Bacteria Are New Targets for Inhibitors of Human Farnesyltransferase

Assessment for antibiotic resistance in Helicobacter pylori: A practical and interpretable machine learning model based on genome-wide genetic variation

Helicobacter pylori (H. pylori) antibiotic resistance poses a global health threat. Accurate identification of antibiotic resistant strains is essential for the control of infection. In the present study, our goal is to leverage the whole-genome data of H. pylori to develop practical and interpretable machine learning (ML) models for comprehensive antibiotic resistance assessment. A total of 296 H. pylori isolates with genome-wide data were downloaded from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) and the National Center for Biotechnology Information (NCBI) databases. By training ML models on feature sets of single nucleotide polymorphisms from SNP calling (SNPs-1), antibiotic-resistance SNP annotated by the Comprehensive Antibiotic Resistance Database (SNPs-2), gene presence or absence (GPA), we generated predictive models for four antibiotics and multidrug-resistance (MDR). Among them, the models that combined SNPs-1, SNPs-2, and GPA data demonstrated the best performance, with the eXtreme Gradient Boosting (XGBoost) consistently outperforming others. And then we utilized the SHapley Additive exPlanations (SHAP) method to interpret the ML models. Furthermore, a free web application for the MDR model was deployed to the GitHub repository (https://H.pylori/MDR/App/). Our study demonstrated the promise of employing whole-genome data in conjunction with ML algorithms to forecast H. pylori antibiotic resistance. In the future, the application of this approach for predicting H. pylori antibiotic resistance would hold the potential to mitigate the empiric administration.

Repurposing High-Throughput Screening Reveals Unconventional Drugs with Antimicrobial and Antibiofilm Potential Against Methicillin-Resistant Staphylococcus aureus from a Cystic Fibrosis Patient

Background/Objectives: Antibiotic therapy faces challenges from rising acquired and biofilm-related antibiotic resistance rates. High resistance levels to commonly used antibiotics have been observed in methicillin-resistant Staphylococcus aureus (MRSA) strains among cystic fibrosis (CF) patients, indicating an urgent need for new antibacterial agents. This study aimed to identify potential novel therapeutics with antibacterial and antibiofilm activities against an MRSA CF strain by screening, for the first time, the Drug Repurposing Compound Library (MedChem Express). Methods/Results: Among the 3386 compounds, a high-throughput screening-based spectrophotometric approach identified 2439 (72%), 654 (19.3%), and 426 (12.6%) drugs active against planktonic cells, biofilm formation, and preformed biofilm, respectively, although to different extents. The most active hits were 193 (5.7%), against planktonic cells, causing a 100% growth inhibition; 5 (0.14%), with excellent activity against biofilm formation (i.e., reduction ≥ 90%); and 4, showing high activity (i.e., 60% ≤ biofilm reduction < 90%) against preformed biofilms. The potential hits belonged to several primary research areas, with "cancer" being the most prevalent. After performing a literature review to identify other, already published biological properties that could be relevant to the CF lung environment (i.e., activity against other CF pathogens, and anti-inflammatory and anti-virulence potential), the most interesting hits were the following: 5-(N,N-Hexamethylene)-amiloride (diuretic), Toremifene (anticancer), Zafirlukast (antiasthmatic), Fenretide (anticancer), and Montelukast (antiasthmatic) against planktonic S. aureus cells; Hemin against biofilm formation; and Heparin, Clemastine (antihistaminic), and Bromfenac (nonsteroidal anti-inflammatory) against established biofilms. Conclusions: These findings warrant further in vitro and in vivo studies to confirm the potential of repurposing these compounds for managing lung infections caused by S. aureus in CF patients.

Advancing Photodynamic Antimicrobial Strategy: Sustainable Fabrication of Novel Lauryl Gallate-Chitosan Hydrophobic Films with Rapid Bacterial Capture and Biofilms Elimination Capabilities for Promoting Wound Healing

Bioinspired photoactive composites, in terms of photodynamic inactivation, cost-effectiveness, and biosafety, are promising alternatives to antibiotics for combating bacterial infections while avoiding antibacterial resistance. However, the weak bacterial membrane affinity of the photoactive substrate and the lack of synergistic antibacterial effect remain crucial shortcomings for their antibacterial applications. Herein, we developed a hydrophobic film from food antioxidant lauryl gallate covalently functionalized chitosan (LG-g-CS conjugates) through a green radical-induced grafting reaction that utilizes synergistic bacteria capture, contact-killing, and photodynamic inactivation activities to achieve enhanced bactericidal and biofilm elimination capabilities. Besides, the grafting reaction mechanism between LG and CS in the ascorbic acid (AA)/H2O2 redox system was further proposed. The LG-g-CS films feature hydrophobic side chains and photoactive phenolic hydroxyl groups, facilitating dual bactericidal activities through bacteria capture and contact-killing via strong hydrophobic and electrostatic interactions with bacterial membranes as well as blue light (BL)-driven photodynamic bacterial eradication through the enhanced generation of reactive oxygen species. As a result, the LG-g-CS films efficiently capture and immobilize bacteria and exhibit excellent photodynamic antibacterial activity against model bacteria (Escherichia coli and Staphylococcus aureus) and their biofilms under BL irradiation. Moreover, LG-g-CS films could significantly promote the healing process of S. aureus-infected wounds. This research demonstrates a new strategy for designing and fabricating sustainable bactericidal and biofilm-removing materials with a high bacterial membrane affinity and photodynamic activity.

Regulation of protein prenylation

Prenyltransferases (PTases) are known to play a role in embryonic development, normal tissue homeostasis and cancer by posttranslationally modifying proteins involved in these processes. They are being discussed as potential drug targets in an increasing number of diseases, ranging from Alzheimer's disease to malaria. Protein prenylation and the development of specific PTase inhibitors (PTIs) have been subject to intense research in recent decades. Recently, the FDA approved lonafarnib, a specific farnesyltransferase inhibitor that acts directly on protein prenylation; and bempedoic acid, an ATP citrate lyase inhibitor that might alter intracellular isoprenoid composition, the relative concentrations of which can exert a decisive influence on protein prenylation. Both drugs represent the first approved agent in their respective substance class. Furthermore, an overwhelming number of processes and proteins that regulate protein prenylation have been identified over the years, many of which have been proposed as molecular targets for pharmacotherapy in their own right. However, certain aspects of protein prenylation, such as the regulation of PTase gene expression or the modulation of PTase activity by phosphorylation, have attracted less attention, despite their reported influence on tumor cell proliferation. Here, we want to summarize the advances regarding our understanding of the regulation of protein prenylation and the potential implications for drug development. Additionally, we want to suggest new lines of investigation that encompass the search for regulatory elements for PTases, especially at the genetic and epigenetic levels.