BB0323-BB0238 PPI assay protocol.

Borrelia burgdorferi, one of the most prevalent tick-borne pathogens, can cause a complex and multisystem illness called Lyme disease, where there has been an unmet need for novel therapeutic or preventive strategies. We previously identified an essential protein-protein interaction (PPI) event in B. burgdorferi involving two unique proteins, BB0323 and BB0238; herein, we show that this PPI is indispensable for long-term borrelial survival in mammals and explore its potential as a novel target for small molecule therapeutics. Using X-ray crystallography, we solved the structure of the BB0238-BB0323 complex and identified the hotspot residues that form the biomolecular PPI interface area of ~1000 square Ångstroms. We then performed quantitative high-throughput drug screens of 62,740 diverse small molecules utilizing an amplified luminescent proximity homogeneous assay linked immunosorbent assay (AlphaLISA). Following a comprehensive pipeline to confirm small molecule hits, we short-listed three distinct PPI inhibitors of BB0238-BB0323. One of these inhibitors, called lomibuvir (VX-222, VCH-222), displayed robust PPI inhibition inside B. burgdorferi cells and was shown to affect pathogen persistence in a tick-borne murine model of Lyme disease. Our study highlights targeted PPI disruption as a new therapeutic strategy against B. burgdorferi and may foster future antimicrobial discovery efforts to resolve clinical complications associated with Lyme disease.