Ligand-based pharmacophore modelling and screening of DNA minor groove binders targeting Staphylococcus aureus.

The recognition of DNA by small molecules is of special importance in the design of new drugs. Many natural and synthetic compounds have the ability to interact with the minor groove of DNA. In the present study, identification of minor groove binding compounds was attained by the combined approach of pharmacophore modelling, virtual screening and molecular dynamics approach. Experimentally reported 32 minor groove binding compounds were used to develop the pharmacophore model. Based on the fitness score, best three pharmacophore hypotheses were selected and used as template for screening the compounds from drug bank database. This pharmacophore-based screening provides many compounds with the same pharmacological properties. All these compounds were subjected to four phases of docking protocols with combined Glide-quantum-polarized ligand docking approach. Molecular dynamics results indicated that selected compounds are more active and showed good interaction in the binding site of DNA. Based on the scoring parameters and energy values, the best compounds were selected, and antibacterial activity of these compounds was identified using in vitro antimicrobial techniques.

Exploration of fluoroquinolone resistance in Streptococcus pyogenes: comparative structure analysis of wild-type and mutant DNA gyrase.

Quinolone resistance-determining region is known to be the druggability site of the target protein that undergoes frequent mutation and thus renders quinolone resistance. In the present study, ligands were tested for their inhibitory activity against DNA gyrase of Streptococcus pyogenes involved in DNA replication. In silico mutational analysis on modelled gyrase A revealed that GLU85 had the most possible interactions with all the ligands used for the study. The amino acid residue GLU85 had also been predicted with an essential role of maintaining the three-dimensional structure of the protein. When introduced with a mutation (GLU 85 LYS) on this particular residue, it had readily denatured the whole α-helix (from 80 to 90 amino acids). This was confirmed through the molecular dynamics simulation and revealed that this single mutation can cause many functional and structural changes. Furthermore, LYS85 mutation has altered the original secondary structure of the protein, which in turn led to the steric hindrance during the ligand-receptor interaction. The results based on the G-score revealed that ligands have reduced interaction with the mutant protein. The semisynthetic fluoroquinolone 6d, which is an exception, forms a strong interaction with the mutant protein and was experimentally verified using the antimicrobial test. Hence, the present study unravels the fact that mutation at the drug binding site is the major cause for different level of resistance by the S. pyogenes when exposed against the varying concentrations of the fluoroquinolones. Furthermore, a comparative assessment of quinolone derivative with the older generation fluoroquinolones will be of great impact for S. pyogenes-related infections.

Biofilm formation by Streptococcus pyogenes: modulation of exopolysaccharide by fluoroquinolone derivatives.

Biofilm formation by Streptococcus pyogenes has been demonstrated as a potentially important mechanism contributing to antibiotic treatment failure. S. pyogenes is the frequent cause of purulent infections in humans and also, it could play a significant role in recurrent and chronic infections. S. pyogenes biofilm communities tend to exhibit significant tolerance to antimicrobial challenge during infections. The fluoroquinolone derivatives have been previously reported from our laboratory as effective agents against human bacterial pathogens. Therefore, in the present study, we observed the effect of these fluoroquinolones on biofilm formation. Quantitative analysis using 2,3-bis (2-methoxy-4-nitro-5-sulfo-phenyl)-2H-tetrazolium-5-carboxanilide (XTT) at the biofilm inhibitory concentrations (BIC), the compounds 6a, 6c, 7b and 7c reduced 61-71% biofilm and sub-BIC (0.5 and 0.25 BIC) significantly reduced biofilm formation by up to 30-38% and 16-18%, respectively. The Fourier Transform Infrared (FTIR) spectrum of the control and treated S. pyogenes revealed the shift in the chemical entity corresponding to the exopolysaccharide (EPS). The GC/MS analysis showed that the EPS of S. pyogenes has the most abundant neutral sugars l-glucose and d-mannose which is not detected in the fluoroquinolone treated EPS.