(586c) Discovery of Inhibitors for Mura Protein As Antimicrobials through an Integrated Computational and Experimental Approach

Peptidoglycan is a component of the bacterial cell wall responsible for mechanical strength and resistance to environmental stress [1]. The fact that peptidoglycan biosynthesis is necessary for bacterial growth and is well conserved across bacterial species makes it a common target for antimicrobial development [1]. In particular, the MurA enzyme is an essential enzyme involved in bacterial cell wall synthesis so that it could be a good drug target for antibiotics. This is implied by the conservation of the structure of the MurA structure across a variety of bacterial strains.[2] Although Fosfomycin is used clinically as a MurA inhibitor, pathogens’ resistance to this antibiotic is a concern. This study aims to find effective inhibitors of the MurA enzyme that can be used as new antibiotics.

Since millions of molecules exist in chemical compound libraries, [3,4] It is costly and time-consuming to evaluate each compound for its inhibition against the MurA protein experimentally. Automated molecular docking provides a solution for this, as it offers a quick computational evaluation of the binding affinity between small-molecule ligand and the MurA protein with a known three-dimensional crystalline structure. Recent optimization of algorithms and scoring functions permit more reliable assessments.[5] Previous studies and tests have indicated that Molsoft ICM performs the outstanding for covalent docking, docking pose, and energy prediction.[5] Here we developed a ICM-based computational pipeline to identify potential MurA inhibitors from 1.412 million compounds from three databases. Thirty-three top compounds from virtual screening were experimentally tested in Listeria innocua (gram-positive bacterium) and Escherichia coli (gram-negative bacterium). The compounds showing growth inhibition effect in and/or L. innocua and E. coli, were further tested for their Minimum Inhibitory Concentration (MIC) value. New potential applications of several FDA-approved drugs as potential antimicrobials have been discovered. The identified MurA inhibitors could be the potential novel antibiotics against foodborne pathogen L. monocytogenes, which is genetically, morphologically, and biochemically similar to L. innocua. Since structures between MurA proteins across species are similar. The compounds identified from this study could be potential Fosfomycin substitutes for the Fosfomycin resistant strains.

References

[1] Radkov, A.D.; Hsu, Y.-P.; Booher, G.; VanNieuwenhze, M.S. Imaging Bacterial Cell Wall Biosynthesis. Annual review of biochemistry, 2018, 87, 991–1014.

[2] Bensen, D.C.; Rodriguez, S.; Nix, J.; Cunningham, M.L.; Tari, L.W. Structure of MurA (UDP-N-Acetylglucosamine Enolpyruvyl Transferase) from Vibrio Fischeri in Complex with Substrate UDP-N-Acetylglucosamine and the Drug Fosfomycin. Acta crystallographica. Section F, Structural biology and crystallization communications, 2012, 68, 382–385.

[3] Kim, S.; Thiessen, P.A.; Bolton, E.E.; Chen, J.; Fu, G.; Gindulyte, A.; Han, L.; He, J.; He, S.; Shoemaker, B.A.; Wang, J.; Yu, B.; Zhang, J.; Bryant, S.H. PubChem Substance and Compound Databases. Nucleic Acids Research, 2016, 44, D1202–D1213.

[4] Allen, F.H.; IUCr. The Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising. urn:issn:0108-7681, 2002, 58, 380–388.

[5] Lionta, E.; Spyrou, G.; Vassilatis, D.K.; Cournia, Z. Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances. Current Topics in Medicinal Chemistry, 2014, 14, 1923–1938.