A versatile technology platform for identification and development of novel bio-antibiotics

The rise of multidrug-resistant bacteria threatens the achievements of modern medicine. Particularly problematic in this context is the increasing resistance of the pathogens Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. Antibiotics with novel modes of action are urgently needed to combat these bacterial species. We will establish a technology that enables the identification of high-affinity binders for targets on the surface of these pathogens. These binders are potential novel antibiotics. As a key application, we will target the outer membrane protein insertase BamA. Using the platform, we will select single-domain antibodies, which will be generated either by immunization of alpacas (nanobodies) or in vitro from synthetic nanobody libraries (sybodies), and we will then screen large libraries of such binder molecules for antibiotic activity. We refer to such biomolecular drugs against pathogenic bacteria as "bio-antibiotics". Our technology platform rests on two pillars. In a first step, sybody and nanobody selections are carried out against a purified sample of the target. Notably, only a small subset of the resulting binders will bind the OMP targets in the native context of the bacterial outer membrane, where some accessible epitopes are covered underneath a dense lipopolysaccharide layer. Therefore, in a second step our recently developed binder screening and characterization technology NestLink is applied, which is uniquely available to the Seeger lab. NestLink allows to deep-mine an enriched binder pool in a single experiment, which is impossible by conventional technologies. The utility of our bio-antibiotic technology platform will be demonstrated by the identification of lead molecules that inhibit the growth of clinical Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa strains. Suitable lead molecules will enter pre-clinical trials to treat life-threatening blood stream infections and frequently observed urinary tract infections.