Computational Study of 16S rRNA of Microbe Cluster Implicated in Diarrhoeal: Phylogeny, Docking, and Dynamics

Abstract In this study, 16S rRNA of diarrhoea microbial cluster was investigated computationally. The phylogeny, two- and three-dimensional structures, molecular docking and dynamics simulations were carried out. The result showed that Escherichia coli, Campylobacter jejuni, Campylobacter upsaliensis, Streptococcus lutetiensis 033, Streptococcus infantarius, Enterococcus ratti, Helicobacter sp. 'feline isolate, Helicobacter canadensis, Anaerobiospirillum sp. B0101, Anaerobiospirillum sp. 3J102 as well as uncultured bacterium (Prevotella) and unidentified bacterium (Lactobacillus) were involved in diarrhoea infection. Optimal secondary structure alignment from ClustalO has a minimum free energy (MFE) of -764.31 kcal/mol while that Aligner has MFE of -592.43 kcal/mol. The free energies from molecular docking reveal possible efficacy in the order of doxycycline > metacycline > streptomycin > rolitetracycline > tetracycline > tigecycline. Out of 17 antibiotics used in this study, chlortetracycline and minocycline have high affinity for methyltransferase KsgA (PDB ID: 3TPZ), kanamycin has almost equal affinity for both enzymes, while the remaining 14 antibiotic compounds have high affinity for pseudouridine synthase RsuA (PDB ID: 1KSV). The modelled three-dimensional structure of 16S rRNA bind to 1KSV and 3TPZ with free energy of -367.52 kcal/mol and-371.55 kcal/mol respectively. Moreover, the active site nucleotide residues were found to have direct interaction with amino acid residues in the active site of the enzymes. This study provides insight on the mechanism of action of antibiotics that targeted 16S rRNA by inhibition of key enzymes that involve in protein synthesis.