Exploration of zinc-binding groups for the design of inhibitors for the oxytocinase subfamily of M1 aminopeptidases

Article abstract of DOI:10.1016/j.bmc.2019.115177

The oxytocinase subfamily of M1 aminopeptidases consists of three members, ERAP1, ERAP2 and IRAP that play several important biological roles, including key functions in the generation of antigenic peptides that drive human immune responses. They represent emerging targets for pharmacological manipulation of the immune system, albeit lack of selective inhibitors is hampering these efforts. Most of the previously explored small-molecule binders target the active site of the enzymes via strong interactions with the catalytic zinc(II) atom and, while achieving increased potency, they suffer in selectivity. Continuing our earlier efforts on weaker zinc(II) binding groups (ZBG), like the 3,4-diaminobenzoic acid derivatives (DABA), we herein synthesized and biochemically evaluated analogues of nine potentially weak ZBGs, based on differential substitutions of functionalized pyridinone- and pyridinethione-scaffolds, nicotinic-, isonicotinic-, aminobenzoic- and hydrazinobenzoic-acids. Crystallographic analysis of two analogues in complex with a metalloprotease (MMP-12) revealed unexpected binding topologies, consistent with the observed affinities. Our results suggest that the potency of the compounds as inhibitors of ERAP1, ERAP2 and IRAP is primarily driven by the occupation of active-site specificity pockets and their proper orientation within the enzymes.

Full text of DOI:10.1016/j.bmc.2019.115177

Journal Pre-proofs
Exploration of zinc-binding groups for the design of inhibitors for the Oxyto-
cinase Subfamily of M1 Aminopeptidases
Sofia Tsoukalidou, Magdalini Kakou, Ioannis Mavridis, Despoina
Koumantou, Vito Calderone, Marco Fragai, Efstratios Stratikos, Athanasios
Papakyriakou, Dionisios Vourloumis
PII:
S0968-0896(19)31115-0
https://doi.org/10.1016/j.bmc.2019.115177
BMC 115177
DOI:
Reference:
To appear in:
Bioorganic & Medicinal Chemistry
Received Date:
Revised Date:
Accepted Date:
1 July 2019
11 October 2019
17 October 2019
Please cite this article as: S. Tsoukalidou, M. Kakou, I. Mavridis, D. Koumantou, V. Calderone, M. Fragai, E.
Stratikos, A. Papakyriakou, D. Vourloumis, Exploration of zinc-binding groups for the design of inhibitors for
the Oxytocinase Subfamily of M1 Aminopeptidases, Bioorganic & Medicinal Chemistry (2019), doi: https://
doi.org/10.1016/j.bmc.2019.115177
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Exploration of zinc-binding groups for the design of inhibitors for
the Oxytocinase Subfamily of M1 Aminopeptidases
Sofia Tsoukalidou1, Magdalini Kakou1, Ioannis Mavridis1, Despoina Koumantou1, Vito
Calderone2, Marco Fragai2, Efstratios Stratikos1, Athanasios Papakyriakou1,* and Dionisios
Vourloumis1,*
1National Centre for Scientific Research "Demokritos", Agia Paraskevi 15310, Greece
2 Center for Magnetic Resonance, University of Florence, Via L. Sacconi 6, 50019 Sesto
Fiorentino, (FI) - Italy
Abstract
The oxytocinase subfamily of M1 aminopeptidases consists of three members, ERAP1, ERAP2
and IRAP that play several important biological roles, including key functions in the generation of
antigenic peptides that drive human immune responses. They represent emerging targets for
pharmacological manipulation of the immune system, albeit lack of selective inhibitors is hampering
these efforts. Most of the previously explored small-molecule binders target the active site of the enzymes
via strong interactions with the catalytic zinc(II) atom and, while achieving increased potency, they suffer
in selectivity. Continuing our earlier efforts on weaker zinc(II) binding groups (ZBG), like the 3,4-
diaminobenzoic acid derivatives (DABA), we herein synthesized and biochemically evaluated analogues
of nine potentially weak ZBGs, based on differential substitutions of functionalized pyridinone- and
pyridinethione-scaffolds, nicotinic-, isonicotinic-, aminobenzoic- and hydrazinobenzoic-acids.
Crystallographic analysis of two analogues in complex with a metalloprotease (MMP-12) revealed
unexpected binding topologies, consistent with the observed affinities. Our results suggest that the
potency of the compounds as inhibitors of ERAP1, ERAP2 and IRAP is primarily driven by the
occupation of active-site specificity pockets and their proper orientation within the enzymes.

Figure for Graphical Abstract

1. Introduction
The M1 family of aminopeptidases comprises several members of high interest in
pharmaceuticals, such as Aminopeptidase N,1 or the oxytocinase subfamily of M1 aminopeptidases,2 both
emerging as important targets for drug development. The latter consists of 3 members: Endoplasmic
Reticulum aminopeptidase
1
(ERAP1, also called adipose-derived leucine aminopeptidase,
aminopeptidase regulator of TNFR1 shedding and endoplasmic reticulum aminopeptidase associated with
antigen processing), Endoplasmic Reticulum aminopeptidase 2 (ERAP2, also called leukocyte-derived
arginine aminopeptidase) and Insulin Regulated aminopeptidase (IRAP, also known as leucyl-cystinyl
aminopeptidase, placental leucine aminopeptidase and oxytocinase). ERAP1 and ERAP2 are localized
primarily in the ER and IRAP on the cell surface and in endosomic vesicles.3 These three enzymes
perform a variety of biological functions, although their involvement in the correct functioning of the
human immune system has been extensively studied during the last decade. Accordingly, they trim
antigenic peptide precursors and generate peptides that bind onto Major Histocompatibility Class I
4
molecules for presentation to T-lymphocytes.2, With this function, they can influence the human
adaptive immune response and are emerging targets for pharmacological approaches.5 Additional
functions performed by members of this sub-family, include the regulation of blood pressure, glucose
transport and peptide hormone levels, as well as roles in the innate immune responses.6 Although several
inhibitors for these enzymes have been reported in the literature, discovered either by rational design or
screening approaches, a combination of shortcomings in terms of potency, pharmacology and selectivity
has limited their clinical application.5b, 7 As a result, several efforts for optimizing selectivity versus
potency are underway.
Based on our previous successful identification of 3,4-diaminobenzoic acid (DABA) derivatives
with natural and unnatural amino acids as inhibitors of ERAP1, ERAP2 and IRAP (Figure 1C) we
examined the potential improvement of their binding affinity and/or selectivity via modification of their
central scaffold, while maintaining the most successful occupants of the active-site specificity pockets
(Figure 1A, B) from our studies.8 Firstly, in an attempt to stabilize the topology and orientation of the
inhibitors in the binding site of the enzyme, we introduced ligands that could coordinate in a bidentate
fashion with the metal ion.9 Thus, a series of mono-substituted 3-hydroxypyridinone derivatives (P1–P11,
Figure 1C) were targeted, as potential bidentate Zn(II) scaffolds. Slight modification of the electronic
potential of the latter, leading to an expected increase in its binding ability to the metal ion, was
accomplished by the introduction of a 3-OMe group or replacement of the carbonyl oxygen by a sulfur
atom,10 leading to analogues P12–P13 and P14–P15, respectively (Figure 1C). To assess the importance
of the free aniline group in meta- and para-substituted DABAs, we synthesized a small representative

library of 3-aminobenzoic acid analogues (P16–P20, Figure 1C) and 4-aminobenzoic acid analogues
(P21–P25, Figure 1C), lacking either the 4-NH2 or the 3-NH2 group, respectively. Similarly, a series of
NH2-substituted isonicotinic- and nicotinic-acid derivatives were synthesized (P26–P30 and P31–P37,
Figure 1C), combining the potential of a bidentate coordination with the altered electronic density of the
central scaffold. Finally, an analogous bidentate chelation to the catalytic zinc ion was envisioned through
the use of meta- and para-hydrazinobenzoic acid, with simultaneous one-atom extension of the S1-
substitution fragment, in derivatives P38–P44 and P45–P49 (Figure 1C).

Figure 1. A. ERAP1 topology and specificity pockets (S1, S1′, S2′, S3′, …Sn′) illustrated from a high resolution X-
ray structure of ERAP1 with a bound inhibitor (PDB ID: 6Q4R).11 B. Close-up view of the substrate-binding site in
the crystal structure of ERAP2 bound with a DABA inhibitor (PDB ID: 5KIV),8a indicating the specificity subsites
(S1, S1′, S2′, S3′, …Sn′) of ERAP2. The hydrogen bond formed between the N4 anilinic group of the inhibitor and
the carboxylate group of Glu371 is indicated. C. Previously obtained diaminobenzoic acid (DABA) analogues and
currently designed and synthesized products P1-P49 described herein. Expected interactions with the metal ion and
the occupation of active-site specificity pockets within the enzymes (ERAP1, ERAP2 and IRAP) are shown.
Evaluation of these compounds against the three M1 aminopeptidases using an in vitro
fluorogenic-based assay8c revealed moderate to low affinities, including however some low micromolar
inhibitors. In addition, we obtained X-ray crystal structures of MMP-12 complexes with P2 and P4, and a
zinc-bound acetohydroxamic acid (AHA) inhibitor. Taken together, our results provide useful structure-
activity relationships and suggest that all of the evaluated zinc-binding groups examined represent weak
zinc-coordinators for this class of enzymes, allowing sidechain-subsite interactions to be the driving force
in determining inhibitor efficacy.
2. Results and discussion
2.1 Synthesis
Synthesis of analogues P1–P11 commenced from the mono-alkylation of 2,3-dihydroxypyridine
(1) with ethyl bromoacetate furnishing the corresponding adduct,12 which was further hydrolyzed under
basic conditions to produce acid 2 in 47% overall yield (Scheme 1). Coupling of the carboxylic acid
moiety with various amines was envisioned by two different methods, dictated mainly by our ability to
purify the desired products from the reaction mixtures. Firstly, pre-activation of the carboxylic acid with
HBTU, followed by in-situ trapping of the activated ester with selected amines, furnished the expected
products P1–P4 in acceptable yields and purity. Alternatively, the pre-activated pentafluoro-phenyl ester
(Pfp-ester) of the carboxylic acid was formed and isolated, followed, in a separate step, by its reaction
with the desired protected amines and protected amino acids. Necessary deprotections (acidic and/or
reductive) yielded products P5–P11 (some products were synthesized by both methods; specific details
are presented in scheme 1 and the experimental section).

