Antimicrobial potential of different metabolites purified from the Red Sea alga Cystoseira Myrica marine-derived Enterobacter Cloacae strain GH1 supported by metabolomics and docking studies

A plethora of studies have been explored to identify effective, safe, and economical alternatives to potentially hazardous antibiotics. Natural extracts of marine organisms and their secondary metabolites are among the intriguing study topics to address this growing concern. This study aimed to investigate the effects of ten purified metabolites isolated from the isolated marine-derived bacterial strain, Enterobacter cloacae GH1 on various resistant pathogens. E. cloacae GH1 was isolated from Red Sea alga, Cystoseira myrica, together with other strains and has been chosen as a promising isolate based on its high microbial inhibition zones towards tested Gram-positive and -negative bacteria. Moreover, metabolomic analysis using (LC-HRESIMS) was conducted for different fractions of ethyl-acetate extract of E. cloacae GH1 for de-replication of biosynthesized and/or produced metabolites. Most de-replicated metabolites were isolated and purified using advanced preparative techniques followed by subsequent antimicrobial and docking studies. Results indicated that ethyl-acetate extract of E. cloacae GH1 significantly increased microbial growth inhibition, especially Staphylococcus aureus and Sarcina maxima. Moreover, metabolomic profiling showed the presence of diverse phytochemicals, mostly diketopiprazines. In addition, purification of the extract afforded 8 diketopiperazine derivatives, namely cyclo(S-Pro-S-Tyr) (E1), cyclo(S-Pro-S-Val) (E2), Brevianamide F (E3), cyclo(S-hyp-S-Pro-S-Phe) (E4), cyclo(R-hy-S-Pro-R-Phe) (E5), cyclo(S-hy-S-Pro-S-Lue) (E6), cyclo(S-hy-R-Pro-S-Lue) (E7), and cyclo(S-Pro-Gly) (E8) together with 2 indole derivatives, indole-3-aldehyde (E9) and indole-3-acetic acid (E10). In accordance with those purified metabolites, only indole derivatives demonstrated remarkable bioactivity against tested microbes. A docking study on two different virulence proteins showed that E9 and E10 actively bind and interact with virulence proteins, assuring their ability to decrease microbial growth. In conclusion, the identified indole derivatives exhibited promising anti-biofilm and anti-virulence properties, suggesting potential for antibiotic development.