Novel selective inhibitors of aminopeptidases that generate antigenic peptides

Article abstract of DOI:10.1016/j.bmcl.2013.07.024

Endoplasmic reticulum aminopeptidases, ERAP1 and ERAP2, as well as Insulin regulated aminopeptidase (IRAP) play key roles in antigen processing, and have recently emerged as biologically important targets for manipulation of antigen presentation. Taking advantage of the available structural and substrate-selectivity data for these enzymes, we have rationally designed a new series of inhibitors that display low micromolar activity. The selectivity profile for these three highly homologous aminopeptidases provides a promising avenue for modulating intracellular antigen processing.

Full text of DOI:10.1016/j.bmcl.2013.07.024

Bioorganic & Medicinal Chemistry Letters 23 (2013) 4832–4836
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Novel selective inhibitors of aminopeptidases that generate antigenic
peptides
Athanasios Papakyriakou a,b, Efthalia Zervoudi c, Emmanuel A. Theodorakis a, Loredana Saveanu d,
Efstratios Stratikos c, Dionisios Vourloumis b,
⇑
a Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
b Chemical Biology Laboratories, National Center for Scientific Research ‘Demokritos’, Agia Paraskevi Attikis, GR 15310, Greece
c Protein Chemistry Laboratories, National Center for Scientific Research ‘Demokritos’, Agia Paraskevi Attikis, GR 15310, Greece
d Institut National de la Santé et de la Recherché Médicale, Unité 1013 and Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France
a r t i c l e i n f o
a b s t r a c t
Article history:
Endoplasmic reticulum aminopeptidases, ERAP1 and ERAP2, as well as Insulin regulated aminopeptidase
(IRAP) play key roles in antigen processing, and have recently emerged as biologically important targets
for manipulation of antigen presentation. Taking advantage of the available structural and substrate-
selectivity data for these enzymes, we have rationally designed a new series of inhibitors that display
low micromolar activity. The selectivity profile for these three highly homologous aminopeptidases pro-
vides a promising avenue for modulating intracellular antigen processing.
Received 3 June 2013
Revised 12 July 2013
Accepted 15 July 2013
Available online 23 July 2013
Keywords:
Endoplasmic reticulum aminopeptidase
Ó 2013 Elsevier Ltd. All rights reserved.
ERAP1
ERAP2
IRAP
Selective inhibitor
Rational design
Molecular modeling
Human aminopeptidases of the oxytocinase subfamily of M1
aminopeptidases have recently been shown to play important roles
in the function of the human adaptive immune response.1–4 Endo-
plasmic reticulum aminopeptidases 1 and 2 (ERAP1/2), as well as
Insulin regulated aminopeptidase (IRAP) can generate key anti-
genic peptides that help the human body fight pathogens and can-
cer but at the same time they can also destroy several antigenic
peptides by over-trimming.5–7 Both functions can contribute to hu-
man disease by either promoting immune evasion or contributing
to autoimmune responses.8 Genetic polymorphisms in ERAP1 and
ERAP2 have been associated with the individual’s predisposition
to numerous human diseases (reviewed in Ref. 8) and it has been
suggested that this link is due to changes in their specificity and
activity.9–11
Despite the important biological roles of ERAP1/2 on human
health, very little is known on how to pharmacologically manipu-
late their function. Down-regulation of ERAP1 protein expression
in experimental models has been shown to elicit novel cytotoxic
responses in mice,7 to induce Natural Killer cell responses against
malignant cells leading to tumor rejection,12 and to elicit non-
classical Major Histocompatibility Class Ib cytotoxic T-lymphocyte
responses in vivo.13 Some of these effects could be reproduced
using the non-specific metalloprotease inhibitor Leucinethiol.7–13
These findings, along with the recent elucidation of the crystallo-
graphic structures of ERAP1,14,15 ERAP2,16 and the accumulation
of a large amount of specificity data for these peptidases,17 have
spurred interest towards the development of potent and selective
inhibitors for these enzymes that could potentially control the gen-
eration of specific subsets of antigenic epitopes. Achievement of
selectivity may be even more important than high potency in this
case, since complete incapacitation of antigenic peptide generation
may not be desired therapeutically as opposed to subtle modula-
tion of a particular epitope’s generation. This concept has been
supported physiologically by demonstrating that relatively small
changes in the enzymatic activity of ERAP1 due to a single nucleo-
tide polymorphism can be either protective or predisposing to
autoimmunity.8,10,18
Since ERAP1, ERAP2 and IRAP are highly homologous, having
sequencing identity at ꢀ50%, the design of inhibitors that demon-
strate any degree of selectivity between these enzymes is highly
challenging. Towards our goal to achieve selectivity we utilized
the acquired scientific experience from the matrix metalloprotein-
ases (MMPs) family of zinc endopeptidases, which has been inten-
sively pursued during the last three decades.18–20 Specifically, it
has been demonstrated that employing strong zinc chelators,21–23
⇑
Corresponding author. Tel.: +30 210 6503624; fax: +30 210 6511766.
