An antibiotic, lolamycin, has been discovered that kills dangerous bacteria without damaging the intestinal microbiome

A recent study published in Nature has shown that scientists in the US 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, is effective 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 shared by Gram-positive and Gram-negative bacteria. Because the gut microbiome contains a variety of Gram-negative bacteria, promiscuous antibiotics such as colistin can cause significant dysbiosis, limiting their use.

Despite the growing need for new antibacterials for Gram-negative bacteria due to resistant 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 scientists 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 effectiveness of lolamycin was tested against multidrug-resistant clinical isolates of E. Coli, K. Pneumoniae and E. Cloacae. Susceptibility studies have been conducted with lolamycin and other compounds.

Lolamycin-resistant mutants were developed and compared for fitness. The bactericidal effect 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 inhibition of lolamycin.

In addition, mice were treated with pyridine pyrazole (compound 1) and lolamycin intraperitoneally for three days. Pharmacokinetic studies were performed to evaluate the bioavailability of lolamycin. Infection models were used to compare the effectiveness of lolamycin and compound 1 in the treatment of pneumonia and septicemia, with lolamycin also administered orally. The mice's microbiomes were analyzed using their fecal samples through 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, has shown high activity against specific Gram-negative pathogens with low accumulation in E. Coli. Lolamycin showed selectivity, preserving 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, showing a narrow range of minimum inhibitory concentrations and effectiveness 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. The LolC and LolE proteins were identified as targets, with specific mutations associated with resistance. Lolamycin showed either bactericidal or bacteriostatic effects against the tested bacteria. Swelling of cells treated with lolamycin was observed, indicating a disruption in lipoprotein transport. Lolamycin-resistant mutants exhibited altered phenotypic responses to treatment, suggesting the involvement of LolC and LolE.

Lolamycin disrupted lipoprotein transport by competitively inhibiting binding at sites BS1 and BS2. Hydrophobic interactions turned out to be the main ones, explaining the decrease in the effectiveness of compounds with primary amines. Resistance 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 burden and increasing survival in infection models involving multidrug-resistant bacteria such as E. Coli AR0349, K. Pneumoniae and E. Cloacae.

Oral administration of lolamycin showed significant bioavailability and efficacy, reducing the bacterial load and increasing the survival of mice infected with colistin-resistant E. Coli. Lolamycin had minimal effects on the gut microbiome, maintaining its richness and diversity compared to amoxicillin and clindamycin. Minimal C. Difficile colonization was observed in lolamycin-treated mice and control animals. 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 damage to the gut microbiome and prevent secondary infections. Further research and clinical trials are needed to confirm the clinical utility of the drug. In the future, the microbiome-preserving effects of lolamycin may provide significant advantages over current broad-spectrum antibiotics in clinical practice, improving patient outcomes and overall health.