Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation

Abstract

DNA gyrase and topoisomerase IV are well-validated pharmacological targets, and quinolone antibacterial drugs are marketed as their representative inhibitors. However, in recent years, resistance to these existing drugs has become a problem, and new chemical classes of antibiotics that can combat resistant strains of bacteria are strongly needed. In this study, we applied our hit-to-lead (H2L) chemistry for the identification of a new chemical class of GyrB/ParE inhibitors by efficient use of thermodynamic parameters. Investigation of the core fragments obtained by fragmentation of high-throughput screening hit compounds and subsequent expansion of the hit fragment was performed using isothermal titration calorimetry (ITC). The 8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative 13e showed potent activity against Escherichia coli DNA gyrase with an IC50 value of 0.0017 μM. In this study, we demonstrated the use of ITC for primary fragment screening, followed by structural optimization to obtain lead compounds, which advanced into further optimization for creating novel antibacterial agents.

Photocatalytic, Bactericidal and Molecular Docking Analysis of Annealed Tin Oxide Nanostructures

“…The 3D-crystal structures of selected protein targets belonging to E. coli and S. aureus were obtained from protein data bank with accession code: 4KZ9; Res: 1.72 Å [ 43 ], 1MWU; Res: 2.6 Å [ 44 ] for β -lactamase, while 6KZX; Res: 2.1 Å [ 45 ] and 5CTU; Res: 1.45 Å [ 46 ] for DNA gyrase as shown in Fig. 4 .…”

DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization

“…As a test case, we use DNA gyrase B from E. coli in complex with 2-oxo-1,2-dihydroquinoline [18]. Ushiyama et al recently used fragment-based lead optimization to identify several DNA gyrase B inhibitors, including one in the low-nanomolar range [18]. Further, none of the crystal structures associated with the Ushiyama study (PDB IDs: 6KZV, 6KZX, 6KZZ, and 6L01 [18]) were included in the original training, validation, or testing sets used to create the DeepFrag model.…”

“…Ushiyama et al [18] first used a high-throughput screen to identify a 2-quinolinone-based inhibitor (IC 50 : 5.4 μM; Figure 2). Using isothermal titration calorimetry, they discovered that potency could be improved by adding an N-methylamino group at the C8 position of the 2-quinolinone.…”

“…We applied DeepFrag to this same position, using only a single grid for network input rather than a multi-grid ensemble. We started from the 6KZV crystal structure [18] shown in Figure 2. To avoid simply repeating the work of Ushiyama et al, we did not remove the N -cyclohexyl- N -methylaminomethyl moiety present in this initial hit compound.…”

“…The original DeepFrag paper includes four examples showing how the model can be used for lead optimization [9], but we here provide additional examples using the DeepFrag browser app specifically. As a test case, we use DNA gyrase B from E. coli in complex with 2-oxo-1,2-dihydroquinoline [18]. Ushiyama et al recently used fragment-based lead optimization to identify several DNA gyrase B inhibitors, including one in the low-nanomolar range [18].…”