Aspergillomarasmine A inhibits metallo-β-lactamases by selectively sequestering Zn2+

Class B metallo-beta-lactamases (MBLs) are Zn2+-dependent enzymes that catalyze the hydrolysis of beta-lactam antibiotics to confer resistance in bacteria. Several problematic groups of MBLs belong to subclass B1, including the binuclear New Delhi MBL (NDM), Verona integrin-encoded MBL, and imipenemase-type enzymes, which are responsible for widespread antibiotic resistance. Aspergillomarasmine A (AMA) is a natural aminopolycarboxylic acid that functions as an effective inhibitor of class B1 MBLs. The precise mechanism of action of AMA is not thoroughly understood, but it is known to inactivate MBLs by removing one catalytic Zn2+ cofactor. We investigated the kinetics of MBL inactivation in detail and report that AMA is a selective Zn2+ scavenger that indirectly inactivates NDM-1 by encouraging the dissociation of a metal cofactor. To further investigate the mechanism in living bacteria, we used an active site probe and showed that AMA causes the loss of a Zn2+ ion from a low-affinity binding site of NDM1. Zn2+-depleted NDM-1 is rapidly degraded, contributing to the efficacy of AMA as a beta-lactam potentiator. However, MBLs with higher metal affinity and stability such as NDM-6 and imipenemase-7 exhibit greater tolerance to AMA. These results indicate that the mechanism of AMA is broadly applicable to diverse Zn2+ chelators and highlight that leveraging Zn2+ availability can influence the survival of MBL-producing bacteria when they are exposed to beta-lactam antibiotics.

Automated summary

Class B metallo-beta-lactamases (MBLs) are enzymes that confer antibiotic resistance in bacteria by catalyzing the hydrolysis of beta-lactam antibiotics with the help of Zn2+ cofactors. Aspergillomarasmine A (AMA) is a natural inhibitor of class B1 MBLs which selectively removes one catalytic Zn2+ cofactor, causing inactivation of enzymes like NDM-1. The mechanism of action of AMA involves encouraging dissociation of Zn2+ from MBLs, leading to their rapid degradation and improved efficacy as a beta-lactam potentiator, although some MBLs with higher metal affinity show greater tolerance to AMA.