Screening of compound library identifies novel inhibitors against the MurA enzyme of Escherichia coli

Abstract

Bacterial cell has always been an attractive target for anti-infective drug discovery. MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) enzyme of Escherichia coli (E.coli) is crucial for peptidoglycan biosynthetic pathway, as it is involved in the early stages of bacterial cell wall biosynthesis. In the present study we aim to identify novel chemical structures targeting the MurA enzyme. For screening purpose, we used in silico approach (pharmacophore based strategy) for 52,026 library compounds (Chembridge, Chemdiv and in house synthetics) which resulted in identification of 50 compounds. These compounds were screened in vitro against MurA enzyme and release of inorganic phosphate (Pi) was estimated. Two compounds (IN00152 and IN00156) were found to inhibit MurA enzyme > 70% in primary screening and IC50 of 14.03 to 32.30 μM respectively. These two hits were further evaluated for their mode of inhibition studies and whole-cell activity where we observed 2-4 folds increase in activity in presence of Permeabilizer EDTA (Ethylenediaminetetraacetic acid). Combination studies were also performed with known antibiotics in presence of EDTA. Hits are reported for the first time against this target and our report also support the use of OM permeabilizer in combination with antibacterial compounds to address the permeability and efficacy issue. These lead hits can be further optimized for drug discovery.

Key points

Emerging Gram negative resistant strains is a matter of concern.

Need for new screening strategies to cope with drying up antibiotics pipeline.

Outer membrane permeabilizers could be useful to improve potency of molecules to reach its target.

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Availability of data and material

Data will be made available on reasonable request.

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Acknowledgments

Authors are thankful to the repository of CSIR-IIIM for providing library compounds. The manuscript bears Institutional Publication No. CSIR-IIIM/IPR/00232

Funding

This work was supported by Department of Health Research (DHR), New Delhi India (Grant no.GAP-2128)

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Authors

Contributions

DR performed the major experiments and wrote the manuscript.

HT performed the in silico screening of library.

SS and D contributed in cloning and assay optimization studies.

PKC synthesized the compounds.

AN guided the in silico and pharmacophore studies.

PLS designed the synthetic compounds.

KE and UB standardized the MurA assays.

RAV guided in the compound synthesis and overall manuscript.

FGK principal investigator of the project and contributed in the molecular biology studies.

SS provided into in the biological part and helped in the final draft preparation.

IAK conceptualized the whole manuscript and edited the draft and submitted the manuscript.

Corresponding authors

Correspondence to Farrah Gul Khan or Inshad Ali Khan.

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The authors have declared that they have no competing interests.

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Raina, D., Tiwari, H., Sharma, S. et al. Screening of compound library identifies novel inhibitors against the MurA enzyme of Escherichia coli. Appl Microbiol Biotechnol 105, 3611–3623 (2021). https://doi.org/10.1007/s00253-021-11272-4

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Keywords

  • Escherichia coli
  • MurA
  • Peptidoglycan
  • Molecular docking
  • Drug discovery