Scheme 1. Reagents and conditions: (a) BrCH2COOEt (5.0 equiv), reflux, 24 h, 50%; (b) 4 M NaOH (4.0 equiv), 25
°C, 30 min, 95%; (c) amine (1.1 equiv), HBTU (2.0 equiv), DIPEA (3.0 equiv), DMF (0.3-0.4 M), 60 °C, 14 h, 80%
for P1, 43% for P2, 40% for P3, 25% for P4; (d) TFAPfp (1.3 equiv), pyridine (1.2 equiv), DMF (1.5 M), 25 °C, 1
h, 40%; (e) amine or protected amino acid (1.0 equiv), DIPEA (2.0-3.0 equiv), DMF (0.1-0.2 M), 25 °C, 2-18 h,
55% for P5, 33% for P6, 60% for protected-P7, 53% for protected-P8, 71% for P9, 84% for P10; (f) CH2Cl2/TFA
(2/1), 25 °C, 30 min, 87% for P7, 79% for P8; (g) P10 (1.0 equiv), H2, Pd/C (10%), MeOH, 25 °C, 1 h, 65% for
P11. TFAPfp = Pentafluorophenyl trifluoroacetate; HBTU = N,N,N′,N′-Tetramethyl-O-(1H-benzotriazol-1-
yl)uronium hexafluorophosphate; DIPEA = N,N-Diisopropylethylamine; DMF = N,N-Dimethylformamide; TFA =
Trifluoroacetic acid
Attempting to increase the electron-donating ability of the 3-oxygen, and thus the scaffold’s
coordinating potential to the metal center, 2,3-dihydroxypyridine (1) was firstly methylated through the
action of dimethyl sulfate,13 followed by its alkylation with ethyl bromoacetate furnishing ester 3.
Hydrolysis of the latter, followed by HBTU-mediated amide bond formation with selected amines,
produced final products P12-P13 (Scheme 2). Alternatively, treatment of 3 with Lawesson’s reagent14
transformed the pyridinone to the corresponding pyridinethione 4, potentially increasing once more its

binding affinity for the zinc ion. Similarly to the previous case, hydrolysis of the ester moiety and amide
coupling furnishes the analogous products P14 and P15 for direct comparison (Scheme 2).
Scheme 2. Reagents and conditions: (a) 1.6 M NaOH (1.0 equiv), (CH3O)2SO2 (1.1 equiv), 25 °C, 12 h, 65%; (b)
BrCH2COOEt (1.5 equiv), K2CO3 (3.0 equiv), DMF (0.2 M), reflux, 18 h, 60%; (c) 4 M NaOH (4.0 equiv), 25 °C,
30 min, 97%; (d) amine (1.2-1.5 equiv), HBTU (2.0 equiv), DIPEA (3.0 equiv), DMF (0.2-0.3 M), 60 °C, 1-10 h,
50% for P12, 67% for P13; (e) Lawesson’s reagent (0.6 equiv), toluene, reflux, 6 h, 70%; (f) 4 M NaOH (4.0 equiv),
25 °C, 30 min, 97%; (g) TFAPfp (1.5 equiv), pyridine (1.5 equiv), DMF (0.25 M), 25 °C, 18 h; then amine (2.0
equiv), DIPEA (2.0 equiv), DMF (0.2 M), 70 °C, 18 h, 42% for P14, 54% for P15.
In order to evaluate the importance of the second aniline nitrogen, present in the previously
synthesized DABA-derivatives (Figure 1C inset), for binding, we envisioned the synthesis of a small
representative library of analogues, lacking the second nitrogen either at the 4- (P16–P20, Schemes 1, 3)
or the 3-position (P21–P25, Schemes 1, 4), exploring at the same time two different orientations of the
inhibitor at the active site of the enzymes. Specifically, ethyl-3-aminobenzoate (5) was coupled with a
series of N-protected amino acids furnishing products 6 in high yields. Hydrolysis of the ester
functionality, followed by a second amide formation, furnished, after the required deprotections,
analogues P16–P20, as presented in scheme 3. 4-Aminobenzoic acid (7) served as the starting material
for the construction of the P21–P25 analogues in a similar fashion to the 1,3-disubstituted derivatives
P16–P20 for direct comparison. The synthetic sequence is presented in scheme 4.

Scheme 3. Reagents and conditions: (a) properly protected amino acid (1.1–1.5 equiv), HBTU (2.0–3.0 equiv),
°
°
DIPEA (3.0–4.0 equiv), DMF, 4–12 h, 23 C, 65–92%; (b) LiOH 1 M (20 equiv), dioxane/H2O (1:1), 3–6 h, 23 C,
87–95%. (c) properly protected amino acid (1.1–1.5 equiv), HBTU (2.0–3.0 equiv), DIPEA (3.0–4.0 equiv), DMF,
°
4–12 h, 23 C, 65–92%; (d) LiOH 1 M (20 equiv), dioxane/H2O (1:1), 3–6 h, 23 °C, or cat. Pd/C (10% wt), H2,
MeOH, 1–2 h, 23 °C, 92–95%. (e) TFA/CH2Cl2 (1:2), 20–40 min, 23 °C, 95–98%. R1′: side-chain of L-α-amino acid
selected from nor-Leu, h-Phe, Arg(Z)2. R2: side-chain of L-α-amino acid selected from Tyr(O-tBu), Trp(OBn),
Lys(Boc). R1, R2΄: the corresponding deprotected L-amino acid side-chains. X: –H or –Me or –Bn.

Scheme 4. Reagents and conditions: (a) properly protected amino acid (2.0 equiv), HOBt∙H2O (0.5 equiv),
EDC∙HCl (3.0 equiv), DIPEA (5.0 equiv), DMF, 12 h, 25 °C, 65–92%; (b) properly protected amino acid (2.0
equiv), HATU (3.0 equiv), DBU (4.0 equiv), DMF, 24–36 h, 25 °C, 45–72 %; (c) LiOH 1 M (20 equiv),
dioxane/H2O (1:1), 3–6 h, 23 °C, or cat. Pd/C (10% wt), H2, MeOH, 1–2 h, 25 °C, 90–95%; (d) TFA/CH2Cl2 (1:2),
20–40 min, 25 °C, 95–98%. R1′: side-chain of L-α-amino acid selected from nor-Leu, hPhe, Tyr(OBn), Arg(Z)2. R2:
side-chain of L-α-amino acid selected from Tyr(O-tBu), Trp-OBn. R1, R2΄: the corresponding deprotected L-amino
acid side-chains. X: –H or –Me or –Bn.
Attempting to increase the zinc-biding potential of our inhibitors by introducing ligands capable
of bidentate chelation, nicotinic- and isonicotinic acid scaffolds were employed. Their expected
interactions at the active site of the enzyme are presented in figure 1 (P26–P30 and P31–P37).
Specifically, pre-activation of selected N-protected amino acids with HBTU and coupling of the reactive
esters with 2-amino-isonicotinic acid (9) in the presence of DIPEA, furnished derivatives 10 in 65-80%
isolated yields. A second amide-bond formation, followed by the required deprotections, produced final
compounds P26–P30 in good overall yields (Scheme 5).

Scheme 5. Reagents and conditions: (a) properly protected amino acid (1.1 equiv), HBTU (2.0 equiv), DIPEA (3.0
equiv), DMF, 4-12 h, 25 °C, 65–80%; (b) properly protected amino acid (1.5 equiv), HBTU (3.0 equiv), DIPEA (4.0
equiv), DMF, 4–12 h, 25 °C, 50–65 %; (c) LiOH 1 M (20 equiv), dioxane/H2O (1:1), 3–6 h, 25 °C, or cat. Pd/C
(10% wt), H2, MeOH, 1–2 h, 25 °C, 90–95%; (d) TFA/CH2Cl2 (1:2), 20–40 min, 25 °C, 95–98%. R1′: side-chain of
L-α-amino acid selected from nor-Leu, hPhe. R2: side-chain of L-α-amino acid selected from Val, Tyr(O-tBu), Trp-
OBn, Lys(Boc). R1, R2΄: the corresponding deprotected L-amino acid side-chains. X: –Me or –Bn.
Taking advantage of the increased reactivity of aliphatic amines over anilines in coupling
reactions, HBTU-mediated reaction of 6-aminonicotinic acid (11) with selected carboxyl-protected amino
acids produced adducts 12 in 65-80% isolated yields. A second amide formation between the anilinic
nitrogen and N-protected amino acids, followed by the required deprotections whenever necessary,
furnished analogues P31–P37 in acceptable yields and high purity (Scheme 6).

Scheme 6. Reagents and conditions: (a) properly protected amino acid (1.1 equiv), HBTU (3.0 equiv), DIPEA (4.0
equiv), DMF, 4-12 h, 25 °C, 65–80%; (b) properly protected amino acid (1.5 equiv), HBTU (3.0 equiv), DIPEA (4.0
equiv), DMF, 4–12 h, 25 °C, 50–65 %; (c) LiOH 1 M (20 equiv), dioxane/H2O (1:1), 3–6 h, 25 °C, or cat. Pd/C
(10% wt), H2, MeOH, 1–2 h, 25 °C, 90–95%; (d) TFA/CH2Cl2 (1:2), 20–40 min, 25 °C, 95–98%. R1′: side-chain of
L-α-amino acid selected from nor-Leu, hPhe, Tyr(OBn), Arg(Z)2. R2: side-chain of L-α-amino acid selected from
Tyr(O-tBu), Trp-OBn. R1, R2΄: the corresponding deprotected L-amino acid side-chains. X: –H or –Me or –Bn.
Targeting a similar bidentate chelation to the metal center, as well as an extension of the S1-
substitution by one atom, meta- and para-hydrazinobenzoic acid derivatives were enlisted for the same
purpose. Thus, 3-hydrazinobenzoic acid (13) was coupled with selected, pre-activated with HBTU, N-
protected amino acids furnishing adducts 14 in good yields. A second coupling reaction followed by the
required deprotections produced the desired analogues P38–P44, as presented in scheme 7. 1,4-
disubstituted analogues were synthesized in a similar manner starting from 4-hydrazinobenzoic acid, as
presented in scheme 8, furnishing products P45–P49 for direct comparison.

Scheme 7. Reagents and conditions: (a) properly protected amino acid (1.0 equiv), HBTU (1.2 equiv), DIPEA (2.0
equiv), DMF, 4-12 h, 25 °C, 40–60%; (b) properly protected amino acid (1.2 equiv), HBTU (2.0 equiv), DIPEA (3.0
equiv), DMF, 4–12 h, 25 °C, 50–65 %; (c) LiOH 1 M (20 equiv), dioxane/H2O (1:1), 3–6 h, 25 °C, or cat. Pd/C
(10% wt), H2, MeOH, 1–2 h, 25 °C, 90–95%; (d) TFA/CH2Cl2 (1:2), 20–40 min, 25 °C, 95–98%. R1′: side-chain of
L-α-amino acid selected from nor-Leu, hPhe, Tyr(OBn), hTyr(OBn), Arg(Z)2. R2: side-chain of L-α-amino acid
selected from Val(OBn), Tyr(O-tBu), Trp-OBn. R1, R2΄: the corresponding deprotected L-amino acid side-chains. X:
–H or –Me or –Bn.

