The Antibacterial Efficacy of a Compound Extracted from Marine Sediment Bacterium Enterococcus Lactis (S-2): A Comparative Analysis Through In-Vitro and In-Silico Assessments
Authors: Kotakonda Muddukrishnaiah , Marappan Makesh 
Published: June 2024

Background:

Marine sediment bacteria have been generating considerable attention
lately due to their potential as valuable reservoirs of novel antimicrobial agents.

Aim:

In vitro and in silico antibacterial activities of antibacterial compounds isolated from the
marine sediment bacterium Enterococcus Lactis (S-2).

Methods:

Coastal sediment samples were collected from Rameswaram, Ramnathapuram District,
Tamil Nadu, India. Bacteria were isolated using the crowded plate method, and their phenotypic
and genotypic characteristics were studied. Purified bacteria were cultured in large volumes,
secondary metabolites were extracted, and novel antibacterial agents were isolated from
the aqueous extract. Novel compound antibacterial activity was studied through in-silico and invitro.
The mechanism activity of antibacterial activity was confirmed by a high-resolution
transmission electron microscope.

Results:

Genotypic analysis confirmed that the isolated S-2 bacteria were Enterococcus lactis,
and the aqueous extract showed antibacterial activity against Staphylococcus aureus (17 mm
zone of inhibition) and Proteus mirabilis (12 mm zone of inhibition). A bioactive molecule, 13-
hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4dioxapentacyclo[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa-
1(20),5,7,12,14(19), 16-hexane-18-one, was isolated from aqueous extracts of the S-2 bacterium.
Chromatography and spectroscopic analysis confirmed the identity of the isolated compound.
Novel compound potential antibacterial activity showing against S. aureus (18 mm zone
of inhibition) and MIC 250 μg/mL, which was confirmed by tetrazolium staining. The antibacterial
activity mechanism was confirmed by transmission electron microscopy. Molecular docking
studies show good binding (-9.9 kcal/mol) of the compound with 3U2D, while molecular
dynamic simulation studies confirm the conformationally stable structure of the complex between
3U2D and 13-hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo
[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa-1(20),5,7,12,14(19), 16-hexane-18-one. It has been observed from
the docking study of 3U2D with standard drug ciprofloxacin that the lower affinity is compared
to the test ligand, which has a docking score of 7.3 kcal/mol. Out of interacting residues of protein
3U2D residue, Thr173 and Ile86 formed conventional hydrogen bonds.

result:

Genotypic analysis confirmed that the isolated S-2 bacteria were Enterococcus lactis, and the aqueous extract showed antibacterial activity against Staphylococcus aureus (17 mm zone of inhibition) and Proteus mirabilis (12 mm zone of inhibition). A bioactive molecule, 13-hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4dioxapentacyclo[10.7.1.0³,⁷.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),5,7,12,14(19), 16-hexane-18-one, was isolated from aqueous extracts of the S-2 bacterium. Chromatography and spectroscopic analysis confirmed the identity of the isolated compound. Novel compound potential antibacterial activity showing against S. aureus (18 mm zone of inhibition) and MIC 250 µg/mL, which was confirmed by tetrazolium staining. Antibacterial activity mechanism was confirmed by transmission electron microscopy. Molecular docking studies show good binding (-7.7 kcal/mol) of the compound with 3MZF (penicillin-binding protein), while molecular dynamic simulation studies confirm the conformationally stable structure of the complex between 3MZF and 13-hydroxy-9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo [10.7.1.0³,⁷.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),5,7,12,14(19), 16-hexane-18-one.

Conclusion:

Marine bacterium E. lactis produces a novel antibacterial compound (13-hydroxy-
9-(1-hydroxyethyl)-11-methoxy-2,4-dioxapentacyclo[10.7.1.0³,⁴.0⁵,²¹.0¹³,¹⁶]icosa-
1(20),5,7,12,14(19),16-hexane-18-one), which shows antibacterial activity against clinical S.
aureus, confirmed by in vitro and in silico analysis. This molecule can used as a lead molecule
for antibacterial activity.