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

Abstract

Background Amoxicillin-resistant H. pylori strains are increasing worldwide. To explore the potential resistance mechanisms involved, the 3D structure modeling and access tunnel prediction for penicillin-binding proteins (PBP1A) was performed, based on the Streptococcus pneumoniae, PBP 3D structure. Molecular covalent docking was used to determine the interactions between amoxicillin (AMX) and PBP1A. Results The AMX-Ser368 covalent complex interacts with the binding site residues (Gly367, Ala369, ILE370, Lys371, Tyr416, Ser433, Thr541, Thr556, Gly557, Thr558, and Asn560) of PBP1A, non-covalently. Six tunnel-like structures, accessing the PBP1A binding site, were characterized, using the CAVER algorithm. Tunnel-1 was the ultimate access route, leading to the drug catalytic binding residue (Ser368). This tunnel comprises of eighteen amino acid residues, 8 of which are shared with the drug binding site. Subsequently, to screen the presence of PBP1A mutations, in the binding site and tunnel residues, in our clinical strains, in vitro assays were performed. H. pylori strains, isolated under gastroscopy, underwent AMX susceptibility testing by E-test. Of the 100 clinical strains tested, 4 were AMX-resistant. The transpeptidase domain of the pbp1a gene of these resistant, plus 10 randomly selected AMX-susceptible strains, were amplified and sequenced. Of the amino acids lining the tunnel-1 and binding site residues, three (Ser414Arg, Val469Met and Thr556Ser) substitutions, were detected in 2 of the 4 resistant and none of the sequenced susceptible strains, respectively. Conclusions We hypothesize that mutations in amino acid residues lining the binding site and/or tunnel-1, resulting in conformational/spatial changes, may block drug binding to PBP1A and cause AMX resistance.

Genetic variations of penicillin-binding protein 1A: insights into the current status of amoxicillin-based regimens for Helicobacter pylori eradication in Malaysia

“…In this study, none of the previously validated amino acid variants linked to amoxicillin, namely S402G, S414R, V469M, S543R, T556S and N561Y was found in our study [19,23]. This observation was in agreement with the published surveillance data on the primary resistance of H. pylori in Malaysia, which consistently reported a 0 % resistance rate [13][14][15][16][17].…”

“…The transformant carried V469M and F473L showed increased resistance in MIC value for amoxicillin to 1.0 µg ml −1 which was identical to that of amoxicillin-resistant clinical isolate B258 [22]. Apart from that, new mutations in the pbp1A gene were reported in H. pylori isolates from Vietnam, Iran, Taiwan and Myanmar, however their association with resistance still awaits confirmation [11, 19, 27, 28].…”

“…Amoxicillin resistance in H. pylori is mainly linked to amino acid alterations in the PBPs, particularly mutations in the pbp1A gene [19]. A previous study reported that the active site of the transpeptidase activity in PBP1A is formed by a few conserved amino acid PBP-motifs, i.e.…”

Advantages of Whole Genome Sequencing in Mitigating the Helicobacter pylori Antimicrobial Resistance Problem

“…Studies observed that phenotypic AMX resistance is mainly related to mutations that alter the protein encoded by the penicillin-binding protein pbp1A gene [ 18 ] Mutations in pbp1a have been found in three countries. Interestingly, the novel mutations found in each country are diverse.…”

The Potential Use of Antibiotics Against Helicobacter pylori Infection: Biopharmaceutical Implications

“…Moreover, H. pylori can be associated with some non-gastric diseases, such as cardiovascular, respiratory, neurologic, hematologic, dermatologic and allergic disorders ( Gravina et al, 2018 ; Attaran et al, 2021 ). As one example, it was discovered that there was a correlation between H. pylori infection and problems in the digestive tract, such as abdominal pain and diarrhea in Coronavirus disease of 2019 (COVID-19) patients ( Balamtekin et al, 2021 ).…”