Scheme 8. Reagents and conditions: (a) properly protected amino acid (1.0 equiv), HBTU (1.2 equiv), DIPEA (2.0
equiv), DMF, 4-12 h, 25 °C, 50–65%; (b) properly protected amino acid (1.2 equiv), HBTU (2.0 equiv), DIPEA (3.0
equiv), DMF, 4–12 h, 25 °C, 60–75 %; (c) LiOH 1 M (20 equiv), dioxane/H2O (1:1), 3–6 h, 25 °C, or cat. Pd/C
(10% wt), H2, MeOH, 1–2 h, 25 °C, 90–95%; (d) TFA/CH2Cl2 (1:2), 20–40 min, 25 °C, 95–98%. R1′: side-chain of
L-α-amino acid selected from nor-Leu, hPhe, Arg(Z)2. R2: side-chain of L-α-amino acid selected from Tyr(O-tBu),
Trp-OBn. R1, R2΄: the corresponding deprotected L-amino acid side-chains. X: –Me or –Bn.
2.2 Biological activity
Biochemical evaluation of P1–P15 against all three enzymes revealed few analogues with
inhibition potential of >50% at 100 μM, generally favoring activity for ERAP2. Initial screening was
performed at a single concentration (100 μM). For all analogues with substantial inhibition at 100 μM and
some inhibition at 10 μM in at least one of the enzymes, a detailed IC50 determination was performed, as
presented in Table 1. Amongst our analogues, P9 (IC50 8.9 μΜ) and P10 (IC50 1.3 μΜ) exhibit the best
inhibitory potential for ERAP2. Regarding their zinc-binding ability, lack of profound trends towards
increased or decreased binding affinity lead us to believe that the pyridinone, its methylated analogue, or
the analogous pyridinethione rings, originally selected for that purpose, do not occupy the desired
position within the active site of the enzyme.
Our attempts to co-crystalize any of our analogues with either ERAP1 or ERAP2 proved
unfruitful, albeit P2 and P4 were successfully co-crystalized with another zinc-metalloprotease (MMP-
12).15 In both X-ray structures acetohydroxamic acid (AHA), which is present as a stabilizer in the
crystallization buffer, is not displaced by the ligands and is chelated to the catalytic zinc at full occupancy

(Figure 2). AHA establishes two typical hydrogen bonding interactions with the backbone of A182 and
the carboxylate of the catalytic E219. The two ligands, P2 and P4, do not interact with AHA and assume
a similar configuration upon binding to MMP-12; their amide moiety is stabilized via two H-bonds with
the backbone of Leu181 and Pro238, whereas the R1 heterocycle is buried inside the S1΄ specificity
pocket of MMP-12 (Figure 2). It should be noted that the IC50 values for P2 and P4 were measured at 81
± 8 μM and 150 60 μM, respectively, therefore lack of interaction between the hydroxypyridinone and
the catalytic Zn(II) is probably due to competition with the high concentration of AHA used (200 mM), as
previously observed with other MMP-12 inhibitors.16 This is also supported by the results from docking
calculations of P2 and P4 using the X-ray structures of ligand-free MMP-12, which indicate that both
compounds could bind zinc with their R1 moiety accommodated in the S1΄ pocket (Supporting
Information, Figure S1). Although direct comparison is not possible between matrix metalloproteinases
and M1 aminopeptidases, our biochemical results justify our hypothesis regarding the absence of metal
chelation.
Figure 2. Close-up view of the catalytic domain in the X-ray crystal structures of MMP-12 bound with: (A)
acetohydroxamic acid (AHA) and P2 (PDB ID: 6RLY), (B) AHA and P4 (PDB ID: 6RD0). The electron density of
the ligands is contoured at 1.0 σ, while the specificity pocket S1´, the catalytic Zn(II) and the Ca(II) ions are
indicated. Yellow dashed lines indicate H-bonding interactions between the ligands and MMP-12 residues.
3- and 4-Aminobenzoic acid disubstituted derivatives P16-P25 were less active than the
corresponding DABA analogues, more probably due to the loss of a stabilizing H-bonding interaction
with the carboxylate group of Glu354 in the catalytic site of ERAP1 (equivalent to Glu371 in ERAP2,
Figure 1B). Regarding the nicotinic- and isonicotinic-based inhibitors (P26-P37), and assuming a similar
bound configuration with the DABA inhibitor in the X-ray structure of ERAP2 (Figure 1B), our
molecular modeling calculations (Supporting Information, Figure S2) reveal a distance of the heterocyclic

N from the metal of over 5 Å. Consequently, these compounds fail to engage zinc in a bidentate fashion
and thus exhibit lower affinities with respect to their DABA-based analogues. Similarly, for the
hydrazinobenzoic acid derivatives P38-P49, the one-atom extension (acyl hydrazone vs. amide) probably
results in a significant change in the topology and orientation of the inhibitors within the active site of the
enzymes, mainly in the S2′ and the S3′ pockets, leading to an overall reduction in potency, with respect to
their DABA analogues.
To confirm the hypothesized mechanism of action of the synthesized compounds we performed Micaelis-
Menten analysis of compound P45 with IRAP (Figure 3). Presence of 50% saturating concentration of
P45 affected only the KM value and not the Kcat parameter, suggesting that the inhibitor is competitive.
Thus, it likely occupies the catalytic site, even absent of coordinating interactions with the catalytic Zn(II)
atom, in agreement with previous crystallographic analysis of a DABA homologue.8a
Figure 3. Michaelis-Menten analysis of the effect of P45 on the activity of IRAP using L-AMC as
substrate. A. Titration of P45 results in a dose-dependent inhibition of IRAP with an IC50 of 2.5μΜ. B.
Michaelis-Menten curves in the absence or presence of 2.5μM of P45. C. Calculated parameters from
fitting the data in B to a standard Michaelis-Menten model.

Table 1. In vitro evaluation of the designed inhibitors for ERAP1, ERAP2 and IRAP. In parenthesis,
calculated Ki values for competitive inhibition.
IC50 , μΜ (Ki, μΜ)
ERAP1
19.1 ± 6.0 (17.5)
-
48.5 ± 10.0 (44)
20.2 ± 1.2 (18.5)
-
ERAP2
50.3 ± 16.2 (27.4)
31.3 ± 6.7 (17.7)
8.9 ± 2.4 (4.9)
1 .3 ± 0.6 (0.7)
39.3 ± 4.9 (21.4)
31.9 ± 10.6 (17.4)
>10
IRAP
24.8 ± 12.7 (13.0)
-
33.6 ± 2.5 (17.6)
10.9 ± 1.8 (5.7)
-
16.7 ± 5.2 (8.7)
6.2 (3.2)
>10
Compound
P2
P4
P9
P10
P11
P14
P16
P21
P26
P38
P45
P46
25.6 ± 14.8 (23.4)
>100
>100
>10
>10
11.9 (10.9)
5.1± 0.9 (4.7)
8.8 (4.8)
>10
7.9 (4.3)
2.2 (1.2)
8.8 (4.6)
7.2 (3.8)
2.5 (1.3)
>10
>10
3. Conclusions
In this study we explored the efficacy of nine weakly coordinating ZBGs for the development of
active-site inhibitors of the oxytocinase subfamily of M1 aminopeptidases. The pyridinone- and
pyridinethione-based series (P1-P15) displayed low potencies, presumably due to lower affinity for the
catalytic metal ion, but mostly due to their inability to occupy simultaneously the S1 and the Sn′ subsites.
Crystallographic analysis of P2 and P4 in complex with a matrix metalloproteinase (MMP-12) revealed
binding topologies with no zinc engagement (Figure 2), consistent with their low affinities and high
concentration of AHA used in the crystallization media. Removal of the free anilinic group from the
DABA analogues (P16-P25) led to loss of stabilizing interactions within the catalytic center and
significant reduction of the compounds potency. Nicotinic- and isonicotinic-based inhibitors (P26-P37),
as well as hydrazinobenzoic acid derivatives (P38-P49) proved incapable to assume the required topology
and orientation for an efficient bidentate coordination to the metal center and the simultaneous occupation
of the specificity pockets of the enzyme. Overall, our results suggest that the potency of the compounds as
inhibitors of ERAP1, ERAP2 and IRAP is primarily driven by the occupation of active-site specificity
pockets, and none of the tested zinc-binding groups had sufficient affinity to properly orient the inhibitor
on a canonical conformation within the active site. Future optimization of specificity pocket occupancy
may lead to inhibitors that block the active site with little to no engagement of the Zn(II) atom, reducing
off-target effects on other metalloproteases.

4. Experimental
4.1 General methods
Unless stated otherwise, all solvents and reagents were obtained from commercial suppliers and
used without further purification. All reactions were magnetically stirred with Teflon stir bars, and
temperatures were measured externally. Reactions that required anhydrous conditions were carried out in
flame-dried (vacuum <0.5 Torr) glassware under Ar atmosphere and anhydrous, freshly distilled solvents
were used. All reactions were monitored by thin layer chromatography (TLC) carried out on 0.25 mm E.
Merck silica gel plates (60F-254). For flash column chromatography E. Merck silica gel (60, particle size:
0.040-0.063mm) was used. Yields refer to chromatographically and spectroscopically (1H NMR)
homogeneous materials. NMR spectra were recorded on a Bruker Avance DRX-500 instrument. NMR
experiments were performed at 25°C. Chemical shifts are measured in parts per million (δ) relative to the
deuterated solvent used in the experiment. To designate the multiplicities the following abbreviations
were designated: s, singlet; d, doublet; t, triplet; m, multiplet; b, broad.
Quantitation of the final compounds was achieved using an internal standard of 2,5-dimethylfuran
(DMFu, 0.1 mM in MeOD). High resolution mass spectra (HRMS) were measured on Agilent 6224
Accurate Mass TOF LC/MS.
4.2 Synthesis of 3-Hydroxypyridinone analogues P1-P11.
4.2.1. 2-(3-Hydroxy-2-oxopyridin-1(2H)-yl)-acetic acid (2): A mixture of 2,3-dihydroxypyridine 1 (5.5
g, 50.0 mmol, 1.0 eq) and ethyl bromoacetate (27.7 g, 250.0 mmοl, 5.0 eq) was stirred
under Ar atmosphere, at 25 °C, for 1 h. The mixture was then heated under reflux and
stirred for 24h. The reaction was subsequently cooled to ambient temperature and the
precipitate that formed, was filtered, washed with cold acetone (3 x 3 mL) and
recrystallized from warm EtOH 95%. The filtrate, which was kept separate from the washings, was
concentrated, dissolved in the minimum amount of EtOH and cooled to 4 °C. The precipitate that formed
was then collected by filtration and combined with the first batch. This procedure was repeated until no
further precipitate could be obtained. In total the reaction yielded 3.3 g (45%) of the corresponding ester
1
in the form of white solid: Rf = 0.7 (silica gel, 5% MeOH in CH2Cl2); H NMR (500 MHz, d6-DMSO) δ
9.11 (bs, 1H), 7.13 (dd, J = 6.8, 1.5 Hz, 1H), 6.73 (dd, J = 7.2, 1.6 Hz, 1H), 6.11 (t, J = 7.0 Hz, 1H), 4.71
(s, 2H), 4.14 (q, J = 7.1 Hz, 2H), 1.21 (t, J = 7.1 Hz, 3H) ppm; 13C NMR (125 MHz, d6-DMSO) δ 168.0,
158.1, 146.6, 128.8, 115.3, 105.1, 60.9, 50.2, 14.0 ppm.

