Multiscale Design Principles for Noncovalent Heteroaryl Phosphonate Inhibitors Targeting NDM-1

Abstract

The global spread of New Delhi metallo-β-lactamase-1 (NDM-1) poses a significant challenge for β-lactam antibiotics, driving the search for effective molecular inhibitors. In this study, we used a suite of computational techniques—including long-timescale molecular dynamics, principal component analysis, free-energy landscape mapping, binding free-energy calculations (MM/GBSA and SIE), and interaction fingerprint profiling—to investigate how heteroaryl phosphonate scaffolds affect NDM-1’s structure and dynamics. Analysis of nine inhibitors revealed that noncovalent phosphonate binding alters the dynamics of the L3 and L10 loops at the Zn(II) active site. Potent inhibitors (such as C06 and C09) confine NDM-1 to a narrow, inactive conformational state, while weaker inhibitors (such as C13 and C14) allow greater loop flexibility and multiple metastable conformations. Free-energy decomposition showed that van der Waals interactions, rather than electrostatics, are the main drivers of inhibitor binding. Interaction fingerprint analysis identified key hotspot residues—His122, Phe70, Met67, and Asn220—that are consistently involved in ligand binding. These findings establish clear design principles linking scaffold features to conformational control, providing a framework for developing next-generation noncovalent NDM-1 inhibitors.