The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains

Abstract

Objectives Disruption of protein synthesis, by drug‐mediated restriction of the ribosomal nascent peptide exit tunnel (NPET), may inhibit bacterial growth. Here, we have studied the secondary and tertiary structures of domain V of the 23S rRNA in the wild‐type and mutant (resistant) H. pylori strains and their mechanisms of interaction with clarithromycin (CLA). Methods H pylori strains, isolated from cultured gastric biopsies, underwent CLA susceptibility testing by E test, followed by PCR amplification and sequencing of domain V of 23S rRNA. The homology model of this domain in H pylori, in complex with L4 and L22 accessory proteins, was determined based on the E. coli ribosome 3D structure. The interactions between CLA and 23S rRNA complex were determined by molecular docking studies. Results Of the 70 H pylori strains, isolated from 200 dyspeptic patients, 11 (16%) were CLA‐resistant. DNA sequencing identified categories with no (A), A2142G (B), and A2143G (C) mutations. Docking studies of our homology model of 23S rRNA complex with CLA showed deviated positions for categories B and C, in reference to category A, with 12.19 Å and 7.92 Å RMSD values, respectively. In both mutant categories, CLA lost its interactions at positions 2142 and 2587 and gained two new bonds with the L4 accessory protein. Conclusion Our data suggest that, in mutant H pylori strains, once the nucleotides at positions 2142 and 2587 are detached from the drug, CLA interacts with and is peeled back by the L4 accessory protein, removing the drug‐imposed spatial restriction of the NPET.

The penicillin binding protein 1A of Helicobacter pylori, its amoxicillin binding site and access routes

“…One hundred clinical H. pylori isolates were collected from 290 dyspeptic patients, via upper endoscopy, from 2013 to 2018, at Amiralam Hospital, Tehran, Iran. Gastric biopsy specimens were cultured onto Brucella agar medium (Merck, Germany), supplemented with 10% defibrinated sheep blood, amphotericin B (8 mg/L), vancomycin (10 mg/L), and trimethoprim (5 mg/L) and incubated under microaerobic conditions (O2, 5%; CO2, 10%; N2, 85%) at 37 °C for 3–5 days [ 51 ]. Sample collection was performed according to the approved protocols by the Committee on Ethical Issues in Medical Research, Pasteur Institute of Iran (Ref.No.IR.PII.REC.1394.57) and every patient provided written informed consent.…”

Efficacy and safety comparison of Helicobacter pylori eradication between vonoprazan dual therapy versus triple therapy: a systematic review and meta-analysis

“…Then we further performed subgroup analysis on antibiotics dose administration. In our study, we noticed that the actual cure rate of low-dose antibiotics treatment 32 For CLA-resistant H. pylori, frequent exposure to CLA increased the chance of gene mutation. This may increase the probability of mutations in genes encoding penicillin-binding proteins.…”

“…This leads to ribosome allostery, which reduced the affinity of the CLA binding site. 32 For CLA-resistant H. pylori , frequent exposure to CLA increased the chance of gene mutation. This may increase the probability of mutations in genes encoding penicillin-binding proteins.…”

Prediction of Synergistic Antibiotic Combinations by Graph Learning

“…Since we concentrated on the subtle differences among synergy, additive, and antagonism, all 91 pairwise combinations fall into three categories, according to the α-score ( Supplementary Table S1 ). Targets of these antibiotics were collected from previous literature studies ( Pongs et al, 1973 ; Shen and Pernet, 1985 ; Buck and Cooperman, 1990 ; Pan et al, 1996 ; Onodera et al, 2002 ; Aracena et al, 2014 ; Kocaoglu and Carlson, 2015 ; Wekselman et al, 2017 ; Lin et al, 2018 ; Salehi et al, 2020 ; Wróbel et al, 2020 ). Because some antibiotics are RNA-targeted small molecules, ribosomal proteins that affect antibiotic binding are considered targets of antibiotics.…”