To a stirred solution of the ester (750 mg, 3.8 mmol, 1.0 eq) in dioxane (5.0 mL, 0.7 Μ) was added
aqueous solution of 4 Μ ΝaOH (3.8 mL, 15.2 mmol, 4.0 eq). The reaction was stirred at room
temperature for 30 min and the organic solvent was evaporated under reduced pressure. The remaining
aqueous phase was acidified with conc. HCl to pH 1 and extracted with AcOEt (7 × 30 mL). The
combined organic extracts were dried over MgSO4, filtered and evaporated, furnishing the acid 2 (610
1
mg, 95%) in the form of amorphous white solid. 2: Rf = 0.8 (silica gel, 100% MeOH); H NMR (500
MHz, CD3OD) δ 7.06 (dd, J = 6.8, 1.4 Hz, 1H), 6.84 (dd, J = 7.3, 1.5 Hz, 1H), 6.24 (t, J = 7.1 Hz, 1H),
4.74 (s, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ 170.8, 160.1, 148.1, 130.0, 117.47, 108.2, 51.7 ppm.
4.2.2. N-Benzyl-2-(3-hydroxy-2-oxopyridin-1(2H)-yl)acetamide (P1): To a stirred solution of 2 (190
mg, 1.1 mmol, 1.0 eq) in anhydrous DMF (1.0 mL, 1.5 Μ) was added pyridine
(0.11 mL, 1.3 mmol, 1.2 eq) at 0 °C under an Ar atmosphere. After 5 min
TFAPfp (0.25 mL, 1.5 mmol, 1.3 eq) was added and stirring was prolonged for 1
h at 25 οC. The reaction mixture was diluted with AcOEt (50 mL) and then washed with HCl 0.1 Μ (3 × 8
mL), 5% NaHCO3 (3 × 8 mL) and brine (1 × 8 mL). The organic layer was dried over anhydrous Na2SO4,
filtered and evaporated under reduced pressure thus furnishing the corresponding activated ester (148 mg,
40%) as an amorphous white solid.
To a mixture of benzylamine (15.3 μl, 014 mmol 1.0 eq) and DIPEA (49 μl, 0.28 mmol, 2.0 eq) in 0.5 mL
of anhydrous DMF, the activated ester (48 mg, 0.14 mmol, 1.0 eq) was added dropwise as a solution in
DMF (0.5 mL). The reaction was then stirred under an Ar atmosphere at 25 °C for 4 h and evaporated
under reduced pressure. Addition of THF (2 mL) to the residue furnished a precipitate which was then
filtered and washed with THF (3 × 0.5 mL), producing analogue P1 (20 mg, 53%) as an amorphous white
1
solid. P1: Rf = 0.5 (silica gel, 5% MeOH in CH2Cl2); H NMR (500 MHz, d6-DMSO) δ 8.99 (bs, 1H),
8.65 (t, J = 5.4 Hz, 1H), 7.41 – 7.18 (m, 5H), 7.10 (d, J = 6.5 Hz, 1H), 6.70 (d, J = 6.9 Hz, 1H), 6.08 (t, J
= 7.0 Hz, 1H), 4.62 (s, 2H), 4.31 (d, J = 5.8 Hz, 2H) ppm; 13C NMR (125 MHz, d6-DMSO) δ 166.7,
157.9, 146.5, 139.1, 129.4, 128.2 (2C), 127.1 (2 C), 126.7, 114.8, 104.6, 51.2, 42.1 ppm; HRMS calcd for
C14H15N2O3 [M+H+] 259.1083 found 259.1072.
4.2.3. N-(2-(Biphenyl-4-yl)ethyl)-2-(3-hydroxy-2-oxopyridin-1(2H)-yl)acetamide (P2) : A mixture of
2 (62 mg, 0.37 mmol, 1.0 eq), 2-(4-biphenyl)ethylamine (80 mg, 0.41
mmol, 1.1 eq), HBTU (281 mg, 0.74 mmol, 2.0 eq) and DIPEA (195 μl,
1.11 mmol, 3.0 eq) in anhydrous DMF (1.2 mL, 0.3 Μ) was stirred under
an Ar atmosphere at 60 °C for 14 h. The solvent was then evaporated
under reduced pressure and product P2 (55 mg, 43%) was precipitated after addition of AcOEt (5 mL)
and collected by filtration. P2: Rf = 0.5 (silica gel, 5% MeOH in CH2Cl2); 1H NMR (500 MHz, d6-DMSO)

δ 9.10 (s, 1H), 8.41 (t, J = 5.3 Hz, 1H), 7.64 (d, J = 7.4 Hz, 2H), 7.59 (d, J = 8.1 Hz, 2H), 7.46 (t, J = 7.7
Hz, 2H), 7.37 – 7.32 (m, 3H), 7.06 (d, J = 7.0 Hz, 1H), 6.74 (d, J = 7.5 Hz ,1H), 6.07 (t, J = 7.0 Hz, 1H),
4.57 (s, 2H), 3.34 (dd, J = 13.2, 6.8 Hz, 2H), 2.78 (t, J = 7.3 Hz, 2H) ppm; 13C NMR (125 MHz, d6-
DMSO) δ 166.7, 157.9, 146.6, 140.1, 138.7, 138.1, 129.5, 129.3 (2 C), 128.9 (2 C), 127.2, 126.7 (2 C),
126.5 (2 C), 114.9, 104.7, 51.2, 40.4, 34.7 ppm; HRMS calcd for C21H21N2O3 [M+H+] 349.1552 found
349.1541.
4.2.4. N-((1H-Indol-5-yl)methyl)-2-(3-hydroxy-2-oxopyridin-1(2H)-yl)-acetamide (P3): It was
synthesized from (1H-indol-5-yl)methanamine according to the procedure
described for P2. The product (43 mg, 40%) was isolated, as an amorphous
yellow solid, after precipitating it by the addition of MeOH (1 mL), filtration
and washing with AcOEt (2 × 0.5 mL) and Εt2O (3 × 1 mL). P3: Rf = 0.7 (silica gel, 10% MeOH in
1
AcOEt); H NMR (500 MHz, d6-DMSO) δ 11.02 (s, 1H), 8.96 (s, 1H), 8.56 (t, J = 5.4 Hz, 1H), 7.45 (s,
1H), 7.36 – 7.28 (m, 2H), 7.09 (d, J = 6.5 Hz, 1H), 7.02 (d, J = 8.3 Hz, 1H), 6.71 (d, J = 7.1 Hz, 1H), 6.38
(s, 1H), 6.08 (t, J = 7.0 Hz, 1H), 4.61 (s, 2H), 4.36 (d, J = 5.6 Hz, 2H) ppm; 13C NMR (125 MHz, d6-
DMSO) δ 166.4, 157.9, 146.6, 135.0, 129.5, 129.2, 127.5, 125.6, 121.1, 118.9, 114.9, 111.2, 104.6, 100.9,
51.2, 42.8 ppm; HRMS calcd for C16H16N3O3 [M+H+] 298.1192 found 298.1199.
4.2.5. N-(2-(1H-Indol-3-yl)ethyl)-2-(3-hydroxy-2-oxopyridin-1(2H)-yl)-acetamide (P4): It was
synthesized from 2-(1H-indol-3-yl)ethanamine according to the procedure
described for P2. In this case the reaction residue was purified initially by
flash column chromatography (silica gel, 3%→10% MeOH in CH2Cl2) and
consequently by precipitation from EtOAc (2 mL) in order to afford the final product P4 (31 mg, 25%) in
1
the form of amorphous white solid. P4: Rf = 0.5 (silica gel, 5% MeOH in CH2Cl2); H NMR (500 MHz,
d6-DMSO) δ 10.81 (s, 1H), 8.95 (s, 1H), 8.26 (t, J = 5.4 Hz, 1H), 7.53 (d, J = 7.8 Hz, 1H), 7.34 (d, J = 8.1
Hz, 1H), 7.17 (s, 1H), 7.09 – 7.03 (m, 2H), 6.98 (t, J = 7.4 Hz, 1H), 6.71 (dd, J = 7.2, 1.5 Hz, 1H), 6.07 (t,
J = 7.0 Hz, 1H), 4.55 (s, 2H), 3.39 – 3.33 (m, 2H), 2.84 (t, J = 7.4 Hz, 2H) ppm; 13C NMR (125 MHz, d6-
DMSO) δ 166.6, 157.9, 146.6, 136.2, 129.5, 127.2, 122.7, 120.9, 118.2, 118.2, 114.9, 111.6, 111.3, 104.6,
51.2, 39.7, 25.1 ppm; HRMS calcd for C17H18N3O3 [M+H+] 312.1348 found 312.1340.
4.2.6. 2-(3-Hydroxy-2-oxopyridin-1(2H)-yl)-N-(4-hydroxybenzyl)-acetamide (P5): To a mixture of 4-
hydroxybenzylamine (20 mg, 0.16 mmol 1.1 eq) and DIPEA (26 μl, 0.15
mmol, 1.0 eq) in 0.5 mL of anhydrous DMF, the activated ester (shown for
P1, 50 mg, 0.15 mmol, 1.0 eq) was added dropwise as a solution in DMF (0.5
mL). The reaction mixture was then stirred under an Ar atmosphere at 25 °C for 2.5 h and evaporated

