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

Abstract

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.

In Silico and In Vitro Studies on the Protein-Protein Interactions between Brugia malayi Immunomodulatory Protein Calreticulin and Human C1q

“…The BmCRT (Homology model), C1q (crystal structure) and the protein-protein complex (BmCRT–C1q) were analyzed in three separate system to obtain the stable conformation of the protein and protein-protein complex for analyzing three dynamic behavior of these structures. The bad contacts from the 3D structure of the proteins were refined and solvated with the solvent [68]. The system was further relaxed by energy minimization and for the MD simulation studies, the structures were solvated using the TIP3P water model and the solvated structures were energy minimized using the steepest descent method, terminating when maximum force was found smaller than 100 KJ/mol-1/nm-1 [69].…”

Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19

“…The molecular dynamics (MD) is performed for the G3A complex nsp14 containing Guanine-N7 methyltransferase domain and for the top five ligand-bound complexes through the virtual screening using the GROningen MAchine for Chemical Simulations (GROMACS 5.1.4, http://gromacs.org) (Chavez Thielemann et al, 2019;Rakhshani et al, 2019). Both the substrate-bound complex and ligand-bound complexes are simulated for the 50 ns of timescale for understanding the dynamic behavior and to understand the interaction pattern (Selvaraj et al, 2018;Shafreen et al, 2013;Swegat et al, 2003). The top five ligand-bound structures are prepared using the OPLS-AA force field solvated by the TIP3P water model within a periodic boundary box of distance 1.0 nm, fixed in between the protein and cubic box (Bandaru et al, 2017;Nguyen et al, 2014;Umesh et al, 2020).…”

Molecular insights on analogs of HIV PR inhibitors toward HTLV‐1 PR through QM/MM interactions and molecular dynamics studies: comparative structure analysis of wild and mutant HTLV‐1 PR

“…All the simulations were performed in the NPT ensemble at constant temperature (300 K) and pressure (1 bar), with a time step of 2 fs. NVT was performed for 1 ns, and the minimized structure was equilibrated with a timescale of 10 ns (10,000 ps) (Shafreen et al, 2013). The results of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and initial and final conformation of both the wild type and the mutant have been incorporated into the results.…”