The antibiotic lolamycin has been discovered to kill dangerous bacteria without damaging the gut microbiome

A recent study published in the journal Nature found that US scientists have developed and discovered a new selective antibiotic called lolamycin that targets the lipoprotein transport system in gram-negative bacteria. The researchers found that lolamycin is effective against multidrug-resistant gram-negative pathogens, shows efficacy in mouse infection models, preserves the gut microbiome, and prevents secondary infections.

Antibiotics can disrupt the gut microbiome, leading to increased susceptibility to pathogens such as C. difficile and increasing the risks of gastrointestinal, renal, and hematological problems. Most antibiotics, whether gram-positive or broad-spectrum, harm gut commensals and cause dysbiosis. The impact of gram-negative-only antibiotics on the microbiome is unclear due to their rarity. Their detection is difficult because most antibiotic targets are common to both gram-positive and gram-negative bacteria. Because the gut microbiome contains many gram-negative bacteria, promiscuous antibiotics such as colistin can cause significant dysbiosis, limiting their use.

Despite the growing need for new antibacterial agents for Gram-negative bacteria due to persistent infections, no new class has been approved by the Food and Drug Administration (FDA) in the last 50 years. Discovery is complicated by the complex membrane structure and efflux pumps of Gram-negative bacteria. Developing a Gram-negative-only antibiotic that preserves the microbiome requires targeting an important protein unique to Gram-negative bacteria, with significant homology differences between pathogenic and commensal bacteria. In this study, scientists developed and reported a new antibiotic called lolamycin, which targets the periplasmic lipoprotein Lol transport system important for a variety of Gram-negative pathogens.

In this study, the researchers targeted LolCDE, a key component of the Lol system in Gram-negative bacteria. Screens were conducted to find potential inhibitors of this system, which were then synthesized and evaluated. The efficacy of lolamycin was tested against multidrug-resistant clinical isolates of E. coli, K. pneumoniae, and E. cloacae. Susceptibility studies were conducted with lolamycin and other compounds.

Lolamycin-resistant mutants were developed and compared for fitness. The bactericidal activity of lolamycin was studied using growth curves. Confocal microscopy was used to observe phenotypic changes in target bacteria. Molecular modeling and dynamic simulations, ensemble docking and cluster analysis were used to investigate the binding sites and mechanism of lolamycin inhibition.

Additionally, mice were treated with pyridinepyrazole (compound 1) and lolamycin intraperitoneally for three days. Pharmacokinetic studies were conducted to assess the bioavailability of lolamycin. Infection models were used to compare the efficacy of lolamycin and compound 1 in the treatment of pneumonia and septicemia, with lolamycin also administered orally. The microbiomes of mice were analyzed using their fecal samples via 16S ribosomal RNA sequencing. Additionally, antibiotic-treated mice were exposed to C. difficile to assess their ability to clear the pathogen on their own.

Lolamycin, an inhibitor of the LolCDE complex, demonstrated high activity against specific Gram-negative pathogens with low accumulation in E. coli. Lolamycin demonstrated selectivity, sparing both Gram-positive and Gram-negative commensal bacteria. It showed minimal toxicity to mammalian cells and remained effective in the presence of human serum. Lolamycin demonstrated high activity against multidrug-resistant clinical isolates of E. coli, K. pneumoniae, and E. cloacae. Lolamycin outperformed other compounds by showing a narrow range of minimum inhibitory concentrations and efficacy against multidrug-resistant strains.

Sequencing of lolCDE in resistant strains revealed no mutations associated with lolamycin resistance, highlighting its potential as a promising antibiotic candidate. Lolamycin showed a low frequency of resistance among strains. LolC and LolE proteins were identified as targets, with specific mutations associated with resistance. Lolamycin exhibited either bactericidal or bacteriostatic activity against the tested bacteria. Swelling of lolamycin-treated cells was observed, suggesting impaired lipoprotein transport. Lolamycin-resistant mutants showed altered phenotypic responses to treatment, confirming the involvement of LolC and LolE.

Lolamycin impaired lipoprotein transport by competitively inhibiting binding at BS1 and BS2. Hydrophobic interactions were found to be dominant, explaining the reduced efficacy of compounds with primary amines. Resistance-conferring mutations affected the binding affinity of lolamycin, highlighting their role in destabilizing binding sites. Lolamycin showed superior efficacy compared to compound 1 in reducing bacterial load and increasing survival in infection models involving multidrug-resistant bacteria such as E. coli AR0349, K. pneumoniae, and E. cloacae.

Oral administration of lolamycin demonstrated significant bioavailability and efficacy, reducing bacterial load and increasing survival in mice infected with colistin-resistant E. coli. Lolamycin had minimal impact on the gut microbiome while maintaining its richness and diversity compared to amoxicillin and clindamycin. Lolamycin-treated mice and controls showed minimal colonization with C. difficile. In contrast, mice treated with amoxicillin or clindamycin failed to clear C. difficile, showing high colonization throughout the experiment.

In conclusion, this pioneering study identifies lolamycin as a specific antibiotic that has the potential to minimize gut microbiome damage and prevent secondary infections. Further studies and clinical trials are needed to confirm the clinical applicability of the drug. In the future, the microbiome-preserving effect of lolamycin may provide significant advantages over current broad-spectrum antibiotics in clinical practice, improving patient outcomes and overall health.