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Alexander Fleming's accidental discovery of penicillin in 1928 changed the world: Once-common bacterial infections, sometimes deadly, were treatable, and a slew of antibiotics followed. But bacteria have proven a wily adversary, adapting to resist antibiotic treatment.

In a recent scientific advancement, a team led by James Fraser, chair and professor of Bioengineering and Therapeutic Sciences at the University of California, San Francisco, developed a compound that may restore the efficacy of a class of antibiotics known as streptogramins.

To do this, the researchers used bright X-rays at the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy's SLAC National Accelerator Laboratory and the Lawrence Berkeley National Laboratory's Advanced Light Source (ALS) to study molecular structures and interactions between candidate drug compounds and bacteria. Their , published in Structure, point to a promising lead in designing new therapies.

"This discovery is an exciting step forward in the fight against antibiotic resistance," said Aina Cohen, division director of Structural Molecular Biology at SSRL. "By harnessing the intense X-ray beams at synchrotrons, the Fraser group identified previously hidden binding sites that offer a promising path to inhibit a bacterial enzyme that makes antibiotics less effective. This could help bring back the power of certain antibiotics that no longer work against resistant infections."

Narrowing the search with powerful X-rays

Antibiotics kill bacteria by disrupting structures and functions crucial for the bacteria's survival. Over time, bacteria have evolved mechanisms to interfere with this process—with some particularly pesky bacteria able to resist multiple antibiotics. Streptogramins are naturally occurring antibiotics that can overcome these mechanisms in multidrug-resistant Gram-positive bacteria, which often cause blood or severe skin infections. Streptogramins bind to the bacteria's ribosome to hinder critical protein synthesis processes.

In recent years, some multidrug-resistant Gram-positive bacteria strains evolved to produce a protein, Virginiamycin acetyl transferase D (VatD), that interferes with the binding of streptogramin to the ribosome. Fraser's team aims to develop a drug that interrupts VatD's ability to do that.

The first step is to find small molecule fragments that could bind to VatD. These fragments could serve as a foundation for creating drugs that inhibit VatD. Using special libraries that house chemical and structural information on hundreds of small molecules, Pooja Asthana, postdoctoral researcher in the Fraser lab and lead author of the paper, soaked each candidate into a VatD crystal to allow them to interact and hopefully bind.

To check if the binding was successful, she turned to X-ray crystallography at SSRL and ALS. The high-resolution structural information from this technique helped Asthana determine if the candidate bound to the protein target site. More than 30 fragments did bind. Next, she added other chemical groups to the fragments to enhance their binding with VatD.

After creating and testing approximately 70 such compounds, she found one showing moderate activity, indicating it could be further developed to enhance its properties. "I was both excited and a little surprised when we got the hit," said Asthana. "After all the rounds of screening and optimization, seeing a compound that checked all the boxes felt rewarding."

Next, the team will try to increase this compound's inhibition by making small changes to its structure through adding or removing molecular groups.

"This work shows that we can use SSRL to rapidly generate starting points for inhibitors that could potentiate the streptogramin class of antibiotics," said Fraser. "With further development, inhibitors based on these scaffolds might enable streptogramin antibiotics to be used in clinical and agricultural contexts where antibiotic resistance currently renders streptogramins and other classes of antibiotics ineffective."