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Persistence Pays off for Researchers Developing Antibiotic Against Persisters

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By Anette Breindl
Science Editor

An antibiotic that was once dropped from clinical development because bacteria quite easily develop genetic resistance to it may get a second lease on life – because as part of a combination therapy, it can kill so-called bacterial persisters in biofilms.

In combination with rifampicin, acyldepsipeptide-4 (ADEP-4) was able to eradicate Staphylococcus aureus biofilms. “We found complete sterilization,” both in test tubes and in animal models of chronic infection, corresponding author Kim Lewis told BioWorld Today.

In their paper, which was published in the Nov. 14, 2013, issue of Nature, he and his co-authors called such biofilm eradication “unprecedented for such low, clinically achievable concentrations of compounds.”

Antibiotics can become ineffective for two reasons. The development of resistance through mutations is a well-known and much-decried risk to antibiotic effectiveness. A September federal report estimated that the annual death toll from such drug-resistant bacteria tops 20,000, and in March, the Centers for Disease Control and Prevention’s director, Tom Frieden, called one such type of bacteria, carbapenem-resistant Enterobacteriaceae, a “nightmare.” (See BioWorld Today, April 22, 2013.)

But antibiotics can also develop so-called persistence that is not due to any genetic mutation. In fact, it’s not entirely clear at the molecular level what causes persistence. Metabolic changes play a role. So do biofilms, where bacteria band together in a sticky matrix, often on medical devices.

“Antibiotics penetrate the biofilm fairly well,” Lewis said, though immune system cells don’t. But within the biofilm, some of the cells are not dividing – and that makes them indifferent to current antibiotics, which are inhibitors. Different classes of antibiotics inhibit different bacterial enzymes, but their basic approach is always to prevent growth by blocking some process or other that is necessary for the bacteria to survive.

Lewis and his team were able to eradicate so-called persisters by using the opposite approach. Rather than inhibiting a process the bacteria needed to grow, they unleashed one of its proteases, leading the cells to basically eat themselves.

ADEP-4 targets a subunit of the protease ClpP. ClpP, Lewis said “has an important role within the [bacterial] cell – it chews up denatured proteins.” But when the protease is activated by ADEP-4, “it starts chewing up proteins indiscriminately” – not just denatured ones, but ones that are important for bacterial function. Ultimately, that kills the bacteria. (See BioWorld Today, Oct. 28, 2005.)

But although ClpP is important for the cell, it is not critical. And so, bacteria soon get around ADEPs, through mutations that render ClpP nonfunctional altogether. That ease with which bacteria develop resistance, in fact, was one of the reasons that Bayer Healthcare AG dropped development of the compound.

However, if the mutants survive, they don’t exactly thrive. “ClpP null mutants can be killed by almost anything,” Lewis said, including regular antibiotics such as rifampicin, which is usually not used to treat staph infections.

In their experiments, Lewis and his colleagues used ADEP-4 in combination with rifampicin both in cell culture biofilms and in mice with deep-seated infections of methicillin-resistant Staph aureus (MRSA), a drug-resistant version of Staph aureus that infects a million people annually and can be fatal. Staph aureus is usually unimpressed by attempts to get rid of it with rifampicin. But a combination of ADEP-4 and rifampicin completely eliminated such infections.

Lewis is the co-founder of a start-up, Arietis Corp., that wants to develop antibiotics that can eradicate persister cells, including S. aureus and MRSA, gastritis due to H. pylori and infections of implanted medical devices.