A Potential Substrate Binding Conformation of β-Lactams and Insight into the Broad Spectrum of NDM-1 Activity

Abstract

New Delhi metallo-␤-lactamase 1 (NDM-1) is a key enzyme that the pathogen Klebsiella pneumonia uses to hydrolyze almost all ␤-lactam antibiotics. It is currently unclear why NDM-1 has a broad spectrum of activity. Docking of the representatives of the ␤-lactam families into the active site of NDM-1 is reported here. All the ␤-lactams naturally fit the NDM-1 pocket, implying that NDM-1 can accommodate the substrates without dramatic conformation changes. The docking reveals two major binding modes of the ␤-lactams, which we tentatively name the S (substrate) and I (inhibitor) conformers. In the S conformers of all the ␤-lactams, the amide oxygen and the carboxylic group conservatively interact with two zinc ions, while the substitutions on the fused rings show dramatic differences in their conformations and positions. Since the bridging hydroxide ion/water in the S conformer is at the position for the nucleophilic attack, the S conformation may simulate the true binding of a substrate to NDM-1. The I conformer either blocks or displaces the bridging hydroxide ion/water, such as in the case of aztreonam, and is thus inhibitory. The docking also suggests that substitutions on the ␤-lactam ring are required for ␤-lactams to bind in the S conformation, and therefore, small ␤-lactams such as clavulanic acid would be inhibitors of NDM-1. Finally, our docking shows that moxalactam uses its tyrosyl-carboxylic group to compete with the S conformer and would thus be a poor substrate of NDM-1.

Metallo‐β‐lactamase structure and function

“…A recent computational substrate docking study of various β‐lactam antibiotics into the active site of the NDM‐1 enzyme has also produced interesting results 81 . The poses of the docked substrates revealed two major modes of binding that were named “S” and “I” conformers.…”

“…The poses of the docked substrates revealed two major modes of binding that were named “S” and “I” conformers. The S mode has the carbonyl oxygen of the amide of β‐lactam ring coordinated to Zn1 and the carboxylate of the fused ring coordinated with Zn2 and the bridging water/hydroxide positioned for nucleophilic attack and therefore this conformer is optimally positioned for catalysis 81 . The I mode contains the carboxylic acid of the fused ring coordinating with Zn1 and Zn2 and displacing the water/hydroxide and moves the β‐lactam amide group away from the metal ions thus creating an inhibitory binding mode.…”

“…The I mode contains the carboxylic acid of the fused ring coordinating with Zn1 and Zn2 and displacing the water/hydroxide and moves the β‐lactam amide group away from the metal ions thus creating an inhibitory binding mode. Interestingly, the S conformer dominates over the I in the set of docked structures for good substrates while for poor substrates, such as the monobactam aztreonam, virtually all docking structures are in the I mode displacing the catalytic water/hydroxide 81 . This result suggests that monobactams are not hydrolyzed by metallo‐β‐lactamases because they bind with the sulfonate group bridged between Zn1 and Zn2 and displace the catalytic water 81 …”

Exploring the Role of Residue 228 in Substrate and Inhibitor Recognition by VIM Metallo-β-lactamases

“…8,9 In B1MBLs, such as IMP-1 and NDM-1, the adjacent position 224 in so-called active site loop 10 (ASL-10) is a conserved lysine that plays a key role in substrate binding because of its proximity to the active site. 11,12 In the VIM enzymes, position 224 has more allelic variants: histidine in VIM-1, -4, -7, -11, and -12; tyrosine in VIM-2; and leucine in VIM-5 and -13. 13 Because the side chains of these residues are shorter and less basic than that of the lysine, R228, with its extended side chain, is hypothesized to replace K224 in interacting with the carboxylate moiety (C4 or C3) of β -lactam substrates.…”

New β-phospholactam as a carbapenem transition state analog: Synthesis of a broad-spectrum inhibitor of metallo-β-lactamases

“…In the absence of experimental structures of MβL-ligand complexes, docking studies can provide insights into possible binding modes of inhibitors 38 and β-lactam substrates. 39, 40 These studies have shown that substituents with high electron density, such as, thiols, carboxylates, and carbonyl groups interact electrostatically with the zinc ions and the positively-charged Lys224 conserved in many B1 and B2 MβLs. 41, 42 Here we assessed the binding mode of β-phospholactam 1 to the different MβLs using docking.…”