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N-Heterocyclic analogues as peptide deformylase inhibitors: Molecular modeling, synthesis and antibacterial evaluation


Global emergence of worsening antibiotic resistance has become a serious problem because of emergence of multi drug resistance (MDR) strains. The emergence of MDR strains has forced the scientific community to searching of new antibiotics.


A new series of N- heterocyclic compounds has been derived from benzimidazole and pyrimidine nuclei optimized with the Discovery studio 3.0 software to investigate the interactions between the target compounds and the amino acid residues of Escherichia coli PDF Ni (PDB: ID 1G2A), and then synthesized. Further, all compounds were examined for their antibacterial activities against Gram-positive, S.viridians, and Gram-negative bacterial strains, E. coli, P. mirabilis and K. pneumoniae using the microdilution broth susceptibility test method and subjected to polynomial regression.


The compounds showed promising in silico results as reflected by their significant scoring functions and close interatomic contacts through strong H-bonds with Ile 44, Gly 45, Gly 89, Cys 90, Glu95, Cys129 and Arg 97; pi-pi interaction with Arg 97 and His 132. Antibacterial results indicated that these molecules possessed significant activity against all the tested species with MIC values ranging between 0.22 and 2.62 μM. The regression coefficients (R2 = 0.78 to 0.89) derived for each strain were correlated significantly.


The molecules proved as effective inhibitors of bacterial PDF, which has been corroborated by docking studies.

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Correspondence to Ramendra K Singh.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

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Singh, A., Yadav, M., Singh, P. et al. N-Heterocyclic analogues as peptide deformylase inhibitors: Molecular modeling, synthesis and antibacterial evaluation. BMC Infect Dis 14 (Suppl 3), E18 (2014).

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