An antibiotic from an uncultured bacterium

More and more bacterial pathogens are developing resistance. There is an increasing risk that common drugs will no longer be effective against infectious diseases. That is why scientists around the world are searching for new effective substances.

Researchers now have discovered and deciphered the mode of action of a new antibiotic. Clovibactin is derived from a soil bacterium. This antibiotic is highly effective at attacking the cell wall of bacteria, including many multi-resistant “superbugs.” The results have now been published in the renowned journal Cell.

“We urgently need new antibiotics to stay ahead in the race against bacteria that have become resistant,” says the senior author and adds that in recent decades, not many new substances to combat bacterial pathogens have come onto the market.

The soil bacterium Eleftheria terrae subspecies carolina carries its place of origin in its name: It was isolated from a soil sample in the US state of North Carolina and produces the new antibiotic compound clovibactin to protect itself from competing bacteria. “The new antibiotic simultaneously attacks the bacterial cell wall at several sites by blocking essential building blocks,” explains the author. It specifically binds to these building blocks with unusual intensity and kills the bacteria by destroying their cell envelope.

Research groups from different disciplines and countries worked together to unravel exactly how this works. The team discovered clovibactin using the iCHip device. This allows bacteria to be grown in the laboratory that were previously considered unculturable and were not available for the development of new antibiotics.

“Our discovery of this exciting new antibiotic further validates the iCHip culturing technology for finding new therapeutic compounds from previously uncultivated microorganisms,” says the president of NovoBiotic Pharmaceuticals, LLC. The company has demonstrated that clovibactin has very good activity against a broad spectrum of bacterial pathogens and has successfully treated mice in preclinical studies.

The researchers were able to show that clovibactin binds very selectively and with high specificity to pyrophosphate groups of bacterial cell wall components. They uncovered exactly what this interaction looks like. Using solid-state NMR spectroscopy, the researchers deciphered the structure of the complex of clovibactin and the bacterial target structure lipid II - under conditions similar to those found in the bacterial cell. These studies showed that clovibactin grips around the pyrophosphate group. This is where the name “Clovibactin” comes from, derived from the Greek “Klouvi” (cage), because it encloses the target structure like a cage.

Clovibactin acts primarily on gram-positive bacteria. These include “hospital pathogens,” such as MRSA bacteria but also the pathogens of the widespread tuberculosis, which affects many millions of people worldwide. “We are very confident that the bacteria will not develop resistance to clovibactin so quickly,” the author says. This is because the pathogens cannot change the cell wall building blocks so easily to undermine the antibiotic - their Achilles’ heel therefore remains.

But clovibactin can do even more. After docking to the target structures, clovibactin forms supramolecular filamentous structures that tightly enclose and further damage the target structures of the bacteria. Bacteria that encounter clovibactin are also stimulated to release certain enzymes, known as autolysins, which then uncontrollably dissolve their own cell envelope. “The combination of these different mechanisms is the reason for the exceptional resilience to resistance,” says the author. This shows the potential that still exists in the natural diversity of bacteria that are candidates for new antibiotics.

“Without the interdisciplinary cooperation between the partners, this important step in the fight against resistance would not have succeeded,” says another author. The research team now plans to use its findings to further increase the effectiveness of clovibactin. “But there is still a long way to go before a new antibiotic hits the market,” says the senior author.