Structural Insights into Human 5-Lipoxygenase Inhibition:  Combined Ligand-Based and Target-Based Approach

Abstract

The human 5-LOX enzyme and its interaction with competitive inhibitors were investigated by means of a combined ligand-based and target-based approach. First, a pharmacophore model was generated for 16 non redox 5-LOX inhibitors with Catalyst (HipHop module). It includes two hydrophobic groups, an aromatic ring, and two hydrogen bond acceptors. The 3D structure of human 5-LOX was then modeled based on the crystal structure of rabbit 15-LOX, and the binding modes of representative ligands were studied by molecular docking. Confrontation of the docking results with the pharmacophore model allowed the weighting of the pharmacophoric features and the integration of structural information. This led to the proposal of an interaction model inside the 5-LOX active site, consisting of four major and two secondary interaction points: on one hand, two hydrophobic groups, an aromatic ring, and a hydrogen bond acceptor, and, on the other hand, an acidic moiety and an additional hydrogen bond acceptor.

Structure-Based Fragment Hopping for Lead Optimization Using Predocked Fragment Database

“…Compound F was docked into the theoretical 5-LOX binding site and the lowest energy conformation was submitted to LeadOp. This selected conformation possesses similar interactions that have been previously reported 37 and discussed above within at the 5-LOX active site (Figure 4). The oxochromen group favorably interacts with the hydrophobic residue Leu414 (CH 3 3 3 π interaction) in the middle of the cavity, while the fluorophenyl group extends to the hydrogen-bond-acceptor region in the lower cleft of the active site.…”

“…B-Raf kinase (PDB ID: 3idp), a ras-activated proto-oncogene serine/theronione protein kinase, 25 and human 5-LOX enzyme (obtained from the homology model by Caroline et al, 37 a key enzyme in leukotriene biosynthesis, were selected as our model systems to examine the LeadOp approach. Generation of Fragments.…”

“…The hydrogen-bond acceptor probably interacts with the key anchoring points (Tyr181, Asn425, and Arg411) to form the hydrogen bond, while Leu414 and Phe421 form a hydrophobic interaction between the ligand and the binding cavity. 37 The 5-LOX inhibitor compound F (compound 6 in the literature 26 ) was selected as our initial molecule for lead optimization and has a biologically determined IC 50 value of 145 nM. Compound F was docked into the theoretical 5-LOX binding site and the lowest energy conformation was submitted to LeadOp.…”

“…In addition, the oxochromen ring of Frag-1 is in close proximity to Leu414 and is potentially an important CH 3 3 3 π contact, as indicated in the literature. 37 Also, Frag-3 of compound G interacts with 5-LOX hydrophobic residues Leu420 and Leu607, which have been suggested to improve binding in the 5-LOX system via complementary hydrophobic interaction between the ligand and receptor, which probably explains compound G's better inhibition compared to compounds F, H, and I. These optimized results indicate that hydrogen-bonding and hydrophobic interactions are important for ligands binding to and inhibition of 5-LOX, as previously reported.…”

“…These optimized results indicate that hydrogen-bonding and hydrophobic interactions are important for ligands binding to and inhibition of 5-LOX, as previously reported. 37 The diversity of the fragment database is a critical factor when searching for substituent fragments. The number of different poses determined by docking fragments to each binding location is always important.…”