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ORIGINAL RESEARCH article
Front. Bioinform.
Sec. Drug Discovery in Bioinformatics
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1544800
This article is part of the Research Topic Expert Opinions in bioinformatics drug discovery View all 3 articles
Streptomyces sp. VITGV156 secondary metabolite binds pathogenic protein PBP2a and Beta-lactamase
Provisionally accepted
Pattapulavar Veilumuthu 1
Manisha Shah 1
SIVAKUMAR A 1
Ramanathan Karuppasamy 1
Muthu Kumar Thirunavukkarasu 1
Antony V Samrot 2
Deepasree K 1
Subhashree Venugopal 1
Godwin J 1*- 1 School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
- 2 Faculty of Medicine, Manipal University College Malaysia, Melaka, Malaysia
The genus Streptomyces sp. emerged as the dominant group. Among these, Streptomyces sp. VITGV156 was selected for the analysis of its bioactive compounds. The genomic size of Streptomyces sp. VITGV156 is 8.18 Mb genome with a G+C content of 72.61%, containing 29 biosynthetic gene clusters (BGCs), including those responsible for the production of antimicrobial agents like nystatin and fluostatins. This genome harbors unique genes with potential roles in secondary metabolite biosynthesis, including terpenoids and polyketides, which could contribute to antimicrobial mechanisms. In vitro, antimicrobial assays confirmed the efficacy of the crude extracts against Grampositive and Gram-negative pathogens. Among these pathogens, Escherichia coli showed the highest susceptibility. Furthermore, a comprehensive ADME analysis and molecular docking studies on the 45 selected secondary metabolites identified via GC-MS supported the drug-like properties of several bioactive compounds, particularly in their interaction with bacterial target proteins. The range of binding affinities against 5M18 and 6NVU were determined to be, respectively, -4.0 to -7.5 kcal/mol and -3.9 to -7.2 kcal/mol. The compound fumaric acid, monoamide, N-benzyl-N-phenylethyl-, and ethyl ester (ligand 38) shows poor antifungal activity. Squalene (ligand 43) has good antibacterial and antifungal activity. The compound 2,5-Piperazinedione, 3-(hydroxymethyl)-6-(phenylmethyl)-(ligand 40) exhibits good antifungal activity. This study underscores the potential of Streptomyces sp. VITGV156 as a valuable source of novel organism.
Keywords: Streptomyces, secondary metabolites, Tomato plant, antiSMASH, terpenoids, gene ontology, molecular docking
Received: 13 Dec 2024; Accepted: 27 Feb 2025.
Copyright: © 2025 Veilumuthu, Shah, A, Karuppasamy, Thirunavukkarasu, Samrot, K, Venugopal and J. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Godwin J, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
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