Design and Combinatorial Development of Shield-1 Peptide Mimetics Binding to Destabilized FKBP12

Article abstract of DOI:10.1021/acscombsci.9b00197

On the basis of computational design, a focused one-bead one-compound library has been prepared on microparticle-encoded PEGA₁₉₀₀ beads consisting of small tripeptides with a triazole-capped N-terminal. The library was screened towards a double

Full text of DOI:10.1021/acscombsci.9b00197

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Article
Design and Combinatorial Development of Shield-1
Peptide Mimetics Binding to Destabilized FKBP12
Daniel Madsen, Frederik Præstholm Jørgensen, Daniel Palmer, Milena Roux, Jakob
V. Olsen, Mikael Bols, Sanne Schoffelen, Frederik Diness, and Morten Meldal
ACS Comb. Sci., Just Accepted Manuscript • DOI: 10.1021/acscombsci.9b00197 • Publication Date (Web): 06 Feb 2020
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Design and Combinatorial Development of Shield-1
Peptide Mimetics Binding to Destabilized FKBP12
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Daniel Madsen,†⊥ Frederik P. Jørgensen,† Daniel Palmer,†⊥ Milena E. Roux,‖ Jakob V. Olsen,‖
Mikael Bols,† Sanne Schoffelen, †⊥ Frederik Diness,*†⊥ Morten Meldal*†⊥
†Department of Chemistry
⊥Center for Evolutionary Chemical Biology,
‖ Department of Biology
University of Copenhagen
Universitetsparken 5, 2100 Copenhagen, Denmark
E-mail: meldal@nano.ku.dk, fdi@chem.ku.dk
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ABSTRACT: Based on computational design, a focused one-bead one-compound library has been
prepared on microparticle encoded PEGA1900 beads consisting of small tripeptides with a triazole
capped N-terminal. The library was screened towards a double point-mutated version of the human
FKBP12 protein, known as the destabilizing domain (DD). Inspired by the decoded library hits,
unnatural peptide structures were screened in a novel on-bead assay, which was useful for a rapid
structure evaluation prior to off-bead resynthesis. Subsequently, a series of 19 compounds were
prepared and tested using a competitive fluorescence polarization assay, which led to the discovery
of peptide-ligands with low micromolar binding affinity towards the DD. The methodology
represents a rapid approach for identification of a novel structure scaffold, where the screening
and initial structure refinement was accomplished using small quantities of library building blocks.
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KEYWORDS: Destabilizing domain, one-bead one-compound library, encoded beads, solid phase
synthesis.
INTRODUCTION
The engineered and double point-mutated version of the human FK506-binding protein, F36V-
L106P-FKBP12, is known as the destabilizing domain (DD).1 This domain can confer its
instability to proteins-of-interests (POIs) when fused to it.2, 3 When expressed in cells, the DD and
the fusion protein will rapidly be degraded by the proteasome, resulting in low levels of the POI.1
Upon stabilization of the DD by addition of a small ligand, the degradation is reduced which
induces a dose-dependent accumulation of the POI within the cell. Hereby, the level of gene
product can be chemically controlled, creating a powerful tool for interrogating biological systems.
The compound Shield-1 (Shld1, Figure 1) is a small molecule derived from the natural ligand
FK506 and has been shown to interact selectively with the DD.4, 5 The Shld1-DD system has
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proven its vast utility in several biological systems, including living mice,6 plants,7, 8 parasites,9,
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mammalian cells,1 and yeast.12 Previous studies have reported Ki values of 7.5 nM from in
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vitro experiments between shld1 and the DD.13 However, in plant systems genetically modified to
express DD-POI fusion proteins, high concentrations of shld1 was required for induce
accumulation of the destabilized complex.7 In studies with rice and wheat, treatment with 3-10 µM
Shld1 solutions were required for achieving sufficient diffusion of the small Shld1 molecule
through the plant cuticle and subsequently stabilization of DD-POI.8 A recent study highlighted
the challenges of improving the plant cell penetrating properties of Shld1 derivatives, while
preserving sufficient potency of the modified compounds.13 In connection to this project,
alternative and novel stabilizing compounds with less demanding synthetic route were envisioned.
We describe in this study, a method for using computational design combined with a series of
encoded combinatorial synthesis and screening steps, as a rapid approach for developing new
peptide-based ligands that stabilizes the DD protein.
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O
O
O
O
'Previous Work'
Structure
based design
OH
O
MeO
MeO
O
N
O
O
N
O
O
O
R
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O
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OH
OH
O
O
O
FK506
O
Ligand for FKBP12
N
R =
R =
O
HO
SLF*
Shield-1
Ligands for DD
This Project
Peptide mimetics
Strategy 2
Strategy 1
R2
R2
N
N
N
N
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R1
R1
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HN
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HN
H
N
O
H
H
N
N
R
R
H
O
O
2
1
Figure 1. Illustration of the development process for small molecule peptide mimetics and their
respectively attachment strategies. Prior to this study, DD-ligands such as SLF* and Shield-1
(Shld1) were derived by structure-based design originating from the natural product FK506.
Strategy 1 of the peptide mimetics involve standard solid-phase synthesis in the C- to N-direction,
whereas in strategy 2 the ligand is anchored via a carboxylate linker attached to a tyrosine side-
chain.
The FKBPs have been described as being “undruggable” for low molecular mass ligands with
sufficient affinity14 and most synthetic ligands of the FKBPs are derived from the natural product
FK506 (Figure 1). Reported strategies include the use of macrocyclic peptide scaffolds15, 16 and
structure-based design of the FK506-FKBP12 pharmacophore.17 Different synthetic approaches
have been reported for the synthesis of Shld1-like structures, in which chiral reducing agents,18
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chiral auxiliaries,19 addition of stoichiometric amount of chiral complexing agents,20 and
