Macrocyclic inhibitor 1 {methyl
[cyclo-7[(2R)-((N-valyl)
amino)-2-(hydroxyl-(1S)-1-methyoxycarbonyl-2-phenylethoxy)phosphinyloxyethyl]-1-naphthaleneacetamide]
sodium salt} was designed according to
the conformation of the acyclic analogue
Iva-l-Val-l-Val-l-LeuP-(O)Phe-OMe
[LeuP = the phosphinic acid
and analogue of l-leucine; (O)Phe =
l-3-phenyllactic acid; OMe = methyl ester]
(4) bound to penicillopepsin,
by linking the P1 and P3 side chains of the penicillopepsin inhibitor.
This compound and its two acyclic
derivatives, {methyl
(2S)-[1-(((N-Formyl)-l-valyl)amino-2-(2-naphthyl)ethyl)hydroxyphosphinyloxy]-3-phenylpropanoate, sodium salt} (2) and {methyl
(2S)-[1-(((N-(1-naphthaleneacetyl))-l-valyl)aminomethyl)hydroxyphosphinyloxy]-3-phenylpropanoate, sodium salt} (3), have
been synthesized and evaluated as inhibitors of
penicillopepsin. Their binding affinity to the enzyme was found to
be inversely related to the predicted degree
of conformational flexibility across the series: 3
(K
i = 110 μM), 2
(K
i = 7.6 μM), 1
(K
i = 0.8 μM). The
X-ray crystallographic structures of penicillopepsin complexed with the
macrocyclic peptidyl phosphonate 1
and with its two derivatives 2 and 3 have been
determined and refined to crystallographic agreement
factors
R (=Σ||F
o| −
|F
c||/Σ|F
o|)
of 15.9%, 16.0%, and 15.2% and R
free of
19.8%, 20.3%, and 21.4%, respectively.
The intensity data for all complexes were collected to 1.5 Å
resolution. One 1.25 Å resolution data set was
obtained for the complex with 1 at 110 K; the structure was
refined to an R factor of 15.0%
(R
free of 19.7%).
The binding interactions that 1 and 2 make
with penicillopepsin are similar to those that have been
observed
for other transition-state mimics with aspartyl proteinases. On
the other hand, the acyclic linear inhibitor 3
exhibits distinctive binding to penicillopepsin with the phosphonate
group shifted ∼3.0 Å from the average
position observed for the other complexes. These structural
results show that the macrocyclic constraint of
1
enhances its binding affinity over those of the acyclic analogues but
the differences in the observed bound
dispositions mean that the effect has yet to be
quantified.