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development of compounds that selectively interact with PDE2 allosteric sites
(Erneux et al.
1982
; Yamamoto et al.
1983
). Recent insights derived from X-ray
crystallographic and NMR structures of several cN-binding GAFs have further
defined topographical features that could lead to design of pharmacophores target-
ing these sites (Heikaus et al.
2008
; Martinez et al.
2005
; Pandit et al.
2009
; Wang
et al. 2011), and high throughput screening assays to identify compounds that might
interact with these sites are currently being developed (see Demirbas et al. and Schultz
et al. in Chapters 5 and 6, respectively, in this volume). Likewise, the
U
pstream
C
onserved
R
egions (UCRs), which profoundly impact catalytic functions in PDE4
isoforms, and the Rec and PAS subdomains in PDE8 are considered to be promising
pharmacological targets for modulation of the catalytic activities of these PDEs.
1.2 Quaternary Structure of PDEs
PDEs exist as monomers, dimers, or higher oligomers, and in most instances, the
contribution of this physical status to function, regulation, localization, and stability
is poorly understood. Most PDEs appear to exist as homodimers except in the case
of PDEs 1 and 6. Under physiological conditions, PDE1 is thought to occur as a
heterotetramer comprising two identical catalytic subunits and two molecules of
calmodulin. PDE6 isoforms in the outer segments of the photoreceptors also
commonly exist as heterotetramers. The PDE6 in rod outer segments is composed
of two closely related gene products (PDE6
a
and PDE6
b
) that form a catalytic
heterodimer that is in complex with two small rod-specific inhibitory subunits (P
g
)
to form an inactive heterotetramer (Cote
2006
). The PDE6 in cone outer segments is
also a heterotetramer that comprises two identical catalytic subunits (PDE6
a
0
) and
two cone-specific P
g
subunits.
The mechanisms employed for oligomerization of PDEs vary; some interact
through their catalytic domains (Huai et al.
2003
; Scapin et al.
2004
), others make
contacts through portions of their regulatory domains including GAFs or UCRs
(Huai et al.
2003
; Martinez 2002; Richter and Conti
2002
; Zoraghi et al.
2005
), and
still others dimerize through contacts in both regions (Pandit et al.
2009
). In all
instances, the contacts and quaternary state appear to be very stable. For most
PDEs, catalytic activity is retained in constructs that include only the catalytic
domain; in several instances, these truncated constructs are monomeric indicating
that oligomeric status is not required for catalytic function. For the isolated catalytic
domains of some PDEs, many functional characteristics (
k
cat
,
K
m
, and IC
50
values
for certain inhibitors) are similar to those of the respective holoenzymes, but in
others, there are important functional differences (Blount et al.
2006
,
2007
; Fink
et al. 1999; Richter and Conti
2004
; Saldou et al.
1998
).
Almost all inhibitors that have been developed to date compete with cN substrate
for access to the PDE catalytic sites. This region continues to be a major focus of
medicinal chemists for development of inhibitors (Ke and Wang
2007b
;Owenetal.
2009
; Verhoest et al.
2009
; Zhang
2006
). The catalytic domain, which is conserved
