proteins incorporated in DNA replication, antibiotic resistance, and virulence. Biovia Discovery Studio was utilized to assess the pharmacokinetic properties of the compounds applying ADMET protocol. Four compounds were isolated and identified from Alternaria destruens NGB-AvF1 including one previously undescribed perylene quinone epoxide ( 1) and three known polyketides ( 2–3 , 4). Metabolic profiling of the extract using UPLC-Q-Tof in the negative mode resulted in the tentative identification of 18 secondary metabolites belonging to different chemical classes with high percentages of polyketides, perylene quinones and isocoumarins. Antimicrobial evaluation revealed strong and selective antimicrobial activities for compounds 2 and 3 against Staphylococcus aureus , with inhibition zones of 28 mm and 30 mm, respectively. In silico assessment revealed favourable binding affinities for 2 and 3 with several key enzymes. Compound 2 exhibited the strongest binding with DNA ligase, β-lactamase, and Clumping factor A, while compound 3 showed high affinity for ClfA, DNA ligase and β-lactamase. Both compounds also interacted moderately with Sortase A, PBP2a, and BlaR1. These results suggest that compounds 2 and 3 possess multitarget antibacterial activity. A. destruens extract revealed wide chemical diversity and displayed a potent antimicrobial activity; in silico studies revealed the potential bacterial targets for the antimicrobial compounds. Compounds 2–3 displayed selective and potent antibacterial activity reinforcing their candidacy as lead compounds for further drug development.
SN - 2314-8535
SN - 2314-8543
ER -