Discovery of a Novel Natural Allosteric Inhibitor That Targets NDM-1 Against Escherichia coli

Abstract

At present, the resistance of New Delhi metallo-β-lactamase-1 (NDM-1) to carbapenems and cephalosporins, one of the mechanisms of bacterial resistance against β-lactam antibiotics, poses a threat to human health. In this work, based on the virtual ligand screen method, we found that carnosic acid 1 (CA), a natural compound, exhibited a significant inhibitory effect against NDM-1 (IC 50 = 27.07 μM). Although carnosic acid did not display direct antibacterial activity, the combination of carnosic acid and meropenem still showed bactericidal activity after the loss of bactericidal effect of meropenem. The experimental results showed that carnosic acid can enhance the antibacterial activity of meropenem against Escherichia coli ZC-YN3. To explore the inhibitory mechanism of carnosic acid against NDM-1, we performed the molecular dynamics simulation and binding energy calculation for the NDM-1-CA complex system. Notably, the 3D structure of the complex obtained from molecular modeling indicates that the binding region of carnosic acid with NDM-1 was not situated in the active region of protein. Due to binding to the allosteric pocket of carnosic acid, the active region conformation of NDM-1 was observed to have been altered. The distance from the active center of the NDM-1-CA complex was larger than that of the free protein, leading to loss of activity. Then, the mutation experiments showed that carnosic acid had lower inhibitory activity against mutated protein than wild-type proteins. Fluorescence experiments verified the results reported above. Thus, our data indicate that carnosic acid is a potential NDM-1 inhibitor and is a promising drug for the treatment of NDM-1 producing pathogens.

Discovery of an Effective Small-Molecule Allosteric Inhibitor of New Delhi Metallo-β-lactamase (NDM)

“…Our characterization of the inhibition mechanism is consistent with describing QDP-1 as a slow-binding, noncompetitive, reversible inhibitor that binds outside of the active site, resulting in a reversible enzyme isomerization to a less thermostable state and inhibition. There are only a limited set of inhibitors with noncompetitive or uncompetitive modes of inhibition for MBLs, and these compounds are mostly peptides or macromolecules. − Some small-molecule reversible inhibitors with these modes of inhibition have also been reported, with just three reports of such inhibitors for NDM-1 to our knowledge: azolylthioacetamides, carnosic acid, and thiosemicarbazone derivatives (each is discussed below). − QDP-1 differs significantly in structure from these other inhibitors and represents a promising alternative to the more common competitive and metal-stripping MBL inhibitors.…”

“…A nitro substituent in the most potent derivative was modeled to interact with the dizinc active site, but the allosteric binding site was not identified. Carnosic acid was proposed as an allosteric inhibitor by virtual docking to NDM-1 at a binding site adjacent to the substrate-binding β-hairpin loop . However, this work has some features that complicate interpretation.…”

“…Carnosic acid was proposed as an allosteric inhibitor by virtual docking to NDM-1 at a binding site adjacent to the substrate-binding β-hairpin loop. 45 However, this work has some features that complicate interpretation. The protein structure used for docking contains 11 amino acid differences from NDM-1 and is not a known clinical variant.…”

In vitro and in silico β-lactamase inhibitory properties and phytochemical profile of Ocimum basilicum cultivated in central delta of Egypt

“…Yang et al. ( 2020 ) stated that carnosic acid, a natural compound, did not possess direct antibacterial activity but demonstrated a significant inhibitory effect against NDM-1 recording an IC 50 of 27.07 mM (Yang et al. 2020 ).…”

Mulberrin inhibitsBotrytis cinereafor strawberry storage by interfering with the bioactivity of 14α-demethylase (CYP51)

“…36 The detailed docking and MD simulation processes were referenced from previous studies. 37,38 2.5.2 Virtual screening. The 3D structure of CYP51 with heme based on homology modeling was used as a receptor, and standard molecular docking was performed for high throughput virtual screening via the Autodock vina software.…”