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Exploring the in silico studies of the endophyte fungus Phoma herbarum against mur enzymes of Staphylococcus aureus – a computational approach

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Abstract

Endophyte fungus Phoma herbarum (NFCCI 4035) was previously isolated and identified from healthy leaf tissue of Meriandra bengalensis Benth plant from Manipur. We recently established the antibacterial activity of ethyl acetate extracts of endophyte fungus P. herbarum in vitro and identified some potentially active components using GC-MS. The current study aims to perform molecular docking of the discovered P. herbarum compounds against Mur enzymes (Mur A, Mur C, Mur D, and Mur F) of Staphylococcus aureus using Auto Dock Tools 1.5.6. SwissADME online tool was used to calculate the drug-likeness characteristics. According to the findings, only 14 of 23 bioactive compounds evaluated from P. herbarum extract adhered to Lipinski’s Rule of Five (LRo5) and had binding affinity ranged between − 3.5 to -6.5 (kcal/mol) with at least one of the four targeted Mur enzymes. When compared to all other bioactive compounds that interact with target Mur enzymes, 2-Palmitoylglycerol molecule demonstrated highest binding affinity (-6.5 kcal/mol) with Mur F ligase. However, (1R,2R,3R,5 S)-2,6,6-Trimethylbicyclo[3.1.1]heptan-3-amine has shown excellent binding affinity for all selected target (Mur A, Mur C, Mur D, and Mur F) enzymes. Also, this study confirmed that the bioactive compounds can be developed into more potent inhibitors targeting S. aureus-related infections.

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Acknowledgements

The author (WSD) wishes to express her gratitude to the Head of the Department of Life Sciences (Botany), Manipur University, for providing lab space for her Ph.D. research.

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Authors and Affiliations

  1. Department of Life Sciences (Botany), Manipur University, Canchipur, Manipur, 795003, Imphal, India

    Kannaiah Surendirakumar & Wairokpam Sanahal Devi

  2. Department of Microbiology, JJ College of Arts and Science (Autonomous), (Affiliated to Bharathidasan University Tiruchirappalli), Pudukkottai, 622 422, Tamil Nadu, India

    Kannaiah Surendirakumar

  3. Department of Biotechnology, JJ College of Arts and Science (Autonomous), (Affiliated to Bharathidasan University Tiruchirappalli), Pudukkottai, 622 422, Tamil Nadu, India

    Subramaniyan Vaithilingam

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  1. Kannaiah Surendirakumar
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  3. Subramaniyan Vaithilingam
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Correspondence to Kannaiah Surendirakumar.

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Surendirakumar, K., Devi, W.S. & Vaithilingam, S. Exploring the in silico studies of the endophyte fungus Phoma herbarum against mur enzymes of Staphylococcus aureus – a computational approach. Vegetos (2023). https://doi.org/10.1007/s42535-023-00738-7

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