Secondary metabolites extracted from marine sponge associated Comamonas testosteroni and Citrobacter freundii as potential antimicrobials against MDR pathogens and hypothetical leads for VP40 matrix protein of Ebola virus: an in vitro and in silico investigation

Abstract

The current study explores therapeutic potential of metabolites extracted from marine sponge (Cliona sp.)-associated bacteria against MDR pathogens and predicts the binding prospective of probable lead molecules against VP40 target of Ebola virus. The metabolite-producing bacteria were characterized by agar overlay assay and as per the protocols in Bergey’s manual of determinative bacteriology. The antibacterial activities of extracted metabolites were tested against clinical pathogens by well-diffusion assay. The selected metabolite producers were characterized by 16S rDNA sequencing. Chemical screening and Fourier Transform Infrared (FTIR) analysis for selected compounds were performed. The probable lead molecules present in the metabolites were hypothesized based on proximate analysis, FTIR data, and literature survey. The drug-like properties and binding potential of lead molecules against VP40 target of Ebola virus were hypothesized by computational virtual screening and molecular docking. The current study demonstrated that clear zones around bacterial colonies in agar overlay assay. Antibiotic sensitivity profiling demonstrated that the clinical isolates were multi-drug resistant, however; most of them showed sensitivity to secondary metabolites (MIC-15 μl/well). The proximate and FTIR analysis suggested that probable metabolites belonged to alkaloids with O–H, C–H, C=O, and N–H groups. 16S rDNA characterization of selected metabolite producers demonstrated that 96% and 99% sequence identity to Comamonas testosteroni and Citrobacter freundii, respectively. The docking studies suggested that molecules such as Gymnastatin, Sorbicillactone, Marizomib, and Daryamide can designed as probable lead candidates against VP40 target of Ebola virus.

Keywords:

• marine sponges
• Cliona sp
• secondary metabolites
• multi-drug resistant
• 16S rDNA sequencing
• Ebola virus
• computational virtual screening
• VP40 targets
• molecular docking

Acknowledgements

The authors acknowledge to Mr. Lenin Augustin, M.D., Managing Director, Monarch Food, Pvt. Ltd. for assisting them during collection of the samples. The authors are also thankful to Ms. Sonia, Research Associate, CMFRI, for her assistance and contribution in the attainment of samples and Dr. Deepak V. Samuel, Senior Scientist, Central Marine Fisheries Research Institute, for guiding us throughout the project work.

Disclosure statement

No potential conflict of interest was reported by the authors.