Discovery of novel inhibitors for Pseudomonas aeruginosa lipase enzyme from in silico and in vitro studies

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen prone to developing drug-resistance and is a major cause of infection for burn patients and patients suffering from cystic fibrosis or are hospitalized in intensive care units. One of the virulence factors of this bacterium is the lipase enzyme that degrades the extracellular matrix of the host tissue and promotes invasion. Bromhexine is a mucolytic drug and has recently been reported to function as a competitive inhibitor of lipase with an IC₅₀ value of 49 µM. In the present study, an attempt was made to identify stronger inhibitors from the ChEMBL database of bioactive compounds, as compared to the reference compound Bromhexine. Following docking and MD simulations, four hit compounds (N1-N4) were selected that showed promising binding modes and low RMSD values indicative of stable protein-ligand complexes. From subsequent binding pose metadynamics (BPMD) simulations, two of these (N2 and N4) stood out as more potent than Bromhexine, displaying stable interactions with residues in the catalytic site of the enzyme. Biological investigations were performed for all four compounds. Among them, the same two hit compounds were found to be the most effective binders with IC₅₀ values of 22.1 and 27.5 µM, respectively; i.e. roughly twice as efficient as the reference Bromhexine. Taken together, our results show that these hits can be promising new candidates to use as leads for the development of drugs targeting the P. aeruginosa lipase enzyme.

Communicated by Ramaswamy H. Sarma

Keywords:

• Pseudomonas aeruginosa
• lipase
• inhibitors
• bromhexine
• docking
• molecular dynamics simulations
• binding pose metadynamics

Acknowledgments

The authors acknowledge funding from the Swedish Research Council (VR), grant number 2019-3684 (L.A.E.), and generous allocation of computing time at the supercomputing centers C3SE and NSC by the Swedish National Infrastructure for Computing (SNIC), in part funded by the Swedish Research Council through grant agreement no 2018-05973.

Authors’ contributions

All authors designed the initial study and contributed with the analysis of data. AG performed all calculations and in vitro experiments. The manuscript was written and revised through the contributions of all authors. All authors have given approval to the final version of the manuscript.

Data availability

All docked structures, MD simulation trajectories, and BPMD data are available as free download from Zenodo.org, DOI: 10.5281/zenodo.7003747.

Disclosure statement

The authors declare no conflicts of interest.

Additional information

Funding

Vetenskapsrådet.