Development of new inhibitors of bacterial topoisomerases to overcome antimicrobial resistance

Code:

J1-3031

Range:

01. October 2021 - 30. September 2024

Range:

1,38 FTE

Leader:

Nace Zidar

Field:

1-09 Natural sciences and Mathematics - Pharmacy

Research Organisation:

https://cris.cobiss.net/ecris/si/en/project/18652

Researchers:

https://cris.cobiss.net/ecris/si/en/project/18652

Content:

https://cris.cobiss.net/ecris/si/en/project/18652

Abstract:

In recent years, we observed an alarming increase in life-threatening infections due to resistant Gram-positive and Gram-negative pathogens and mycobacteria. Resistance has evolved to every single antibacterial   drug that has been introduced to the clinic, which strongly limits our treatment options. New antibacterials specifically aimed at resistant infections are thus urgently needed. Bacterial type II topoisomerases - DNA gyrase and topoisomerase IV - are enzymes that control the topological state of DNA during cell division and DNA   replication, and are essential for bacterial growth. The ATP binding site located on the GyrB subunit of DNA gyrase and ParE subunit of topoisomerase IV is an attractive target for the development of new antibacterial agents. DNA gyrase and topoisomerase IV   share 40% overall sequence identity and possess similar active sites, which offers exceptional opportunity for dual targeting, thereby reducing the probability of bacteria to develop target-based resistance. In recent years, several small-molecule ATP-competitive   inhibitor classes have been discovered but none has so far reached the market. Further research is needed to produce drug candidates with stronger in vitro and in vivo antibacterial activities, low toxicity and good ADMET properties. Therefore, the overall aim of the project is to discover new ATP-competitive small-molecule inhibitors of DNA gyrase and topoisomerase IV with activity against resistant bacterial strains. The project is highly multidisciplinary and gathers a group of experts on the whole cycle of modern hit and hit-to-lead drug discovery of antibacterial compounds. Past and present cooperative connections   between different members of the core team provide a broad platform not only for biological screening but also for knowledge transfer, and are good promise for successful realisation and international relevance of the proposed project. The result of the project will be new lead compounds with potential to be developed into clinical candidates for the treatment of infections caused by resistant bacterial strains.

Phases:

To achieve the overall goal of the project, we will combine several innovative approaches. We will start from our recently discovered N-phenylpyrrolamide GyrB/ParE inhibitors and optimise them using innovative structure-based design. We will design original   new compounds with balanced dual-targeting activity towards GyrB and ParE, by interacting with multiple, functionally essential amino acids of both target proteins, with low probability of resistance development. Compounds will be synthesized using state-of-the-art   organic chemistry strategies. We will determine the inhibitory activities of the prepared compounds on bacterial topoisomerases and on various off-targets. Potent and selective inhibitors will be subjected to detailed microbiological evaluation on selected   Gram-positive and Gram-negative bacteria and mycobacteria, including multidrug resistant (MDR) strains. Using original method DIvERGE, we will assess the probability of resistance development and underlying mutational mechanisms. We will later use this data   to identify less resistance-prone antibiotics. For the most promising hits with potent antibacterial activity, a comprehensive medicinal chemistry programme will be pursued to develop them towards lead compounds, which will involve determination and optimisation   of compounds’ physicochemical (logP, logD, thermodynamic and kinetic solubility) and ADMET properties. Crystal structures of GyrB or ParE in complex with selected most promising inhibitors will be prepared. Using the generated data, new analogues will be designed, prepared and evaluated in several cycles, until compounds with desired activity on GyrB/ParE and against selected bacteria with optimized ADMET properties will be obtained.

Bibliographical references, arising directly from the implementation of the project:

https://cris.cobiss.net/ecris/si/en/project/18652

Financed by:

Research projects (co)funded by the Slovenian Research Agency.