Computer-Aided Fragment Growing Strategies to Design Dual Inhibitors of Soluble Epoxide Hydrolase and LTA4 Hydrolase

Abstract

Multitarget ligands are interesting candidates for drug discovery and development due to improved safety and efficacy. However, rational design and optimization of multitarget ligands is tedious because affinity optimization for two or more targets has to be performed simultaneously. In this study, we demonstrate that, given a molecular fragment, which binds to two targets of interest, computer-aided fragment growing can be applied to optimize compound potency, relying on either ligand- or structure-derived information. This methodology is applied to the design of dual inhibitors of soluble epoxide hydrolase and leukotriene A4 hydrolase.

Figure 1

Identification of dual fragments using a self-organizing map. Training a SOM (50 × 50 neurons) with known active sEH (red circles) and LTA4H (blue circles) ligands led to identification of 1, a previously reported sEH inhibitor, which is located within the LTA4H cluster. The reference sEH inhibitor 2 (TPPU) and the LTA4H inhibitor 3 (bestatin) were located within the respective cluster.

Figure 2

Starting point for fragment growing. (A) Cocrystal structure of 1 with sEH hydrolase domain (PDB code: 4Y2T). (B) Proposed binding mode of 1 in complex with LTA4H, based on cocrystal structure of a similar fragment (PDB code: 3CHO). 1 is shown as orange sticks, the molecular surface of the binding site is colored by lipophilicity (green: lipophilic; magenta: hydrophilic), and a gray dashed circle indicates an unoccupied space in the binding site. (C) Fragment growing strategy toward amides 4a–k. Red arrows indicate H-bond acceptor, and blue arrows indicate H-bond donor capabilities of the hydroxyl moiety, which is bioisosterically replaced by the secondary amide.

Figure 3

Fragment growing. (A) Compilation of data sets for training various machine learning algorithms. (B) Computational workflow for structure- and ligand-based fragment growing. (C) Reaction conditions for amide coupling. 4a, 4f, 4g, 4j (i) 1.1 equiv of PyBOP, 0.5–1.1 equiv of HOBt·H₂O, 1.5–3.0 equiv of DIPEA, THF, rt, 16 h; 4b–e, 4h, 4i (ii) 1.2 equiv of EDC·HCl, 4-DMAP, DCM, 60 °C μw irradiation, 1 h; 4k (iii) (a) 1.5 equiv of 3-(4-(benzyloxy)phenyl)propionic acid, 1.5 equiv of fluoro-N,N,N′,N′-bis(tetramethylen)formamidinium hexafluorophosphate, 4.5 equiv of DIPEA, DCM, 50 °C, 4 h, (b) 1.0 equiv of 4-trifluoromethyl-oxazol-2-ylamine, DCM, 50 °C, 72 h.