Discovery of novel inhibitor via molecular dynamics simulations against D-alanyl-D-alanine carboxypeptidase of Enterobacter cloacae

Abstract

Antibiotics resistance by bacterial pathogens is a major concern to public health worldwide resulting in high health care costs and rising mortality. Subtractive proteomics prioritized D-alanyl-D-alanine carboxypeptidas (DacB) enzyme from Enterobacter cloacae ATCC 13047 as a potential candidate for drugs designing to block pathogen cell wall biosynthesis. Virtual screening of an antibacterial library against the target unraveled a hit compound (2-[(1-methylsulfonylpiperidin-3-yl)methyl]-6-(1H-pyrazol-4-yl) pyrazine) showing high affinity and stability with the target. The N-methyl-N-propyl-methanesulfonamide of the compound is seen as a closed affinity towards domain involving strong hydrogen bonds with Ser41, Lys44, Ser285, and Asn287. The 4-methyl-1H-pyrazole is posed towards the open cavity of domain I and II and formed hydrophobic and hydrophilic contacts. The system is highly stable with average carbon-alpha deviations of 1.69 Å over trajectories of 400-ns. Three vital residues projected: Arg437, Arg438 and Leu400 from enzyme pocket via Radial distribution function (RDF) assay, which actively engaged the inhibitor. Further confirmation is done by estimating binding free energies, which confirms the very low delta energy of −7.24 kcal/mol in Generalized Born (GB) method and −7.4363 kcal/mol in Poisson-Boltzmann (PB) method. WaterSwap calculations were performed that revealed the energies highly converged, an agreement on good system stability. Lastly, three DacB mutants were created to investigate the role of functional active residues and a decline in binding affinity of the residues was noticed. These computational results provide a gateway for experimentalists to further confirm their efficacy both in-vitro and in-vivo.

Communicated by Ramaswamy H. Sarma

Keywords:

• Subtractive proteomics
• hydrogen bonds
• binding energies
• trajectories analysis
• axial frequency distribution

Acknowledgment

Authors are highly grateful to the Higher Education Pakistan (HEC) for granting financial assistance. Authors dedicate this paper to Prof. Dr. Bernd Michael Rode who passed away on August 29th, 2022, for his excellent contribution towards science and specifically for Theoretical and Computational Chemistry.

Disclosure statement

No potential conflict of interest was reported by the authors.

Authors contributions

The whole work was designed by Dr Syed Sikander Azam and the computational analysis was done by Mr. Faisal Ahmad that include Molecular docking and simulation along its statistical analysis. Followed by the manuscript writing as well. Whereas Saba Ismail has performed some of the analysis which include binding energies and manuscript formatting. All the authors contributed equally and reviewed the manuscript.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.