E-mail address: vourloumis@chem.demokritos.gr (D. Vourloumis).
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.07.024

A. Papakyriakou et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4832–4836
4833
such as the hydroxamic acid zinc-binding group, usually raises
undesirable off-target activity against other metalloproteins, as
exemplified by the first generation of MMP inhibitors.24,25 Addi-
tionally, it has been proposed that since the metal site is the most
conserved feature across all MMPs, inhibition based on non-zinc
chelating inhibitors would minimize or even eliminate the interac-
tion with the catalytic zinc, leading to improved selectivity.26–28
The latter was proven to be very successful for targeting enzymes
with deep pockets, such as the S10 subsite of MMP-13.29
It has become clear that a careful consideration of inhibitor
backbones for targeting the substrate pockets of individual metal-
loenzymes, can lead to the development of highly selective inhib-
itors, irrespective of the zinc-binding group used. On these
grounds, we based our design strategy on a relatively weak zinc
chelator, aminobenzamide, borrowed from class I histone deacetyl-
ase inhibitors.30 The amino-functionality at position 1 (numbering
as of Fig. 1A) could either coordinate to the active-site zinc ion, or
probably interact with a catalytically important glutamic acid res-
idue (Glu-354/371/465 for ERAP1/ERAP2/IRAP), which is engaged
in most zinc metalloproteases to polarize the water molecule for
nucleophilic attack on the carbonyl group of the scissile bond.31
The 2-benzamide functionality incorporates the coordinating
another, based on their individual spatial and electrostatic require-
ments. Expansion towards the primed subsites could be achieved
through functionalization of the carboxylic acid at position 4, prop-
erly directing the inhibitor side-chain(s) Pn0 to target the corre-
sponding substrate pockets.
The selectivity profile of the S1 subsite of ERAP1, ERAP2 and
IRAP was recently investigated using a library of 82 fluorogenic
substrates.17 These studies suggested that ERAP1 displays a gen-
eral preference for substrates comprising long, aromatic or hydro-
phobic P1 side-chains. In contrast, the S1 subsite of ERAP2
exhibits higher selectivity for positively charged groups (e.g., L-
Arg), whereas IRAP combines the specificity of ERAP1 and
ERAP2.17 For these reasons we selected
L-homo-phenylalanine
(hPhe) as one of the preferred occupants for the S1 subsite. This
decision was further supported by our molecular modeling calcu-
lations, which indicated that the long side-chain of hPhe would
be ideally accommodated in the S1 pocket of ERAP1, providing
p-stacking interactions with a conserved aromatic residue (Phe-
433/Phe-450/Phe-544 for ERAP1/ERAP2/IRAP). Higher flexibility
was allowed for the Pn0 position by employing a compilation of
polar, non-polar and aromatic natural amino acids to attain the
desired selectivity.
carbonyl group and the
for the enzymatic function in all natural substrates. Thus, the
strong electrostatic interaction with the two conserved glutamic
acid residues that harbor the
strates is preserved (Fig. 1). The P1 side-chain could be selected
according to the target member and is expected to significantly
contribute in achieving selectivity for one aminopeptidase over
a
-amino acid-based moiety, as required
The targeted analogues were synthesized according to the
procedure presented in Scheme 1. Thus, Boc-protected L-
homo-phenylalanine 2, selected as the amino acid of choice for
optimizing the S1 lipophilic interactions as presented before, was
coupled with di-aniline 1 under standard coupling conditions
(HBTU, DIPEA) furnishing the corresponding amide in 82% yield.