under reduced pressure. The product P5 (23 mg, 55%) was isolated as amorphous white solid after the
addition of THF (2 mL), filtration of the formed precipitate and washing of the solid with THF (3 × 0.5
mL). P5: Rf = 0.3 (silica gel, 5% MeOH in CH2Cl2); 1H NMR (500 MHz, d6-DMSO) δ 9.29 (s, 1H), 8.98
(s, 1H), 8.52 (t, J = 6.4 Hz, 1H), 7.08 (d, J = 7.5 Hz, 3H), 6.70 (d, J = 7.5 Hz, 3H), 6.07 (t, J = 7.5 Hz,
1H), 4.58 (s, 2H), 4.18 (d, J = 5.1 Hz, 2H) ppm; 13C NMR (125 MHz, d6-DMSO) δ 166.6, 157.9, 156.3,
146.6, 129.5, 129.2, 128.6 (2 C), 115.0 (2 C), 114.9, 104.7, 51.3, 41.8 ppm; HRMS calcd for C14H15N2O4
[M+H+] 275.1032 found 275.1028.
4.2.7. N-(Biphenyl-4-ylmethyl)-2-(3-hydroxy-2-oxopyridin-1(2H)-yl)-acetamide (P6): Analogue P6
(16 mg, 33%) was synthesized from 4-phenylbenzylamine according to the
procedure described for P5. P6: Rf = 0.5 (silica gel, 5% MeOH in CH2Cl2);
1H NMR (500 MHz, d6-DMSO) δ 9.01 (s, 1H), 8.70 (t, J = 6.5 Hz, 1H),
7.64 (dd, J = 16.2, 7.9 Hz, 4H), 7.46 (t, J = 7.6 Hz, 2H), 7.34 – 7.39 (m, J =
17.2, 7.8 Hz, 3H), 7.11 (d, J = 5.9 Hz, 1H), 6.72 (d, J = 6.6 Hz, 1H), 6.09 (t, J = 6.6 Hz, 1H), 4.65 (s, 2H),
4.36 (d, J = 5.6 Hz, 2H) ppm; 13C NMR (125 MHz, d6-DMSO) δ 166.9, 158.0, 146.6, 140.0, 138.8, 138.4,
129.5, 128.9 (2 C), 127.9 (2 C), 127.3 (2 C), 126.6 (2 C), 115.0, 106.2, 104.7, 51.4, 41.9 ppm; HRMS
calcd for C20H19N2O3 [M+H+] 335.1396 found 335.1405.
4.2.8. N-((4'-aminobiphenyl-4-yl)methyl)-2-(3-hydroxy-2-oxopyridin-1(2H)-yl) acetamide (P7): To
a mixture of t-butyl (4'-(aminomethyl)-[1,1'-biphenyl]-4-yl)-carbamate
(36 mg, 0.12 mmol, 0.8 eq) and DIPEA (40 μl, 0.23 mmol, 1.5 eq) in
0.5 of anhydrous DMF, the activated ester (presented for P1, 50 mg,
0.15 mmol, 1.0 eq) was added dropwise as a solution in DMF (0.5
mL). The reaction was stirred under Ar atmosphere at 25 °C for 1 h, evaporated under reduced pressure
and purified by column chromatography (silica gel, 6%→10% MeOH in CH2Cl2). The N-Boc protected
intermediate, isolated in the form of an amorphous white solid (40 mg, 60%, Rf = 0.6 (5%
MeOH/CH2Cl2)), was dissolved in a mixture of CH2Cl2/TFA (2:1, 0.033 mM) and stirred at 25 °C for 30
min. The solution was then concentrated under reduced pressure, dissolved in a mixture of HCl 1.0 M
(0.5 mL) and toluene (2 mL) and again concentrated. This procedure was repeated twice in order to afford
1
the hydrochloride salt of P7 (27 mg, 87%) in the form of an amorphous yellow solid. P7: H NMR (500
MHz, d6-DMSO) δ 8.75 (t, J = 5.7 Hz, 1H), 7.77 (d, J = 8.3 Hz, 2H), 7.63 (d, J = 8.0 Hz, 2H), 7.48 (d, J =
8.3 Hz, 2H), 7.39 (d, J = 7.9 Hz, 2H), 7.11 (d, J = 6.8 Hz, 1H), 6.72 (d, J = 7.2 Hz, 1H), 6.08 (t, J = 7.0
Hz, 1H), 4.64 (s, 2H), 4.35 (d, J = 5.6 Hz, 2H) ppm; 13C NMR (125 MHz, d6-DMSO) δ 166.9, 158.0,
146.6, 139.6, 138.9, 137.5, 131.2, 129.6, 128.0 (2 C), 127.8 (2 C), 126.6 (2 C), 123.8 (2 C), 115.0, 104.7,
51.4, 41.9 ppm; HRMS calcd for C20H20N3O3 [M+H+] 350.1505 found 350.1500.

4.2.9. (S)-Methyl-6-amino-2-(2-(3-hydroxy-2-oxopyridin-1(2H)-yl)acetamido)-hexanoate (P8): To a
stirred solution of (S)-Lys(N-Boc)-OMe•HCl (50 mg, 0.16 mmol, 1.1 eq)
and DIPEA (65 μl, 0.37 mmol, 2.5 eq) in 0.5 mL of anhydrous DMF, was
added dropwise a solution of the activated ester (presented for P1, 50 mg,
0.15 mmol, 1.0 eq) in 0.5 mL DMF. The reaction was then stirred under Ar atmosphere at 25 °C for 18 h
and evaporated under reduced pressure. The residue was dissolvent in 40 mL CH2Cl2 and washed with aq.
HCl 1 M (1 × 5 mL) and brine (1 × 5 mL). The organic layer was evaporated under reduced pressure and
the residue was purified by column chromatography (silica gel, 4%→10% MeOH in CH2Cl2). The N-Boc
protected intermediate, isolated in the form of amorphous white solid (33 mg, 53%, Rf = 0.6 (silica gel,
°
5% MeOH in CH2Cl2)), was dissolved in a mixture of CH2Cl2/TFA (2:1, 0.033 mM) and stirred at 25 C
for 30 min. The solution was then concentrated under reduced pressure, dissolved in a mixture of HCl 1.0
M (0.5 mL) and toluene (2 mL) and again concentrated. This procedure was repeated twice in order to
afford the hydrochloric salt of P8 (20 mg, 79%) in the form of an amorphous yellow solid. P8: 1H NMR
(500 MHz, CD3OD) δ 7.15 (d, J = 6.6 Hz, 1H), 6.92 (d, J = 7.0 Hz, 1H), 6.31 (t, J = 7.1 Hz, 1H), 4.85 (s,
2H), 4.63 (d, J = 15.5 Hz, 1H), 4.55-4.49 (m, 1H), 3.73 (s, 3H), 2.94 (t, J = 7.0 Hz, 2H), 2.00 – 1.88 (m,
1H), 1.83 – 1.73 (m, 1H), 1.74 – 1.64 (m, 2H), 1.59 – 1.50 (m, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ
173.5, 168.5, 158.6, 147.3, 131.4, 121.5, 111.5, 54.3, 53.5, 52.9, 40.5, 31.9, 27.8, 23.6 ppm; HRMS calcd
for C14H22N3O5 [M+H+] 312.1559 found 312.1567.
4.2.10. (S)-Benzyl 2-(2-(3-hydroxy-2-oxopyridin-1(2H)-yl)acetamido)-3-methylbutanoate (P9):
Analogue P9 (40 mg, 71%) was synthesized from (S)-Val-OBn•HCl according
to the procedure described for P8 and was isolated in the form of white
amorphous solid. P9: Rf = 0.6 (silica gel, 5% MeOH in CH2Cl2); 1H NMR (500
MHz, d6-DMSO) δ 8.97 (s, 1H), 8.57 (d, J = 8.2 Hz, 1H), 7.41 – 7.32 (m, 5H), 7.05 (d, J = 6.4 Hz, 1H),
6.69 (d, J = 7.0 Hz, 1H), 6.06 (t, J = 6.9 Hz, 1H), 5.14 (q, J = 12.4 Hz, 2H), 4.67 (dd, J = 44.8, 15.7 Hz,
2H), 4.27 (t, J = 7.1 Hz, 1H), 2.11 – 2.04 (m, 1H), 0.88 (t, J = 7.2 Hz, 6H) ppm; 13C NMR (125 MHz d6-
DMSO,) δ 170.2, 166.2, 156.9, 145.6, 134.8, 128.5, 127.5 (2 C), 127.1 (2 C), 127.1, 113.9, 103.6, 65.0,
56.5, 49.9, 29.3, 17.9, 17.1 ppm; HRMS calcd for C19H23N2O5 [M+H+] 359.1607 found 359.1601.
4.2.11. (S)-Benzyl 2-(2-(3-hydroxy-2-oxopyridin-1(2H)-yl) acetamido)-3-(1H-indol-3-yl)-propanoate
(P10): Analogue P10 (60 mg, 84%) was synthesized from (S)-Trp-OBn
according to the procedure described for P8 and was isolated in the form of
1
white amorphous solid. P10: Rf = 0.6 (silica gel, 5% MeOH in CH2Cl2); H
NMR (500 MHz, CD3OD) δ 7.50 (d, J = 7.8 Hz, 1H), 7.33 (d, J = 8.0 Hz, 1H),
7.26 (d, J = 2.1 Hz, 3H), 7.12 (d, J = 3.7 Hz, 2H), 7.09 (t, J = 7.7 Hz, 1H), 7.00 (t, J = 7.2 Hz, 2H), 6.78

(d, J = 6.9 Hz, 2H), 6.12 (t, J = 6.9 Hz, 1H), 5.00 (s, 2H), 4.80 (t, J = 6.4 Hz, 1H), 4.67 – 4.57 (m, 2H),
13
3.26 (dd, J = 15.9, 6.5 Hz, 2H) ppm; C NMR (125 MHz, CD3OD) δ 173.0, 169.1, 160.2, 148.2, 138.0,
136.9, 129.9, 129.5, 129.3 (2 C), 129.2 (2 C), 128.7, 124.8, 122.4, 119.9, 119.2, 117.2, 112.4, 110.2,
107.9, 68.1, 55.2, 52.3, 28.6 ppm; HRMS calcd for C25H24N3O5 [M+H+] 446.1716 found 446.1704.
4.2.12. (S)-2-(2-(3-Hydroxy-2-oxopyridin-1(2H)-yl)acetamido)-3-(1H-indol-3-yl)-propanoic acid
(P11): Analogue P10 (25 mg, 0.05 mmol) was dissolved in ΜeOH (4.0 ml, 0.0125 M) and the solution
was degassed under Ar. Catalytic quantity of Pd/C 10% was added, after which
Ar was replaced with H2 and the reaction mixture was stirred for 1 h at 25 °C.
The heterogeneous mixture was filtered through celite and the filtrate was
concentrated under reduced pressure to afford product P11 (13 mg, 65%) in the
form of amorphous white solid. P11: 1H NMR (500 MHz, CD3OD) δ 7.58 (d, J = 7.8 Hz, 1H), 7.32 (d, J
= 8.0 Hz, 1H), 7.13 (s, 1H), 7.08 (t, J = 7.5 Hz, 1H), 7.01 (t, J = 7.4 Hz, 1H), 6.80 (d, J = 7.0 Hz, 2H),
6.15 (t, J = 7.0 Hz, 1H), 4.73 (t, J = 5.9 Hz, 1H), 4.63 (s, 2H), 3.36 (dd, J = 14.6, 7.2 Hz 1H), 3.22 (dd, J
= 14.6, 7.2 Hz, 1H) ppm; 13C NMR (125 MHz, CD3OD) δ 174.9, 168.9, 160.2, 148.2, 138.0, 129.9, 129.0,
124.7, 122.3, 119.8, 119.3, 117.2, 112.3, 110.7, 107.8, 55.0, 52.6, 28.5 ppm; HRMS calcd for C18H18N3O5
[M+H+] 356.1246 found 356.1235.
4.3 Synthesis of 3-Methoxypyridinone analogues P12-P13.
4.3.1. Ethyl 2-(3-methoxy-2-oxopyridin-1(2H)-yl)-acetate (3): 2,3-Dihydroxy pyridine (3.0 g, 27.0
mmol, 1.0 eq) was added to a stirred aqueous solution of ΝaOH 1.6 M (17 ml, 27.0 mmol,
1.0 eq) at 0 °C. After 15 min, dimethyl sulfate (3 ml, 31 mmol, 1.1 eq) was injected
dropwise and stirring continued for 14 h at 25 °C. During this period the solution’s pH
was frequently measured and adjusted with the addition of aq. NaOH 1 M in order to
prevent it from becoming overly acidic. Upon completion, the pH was adjusted to 7 and the reaction
mixture was extracted with CHCl3 (6 × 40 ml). The combined organic extracts were dried over anhydrous
MgSO4, filtered and evaporated under reduced pressure. The solid residue was recrystallized from CHCl3,
furnishing the corresponding ether (2.1 g, 62%) in the form of white crystals. Rf = 0.4 (5%
MeOH/CH2Cl2); 1H NMR (500 MHz, CDCl3) δ 13.49 (bs, 1H), 6.95 (d, J = 6.1 Hz, 1H), 6.66 (d, J = 7.2
Hz, 1H), 6.12 (t, J = 6.9 Hz, 1H), 3.73 (s, 3H) ppm; 13C NMR (125 MHz, CDCl3) δ 160.2, 149.6, 125.3,
114.6, 106.3, 55.6 ppm.
To a stirred solution of the intermediate ether (250 mg, 2.0 mmol, 1.0 eq) in anhydrous DMF (10.0 ml,
0.2 M), at 25 °C under Ar atmosphere, was added Κ2CO3 (830 mg, 6.0 mmol, 3.0 eq). After 10 min, ethyl
bromoacetate (0.33 ml, 3.0 mmol, 1.5 eq) was added dropwise, and the reaction mixture was heated at

