Rational design of novel compounds to serve as potential NDM-1 inhibitors using molecular docking, molecular dynamics simulation, and physicochemical studies

Abstract

New Delhi Metallo-β-lactamase (NDM-1) is an enzyme that hydrolyses a wide range of β-lactam antibiotics, including most carbapenems, leading to antimicrobial resistance. The development of a novel NDM-1 inhibitor for use in combination with carbapenems may help to combat drug-resistant pathogens. Twenty compounds were designed based on the structural features of the NDM-1 active site to inhibit bacterial NDM-1 and protect β-lactam antibiotics from enzyme attack. The designed molecules were naphthalene, thiazole, and sulfone derivatives because they could coordinate with the zinc ions and form hydrophobic contracts with the enzyme’s active site. A molecular docking protocol was used to identify potential inhibitor(s) of the NDM-1 target protein. Furthermore, drug-likeness and pharmacokinetic properties of the designed molecules were predicted. Three compounds with the more negative ΔGbinding results were selected for further investigation using molecular dynamic (MD) simulations. T016 had a significantly more negative binding free energy than the positive control and other designed molecules, had stable MD simulations (Root-mean-square deviation < 0.5 Å), passed Lipinski’s rule of five, and had favourable physicochemical and pharmacokinetic properties. The findings can be used to inform the synthesis and in vitro testing of the selected molecules.