Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium

Abstract

Antibiotic resistance is widely seen as one of the biggest threats to global health for the next decades. WHO estimates that in 2050, up to 10 millions deaths per year will be caused by multi-resistant bacteria, unless action is taken. Therefore, it is of vital importance to analyse and elucidate the mechanisms that bring resistance to microorganisms, in order to plan strategies that will lead, eventually, to the development of new generations of antibiotics. Metallo-β-lactamases (MBLs) are bacterial enzymes that generate resistance towards a wide variety of antibiotics. The response of the immune system consists in supplying metal chelators, which retrieve zinc ions, causing the degradation of MBLs. New Delhi MBL 1 (NDM-1) is a B1 subclass MBL that came to the fore in the last years because of its resistance to metal chelators. It was demonstrated that a lipidated version of NDM-1 is able to anchor to the outer bacterial membrane, hence providing resistance towards zinc starvation. However, the molecular mechanisms that lie beyond this phenomenon remain elusive. Molecular simulations show that, although lipidation is essential for stabilizing membrane anchoring, the first interaction is driven by simple electrostatics. The natural affinity of NDM-1 for the membrane could explain why, among MBLs, this peculiar mechanism evolved within NDM-1 only, eventually helping to predict which other MBLs are likely to develop similar features. Indeed, the affinity for the membrane presents ample variability across different MBLs, as we highlighted by comparing NDM-1 to other enzymes of the same class, such as VIM-2. The simulations also show that a specific lipid patch is necessary to drive the protein/membrane recognition, and that removing charged lipids can strongly affect the binding. Experimental tests were conducted to support and confirm these findings.