100 °C for 14 h. After cooling to ambient temperature, the reaction was diluted with H2O (30 ml) and
extracted with CHCl3 (60 ml). The organic layer was washed with H2O (3 × 30 ml) and brine (1 × 40),
dried with anhydrous MgSO4, filtered and evaporated under reduced pressure. The residue was purified
by column chromatography (50%→80% ΑcOEt/CH2Cl2) furnishing ester 3 (250 mg, 60%) in the form of
a beige amorphous solid. 3: Rf = 0.5 (50% AcOEt/CH2Cl2); 1H NMR (500 MHz, CDCl3) δ 6.79 (d, J = 7.2
Hz, 1H), 6.53 (d, J = 7.4 Hz, 1H), 6.01 (t, J = 7.1 Hz, 1H), 4.56 (s, 2H), 4.08 (q, J = 7.1 Hz, 2H), 3.67 (s,
3H), 1.14 (t, J = 7.2 Hz, 3H) ppm; 13C NMR (125 MHz, CDCl3) δ 167.3, 157.6, 149.5, 128.6, 112.5,
104.5, 61.22, 55.4, 50.0, 13.7 ppm.
4.3.2. N-(2-(Biphenyl-4-yl) ethyl)-2-(3-methoxy-2-oxopyridin-1(2H)-yl)-acetamide (P12): Compound
3 (295 mg, 1.4 mmol. 1.0 eq) was dissolved in dioxane (5.0 ml, 0.3 Μ), followed by the addition of aq.
ΝaOH 1 M (5.6 ml, 5.6 mmol, 4.0 eq). The reaction mixture was stirred
at ambient temperature for 30 min and the organic solvent was
evaporated under reduced pressure. The remaining aqueous solution was
acidified with conc. HCl to pH = 1 and extracted with AcOEt (7 × 30 mL). The combined organic extracts
were dried over anhydrous MgSO4, filtered and evaporated to produce the corresponding carboxylic acid
(250 mg, 97%) as amorphous white solid. Rf = 0.5 (100% MeOH); 1H NMR (500 MHz, CD3OD) δ 7.16
(dd, J = 6.9, 1.4 Hz, 1H), 6.93 (d, J = 7.5 Hz, 1H), 6.31 (dd, J = 10.2, 4.2 Hz, 1H), 4.73 (s, 2H), 3.81 (s,
3H) ppm; 13C NMR (125 MHz, CD3OD) δ 170.8, 160.0, 150.9, 130.8, 115.4, 107.2, 56.4, 51.6 ppm.
To a stirred solution of the intermediate acid (65 mg, 0.36 mmol, 1.0 eq) in anhydrous DMF (1.5 ml, 0.2
Μ) were added 2-(4-biphenyl)ethylamine (85 mg, 0.43 mmol, 1.2 eq), HBTU (270 mg, 0.71 mmol, 2.0
eq) and DIPEA (189 μl, 1.1 mmol, 3.0 eq), and the resulting mixture was heated to 50 °C, under Ar for 1
h. The precipitate that formed was filtrated and washed with DMF (3 × 1 ml) producing 65 mg (50%) of
analogue P12 as amorphous white solid. P12: 1H NMR (500 MHz, d6-DMSO) δ 8.24 (t, J = 5.4 Hz, 1H),
7.64 (dd, J = 8.2, 1.4 Hz, 2H), 7.59 (d, J = 8.2 Hz, 2H), 7.45 (t, J = 7.7 Hz, 2H), 7.39 – 7.29 (m, 3H), 7.15
(dd, J = 6.9, 1.6 Hz, 1H), 6.81 (dd, J = 7.5, 1.5 Hz, 1H), 6.11 (t, J = 7.1 Hz, 1H), 4.51 (s, 2H), 3.69 (s,
3H), 3.36 – 3.33 (m, 2H), 2.76 (t, J = 7.3 Hz, 2H) ppm; 13C NMR (125 MHz, d6-DMSO) δ 166.7, 156.9,
149.0, 140.1, 138.64, 138.0, 130.8, 129.3 (2 C), 128.9 (2 C), 127.2, 126.6 (2 C), 126.5 (2 C), 113.4,
103.4, 55.4, 51.0, 40.3, 34.6 ppm; HRMS calcd for C22H23N2O3 [M+H+] 363.1709 found 363.1701.
4.3.3. N-(2-(1H-Indol-3-yl)ethyl)-2-(3-methoxy-2-oxopyridin-1(2H)-yl)-acetamide (P13): Analogue
P13 (50 mg, 67%) was synthesized from 2-(1H-indol-3-yl)-ethanamine
according to the procedure described for P12. An additional flash column
chromatography (4%→10→20% MeOH in CH2Cl2) was performed for
high purity. P13: Rf = 0.3 (10% MeOH/AcOEt); 1H NMR (500 MHz, CD3OD) δ 7.53 (d, J = 7.9 Hz, 1H),

7.32 (d, J = 8.1 Hz, 1H), 7.07 (t, J = 7.5 Hz, 1H), 7.06 (s, 1H), 6.99 (t, J = 7.5 Hz, 2H), 6.85 (dd, J = 7.5,
1.2 Hz, 1H), 6.24 (t, J = 7.2 Hz, 1H), 4.57 (s, 2H), 3.75 (s, 3H), 3.48 (t, J = 7.2 Hz, 2H), 2.93 (t, J = 7.2,
2H) ppm; 13C NMR (125 MHz, CD3OD) δ 169.0, 161.0, 150.6, 138.1, 131.1, 128.7, 123.6, 122.1, 119.7,
119.2, 115.5, 113.0, 112.3, 107.2, 56.5, 53.0, 41.5, 26.0 ppm; HRMS calcd for C18H20N3O3 [M+H+]
326.1505 found 326.1515.
4.4 Synthesis of 3-Methoxypyridinethione analogues P14-P15.
4.4.1. Ethyl 2-(3-methoxy-2-thioxopyridin-1(2H)-yl)-acetate (4): Pyridinone 3 (380 mg, 1.8 mmol, 1.0
eq) was dissolved in anhydrous toluene (15.0 ml, 0.12 M) under Ar, followed by the
addition of Lawesson’s reagent (437 mg, 1.08 mmol, 0.6 eq). The reaction mixture was
heated under reflux for 6 h. Then it was allowed to cool to ambient temperature and the
solvent was evaporated under reduced pressure. The residue was purified by column
chromatography (60% ΑcOEt/CH2Cl2→100% ΑcOEt) furnishing intermediate 4 (295 mg, 72%) as an
1
amorphous white solid. 4: Rf = 0.6 (60% AcOEt/CH2Cl2); H NMR (500 MHz, CDCl3) δ 7.34 (dd, J =
6.6, 1.2 Hz, 1H), 6.7 (d, J = 7.9 Hz, 1H), 6.61 (t, J = 7.7, 6.7 Hz, 1H), 5.24 (s, 2H), 4.24 (q, J = 7.1 Hz,
2H), 3.90 (s, 3H), 1.27 (t, J = 7.1 Hz, 3H) ppm; 13C NMR (125 MHz, CDCl3) δ 172.9, 166.0, 158.5,
132.9, 111.4, 110.2, 61.5, 58.0, 56.4, 13.7 ppm.
4.4.2. N-(2-(Biphenyl-4-yl)ethyl)-2-(3-methoxy-2-thioxopyridin-1(2H)-yl)-acetamide (P14): Ethyl
ester 4 (290 mg, 1.3 mmol, 1.0 eq) was dissolved in dioxane (6.0 ml, 0.2
Μ), followed by the addition of aq. ΝaOH 1 M (5.2 ml, 5.2 mmol, 4 eq).
The reaction mixture was stirred at ambient temperature for 30 min and
then the organic solvent was evaporated under reduced pressure. The
remaining aqueous solution was acidified with conc. HCl to pH = 1 and extracted with AcOEt (7 × 30
mL). The combined organic extracts were dried over anhydrous MgSO4 to produce the corresponding
acid (245 mg, 97%) as an amorphous yellow solid. Rf = 0.3 (100% MeOH); 1H NMR (500 MHz, CD3OD)
δ 7.70 (d, J = 6.6, 1H), 7.00 (d, J = 7.9 Hz, 1H), 6.79 (t, J = 7.2 Hz, 1H), 5.35 (s, 2H), 3.87 (s, 3H) ppm;
13C NMR (125 MHz, CD3OD) δ 173.8, 169.9, 159.9, 135.3, 113.4, 112.8, 59.0, 57.1 ppm.
The acid (100 mg, 0.5 mmol. 1.0 eq) was dissolved in anhydrous DMF (2.0 ml, 0.25 Μ) under Ar and the
solution was cooled to 0 °C with stirring. Pyridine (0.08 ml, 1.0 mmol, 2 eq) was then added, followed,
after 5 min, by ΤFAPfp (0.17 ml, 1.0 mmol, 2.0 eq). Stirring continued for 18 h at 25 °C and the mixture
was then diluted with 50 ml AcOEt and filtered in order to remove the formed precipitate. The filtrate was
consecutively washed with aq. HCl 0.1 M (2 × 10 ml), 5% NaHCO3 (2 × 10 ml) and brine (1 × 10 ml),
dried over anhydrous Na2SO4, filtered and evaporated under reduced pressure. The isolated activated ester
was used in the next step without further purification.

