Screening of exogenous nutrients for pathogenic bacteria and development of highly active bactericides

The inherent barriers posed by bacterial outer membranes, efflux pumps, and biofilm matrices significantly limit the clinical efficacy of antimicrobial agents, underscoring the urgent need for strategies to enhance drug penetration. Integrating pathogen-specific exogenous nutrients with conventional antibiotics has emerged as a promising approach, facilitating the targeted delivery and enhanced efficacy of antimicrobial compounds. In this study, we aimed to improve antimicrobial efficacy by enhancing transmembrane transport. First, we comprehensively compared various genome-scale metabolic reconstruction methods to identify the optimal approach. Subsequently, we enhanced our previous approach to identify exogenous nutrients by integrating topological screening, flux scoring, and chemical structure analysis. Key exogenous nutrients were identified for three pathogens: urea for <i>Acinetobacter baumannii</i>, acetamide for <i>Pseudomonas aeruginosa</i>, and succinic acid for <i>Salmonella enterica</i>. Growth assays confirmed that these nutrients significantly promoted bacterial proliferation. Leveraging these findings, four novel antimicrobial compounds (NC, NA, MA, and MN) were synthesized by conjugating membrane-resistant nalidixic acid or magnolol with the respective nutrients. MN enhanced the antimicrobial activity against wild-type <i>S. enterica</i> by 56.5%, while MA and NA boosted the activity against wild-type <i>P. aeruginosa</i> by 51.4% and 70.4%, respectively. Moreover, NC improved efficacy against drug-resistant <i>A. baumannii</i> by fourfold. These results demonstrate that conjugating exogenous nutrients with antibiotics can effectively enhance antimicrobial activity and help overcome membrane-associated resistance. This nutrient-conjugation strategy offers a promising avenue for developing new antimicrobial agents.IMPORTANCEThe difficulty of achieving effective drug penetration into bacterial cells is a major obstacle limiting antimicrobial efficacy and posing a significant global health challenge. This study demonstrates a novel strategy to combat resistance by "hijacking" nutrients that pathogens rely on for growth. By combining antibiotics with these nutrients, drugs can bypass membrane barriers and effectively reach their targets. The preferred exogenous nutrients of the high-priority pathogens <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, and <i>Salmonella enterica</i> were identified. Combining these with the existing antibiotics markedly enhanced antimicrobial efficacy against both susceptible and resistant strains. This approach offers a practical way to revitalize existing antibiotics and design new ones, potentially slowing the spread of resistance. Importantly, it highlights how understanding bacterial metabolism can lead to smarter drug design, addressing a critical need in global health.