The high regioselectivity of the coupling transformation is
a-amino terminus of natural sub-
Figure 1. Inhibitor design strategy. (A) Schematic representation of the designed inhibitors (black) showing the interacting residues of the enzyme in blue. P1 and Pn0
represent amino acid side-chains that are accommodated at the S1 and Sn0 subsites of the aminopeptidases, respectively. (B) Molecular model of the designed scaffold with
carbon atoms shown in orange. The active-site residues of ERAP1 are shown with cyan-stick carbons and Zn2+ with a green sphere; all oxygen and nitrogen atoms are red and
blue, respectively. The
a-amino terminal docking residues are Glu-183 and Glu-320. The zinc-coordinated residues His-353, His-357 and Glu-376, and the catalytically
important Tyr-438 are shown transparent. (C) Surface representation of the active site of ERAP1 indicating the S1 and the putative S10–S30 subsites.

4834
A. Papakyriakou et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4832–4836
inhibitors exhibit low micromolar affinity and a high degree of
selectivity between the three enzymes (Table 1). In particular, 16
proved to be the most potent ERAP1 inhibitor with >10-fold selec-
tivity with respect to ERAP2 (Fig. 2A), whereas 20 is the most po-
tent and selective inhibitor for IRAP. On the other hand,
compounds with a short P10 side-chain (12–15) proved to be inac-
tive for all three aminopeptidases, with the exception of 13 that
carries a C-terminus benzylic group and exhibits comparable affin-
ity for ERAP2 and IRAP. Finally, the non-substituted derivatives 21
and 22 were not able to inhibit ERAP1 or ERAP2 at easily achiev-
able concentrations, albeit 21 is a modest inhibitor of IRAP. These
results verify the value of the L-amino acid incorporation for both
potency and selectivity, although they indicate that some selectiv-
ity for IRAP can be achieved even in the absence of the additional
amino acid.
To investigate the mechanism of inhibition of ERAP1 by the
most potent compound we performed a standard Michaelis–Men-
ten (MM) analysis. Since the KM value for
methyl coumarin (L-AMC) is very high to allow reliable calculation
of MM kinetics, we instead used the chromogenic substrate -Leu-
L-Leucine-7-amido-4-
L
cine-4-nitroanilide (L-pNA) as described before.14 Analysis indi-
cated that compound 16, only affected the KM parameter of the
enzymatic reaction and not the Vmax or kcat parameters (Fig. 2B),
consistent with a competitive inhibition mechanism. A major con-
cern for this type of inhibitors was whether they can be hydrolyt-
ically cleaved by the enzymes. In order to investigate their stability
we incubated the most potent ERAP1-inhibitor 16 with active en-
zyme and analyzed the reaction products on reversed-phase HPLC.
This analysis suggested that 16 was resistant towards hydrolysis
by ERAP1 (see Supplementary data, Fig. S2).
