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

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

BACKGROUND

As a novel drug, vonoprazan (VPZ) has been developed as a new strategy against Helicobacter pylori (H. pylori) infections. However, whether VPZ + amoxicillin (AMO) dual therapy has a clear advantage is still unclear.

OBJECTIVE

To review and meta-analyze the available literature investigating the efficacy and safety of H. pylori eradication in VPZ dual therapy.

DESIGN

A systematic review and meta-analysis were conducted.

DATA SOURCES AND METHODS

We performed a systematic search in the PubMed, Embase, EIsevier/Science Library, and Cochrane Library databases from 2015 to 2022. Meta-analyses were conducted to evaluate the actual cure rate and the incidence rate of adverse reactions in dual therapy and VPZ + AMO + clarithromycin (CLA) triple therapy; furthermore, eradication rates in CLA-resistant infections and different doses of antibiotics were evaluated in subgroup analysis.

RESULTS

Seven studies with 1490 patients were included in this meta-analysis. According to intention-to-treat analysis, the actual cure rates of VPZ dual and triple therapy were 82.8% and 84.6%, respectively [p = 0.29, odds ratio (OR): 0.86, 95% confidence interval (CI): 0.64-1.14]. And in the per-protocol analysis, the actual cure rates of these two therapies were 84.8% and 87.0%, respectively (p = 0.21, OR: 0.80, 95% CI: 0.57-1.13). The incidence of adverse reactions between VPZ dual and triple therapy was 26.1% versus 29.6% (p = 0.04, OR: 0.78, 95% CI: 0.61-0.99). In subgroup analysis, the eradication rates in CLA-resistant infections were dual therapy: 85.7% for VPZ versus 71.0% for triple therapy (p = 0.03, OR: 2.36, 95% CI: 1.10-5.05). And the actual cure rate of VPZ with high-dose antibiotics was lower than with low-dose antibiotics (p = 0.000 in dual therapy; p = 0.011 in triple therapy).

CONCLUSION

A combination of VPZ and a low dose of AMO should be prioritized as a treatment option for H. pylori eradication.

REGISTRATION

PROSPERO registration number CRD42022346100.

Prediction of Synergistic Antibiotic Combinations by Graph Learning

Antibiotic resistance is a major public health concern. Antibiotic combinations, offering better efficacy at lower doses, are a useful way to handle this problem. However, it is difficult for us to find effective antibiotic combinations in the vast chemical space. Herein, we propose a graph learning framework to predict synergistic antibiotic combinations. In this model, a network proximity method combined with network propagation was used to quantify the relationships of drug pairs, and we found that synergistic antibiotic combinations tend to have smaller network proximity. Therefore, network proximity can be used for building an affinity matrix. Subsequently, the affinity matrix was fed into a graph regularization model to predict potential synergistic antibiotic combinations. Compared with existing methods, our model shows a better performance in the prediction of synergistic antibiotic combinations and interpretability.

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

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.