A solution of the activated ester (96 mg, 0.26 mmol, 1.0 eq), 2-(4-biphenyl)ethylamine (104 mg, 0.52
mmol, 2.0 eq) and DIPEA (91 μl, 0.58 mmol, 2.0 eq) in anhydrous DMF (1.0 ml, 0.3 M) under Ar was
heated to 70 °C and left to stir for 18 h.. The solvent was then evaporated under reduced pressure and the
residue was dissolved in AcOEt (40 ml). This solution was washed with aq. HCl 1.0 M (1 × 7 ml),
saturated aq. NaHCO3 (1 × 7 ml) and brine (1 × 7 ml), dried over anhydrous Na2SO4, filtered and
evaporated under reduced pressure. Product P14 (42 mg, 42% over two steps) was isolated after column
chromatography (4%→6% MeOH/AcOEt) as an amorphous yellow solid. P14: Rf = 0.4 (5%
MeOH/AcOEt); 1H NMR (500 MHz, CDCl3) δ 7.55 (d, J = 7.8 Hz, 2H), 7.51 (d, J = 6.4 Hz, 1H), 7.46 (d,
J = 8.1 Hz, 2H), 7.42 (t, J = 7.6 Hz, 2H), 7.32 (t, J = 7.3 Hz, 1H), 7.22 (d, J = 8.1 Hz, 2H), 6.69 (d, J =
7.5 Hz, 1H), 6.64 (m, 1H), 5.25 (s, 2H), 3.87 (s, 3H), 3.50 (t, J = 6.9, 2H), 2.82 (t, J = 7.1 Hz, 2H) ppm;
13C NMR (125 MHz, CDCl3) δ 172.3, 166.1, 159.2, 140.9, 139.3, 137.7, 132.7, 129.3 (2 C), 128.8 (2 C),
127.2 (2 C), 127.2, 127.0 (2 C), 112.5, 110.8, 59.8, 56.9, 40.8, 35.0 ppm; HRMS calcd for C22H23N2O2S
[M+H+] 379.1480 found 379.1471.
4.4.3.
N-(2-(1H-Indol-3-yl)ethyl)-2-(3-methoxy-2-thioxopyridin-1(2H)-yl)-acetamide
(P15):
Analogue P15 (43 mg, 54% over two steps) was synthesized from 2-(1H-
indol-3-yl)-ethanamine according to the procedure presented for P14, and
isolated as an amorphous white solid. P15: Rf = 0.5 (5% MeOH/AcOEt); 1H
NMR (500 MHz, CD3OD) δ 7.57 (ddd, J = 8.8, 7.2, 1.1 Hz, 2H), 7.32 (d, J = 8.1 Hz, 1H), 7.11 (s, 1H),
7.08 (t, J = 7.6, Hz, 1H), 6.99 (t, J = 7.4 Hz, 2H), 6.72 (dd, J = 7.8, 6.7 Hz, 1H), 5.23 (s, 2H), 3.84 (s,
3H), 3.51 (t, J = 7.2 Hz, 2H), 2.97 (t, J = 7.1 Hz, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ 173.6, 168.2,
159.8, 138.1, 135.7, 128.8, 123.7, 122.3, 119.6, 119.3, 113.3, 113.1 112.8, 112.2, 60.2, 57.0, 41.6, 26.1
ppm; HRMS calcd for C18H20N3O2S [M+H+] 342.1276 found 342.1263.
4.5 Synthesis of analogues P16-P20
4.5.1. General procedure for the HBTU-mediated amide coupling. Synthesis of intermediates 6: A
mixture of aniline 5 (1.0 eq), the appropriately protected amino acid (1.1-1.5 eq), HBTU (2.0-3.0 eq) and
DIPEA (3.0-4.0 eq) in anhydrous DMF (0.25 Μ) was stirred under an Ar atmosphere at ambient
temperature for 4-12 h. The mixture was then diluted with EtOAc and sequentially washed with HCl (1.0
M), saturated NaHCO3 and brine. The organic layer was dried over anhydrous Na2SO4, filtered and
evaporated under reduced pressure and the resulting residue was purified by column chromatography
(silica gel, EtOAc/Hexanes 20%→50%) to furnish intermediates 6 in 65-92% isolated yields.
4.5.2. General procedure for the LiOH-mediated ester hydrolysis: The corresponding ester was
dissolved in a 1:1 mixture of dioxane / aq. LiOH 1.0 M (20 eq) under vigorous stirring at ambient

temperature. After 3-6 h brine was added to the reaction mixture and the organic solvent was removed
under reduced pressure. The aqueous solution (pH=12) was washed once with EtOAc and acidified by the
addition of HCl 1.0 M to pH = 2. Subsequently, the aqueous layer was extracted with EtOAc (×3) and the
combined organic extracts were dried over anhydrous Mg2SO4, filtered and concentrated under reduced
pressure. The corresponding acids obtained (87-95% yields) were used without the need for further
purification (>95% purity according to NMR data).
4.5.3. General procedure for the hydrogenolysis of benzylic esters and carbamates: The
corresponding ester or carbamate was dissolved in ΜeOH (0.025 M) and the solution was degassed under
Ar. Catalytic quantity of Pd/C 10% was added, after which Ar was replaced with H2 and the reaction
mixture was stirred for 1-2 h at 25 °C. The heterogeneous mixture was filtered through celite and the
filtrate was concentrated under reduced pressure to afford the desired products in excellent yields (90-
95%) and purities.
4.5.4. General procedure for the acidic hydrolysis of tert-Butyl ethers and carbamates: The
corresponding intermediate was dissolved in a mixture of CH2Cl2/TFA (2:1, 0.033 M) and the solution
was stirred at ambient temperature for 20-40 min. The solvent was then evaporated to dryness under
reduced pressure. The residue was dissolved in a mixture of HCl 1.0 M (0.5 mL) and toluene (2 mL) and
the solution was concentrated under reduced pressure. The latter was repeated 2-3 times to ensure
complete conversion of the product to the hydrochloride salt. Final analogues were isolated in excellent
yields (95-99%) and purities.
4.5.4.1. (S)-Benzyl 2-(3-((S)-2-aminohexanamido)benzamido)-3-(1H-indol-3-yl)-propanoate (P16):
1
Isolated 21 mg (73%) in the form of yellow oil. H NMR (500 MHz,
CD3OD) δ 8.07 (s, 1H), 7.76 (d, J = 8.0 Hz, 1H), 7.54 (d, J = 7.8 Hz,
1H), 7.48 (d, J = 7.7 Hz, 1H), 7.39 – 7.31 (m, 2H), 7.28 – 7.20 (m, 3H),
7.18 – 7.12 (m, 2H), 7.11 – 7.03 (m, 2H), 6.98 (t, J = 7.4 Hz, 1H), 5.06
(s, 2H), 4.98 – 4.92 (m, 1H), 4.09 (t, J = 6.3 Hz, 1H), 3.43 (dd, J = 14.5,
6.2 Hz, 1H), 3.37 – 3.32 (m, 1H), 2.03 – 1.87 (m, 2H), 1.50 – 1.34 (m, 4H), 0.92 (t, J = 7.1 Hz, 3H) ppm;
13C NMR (125 MHz, CD3OD) δ 173.4, 169.8, 168.9, 139.2, 138.0, 136.9, 136.0, 130.2, 129.4, 129.4,
129.1, 129.1, 129.0, 128.6, 124.6, 124.5, 124.3, 122.4, 120.3, 119.9, 119.1, 112.4, 110.6, 68.0, 55.8, 55.2,
32.4, 28.3, 27.9, 23.3, 14.1 ppm; HRMS calcd for C31H35N4O4 [M+H+] 527.2658 found 527.2667.
4.5.4.2.
(S)-Benzyl
2-(3-((S)-2-amino-4-phenylbutanamido)benzamido)-3-(1H-indol-3-yl)-
propanoate (P17): Isolated 21 mg (74%) in the form of yellow oil. 1H NMR (500 MHz, CD3OD) δ 8.03
(s, 1H), 7.72 (d, J = 7.9 Hz, 1H), 7.54 (d, J = 7.9 Hz, 1H), 7.48 (d, J = 7.7 Hz, 1H), 7.39 – 7.30 (m, 2H),

7.27 – 7.12 (m, 10H), 7.06 (t, J = 7.5 Hz, 1H), 7.03 (s, 1H), 6.98 (t, J =
7.4 Hz, 1H), 5.07 (s, 2H), 4.95 (t, J = 6.9 Hz, 1H), 4.12 (t, J = 6.3 Hz,
1H), 3.43 (dd, J = 14.6, 6.3 Hz, 1H), 3.37 – 3.32 (m, 1H), 2.81 – 2.69
(m, 2H), 2.31 – 2.17 (m, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ
173.4, 169.8, 168.5, 141.1, 139.2, 138.0, 137.0, 136.1, 130.2, 129.7,
129.7, 129.7, 129.4, 129.4, 129.2, 129.2, 129.2, 129.1, 129.1, 128.7, 127.5, 124.5, 124.4, 122.5, 120.5,
119.9, 119.2, 112.4, 110.7, 68.0, 55.8, 55.1, 34.5, 32.0, 28.3 ppm; HRMS calcd for C35H35N4O4 [M+H+]
575.2658 found 575.2648.
4.5.4.3. (S)-Methyl 6-amino-2-(3-((S)-2-amino-4-phenylbutanamido)benzamido)-hexanoate (P18):
1
Isolated 16 mg (70%) in the form of yellow oil. H NMR (500
MHz, CD3OD) δ 8.11 (s, 1H), 7.78 (d, J = 7.8 Hz, 1H), 7.64 (d, J
= 7.5 Hz, 1H), 7.46 (t, J = 7.9 Hz, 1H), 7.29 – 7.18 (m, 4H), 7.17
(t, J = 7.1 Hz, 1H), 4.62 (dd, J = 9.3, 5.1 Hz, 1H), 4.16 (t, J = 5.8
Hz, 1H), 3.75 (s, 3H), 2.94 (t, J = 7.2 Hz, 2H), 2.78 (t, J = 8.1 Hz, 2H), 2.34 – 2.20 (m, 2H), 2.05 – 1.82
(m, 2H), 1.76 – 1.68 (m, 2H), 1.61 – 1.43 (m, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ 174.0, 170.1,
168.7, 141.2, 139.3, 136.1, 130.3, 129.7, 129.7, 129.3, 129.3, 127.5, 124.6, 124.6, 120.5, 55.1, 54.2, 52.8,
40.5, 34.6, 32.0, 31.7, 28.0, 24.1 ppm; HRMS calcd for C24H33N4O4 [M+H+] 441.2502 found 441.2491.
4.5.4.4. (S)-Methyl 2-(3-((S)-2-amino-5-guanidinopentanamido)benzamido)-3-(4-hydroxyphenyl)-
propanoate (P19): Isolated 12 mg (66%) in the form of yellow oil. 1H NMR (500 MHz, CD3OD) δ 8.06
(s, 1H), 7.79 (d, J = 7.0 Hz, 1H), 7.50 (d, J = 7.0 Hz, 1H), 7.44
– 7.36 (m, 1H), 7.08 (d, J = 8.3 Hz, 2H), 6.72 (d, J = 8.3 Hz,
2H), 4.76 (dd, J = 9.1, 5.5 Hz, 1H), 4.25 – 4.17 (m, 1H), 3.71
(s, 3H), 3.30 – 3.27 (m, 2H), 3.18 (dd, J = 13.9, 5.4 Hz, 1H),
3.04 (dd, J = 13.7, 9.4 Hz, 1H), 2.14 – 1.96 (m, 2H), 1.86 – 1.73 (m, 2H) ppm; 13C NMR (125 MHz,
CD3OD) δ 173.7, 169.8, 168.5, 158.6, 157.3, 139.2, 136.0, 131.2, 131.2, 130.2, 129.0, 124.5, 124.5,
120.3, 116.3, 116.3, 56.2, 54.6, 52.8, 41.7, 37.3, 29.8, 25.5 ppm; HRMS calcd for C23H31N6O5 [M+H+]
471.2356 found 471.2361.
4.5.4.5.
(S)-2-(3-((S)-2-Amino-5-guanidinopentanamido)benzamido)-3-(1H-indol-3-yl)-propanoic
acid (P20): Isolated 10 mg (61%) in the form of yellow oil. 1H NMR (500 MHz, CD3OD) δ 8.04 (s, 1H),
7.77 (d, J = 7.8 Hz, 1H), 7.59 (d, J = 7.8 Hz, 1H), 7.45 (d, J = 7.7 Hz, 1H), 7.40 – 7.32 (m, 2H), 7.17 (s,
1H), 7.07 (t, J = 7.5 Hz, 1H), 6.98 (t, J = 7.3 Hz, 1H), 4.91 (dd, J = 8.2, 4.9 Hz, 1H), 4.20 – 4.12 (m, 1H),
3.49 (dd, J = 14.7, 4.8 Hz, 1H), 3.37 – 3.33 (m, 1H), 3.30 – 3.24 (m, 2H), 2.12 – 1.96 (m, 2H), 1.85 –

