Fifty years ago, researchers plucked a highly potent antibiotic out of a bacterial broth and named it borrelidin. Although scientists soon discovered that it blocked the activity of an enzyme involved in protein synthesis, no one could figure out exactly how it did so.
Now, researchers led by Min Guo at Scripps Research Institute Florida report they have used X-ray crystallography to determine how borrelidin jams its protein target, threonyl-tRNA synthetase (Nat. Commun. 2015, DOI: 10.1038/ncomms7402). The structural insights could enable drug developers to massage the molecule, which also has potent antifungal, antimalarial, and anticancer properties, into a viable therapeutic.
Borrelidin is one of several molecules that target transfer RNA synthetases, the protein machines that attach amino acids to tRNA, so that the ribosome can then add the amino acids to a growing protein chain. Other tRNA synthetase-blocking compounds are therapeutics, such as the topical ointment mupirocin (or bactroban), which can kill MRSA, the notorious methicillin-resistant Staphylococcus aureus.
“For decades, borrelidin remained one of the most potent molecules in its class, yet people didn’t know how it worked,” comments Roger G. Linington, a natural products chemist at the University of California, Santa Cruz.
Guo’s team discovered that borrelidin shuts down its target by being an impressive multitasker: The molecule simultaneously blocks three substrate binding sites and creates its own fourth site by jamming its macrolide ring into the protein’s hydrophobic core. “The fact that it binds these four sites is incredible,” comments Michael Ibba, an Ohio State University microbiologist who studies tRNA synthetases.
“Nobody would have designed this molecule using a rational design strategy,” Linington says. Only extensive evolutionary experimentation could lead to such a blocking mechanism, he adds. “Now we need to find out whether this is a common mode of action or just something freaky and weird about borrelidin,” Ibba says.
Borrelidin is currently too unselective to be a drug. The molecule targets tRNA synthetases in humans, which could make for undesirable toxic side effects. It is also metabolized too quickly by the body, so its pharmacokinetic properties are poor, Guo adds.
Guo hopes that the atomic-level structure of borrelidin in its target’s binding pocket will help researchers design more inhibitors of the tRNA synthetase and develop borrelidin analogs that get around its selectivity and pharmacokinetic problems. Tweaking borrelidin may be challenging synthetically, Linington notes, because the molecule contains an unusual but important nitrile motif and conjugated olefins, all of which medicinal chemists may find hard to modify. One way to help borrelidin avoid human synthetases, Guo adds, could be to encapsulate the molecule chemically and target those bundles to pathogenic or cancerous cells.