New insights into resistance of Helicobacter pylori against third‐ and fourth‐generation fluoroquinolones: A molecular docking study of prevalent GyrA mutations

Abstract

Background: Fluoroquinolones hinder bacterial DNA replication by inhibiting DNA gyrase. However, mutations, in the QRDR segment of its A subunit (GyrA), cause antibiotic resistance. Here, the interactions of levofloxacin (LVX), gemifloxacin (GXN), and moxifloxacin (MXN) with Helicobacter pylori GyrA, in LVX-resistant vs -sensitive strains, were studied. Methods: Levoflixacin-sensitive (n = 4) and -resistant (n = 9) H pylori strains, randomly selected from another antibiotic susceptibility study, underwent PCR amplification of gyrA gene, spanning the QRDR segment. The amplified gene fragments were sequenced and aligned. The homology model of H pylori GyrA was built based on that of Escherichia coli, and energy minimization was done. The interaction patterns of LVX, GXN, and MXN with GyrA were analyzed via molecular docking studies. Results: Sequence alignment of the 13 studied strains, created 5 categories of strains: (A) wild type-like (H pylori ATCC26695), (B) N87K-only, (C) D91N-only, (D) N87K + V94L, and (E) D91N + A97V mutations. The minimum inhibitory concentrations (MIC) for LVX-sensitive (category A) and -resistant (categories B-E) strains were <1 mg/L and ≥32 mg/L, respectively. The binding mode of GyrA in category A withLVX identified G35/N87/Y90/D91/V94/G114/S115/I116/D117/G118/D119, as key residues, some residing outside the QRDR segment. Category B strains lost only one interaction (G35), which led to elevated binding free energy (∆G) and full LVX resistance. Categories C-E lost more contacts, with higher ∆G and again full LVX resistance. GXN bound to GyrA of categories A and B via a different set of key residues, while MXN retained the lost contact (G35) in LVX-resistant, category B strains. Conclusion:Using molecular docking tools, we identified the key residues responsible for interaction of GyrA with LVX, GXN, and MXN. In the presence of N87K-only mutation, the loss of one of these contacts (ie, G35) led to full LVX resistance. Yet, GXN and MXN overcame this mutation, by retaining all key contacts with GyrA.

Pharmacoinformatics-Based Approach for Uncovering the Quorum-Quenching Activity of Phytocompounds against the Oral Pathogen, Streptococcus mutans

“…In silico and in vitro agonistic activity of ligands have been studied for the treatment of diabetes [ 44 , 45 ], Parkinson’s disease [ 46 ], and cardiac diseases [ 47 ]. The antagonistic activity of ligands against S. mutans [ 48 , 49 ], Leishmania donovani [ 50 ], Helicobacter pylori [ 51 ], and SARS-CoV-2 [ 52 ] has also been studied. All these research works corroborate the necessity of in vitro experiments in the validation of computational analysis.…”

Helicobacter pylori resistance to antibiotics before and after treatment: Incidence of eradication failure

“…Levofloxacin resistance is due to changes in gyrA component of H . pylori [ 22 – 25 ] that renders even fluoroquinolones inactive to suppress H . pylori growth [ 22 , 25 , 26 ].…”

“…pylori [ 22 – 25 ] that renders even fluoroquinolones inactive to suppress H . pylori growth [ 22 , 25 , 26 ].…”

The outward shift of clarithromycin binding to the ribosome in mutantHelicobacter pyloristrains

“…The docking box (with 27 × 25 × 25 Å dimensions) was defined around mutated nucleotides, L4, and L22 accessory proteins, to calculate the affinity of CLA, to the reference and mutated complexes. All complex conformations, root‐mean‐square deviation (RMSD) values 42 and distances were depicted and measured by VMD1.9.3 43 . The nucleotides and amino acid residues of the 23S rRNA complex in interaction with CLA and their interaction types were determined by LigPlot + v.1.4 44 …”