1.69 (m, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ 175.3, 169.8,
168.5, 158.4, 139.2, 137.9, 136.1, 130.2, 128.7, 124.5, 124.3,
122.4, 120.2, 119.8, 119.2, 119.1, 112.4, 111.0, 55.6, 54.6, 41.7,
29.8, 28.2, 25.5 ppm; HRMS calcd for C24H30N7O4 [M+H+] 480.2359 found 480.2351.
4.6. Synthesis of analogues P21-P25
4.6.1. General procedure for the HOBt/EDC-mediated amide coupling. Synthesis of intermediates
8: A solution of aniline 7 (1.0 eq), the appropriately protected amino acid (2.0 eq), HOBt∙H2O (0.5 eq),
EDC∙HCl (3.0 eq) and DIPEA (5.0 eq) in anhydrous DMF (0.25 M) was stirred under Ar at 25 °C for 12
h. The reaction mixture was then diluted with EtOAc and consecutively washed with HCl 1.0 M,
saturated NaHCO3 and brine. The organic layer was dried over anhydrous Na2SO4, filtered and
evaporated under reduced pressure. The residue was purified by column chromatography in order to
furnish intermediates 8 in 65-92% yields.
4.6.2. General procedure for the HATU/BTU-mediated amide coupling. Synthesis of analogues P21-
P25: A solution of intermediates 8 (1.0 eq), a properly protected amino acid (2.0 eq), HATU (3.0 eq) and
DBU (4.0 eq) in anhydrous DMF (0.25 M) was stirred under Ar at 25 °C for 24-36 h. The reaction
mixture was then diluted with EtOAc and consecutively washed with HCl 1.0 M, saturated NaHCO3 and
brine. The organic layer was dried over anhydrous Na2SO4, filtered and evaporated under reduced
pressure. The resulting residue was purified by column chromatography (silica gel, EtOAc/Hexanes
20%→50%) to produce the desired intermediates in 45-72% yields. Final deprotections were performed
as needed similarly to the ones described for analogues P16-P20.
4.6.2.1. (S)-Benzyl 2-(4-((S)-2-aminohexanamido)benzamido)-3-(1H-indol-3-yl)-propanoate (P21):
1
Isolated 18 mg (76%) as yellow oil. H NMR (500 MHz, CD3OD) δ
7.76 – 7.63 (m, 4H), 7.55 (d, J = 7.9 Hz, 1H), 7.34 (d, J = 8.0 Hz, 1H),
7.30 – 7.22 (m, 3H), 7.21 – 7.14 (m, 2H), 7.09 (t, J = 7.5 Hz, 1H), 7.03
(s, 1H), 6.99 (t, J = 7.5 Hz, 1H), 5.09 (s, 2H), 4.96 – 4.92 (m, 1H), 3.77
– 3.70 (m, 1H), 3.47 – 3.38 (m, 1H), 3.38 – 3.33 (m, 1H), 1.89 – 1.68
(m, 2H), 1.44 – 1.30 (m, 4H), 1.15 – 1.08 (m, 3H) ppm; 13C NMR (125 MHz, CD3OD) δ 173.6, 172.9,
169.5, 142.7, 138.1, 137.1, 130.6, 129.5, 128.7, 124.6, 124.4, 122.6, 122.4, 120.4, 120.0, 119.8, 119.2,
112.4, 110.8, 68.0, 56.1, 55.8, 34.4, 28.5, 28.3, 23.5, 14.1 ppm; HRMS calcd for C31H35N4O4 [M+H+]
527.2658 found 527.2644.

4.6.2.2.
(S)-Benzyl
2-(4-((S)-2-amino-4-phenylbutanamido)benzamido)-3-(1H-indol-3-yl)-
1
propanoate (P22): Isolated 18 mg (71%) as yellow oil. H NMR (500 MHz, CD3OD) δ 7.76 – 7.66 (m,
4H), 7.55 (d, J = 7.9 Hz, 1H), 7.34 (d, J = 7.9 Hz, 1H), 7.29 – 7.19 (m,
7H), 7.19 – 7.14 (m, 3H), 7.08 (t, J = 7.6 Hz, 1H), 7.02 (s, 1H), 6.98 (t, J
= 7.5 Hz, 1H), 5.07 (s, 2H), 4.94 (dd, J = 7.8, 6.4 Hz, 1H), 4.18 (t, J =
6.4 Hz, 1H), 3.43 (dd, J = 14.6, 6.4 Hz, 1H), 3.36 – 3.31 (m, 1H), 2.81 –
2.73 (m, 2H), 2.30 – 2.20 (m, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ 173.5, 169.4, 168.5, 142.3,
141.2, 138.1, 137.0, 130.9, 129.7, 129.7, 129.5, 129.5, 129.4, 129.4, 129.3, 129.3, 129.2, 129.2, 129.2,
128.7, 127.5, 124.5, 122.5, 120.5, 120.5, 119.9, 119.2, 112.4, 110.8, 68.0, 55.8, 55.2, 34.6, 32.0, 28.3
ppm; HRMS calcd for C35H35N4O4 [M+H+] 575.2658 found 575.2669.
4.6.2.3. (S)-Methyl 2-(4-((S)-2-amino-5-guanidinopentanamido)benzamido)-3-(4-hydroxyphenyl)-
1
propanoate (P23): Isolated 14 mg (61%) as yellow oil. H NMR (500 MHz, CD3OD) δ 7.78 – 7.61 (m,
4H), 7.06 (d, J = 8.4 Hz, 2H), 6.70 (d, J = 8.4 Hz, 2H), 4.78 –
4.72 (m, 1H), 3.92 – 3.84 (m, 1H), 3.72 (s, 3H), 3.26 – 3.14
(m, 3H), 3.05 – 2.95 (m, 1H), 2.01 – 1.83 (m, 2H), 1.78 – 1.66
(m, 2H) ppm; 13C NMR (125 MHz, CD3OD) δ 173.9, 172.4,
169.4, 157.4, 156.6, 141.5, 131.2, 131.2, 129.5, 129.5, 129.4, 129.1, 120.5, 120.5, 116.3, 116.3, 56.2,
55.3, 52.7, 42.0, 37.5, 30.9, 25.7 ppm; HRMS calcd for C23H31N6O5 [M+H+] 471.2356 found 471.2345.
4.6.2.4. (S)-Benzyl 2-(4-((S)-2-amino-4-(4-(benzyloxy)phenyl)butanamido)benzamido)-3-(1H-indol-
3-yl)-propanoate (P24): Isolated 15 mg (67%) as yellow oil. 1H NMR (500 MHz, CD3OD) δ 7.77 – 7.70
(m, 2H), 7.69 – 7.63 (m, 2H), 7.55 (d, J = 7.9 Hz, 1H), 7.41 – 7.23
(m, 9H), 7.22 – 7.05 (m, 5H), 7.03 – 6.97 (m, 2H), 6.90 – 6.82 (m,
2H), 5.12 – 5.03 (m, 2H), 4.98 – 4.89 (m, 3H), 4.15 – 4.05 (m, 1H),
3.48 – 3.34 (m, 2H), 2.77 – 2.61 (m, 2H), 2.29 – 2.15 (m, 2H) ppm;
13C NMR (125 MHz, CD3OD) δ 173.5, 172.9, 169.5, 159.4, 142.4,
138.7, 138.7, 138.1, 137.1, 131.5, 130.7, 129.7, 129.5, 129.4, 129.2, 129.2, 128.8, 128.5, 124.5, 122.5,
120.6, 119.9, 119.2, 116.3, 112.4, 110.9, 106.9, 71.1, 68.0, 57.8, 55.8, 43.8, 40.4, 28.3 ppm; HRMS calcd
for C42H41N4O5 [M+H+] 681.3077 found 681.3071.
4.6.2.5. (S)-2-(4-((S)-2-Aminohexanamido)benzamido)-3-(1H-indol-3-yl)-propanoic acid (P25):
Isolated 11 mg (61%) as yellow oil. 1H NMR (500 MHz, CD3OD) δ 7.70 – 7.62 (m, 4H), 7.57 (d, J = 7.9
Hz, 1H), 7.30 (d, J = 7.9 Hz, 1H), 7.12 (s, 1H), 7.04 (t, J = 7.5 Hz, 1H), 6.92 (t, J = 7.4 Hz, 1H), 4.84 –
4.80 (m, 1H), 4.06 – 3.98 (m, 1H), 3.51 – 3.43 (m, 1H), 3.37 – 3.33 (m, 1H), 1.99 – 1.82 (m, 2H), 1.49 –