1,3-Dichloroadamantyl-Containing Ureas as Potential Triple Inhibitors of Soluble Epoxide Hydrolase, p38 MAPK and c-Raf

Abstract

Soluble epoxide hydrolase (sEH) is an enzyme involved in the metabolism of bioactive lipid signaling molecules. sEH converts epoxyeicosatrienoic acids (EET) to virtually inactive dihydroxyeicosatrienoic acids (DHET). The first acids are "medicinal" molecules, the second increase the inflammatory infiltration of cells. Mitogen-activated protein kinases (p38 MAPKs) are key protein kinases involved in the production of inflammatory mediators, including tumor necrosis factor-α (TNF-α) and cyclooxygenase-2 (COX-2). p38 MAPK signaling plays an important role in the regulation of cellular processes, especially inflammation. The proto-oncogenic serine/threonine protein kinase Raf (c-Raf) is a major component of the mitogen-activated protein kinase (MAPK) pathway: ERK1/2 signaling. Normal cellular Raf genes can also mutate and become oncogenes, overloading the activity of MEK1/2 and ERK1/2. The development of multitarget inhibitors is a promising strategy for the treatment of socially dangerous diseases. We synthesized 1,3-disubstituted ureas and diureas containing a dichloroadamantyl moiety. The results of computational methods show that soluble epoxide hydrolase inhibitors can act on two more targets in different signaling pathways of mitogen-activated protein kinases p38 MAPK and c-Raf. The two chlorine atoms in the adamantyl moiety may provide additional Cl-π interactions in the active site of human sEH. Molecular dynamics studies have shown that the stability of ligand-protein complexes largely depends on the "spacer effect." The compound containing a bridge between the chloroadamantyl fragment and the ureide group forms more stable ligand-protein complexes with sEH and p38 MAPK, which indicates a better conformational ability of the molecule in the active sites of these targets. In turn, a compound containing two chlorine atoms forms a more stable complex with c-Raf, probably due to the presence of additional halogen bonds of chlorine atoms with amino acid residues.

Keywords: c-Raf; cancer; inhibitors; p38 MAPK; signaling pathway; soluble epoxide hydrolase (sEH); ureas.

Figure 1

Signaling pathways that unite the described targets.

Figure 2

Known inhibitors with activity against soluble epoxide hydrolase sEH, p38 MAPK and c-Raf [73,74,77,78,79,80].

Scheme 1

Preparation of 3,5-dichloroadamant-1-yl isocyanate.

Scheme 2

Preparation of 1,3-dichloroadamantyl containing diureas 7a–i.

Scheme 3

Preparation of symmetrical 1,3-disubstituted urea 9 and 11.

Figure 3

(a) Molecular docking of 11 with sEH. MM/GBSA binding free energy −56.52 kcal/mol. (b) Molecular docking of 12 with sEH. MM/GBSA binding free energy −57.26 kcal/mol. Purple dotted lines show the distance between atoms.

Figure 4

RMSD of 11 and 12 with sEH.

Figure 5

RMSF of 11 and 12 and protein-ligand contacts with sEH.

Figure 6

Protein–ligand contacts of 11 and 12 with sEH.

Figure 7

(a) Molecular docking of 11 with p38 MAPK (1KV1). MM/GBSA binding free energy −23.63 kcal/mol. (b) Molecular docking of 12 with p38 MAPK (1KV1). MM/GBSA binding free energy −35.34 kcal/mol. Purple dotted lines show the distance between atoms.

Figure 8

RMSD of 11 and 12 with p38 MAPK (PDB ID: 1KV1).

Figure 9

RMSF of 11 and 12 and protein–ligand contacts with p38 MAPK (PDB ID: 1KV1).

Figure 10

Protein–ligand contacts of 11 and 12 with p38 MAPK (PDB ID: 1KV1).

Figure 11

(a) Molecular docking of 11 with p38 MAPK (PDB ID: 3HEG). MM/GBSA binding free energy −27.60 kcal/mol. (b) Molecular docking of 12 with p38 MAPK (PDB ID: 3HEG). MM/GBSA binding free energy −26.33 kcal/mol. Purple dotted lines show the distance between atoms.

Figure 12

RMSD of 11 and 12 with p38 MAPK (PDB ID: 3HEG).

Figure 13

RMSF of 11 and 12 with p38 MAPK (PDB ID: 3HEG).

Figure 14

Diagram of protein–ligand contacts of 11 and 12 with p38 MAPK (PDB ID: 3HEG).

Figure 15

Protein–ligand contacts of 11 and 12 with p38 MAPK (PDB ID: 3HEG).

Figure 16

(a) Molecular docking of 11 with c-Raf. MM/GBSA binding free energy −29.78 kcal/mol. (b) Molecular docking of 12 with c-Raf. MM/GBSA binding free energy −32.75 kcal/mol. Purple dotted lines show the distance between atoms.

Figure 17

RMSD of 11 and 12 with c-Raf.

Figure 18

RMSF of 11 and 12 with c-Raf.

Figure 19

Protein–ligand contacts of 11 and 12 with c-Raf.