ACS Medicinal Chemistry Letters
Letter
active.25 In contrast, Walker et al. found that phosphinate
esters with a single amino acid in the P1 position displayed
consistently higher activity than their phosphonate counter-
parts.26
To shed more light on the difference in activity of
phosphinate and phosphonate esters, we made a comparable
assessment of the potency of the here described compounds as
well as their diphenyl phosphonate ester counterparts 1a and
1b. To this end, we performed inhibition kinetics experiments.
Because of the covalent, irreversible nature of the inhibitors, we
used a two-step binding model (Figure S2) consisting of a first,
reversible, non-covalent interaction and a second, irreversible
reaction between enzyme and inhibitor. Applying this binding
model, we determined kinact and KI. kinact is the rate constant of
the second, irreversible step in this process at infinite inhibitor
concentration and as such an indicator of compound reactivity.
The inhibitor concentration that results in an observed rate
constant of 1/2kinact is called KI. It reflects the reversible binding
process between inhibitor and enzyme before reaction. The
overall inhibitory potency is reflected in the ratio of these two
values with better inhibitors possessing higher kinact/KI values.
Valine derivatives 12a and 1a were tested against three
enzymes with elastase-like activity (NE, PR3, and PPE).
Additionally, 12b was tested against PR3. Whereas 12a showed
activity with the highest kinact/KI against PR3, the diphenyl
phosphonate was mostly inactive, in line with previous
reports,23 except against NE (Table 1, entries 1−7).
Compound 12b, which only showed activity against PR3 in
the gel-based experiments (Figure 2), displayed much lower
activity than 12a.
Figure 3. Proposed binding models by in silico covalent docking.
Shown are close-ups of the active site with the protein in cartoon
format (α-helices in cyan, β-sheets in magenta, loops in pink),
molecular surface depicted as gray transparent, and inhibitors as stick
models. All phosphinates are colored yellow. Water molecules and
inhibitor molecules originally present in the structure were removed
prior to docking. (a) Compound 12a covalently bound to S195 of
human NE (PDB code: 4WVP). (b) Compound 12a covalently
bound to S195 of human PR3 (PDB code: 1FUJ). (c) Compound
13a and diphenyl phosphonate 1b (in magenta) bound to S195 of
bovine α-chymotrypsin (PDB code: 4Q2K). (d) Chirality at the
phosphorus atom with priorities of the substituents (the PO bond
is treated as a normal single-bonded substituent according to IUPAC
rules). Here, the S-enantiomer is depicted. Note that the chirality is
inverted upon reaction with the enzyme in an SN2P-type mechanism.
Unfortunately, the kinetic experiments with cathepsin G
gave no good progression curves and thus no good fitting was
possible in that case. Hence, phosphinates with large
hydrophobic P1 residues (Leu, Phe, Phg) were tested against
chymotrypsin, as this protease was inhibited by the largest
number of compounds (Figure 2) and may be able to give
more insight into the primed site effect. Phe in the P1 position
is clearly preferred with its kinact/KI value being 5−20-fold
higher than the values of the corresponding Phg and Leu
derivatives with the same primed site element (Table 1, entries
9−13). Additionally, it is twice as active as the corresponding
diphenyl phosphonate inhibitor 1b, which is especially due to a
higher kinact. Unfortunately, the Phe phosphinates could only
be synthesized with one R2 group. Therefore, comparison of
the primed site binding elements can only be made with the
Leu and Phg derivatives. In both cases, the inhibitors with a
phenyl R2 substituent displayed higher potency. Interestingly,
for the Leu phosphinate esters, the difference was mainly
caused by a higher kinact for the R2=Ph, whereas, for the Phg
phosphinate esters, the underlying potency difference had its
cause in a better KI for the R2=Ph compound.
For further insight into the different binding modes, we
performed covalent docking with AutoDock 4.230 of some
selected compounds in crystal structures of NE, PR3, and ChT
(Figure 3). In these experiments, only the R-configurations at
the α-carbon to the phosphorus were assessed, because these
reflect the natural L-configuration of amino acids and
correspond to the active species, as previously shown in
structural and kinetics studies.27,31 However, we included both
configurations at the phosphorus atom: the bound RR- and RS-
diastereomers. Note that the R-configuration at the phospho-
rus bound to the enzyme originates from the S-configuration at
the phosphorus in the inhibitor, because the stereochemistry
inverts upon reaction with the active site serine in an SN2P-
type mechanism with trigonal bipyramidal transition state
(Figure 3D) Strikingly, we found the RS-diastereomer to be
consistently superior to the RR-diastereomer in binding energy,
with the only exception being 11a (Table S1). Additionally, a
visual inspection of the top scoring poses showed that the RR-
derivatives generally displayed unlikely binding modes (Figure
S3). Therefore, we propose that the RS-diastereomers are
probably the (most) active species. Future efforts in synthesis
toward enantiomerically pure phosphinate esters may address
this further and result in compounds with higher potency.
For NE and PR3 we took a closer look at the interactions of
12a. In both proteases the valine side chain docks well into the
S1 pocket and the Cbz group occupies the S2 pocket, whereas
the phenyl substituent at the phosphorus atom reaches toward
the primed site (Figure 4A,B). The better KI value seen for
PR3, as measured in the kinetics experiments, may be
explained by the somewhat different orientation of the Cbz
and Ph groups as well as the preference of PR3 for slightly
larger P1 and P2 residues, as has been shown before.21,22,31
For ChT, we compared the most active compound 13a with
the reference diphenyl phosphonate 1b. For both compounds,
the Phe side chain reaches deep into the S1 pocket and the
carboxybenzyl substituent interacts with the S2 pocket. The
phenoxy as well as the phenyl group are both oriented toward
the S1′ pocket. The overall very similar binding mode may
explain their comparable KI values.
In conclusion, we report a straightforward synthetic
procedure to synthesize phenyl phosphinates in one to two
steps from commercially available aldehydes and dichloro-
phosphines. These compounds inhibit S1 family serine
D
ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX