Development of fragment-based inhibitors of the bacterial deacetylase LpxC as novel antibiotics

• Applicants: Professor Dr. Ralph Holl; Professor Dr. Wolfgang Sippl
• Subject Area: Pharmacy
• Term: from 2020 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 434601098

The constantly increasing number of multidrug-resistant Gramnegative bacteria poses a pressing threat to human health and welfare. Therefore, novel antibiotics possessing so far unexploited mechanisms of action are urgently required. As lipid A, the hydrophobic membrane anchor of lipopolysaccharides, is essential for growth and viability of Gram-negative bacteria, the inhibition of its biosynthesis represents a promising strategy for the development of antibiotics being selective for Gram-negative germs. The deacetylase LpxC catalyzes the first committed step of lipid A biosynthesis and could be validated as an antibacterial drug target. In the proposed project, small molecule LpxC inhibitors shall be developed using innovative fragment-based methods combined with structure-based approaches. NMR-based fragment screening against LpxC will be performed to identify fragments binding to the so far unoccupied UDP-binding pocket of LpxC. Fragment libraries comprising nature-inspired fragments will be screened in the presence of probes being derived from known as well as novel inhibitors. To generate potent enzyme inhibitors, the identified structures will be merged in the most beneficial way using the knowledge of the structural information derived from experimental NMR data such as Interligand NOEs and molecular docking studies. The envisaged merged compounds will be prepared in a stereocontrolled manner employing state of the art divergent syntheses. Besides benzyloxyacetohydroxamic acid-based LpxC inhibitors, novel 3,4-disubstituted morpholine derivatives being devoid of the pharmacokinetically unfavorable hydroxamate moiety will be synthesized. Structure-activity relationships will be elaborated for all of the synthesized LpxC inhibitors and rationalized by molecular docking studies. In subsequent optimization steps, the inhibitory activity of the compounds, their antibacterial spectrum against various Gram-negative bacteria as well as their metabolic stability will be improved. Preliminary experiments have been performed to ensure the feasibility of the project. Protein purification, enzymatic assays, first LpxC inhibitors synthesis, biological activities, interligand-NOE NMR experiments, and docking studies with known and designed inhibitors have been carried out successfully.

• DFG Programme: Research Grants
• International Connection: France
• Cooperation Partner: Dr. Isabelle Krimm