Drug Design and Optimisation

The methyl erythritol phosphate (MEP) pathway is a rich, underexplored source of anti-infective targets that are absent from humans but essential in many pathogenic bacteria, protozoa and plants. This opens up the possibility of developing highly selective inhibitors that are active against clinically relevant pathogens such as four ESKAPE pathogens: Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp., all of which have highest priority according to the WHO Global Priority List of antibiotic-resistant bacteria – as well as Mycobacterium tuberculosis and Plasmodium falciparum. In these pathogens, the MEP pathway is the sole source of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). The latter are the universal building blocks for the biosynthesis of isoprenoids, a large and diverse class of natural products fulfilling a myriad of indispensable functions. With DXS, IspD, IspE we address three essential enzymes of this pathway. Our best compounds are highly active against the mentioned pathogens and show nanomolar IC50 values.

Antibacterial drugs targeting essential multi-enzyme complexes are less prone to resistance development, since their malfunctioning is hard to bypass. In this context, the bacterial replisome machinery, which consists of at least twelve interacting enzymes that are highly conserved in bacteria, contains several attractive and promising antibacterial targets – including the bacterial β-sliding clamp DnaN. DnaN is a crucial subunit of the DNA polymerase III holoenzyme, preventing polymerase dissociation and enhancing polymerase activity. Furthermore, the β-sliding clamp shows interactions with a variety of other enzymes involved in replication and DNA repair processes. Its important functionality in the replication process and its highly conserved structure across bacterial species and its significant structural divergence to the mammalian counterpart (PCNA) make DnaN an attractive target for the treatment of various pathogens including Mycobacterium tuberculosis. Based on the natural product griselimycin (GM), a known DnaN binder, we adopted a semisynthetic approach, which resulted in a set of GM derivatives with promising antibacterial activities. Furthermore, we identified diverse small organic molecules binding to DnaN. The optimization of the most promising compounds is ongoing.

Clostridia represent a family of ubiquitously occurring gram-positive bacteria comprising perilous pathogens causing serious infectious diseases. The high lethality of these bacteria is related to collagenases, which are crucial for clostridial virulence, given their critical role in colonisation and evasion of host immune defence, acquisition of nutrients, facilitation of dissemination, or tissue damage during infection. The inhibition of these extracellular collagenases is conceptually attractive, as it does not attack the pathogen directly but rather blocks the colonisation and infiltration of the host by the clostridia. Targeting extracellular enzymes has the added benefit that inhibitors do not need to cross the bacterial cell wall, which has been challenging in many cases. Clostridial collagenases are zinc metalloproteinases with a multi-domain organisation, homologues of which are also found in many bacilli. Our group was the first who published compounds showing not only a highly potent inhibition of clostridial and bacillal collagenases (ColH IC50 in nM range) but also a strong selectivity over human MMPs.

Pseudomonas aeruginosa (PA), a highly problematic gram-negative pathogen, which has been assigned critical priority by the WHO, is responsible for many nosocomial infections. The opportunistic pathogen is also commonly found in burns, and in lungs of COPD and cystic fibrosis patients. PA-derived virulence factors play pivotal roles in mechanisms mediating its pathogenesis and infectivity. The strategy to develop “pathoblockers” targeting such virulence factors is expected to leave the commensal microbiome intact and to be less prone to the development of resistance compared to conventional antibiotics. One of the major virulence factors of PA is the extracellular zinc-metalloprotease elastase LasB. LasB substantially contributes to disease progression in PA-infected individuals by facilitating host invasion and immune evasion, and was furthermore reported to be involved in the formation of PA biofilms. Inhibition of LasB is a promising strategy to effectively reduce virulence of PA without affecting viability of the pathogen and the host microbiome. Our most promising LasB inhibitors show nanomolar IC50 values and a promising safety profile.