Piperine co-crystallizes with human DHODH
Next, we solved the X-ray cocrystal structure of piperine bound to DHODH
at a resolution of 1.98 Å (PDB code: 6IWU). The high-resolution
structure shows that piperine is located in the hydrophobic channel
formed between helix α1 and α2 (Figure 3A). This channel can be roughly
divided into an exclusive hydrophobic entrance and a rather polar narrow
end, and capped by a small hydrophobic pocket formed by side chains of
Val134 and Val143 (Figure 3B). Thus, the amphipathic character of
binding channel is a genuine pocket for potential ligands binding.
Obviously, the electron density unequivocally reveals that piperine
matches this amphipathic requirement well: the 1,3-benzodioxole ring
located in the hydrophobic part of the channel and the
n-piperidinecarbonyl of the piperine deeply buried in the polar
environment. The 1,3-benzodioxole ring of piperine contacting with
residues including Met 43, Val 143,
Val 134, Pro 52, Phe 98, Ala 59, Leu 68, Pro 396 forms a
protruding hydrophobic patch
(Figure 3C). The
N-piperidinecarboxaldehyde moiety
of the piperine bonds to the phenolic hydroxyl group of Tyr 356 through
a hydrogen bond and overlays well in the polar subsite (Figure 3D). The
short hydrogen bond distance (2.7Å) between the oxygen atom of piperine
and the hydroxyl of Tyr 356 in the crystallographic structure indicates
a reliable hydrogen bond interaction. DHODH have two important redox
sites, one where FMN oxidizes dihydroorotate to orotate and the other
where ubiquinone oxidizes FMNH2 to FMN(Liu, Neidhardt, Grossman, Ocain
& Clardy, 2000a). Piperine can occupy the narrow region in the
FMNH2-ubiquinone redox site, which can impact the following DHODH
activity. Polar and hydrophobic interactions were exhibited clearly in
the two-dimensional view of piperine contacting with DHODH, and there is
no water in the binding pocket (Figure 3E).