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Complex crystal structures of analogs 3 (panel A), 2 (panel B), and 13 (panel C) bound to NDM-1. In contrast to the structure of 3 (PDB 9O2W ), the structures of analogs 2 (PDB code 9DEW ) and 13 (PDB code 9DAG ) include two ligands arranged in a head-to-tail stacking interaction. The 2Fo-Fc electron densities for analogs 3 and 2 are shown at 1.5σ.

Journal: ACS Omega

Article Title: Structure-Based Design of Reversible, Quinoline-2(1 H )‑one Inhibitors of Serine- and Metallo-Carbapenemases

doi: 10.1021/acsomega.5c12676

Figure Lengend Snippet: Complex crystal structures of analogs 3 (panel A), 2 (panel B), and 13 (panel C) bound to NDM-1. In contrast to the structure of 3 (PDB 9O2W ), the structures of analogs 2 (PDB code 9DEW ) and 13 (PDB code 9DAG ) include two ligands arranged in a head-to-tail stacking interaction. The 2Fo-Fc electron densities for analogs 3 and 2 are shown at 1.5σ.

Article Snippet: Briefly, the clinical K. pneumoniae KPC-2 strain was provided by Dr. Yohei Doi (University of Pittsburgh) and the K. pneumoniae NDM-1 strain was purchased from ATCC (BAA-2146).

Techniques:

(A) Thermogram of ITC runs performed at 200 μM 13 into 30 μM NDM-1 in 500 μM Zn 2+ buffer (black line). A baseline heat release of 13 directly into the buffer with no protein present was also performed (orange line). Data is plotted with exothermic reactions down. (B) Heat release as a function of compound/protein mole ratio (exotherm up). Data points were then fit to a nonlinear regression (independent model of binding) to determine thermodynamic parameters. (C) Table of thermodynamic parameters measured from ITC curve.

Journal: ACS Omega

Article Title: Structure-Based Design of Reversible, Quinoline-2(1 H )‑one Inhibitors of Serine- and Metallo-Carbapenemases

doi: 10.1021/acsomega.5c12676

Figure Lengend Snippet: (A) Thermogram of ITC runs performed at 200 μM 13 into 30 μM NDM-1 in 500 μM Zn 2+ buffer (black line). A baseline heat release of 13 directly into the buffer with no protein present was also performed (orange line). Data is plotted with exothermic reactions down. (B) Heat release as a function of compound/protein mole ratio (exotherm up). Data points were then fit to a nonlinear regression (independent model of binding) to determine thermodynamic parameters. (C) Table of thermodynamic parameters measured from ITC curve.

Article Snippet: Briefly, the clinical K. pneumoniae KPC-2 strain was provided by Dr. Yohei Doi (University of Pittsburgh) and the K. pneumoniae NDM-1 strain was purchased from ATCC (BAA-2146).

Techniques: Binding Assay

Stacked binding of the 22 (PDB code 9DB7 ) dimer in NDM-1 (panel A). Overlay of 22 with structure of 13 (wheat) illustrating shift in the binding of 22 within the active site (panel B). The greater steric demands of the larger N1 substituent in 22 may force the alternate binding mode, compared to the planar π–π stacking seen with 13 .

Journal: ACS Omega

Article Title: Structure-Based Design of Reversible, Quinoline-2(1 H )‑one Inhibitors of Serine- and Metallo-Carbapenemases

doi: 10.1021/acsomega.5c12676

Figure Lengend Snippet: Stacked binding of the 22 (PDB code 9DB7 ) dimer in NDM-1 (panel A). Overlay of 22 with structure of 13 (wheat) illustrating shift in the binding of 22 within the active site (panel B). The greater steric demands of the larger N1 substituent in 22 may force the alternate binding mode, compared to the planar π–π stacking seen with 13 .

Article Snippet: Briefly, the clinical K. pneumoniae KPC-2 strain was provided by Dr. Yohei Doi (University of Pittsburgh) and the K. pneumoniae NDM-1 strain was purchased from ATCC (BAA-2146).

Techniques: Binding Assay