ArticleSignal transduction and targeted therapy2024
A deep learning-driven discovery of berberine derivatives as novel antibacterial against multidrug-resistant Helicobacter pylori.
Article in Signal transduction and targeted therapy, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Berberine Prevents and Reverses Gastric Spasmolytic Polypeptide-Expressing Metaplasia by Modulating M2 Macrophage Polarization.International journal of molecular sciences · 2026Article
- Berberine as a Promising Antifungal Agent: Insights into Molecular Mechanisms and Therapeutic Potential.ACS omega · 2026Review
- MMP2Mol: a matched molecular pairs-based framework for ligand-based de novo drug design.Briefings in bioinformatics · 2026Article
- Alkaloids Mediate Multi-Level Modulation of Gastric Carcinogenesis: From Antibacterial and Anti-Inflammatory Actions to Antitumor Effects.International journal of molecular sciences · 2026Review
- Berberine and Berberine-Derived Compounds as Promising Weapons AgainstPharmaceuticals (Basel, Switzerland) · 2026Review
- Artificial intelligence drives the identification and screening of novel antibiotics and antimicrobial peptides.Briefings in bioinformatics · 2026Review
- Natural products and their derivatives as candidate treatments for hair greying: from drug discovery to molecular mechanisms.Chinese medicine · 2026Review
- Development and application of artificial intelligence in traditional Chinese medicine research and development.Chinese medicine · 2026Review
- AI-Powered Discovery of Rosmarinic Acid as a Novel Ferroptosis Inhibitor for Ulcerative Colitis via Targeting the ALOX15-VDAC1 Axis.Research (Washington, D.C.) · 2026Article
- A review of advances in research on mechanisms inhibiting kidney stone formation from a network pharmacology perspective.Frontiers in pharmacology · 2026Review
- Ultrasound-Responsive Microcapsules Delivering Oxygen and Traditional Chinese Medicine for Wound Healing.Smart medicine · 2025Article
- Integrative Computational Approaches for the Discovery of Triazole-Based Urease Inhibitors: A Machine Learning, Virtual Screening, and Meta-Dynamics Framework.International journal of molecular sciences · 2025Article
- Advances of Antimicrobial Peptides in the Treatment of Multidrug-Resistant Bacteria.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2025Review
- Progress of AI-Driven Drug-Target Interaction Prediction and Lead Optimization.International journal of molecular sciences · 2025Review
- Biomaterials mediated 3R (remove-remodel-repair) strategy: holistic management of Helicobacter pylori infection.Journal of nanobiotechnology · 2025Review
- Poor Oral Hygiene: A Hidden Risk Factor for Helicobacter pylori Infection.International dental journal · 2025Article
- Computer-Aided Drug Design in Research on Chinese Materia Medica: Methods, Applications, Advantages, and Challenges.Pharmaceutics · 2025Review
- Review
- Review
- Regulatory Mechanisms of Benzylisoquinoline Alkaloid Biosynthesis in Coptis chinensis Under Light Quality Treatment.Physiologia plantarumArticle
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Helicobacter pylori (H. pylori) is currently recognized as the primary carcinogenic pathogen associated with gastric tumorigenesis, and its high prevalence and resistance make it difficult to tackle. A graph neural network-based deep learning model, employing different training sets of 13,638 molecules for pre-training and fine-tuning, was aided in predicting and exploring novel molecules against H. pylori. A positively predicted novel berberine derivative 8 with 3,13-disubstituted alkene exhibited a potency against all tested drug-susceptible and resistant H. pylori strains with minimum inhibitory concentrations (MICs) of 0.25-0.5 μg/mL. Pharmacokinetic studies demonstrated an ideal gastric retention of 8, with the stomach concentration significantly higher than its MIC at 24 h post dose. Oral administration of 8 and omeprazole (OPZ) showed a comparable gastric bacterial reduction (2.2-log reduction) to the triple-therapy, namely OPZ + amoxicillin (AMX) + clarithromycin (CLA) without obvious disturbance on the intestinal flora. A combination of OPZ, AMX, CLA, and 8 could further decrease the bacteria load (2.8-log reduction). More importantly, the mono-therapy of 8 exhibited comparable eradication to both triple-therapy (OPZ + AMX + CLA) and quadruple-therapy (OPZ + AMX + CLA + bismuth citrate) groups. SecA and BamD, playing a major role in outer membrane protein (OMP) transport and assembling, were identified and verified as the direct targets of 8 by employing the chemoproteomics technique. In summary, by targeting the relatively conserved OMPs transport and assembling system, 8 has the potential to be developed as a novel anti-H. pylori candidate, especially for the eradication of drug-resistant strains.
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