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Researchers find a new way to kill antibiotic-resistant bacteria

Antibiotic-resistant bacteria can now be killed using a new approach, according to researchers. The new method disables bacteria’s natural defense system, making antibiotics more harmful. The research, which was carried out in lab dishes and on mice, suggests a viable technique for combating so-called superbugs without the need to develop new medicines.

“You want to make the already existing antibiotics with good safety profiles more potent,” said senior author Evgeny Nudler, a professor of biochemistry at the New York University Grossman School of Medicine and an investigator with the Howard Hughes Medical Institute. With the help of a few newfound chemicals, the research team did just that.

Staphylococcus aureus and Pseudomonas aeruginosa, two bacteria that demonstrate widespread treatment resistance and are among the top causes of hospital-acquired infections, were the focus of the new study, which was published in the journal Science on Thursday (June 10). To resist the harmful effects of bactericidal antibiotics, these bacteria use an enzyme called cystathionine gamma-lyase (CSE). The enzyme is used by the bacteria to protect themselves from the toxicity of bactericidal antibiotics, which kill bacteria rather than simply halt their development.

The enzyme creates hydrogen sulfide, a substance that protects bacteria from oxidative stress, or the buildup of free radicals. So the researchers combed through over 3 million tiny compounds in search of compounds that might block CSE without interfering with mammalian cells, and they came up with three promising options.

In lab dishes, the novel compounds increased the potency of bactericidal medicines by two to 15 times, depending on the drug and the bacterial strain being targeted. Antibiotic-treated mice infected with S. aureus or P. aeruginosa fared better than those infected with S. aureus or P. aeruginosa.

Given that the research was done on rats in a lab setting, “moving on into a human system is, you know, that huge next step,” said Thien-Fah Mah, a professor and director of the Microbiology Graduate Program at the University of Ottawa who was not involved in the research. More research will be needed, as with any novel drug-like compounds, to determine what dose and delivery method will be the safest and most effective in people, Mah said.

However, because most bacterial species utilize this defense mechanism, targeting hydrogen sulfide production might be a “true game changer” in the fight against antibiotic resistance, according to a commentary published in the journal Science on June 10.

According to Mah, the route to the current study began years ago, when a 2007 publication in the journal Cell proposed that all bactericidal drugs may cause cell death in the same way. “At that point … it kind of blew the lid off of what all of us were thinking,” because each class of bactericidal antibiotics targets distinct regions of the bacterial cell, making it contradictory to believe they all kill microorganisms in the same way, she explained.

Some bactericidal medications, for example, target a cell’s outer wall,, while others impair the ribosome, the cell’s protein-building factory. However, according to a 2007 study, after achieving their initial targets, all of these medications had a common secondary effect: They encourage bacteria to develop “reactive oxygen species,” or free radicals, which are extremely reactive molecular wrecking balls that may cause catastrophic damage.

Following this research, Nudler and his colleagues found hydrogen sulfide, which is one of bacteria’s natural defensive mechanisms against reactive oxygen species. According to their findings, which was published in 2011 in the journal Science, the scientists analyzed the genomes of hundreds of bacteria and discovered that S. aureus and P. aeruginosa p shared similar genes that code for hydrogen sulfide-producing enzymes. They discovered that hydrogen sulfide increased the development of antioxidant enzymes in bacteria, which convert free radicals into non-toxic molecules while simultaneously reducing reactive oxygen species generation.

They also discovered that removing or inhibiting enzymes in bacteria makes them “highly sensitive” to antibiotics. Oxidative stress generated by a buildup of reactive oxygen species killed these sensitive microorganisms. The researchers was looking for “inhibitors” that could attach to and block bacterial enzymes in an infected individual at the time.

“If we combined those inhibitors with antibiotics … we could make those antibiotics more potent,” Nudler suggested. However, “it was very tricky to find those inhibitors targeting these enzymes that were specific to bacteria.”

Human cells rely on hydrogen sulfide since it is produced by mammalian cells. In humans, hydrogen sulfide works as a signaling molecule and interacts with a variety of organs, including the brain and smooth muscle. CSE is used by both human and bacterial cells to produce hydrogen sulfide, however human and bacterial CSE have somewhat distinct tastes. The researchers aimed to identify compounds that had a strong preference for the bacterial CSE, both to guarantee that the compounds were effective against bacteria and to minimize any unwanted side effects in mammalian cells.

They did so by studying the structure of human, bacterial, and other CSE variants in order to locate an appealing target for their molecules to latch onto. Finally, scientists discovered a “nice pocket” on the bacterial CSE where a tiny molecule might slip in and modulate the enzyme’s activity, according to Nudler.

The crew got to work building their weaponry when they located a bull’s-eye to shoot at. They used a virtual screen to find out which of the 3.2 million commercially available tiny molecules would fit into their selected pocket. Three options stood out as promising and advanced to the next phase of testing.

By reducing hydrogen sulfide generation, the inhibitors not only improved the effectiveness of medicines against bacteria, but they also prevented “bacterial tolerance.”

Unlike antibiotic resistance, which describes how bacteria develop to become more resistant to antibiotics, tolerance describes how bacteria slow down their metabolisms in response to stress and go into a semi-dormant condition. The cells cease proliferating and utilize less energy in this stage. Tolerance keeps germs alive until the antibiotics are no longer present since many drugs cause bacteria to short-circuit while proliferating. This implies that even after an infected individual has completed a full course of antibiotics, some bacteria cells might stay, and if their immune system isn’t able to cope with the leftovers, persistent infection might develop, according to Nudler.

However, the authors discovered that the inhibitors prevented many bacteria from entering this protective condition in their trials. “We demonstrate that hydrogen sulfide, clearly, makes a huge impact on tolerance,” Nudler stated. At the moment, “there is no drug specifically targeting … this tolerance phenomenon,” he noted, implying that this may be a new therapeutic option.

“From a mechanistic point of view, it is still not entirely clear how inhibition of hydrogen sulfide leads to the various effects observed,” said Dr. Dao Nguyen, an associate professor in the department of microbiology and immunology at McGill University in Montreal, who was not involved in the study. Nudler agreed, saying that he and his colleagues aim to look into the function of hydrogen sulfide in tolerance further.

The team also has to figure out if the molecules need to be tweaked to make them more effective in people, not just mice, and what the ideal method of administration is, according to Nguyen. “If the inhibitors could be developed into safe and effective drugs, one could imagine that they would be used in combination with existing antibiotics to treat … chronic infections where current antibiotics are not very effective,” she said.

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