Computational Investigation of a Series of Small Molecules as Lead Compounds for Lysyl hydroxylase-2 (LH2) Inhibition

Abstract

The catalytic function of Lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required co-substrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of forty-four small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intra-molecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than the apoenzyme suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.

1,3-diketone analogs as selective lysyl hydroxylase 2 (LH2) antagonists

“…Based on the initial HTS and docking results, a computational study was performed in parallel on forty-four molecules, including most of the compounds of this paper. 59 Based on this previous study, we found that the enolate form of R2 with specific substituents for R1 and R3 showed preferential interactions with LH2. Additionally, tunneling analysis to determine the existence of O2 tunnels to transport the co-substrate to the active site revealed the possible existence of more than one tunnel.…”

“…This suggests that the presence of -CF3 in the para position of the benzene ring in compound 7 (43-c24 in Ref. 59) led to a significant decrease in the interaction energies. At the same time, it was slightly increased for the other three compared with compound 5.…”

“…Interestingly, the number of residues having noncovalent interactions with these four compounds showed a slight decrease compared to compound 5, especially in the case of compounds 7 and 9 (Tables S2 and S10 in Ref. 59). This suggested that our modifications at the para position of benzene ring do not produce favorable interaction effects between the inhibitor and the binding pocket's residues.…”

“…In comparison with compounds 1 and 2, compounds 5 (ID: 18-cpd1php in Ref. 59) and 6 (Table S2) show considerably stronger interactions with the enzyme (-185.2 and -200.1 kcal mol -1 , respectively).…”

“…The more promising candidates from our previous study were observed to partially block these putative tunnels and have negatively charged enolate forms (IDs: 2-cpd1p and 4-cpd2p in Ref. 59), which have considerably strong interactions with the active site (-169.4 and -139.7 kcal mol -1 , respectively) as well as several NCIs (non-covalent interactions) with the residues of the active site including Y655 and R728. To test the role of pyridine in the interaction with the inner residues, compounds 3 and 4 were synthesized and assessed for inhibitory activities.…”