Biology Reference
In-Depth Information
3.2.2
IBMX Binding
IBMX is a nonselective inhibitor of most human PDE families, but it only weakly
inhibits LmjPDEB1, with an IC
50
of 580
m
M. IBMX binds to the active site of
LmjPDEB1: the O6 atom of the xanthine ring of IBMX forms a hydrogen bond with
Ne2 of Gln887 in LmjPDEB1 (Fig.
6
). The xanthine ring stacks against Phe890 of
LmjPDEB1 and also forms van der Waals' contacts with residues Tyr680, Asn838,
Val853, and Phe857. This pattern of IBMX binding is similar to that found in human
PDE-IBMX complexes (Ke and Wang
2007
). In fact, the hydrogen bond with the
invariant glutamine and stacking against phenylalanine are two characteristics for
binding of not only IBMX in LmjPDEB1, but also almost all inhibitors of human
PDEs (Ke and Wang
2007
), whether or not they are selective. Notably, the xanthine
ring of IBMX in the LmjPDEB1 structure has the same orientation as that in PDE3B,
PDE5A, and PDE9A, but is rotated by about 180
in PDE4D, PDE7A, and PDE8A
(Wang et al.
2008
). The different orientations of IBMX in the PDE structures may
just mean that the active site pockets of PDEs, which are much larger than the
volume of most PDE inhibitors, can accommodate multiple inhibitor conformations.
3.2.3 Subtle but Significant Differences Between the Active Sites of
LmjPDEB1 and Human PDEs
A structural comparison shows an overall similarity between the active sites of
LmjPDEB1 and human PDEs, including the four metal-binding residues (His685,
His721, Asp722, and Asp835), the key residues such as His681 and His725 for the
catalysis, and Phe890 for the inhibitor binding. However, Gln887 of LmjPDEB1
shows a significant positional displacement. Since the invariant glutamine (Gln887
of LmjPDEB1) donates hydrogen bonds and plays an essential role in substrate and
inhibitor binding (Ke and Wang
2007
), the positional variation of Gln887 must be
an important factor that diminishes the binding of the human PDE inhibitors to
LmjPDEB1. In addition, alterations in Asn838, Val839, Ser846, Met874, and
Gly886 of LmjPDEB1 are also significant and may thus affect inhibitor binding.
In particular, Met874 and Gly886 appear to serve as two gating residues controlling
access to a unique pocket that may be valuable for the design of LmjPDE-selective
inhibitors.
3.2.4 A Unique Pocket of LmjPDEB1 for Inhibitor Binding
A unique pocket called the L-pocket has been identified in LmjPDEB1 (Wang et al.
2007
). It lies adjacent to the main inhibitor binding pocket and next to the cyclic
pentanyl ring of rolipram in the PDE4 structure (Fig.
7
). This pocket is made up of
residues from the M-loop and helix H14, including Thr854, Tyr858, Met874,
Asn881, Leu883, and Gly886 in LmjPDEB1. Thr854 and Tyr858 of helix H14 and
Leu883 and Gly886 of helix H15 form two walls of the pocket, while the fragment of