In an effort to gain further insight into the structure–activity
relationships of the designed inhibitors, we performed molecular
modeling calculations using the crystallographic structures of
ERAP1, ERAP2 and a homology model of IRAP (Supplementary
data). The large conformational space of such flexible molecules
(16 active torsions for compound 16) represents a challenging task
for most of the widely used molecular docking methods. However,
we were able to predict meaningful structures within the highest
ranked docked poses, in terms of their zinc-binding geometry
within the active site and their interactions with key-catalytic res-
idues. More specifically, the complex between 16 and ERAP1
Scheme 1. Reagents and conditions used: (a) 1 (1.0 equiv), 2 (1.1 equiv), HBTU
(2.0 equiv), DIEA (3.0 equiv), DMF, 4 h, 25 °C, 82%; (b) LiOH 1 M (20 equiv), dioxane/
H2O (1:1), 4 h, 25 °C, 95%; (c) protected amino acid (1.5 equiv), HBTU (2.5 equiv),
DIEA (4.0 equiv), DMF, 12 h, 25 °C, 72–92%; (d) for Lys-OMe: LiOH 1 M (20 equiv),
dioxane/H2O (1:1), 4 h, 25 °C, 95%; for Val-OBn and Arg(Z)2: cat. Pd/C (10% wt), H2
MeOH, 1 h, 25 °C, 90%; (e) TFA/CH2Cl2 (1:2), 30 min, 25 °C, 97%. Protected amino
acids used:
L-Ala-OMe,
L-Val-OBn, L-Thr-OMe, L-Lys(Boc)-OMe, L-Arg(Z)2-OMe, L-
Tyr(O-tBu)-OMe,
L-Trp-OBn.
Table 1
Results of the in vitro evaluation for 12–22
attributed to the increased nucleophilic nature of the meta-NH2
compared to the para-one, resulting in the exclusive formation of
3. Saponification of the methyl ester was followed by a second
IC50 (lM)
amide formation with a series of protected L-amino acids produc-
ID
ing intermediates 5–11 (Scheme 1). In particular for the lysine-
and valine-containing intermediates, their methyl and benzyl es-
ters were cleaved in order to evaluate the potential effect of the
carboxylic acid versus the ester in the binding potential of the de-
R
ERAP1
ERAP2
NI
IRAP
38
12
13
14
15
16
17
18
19
20
NI
3
L
L
L
L
L
L
L
L
L
-Ala-OMe
signed inhibitors. Finally, acidic cleavage of the P1
a-amino pro-
95.5 3.3
NI
11.5 0.6
NI
3.9 0.1
>100a
-Val-OBn
-Val-OH
tecting groups furnished compounds12–20 (Scheme 1) that were
further evaluated for their ability to inhibit the enzymes. In addi-
tion, acidic cleavage of the a-amino Boc-group of intermediates 3
and 4 yielded the non-subsituted derivatives 21 and 22, respec-
NI
NI
46
2
-Thr-OMe
-Lys-OMe
-Lys-OH
2.0 0.6
2.6 0.2
NI
24.9 1.2
8.9 0.5
NI
10.3 0.6
6.0 0.2
9.6 0.5
2.8 0.2
1.3 0.1
tively, which were also evaluated as reference compounds.
-Arg-OMe
-Tyr-OMe
-Trp-OBn
7.7 0.4
NI
>100a
ERAP1, ERAP2 and IRAP were expressed in insect cells (Hi5
cells) as recombinant proteins after infection with recombinant
baculoviruses carrying the desired gene and then purified to homo-
geneity by affinity chromatography (see Supplementary data for
details). The inhibitor potency of all compounds towards the three
enzymes was determined using an established fluorogenic assay
(Supplementary data, Fig. S1). Our initial screen showed that these
23.9 0.8
>100a
>100a
21
22
OMe
OH
NI
NI
16.3 0.8
>100a
NI = No inhibition observed at 50
l
M.
Limited inhibition (up to 20%) was evident in the 50–100
an IC50 value >100 M.
a
l
M range indicating
l

A. Papakyriakou et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4832–4836
4835
Figure 2. (A) Inhibitory potency of 16 for the three enzymes, calculated by titrating increasing amounts of the compound while following the kinetics of hydrolysis of small
fluorigenic substrates (L-AMC for ERAP1 and IRAP, and R-AMC for ERAP2). (B) Effect of 16 on the enzymatic parameters of ERAP1 calculated by Michaelis–Menten analysis
using the chromogenic substrate L-pNA.
Figure 3. Molecular models of the two most potent inhibitors bound into the aminopeptidases’ active site, illustrating the key-interacting residues for (A) ERAP1 complex
with 16 and (B) IRAP complex with 20. Colors are as described in Figure 1.
