Discovery of antibiotic lolamicin that targets deadly bacteria without harming gut microbiome

Antibiotic treatment can disrupt the gut microbiome, leading to increased susceptibility to pathogens like C. difficile and higher risks of gastrointestinal, renal, and hematological issues. Most antibiotics, whether Gram-positive-only or broad-spectrum, harm gut commensals and cause dysbiosis. The impact of Gram-negative-only antibiotics on the microbiome is unclear due to the scarcity of such compounds. Their discovery was challenging because most antibiotic targets are shared by both Gram-positive and Gram-negative bacteria. Since the gut microbiome contains many Gram-negative bacteria, indiscriminate Gram-negative antibiotics such as colistin can cause significant dysbiosis, limiting their use. Despite the rising need for new Gram-negative antibacterial agents due to resistant infections, no new class has been approved by the Food and Drug Administration (FDA) in over 50 years. Discovery is complicated by Gram-negative bacteria’s complex membrane structures and efflux pumps. Developing a Gram-negative-only antibiotic that spares the microbiome calls for targeting an essential protein exclusive to Gram-negative bacteria, with significant homology differences between pathogenic and commensal bacteria. In the present study, researchers designed and reported a Gram-negative-only antibiotic named “lolamicin,” that targets the Lol lipoprotein transport system in the periplasm, which is crucial for various Gram-negative pathogens. About the study In the present study, LolCDE, a key component of the Lol system in Gram-negative bacteria, was targeted. Screening was conducted for potential inhibitors of the system, which were synthesized and assessed. The efficacy of lolamicin was evaluated against multidrug-resistant clinical isolates of E. coli, K. pneumoniae, and E. cloacae. Susceptibility studies were conducted with lolamicin and other compounds. Lolamicin-resistant mutants were developed and compared for fitness. The bactericidal effects of lolamicin were examined using time-kill growth curves. Confocal microscopy was used to observe phenotypic changes in the target bacteria. Molecular modeling and dynamics simulations, ensemble docking, and cluster analysis were used to explore lolamicin’s binding sites and inhibition mechanism. Further, mice were treated with pyridinepyrazole (compound 1) and lolamicin intraperitoneally for three days. Pharmacokinetic studies were conducted to assess lolamicin’s bioavailability. Infection models were used to compare the efficacy of lolamicin and compound 1 in treating pneumonia and septicemia, with lolamicin also administered orally. Microbiomes of mice were analyzed using their fecal samples via16S ribosomal ribonucleic acid (RNA) sequencing. Additionally, antibiotic-treated mice were challenged with C. difficile to assess their ability to clear the pathogen spontaneously. Results and discussion Lolamicin, an inhibitor of the LolCDE complex, showed potent activity against specific Gram-negative pathogens with low accumulation in E. coli. Lolamicin displayed selectivity, sparing both Gram-positive and Gram-negative commensal bacteria. It exhibited minimal toxicity towards mammalian cells and remained effective in the presence of human serum. Lolamicin demonstrated potent activity against multidrug-resistant clinical isolates of E. coli, K. pneumoniae, and E. cloacae. Lolamicin outperformed other compounds, showing a narrow minimum inhibitory concentration range and efficacy against multidrug-resistant strains.