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

In a recent study published in the journal Nature, researchers in the United States of America designed and discovered lolamicin, a selective antibiotic that targets the lipoprotein transport system in Gram-negative bacteria. They found that lolamicin was effective against multidrug-resistant Gram-negative pathogens, showed efficacy in mouse infection models, spared the gut microbiome, and prevented secondary infections.

Study: A Gram-negative-selective antibiotic that spares the gut microbiome. Image Credit: Kateryna Kon / ShutterstockStudy: A Gram-negative-selective antibiotic that spares the gut microbiome. Image Credit: Kateryna Kon / Shutterstock

Background

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.

Sequencing of lolCDE in resistant strains did not reveal mutations associated with lolamicin resistance, highlighting its potential as a promising antibiotic candidate. Lolamicin showed lower resistance frequencies across strains. LolC and LolE proteins were identified as targets, with specific mutations linked to resistance. Lolamicin exhibited bactericidal or bacteriostatic effects against tested bacteria. Swelling was observed in lolamicin-treated cells, indicative of dysfunctional lipoprotein trafficking. Lolamicin-resistant mutants displayed altered phenotypic responses to treatment, supporting LolC and LolE involvement.

Lolamicin was found to disrupt lipoprotein trafficking by competitively inhibiting binding at BS1 and BS2 sites. Hydrophobic interactions were primarily found to drive lolamicin binding, explaining the reduced efficacy of compounds with primary amines. Resistant mutations were found to impact lolamicin binding affinity, highlighting their role in destabilizing binding pockets. Lolamicin demonstrated superior efficacy to compound 1 in reducing bacterial burden and improving survival rates in infection models involving multidrug-resistant bacteria such as E. coli AR0349, K. pneumoniae, and E. cloacae.

Oral administration of lolamicin showed significant bioavailability and efficacy, reducing bacterial burden and increasing survival rates in mice infected with colistin-resistant E. coli. Lolamicin showed minimal impact on the gut microbiome with stable richness and diversity compared to amoxicillin and clindamycin. Lolamicin-treated mice and the vehicle control showed minimal C. difficile colonization. In contrast, amoxicillin or clindamycin-treated mice displayed an inability to clear C. difficile, with high colonization throughout the experiment.

Conclusion

In conclusion, this novel study identifies lolamicin as a pathogen-specific antibiotic that holds promise for minimizing damage to the gut microbiome and potentially preventing secondary infections. Further research and human studies are warranted to confirm the drug's clinical applicability. In the future, the microbiome-sparing effect of lolamicin could offer significant advantages over current broad-spectrum antibiotics in clinical practice, enhancing patient outcomes and overall health.

Journal reference:
Dr. Sushama R. Chaphalkar

Written by

Dr. Sushama R. Chaphalkar

Dr. Sushama R. Chaphalkar is a senior researcher and academician based in Pune, India. She holds a PhD in Microbiology and comes with vast experience in research and education in Biotechnology. In her illustrious career spanning three decades and a half, she held prominent leadership positions in academia and industry. As the Founder-Director of a renowned Biotechnology institute, she worked extensively on high-end research projects of industrial significance, fostering a stronger bond between industry and academia.  

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