(Fig. 3A) displays the accommodation of hPhe side-chain inside the
S1 pocket so that the phenyl group is stacked over Phe-433. The ly-
sine moiety of 16 is extended towards a putative S20 subsite of
ERAP1, with its side-chain amine group interacting electrostati-
cally with two aspartic acid residues (Asp-435 and Asp-439,
Fig. 3A). Interestingly, both of these residues are not conserved in
the other two M1 aminopeptidases (Glu-452 and Asn-454 in
ERAP2, Ser-546 and Phe-550 in IRAP), which might account for
the selectivity of 16 for ERAP1 over ERAP2 and IRAP. The C-termi-
nus methyl ester is probably hydrogen bonded with the hydroxylic
group of Ser-869 (Tyr-892 in ERAP2 and Tyr-961 in IRAP). The cor-
responding hydrolyzed carboxylic acid 17 displays comparable
affinity for ERAP1 with respect to 16, albeit with lower selectivity
for ERAP2 and IRAP. Surprisingly, the longer side-chain of arginine
in 18 displayed no affinity for either ERAP1 or ERAP2, which indi-
cates that the planar guanidinium group might not be suitable for
the electrostatic interactions predicted for the more flexible side-
chain of lysine in 16. Another potentially good candidate for
exploring the primed subsites of ERAP1 is the phenolic group of
tyrosine, though 19 displayed high potency for IRAP, as well.
With regard to the more potent inhibitor of IRAP, compound 20
is predicted to bind within the active site in a similar configuration
as described for 16 (Fig. 3B). The P10 tryptophan side-chain of 20
engaged in aromatic interactions with the catalytically active
Try-549 residue (conserved amongst M1 aminopeptidases), Phe-
550 (Asp-439 in ERAP1 and Asn-454 in ERAP2) and Tyr-961 (Ser-
869 in ERAP1 and conserved in ERAP2). The carboxylate terminus
benzyl group of 20 is found in the assumed S20 subsite, interacting
with Phe-926 (Gln-834 in ERAP1 and Ala-857 in ERAP2) and Tyr-
961, as well. Similar interactions of the terminal O-benzyl group
in 13 might account for its increased affinity for IRAP with respect
to the non-active carboxylic acid 14.
In conclusion, we have rationally designed and synthesized a
novel family of inhibitors for zinc aminopeptidases that display
promising selectivity profiles for three, highly homologous mem-
bers of antigen-processing enzymes. Their facile synthesis and flex-
ibility in incorporating a plethora of P1 and Pn0 moieties may
constitute, after further optimization, a promising avenue to mod-
ulating intracellular antigen processing. Additional examples and
substitution patterns along with co-crystallization efforts and
cell-based inhibition assays are currently underway.
Author contributions
A.P. performed the molecular modeling calculation and the syn-
thesis of the inhibitors. E.Z. prepared the recombinant enzymes,
performed fluorogenic assay measurements and HPLC analysis.
L.S. established the expression system for IRAP. E.S. and D.V. con-
ceived the experiments and analyzed data. E.A.T. co-supervised
the project. All authors contributed to the preparation of the man-
uscript and have approved its final version.
Acknowledgments
This work was supported by the Action ‘Supporting Postdoctoral
Researchers’ grant LS7_2199 of the Operational Program ‘Education
and Lifelong Learning’, and by the ‘ARISTEIA I’ action grant 986, co-
financed by the European Social Fund (ESF) and the General Secre-
tariat for Research and Technology of Greece. L.S. acknowledges
financial support from the French ‘Agence Nationale de Recherche’,
ANR for the IRAP-DC (NT09_522096) project’. We thank Damijana
Urankar and Janez Košmrlj (University of Ljubljana) for the HRMS
analysis.

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A. Papakyriakou et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4832–4836
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Supplementary data (experimental procedures for the synthesis
and characterization of compounds 3–22 along with the enzyme
production and purification; description of the enzymatic activity
assay with characteristic titration curves for 12, 19 and 20; HPLC
analysis of digestion products by ERAP1 with the chromatogram
for 16 and computational modeling details) associated with this
article can be found, in the online version, at http://dx.doi.org/
10.1016/j.bmcl.2013.07.024.
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