Dissertion: "Development of phosphorus-containing metallo-β-lactamase inhibitors: Synthesis and binding studies by solution NMR and molecular docking"

Katarzyna Palica defends her thesis with the title ”Development of phosphorus-containing metallo-β-lactamase inhibitors: Synthesis and binding studies by solution NMR and molecular docking” in the subject of Chemistry, with specialization in Organic Chemistry.

Opponent: Prof. Christopher Schofield, University of Oxford, UK
Supervisors: Prof. Máté Erdélyi, Uppsala University and Prof. Jan Kihlberg, Uppsala University


The rapidly growing bacterial resistance development is turning into one of the main challenges of the 21st century. Our antibiotics are becoming ineffective for the treatment of bacterial infections, and without successful action, simple infections, such as pneumonia or Septicemia, will soon carry a highly probable mortal prognosis. Among the most widely spread mechanisms of bacterial resistance are the degradation and modification of antibiotics, prior to them reaching the target site, by bacterial enzymes.

This thesis work aims to contribute to solving a major societal challenge by providing new knowledge on the binding site of the NDM-1, which is one of the clinically most relevant enzymes used by bacteria to degrade antibiotics. The work includes the design and synthesis of potential β-lactamase inhibitors that mimic the transition state of the enzymatic hydrolysis of β-lactam antibiotics. These bioisosteric transition state analogues are expected to bind and inhibit NDM-1, without being hydrolysable. Thereby they could potentially slow down or even halt the degradation of our β-lactam antibiotics is use.

The first chapter describes the specific aims, whereas the second presents a general overview of bacterial resistance showing the mechanism of β-lactam hydrolysis along with our current knowledge of the structure of metallo-β-lactamases and examples for known inhibitors. The third chapter reviews the key features of the applied methods including those of enzyme assays, NMR protein backbone resonance assignment, chemical shift perturbation, NOESY and molecular docking. Subsequently, the investigation of the three groups of metallo-β-lactamase inhibitors are discussed. First, the design and synthesis of phosphoamidate- and phosphonic acid-based metallo-β-lactamase inhibitors is presented. Subsequently, enzyme - inhibitor binding studies as well as combined solution NMR spectroscopic and computational docking studies aiming the determination of binding site and pose of inhibitor candidates is described. The binding affinities and binding modes for three types of enzyme inhibitors are disclosed along with a comparison of their binding to the New Delhi metallo-β-lactamase (NDM-1) and Verona integron-encoded metallo-β-lactamase (VIM-2), pointing out similarities and differences. The binding pose of a previously developed inhibitor has also been determined with the help of fluorine-labeling. 

The knowledge generated in this thesis work is expected to be useful for the development of wide spectrum metallo-β-lactamase inhibitors, which may become a long-sought relief in an escalating crisis.

Link to the thesis in full text in DiVA.