Identification of novel metallo-β-lactamases inhibitors using ligand-based pharmacophore modelling and structure-based virtual screening

Abstract

Metallo-β-lactamases (MBLs) are a group of enzymes that hydrolyze the most commonly used β-lactam-based antibiotics, leading to the development of multi-drug resistance. The three main clinically relevant groups of these enzymes are IMP, VIM, and NDM. This study aims to introduce potent novel overlapped candidates from a ZINC database retrieved from the 200,583-member natural library against the active sites of IMP-1, VIM-2, and NDM-1 through a straightforward computational workflow using virtual screening approaches. The screening pipeline started by assessing Lipinski’s rule of five (RO5), drug-likeness, and pan-assay interference compounds (PAINS) which were used to generate a pharmacophore model using D-captopril as a standard inhibitor. The process was followed by the consensus docking protocol and molecular dynamic (MD) simulation combined with the molecular mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method to compute the total binding free energy and evaluate the binding characteristics. The absorption, distribution, metabolism, elimination, and toxicity (ADMET) profiles of the compounds were also analyzed, and the search space decreased to the final two inhibitory candidates for B1 subclass MBLs, which fulfilled all criteria for further experimental evaluation.

Communicated by Ramaswamy H. Sarma

Keywords:

• Antibiotic resistance
• Metallo-β-lactamases
• drug discovery
• natural product
• pharmacophore
  
• molecular dynamics simulation

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The authors did not receive support from any organization for the submitted work.