chromatographic separation of diastereomers,5 have been utilized to obtain the enantiopure
compounds. Inspired by the structural insight of these previous studies,1, 5 we selected in silico for
the design new scaffolds that mimic the binding of Shld1 to the DD. The scaffolds should be
assembled from simple amino acid building blocks by solid phase peptide synthesis. The resulting
initial structural design (vide infra) is presented in Figure 1 and consists of tripeptides capped at
the N-terminal with a triazole by CuAAC click chemistry.
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We implemented and report here on a new on-bead binding assay using templated pre-folding of
the labeled, disordered protein target for the evaluation of the target binding by the new scaffolds.
The assay allowed rapid scaffold optimization. The solid-supported ligands could be synthesized
in parallel using only 10 mg of resin per compound, thus enabling a rapid hit structure elucidation
prior to off-bead resynthesis. The scaffold allowed synthesis of one-bead-one-compound (OBOC)
libraries and comprised two strategies with different points of attachment to the support (1 and 2,
Figure 1). The compound SLF* 5 (Figure 1), which is closely related to shld1, has a carboxylic
acid handle for attachment to the solid support, and was selected as a reference for studying the
on-bead target interaction.
The screening of a focused combinatorial library, synthesized on optically encoded beads
containing fluorescent microparticles,21 facilitated rapid identification of hit compounds through
simple optical decoding. This library encoding approach is suitable for synthesis and screening of
small to medium sized libraries (500-50000 beads) and permits, as do other bead based encoding
technologies,22, 23, 24, 25 the identification of library members binding to the fluorescent target. The
method relies on the fact that each bead in the library carries a unique distribution of microparticles
as a code obtained by recording the microparticle coordinates that distinguish it from all other
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beads in the library. The encoded library technology is particularly useful for bead-based libraries
of compounds for which conventional mass-spectrometry methods are complicated and inefficient,
as was the case in the presented study.26
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The structural insight gained from the on-bead assay assisted the design of 19 unnatural peptides
which were screened in a competitive fluorescence polarization assay, and our findings has led to
the discovery of novel and small unnatural peptides with low micromolar binding affinity towards
the DD.
RESULTS AND DISCUSSION
With the aim of developing a core structure with modifiable moieties for combinatorial library
development, a tripeptide with a triazole capped N-terminal was designed by computer modelling
to adopt a similar binding pose to that of Shld1 in the DD binding site.5 The reference compound
SLF* and an example of the computational designed ligand 1 is depicted in Figure 2. Modelling
was performed with Molecular Operating Environment (MOE, CCG) using the crystal structure
of SLF* bound to F36V-FKBP12 (PDB: 1BL4) as a starting point.5 Upon fixing the coordinates
of the protein, the SLF* compound was replaced with peptide mimetics, soaked in a water droplet,
and relaxed by energy minimization as described in detail in the supporting information.
Modifications were explored on key features of the peptides during structural development. The
pipecolic moiety is located in a groove on the active site of the protein and has in several studies
shown to be important for binding to the protein.14, 17, 18
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, 27 A range of alternative ring sizes and substitution patterns were sampled during the modelling,
but the pipecolic residue presented a superior fit to the pocket. Originating from an α-aminobutyric
acid, the ethyl part adjacent to the triazole is designed to dock into the hydrophobic cavity formed
after the F36V mutation,5 and various lengths of alkyl groups were investigated and selected in
order to explore its capacity. Those alkyl groups providing favorable interactions in the pocket
during modelling were included in subsequent library synthesis. For the remaining residues,
interaction over the entire binding site was evaluated and structural components displaying
appropriate contact with the protein were selected for combinatorial library synthesis.
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Figure 2. Comparison of the binding modes of SLF* (A), and an example of peptide mimetic 1
(B) to the crystal structure of the SLF*-stabilized F36V-FKBP12 complex. In the modelling of the
complex between F36V-FKBP12 and the peptide mimetic, key features of the ligand was
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maintained while building the structure. The water-soaked complexes of F36V-FKBP12 with the
peptide mimetic was subjected to several rounds simulated annealing (MOE, Amber 10, ETH; T:
430 K, 1 ns, 430-230 K, 1 ns, 230 K, 3 ns). In the first round, the coordinates of F36V-FKBP12
were fixed and in the subsequent rounds, the contact residues in F36V-FKBP12 were relaxed to
allow an induced fit of F36V-FKBP12 and the ligand.
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The design of the peptide mimetic scaffold allowed usage of the large pool of natural and
unnatural amino acid building blocks in combination with the orthogonal CuAAC click chemistry
to survey the pharmacophore interactions. In order to screen for optimal interaction with the
protein for the immobilized substrates in the library, two different linker strategies were employed.
As presented in Scheme 1, Strategy 1 involve standard solid-phase peptide synthesis (SPPS) in
the C- to N-direction. Whereas Strategy 2 is anchored via a linker piece from the tyrosine sidechain,
protruding from the other end of the compound and resembling the part of the SLF* used for
immobilization of 18. Presumably, attachment from this part of the peptide would exhibit a smaller
degree of steric interaction with the DD. In order to initially verify the scaffold design and test the
two linking strategies, 2-3 examples of the scaffold linked by each of the methods were synthesized
on solid support (Scheme 1). The building block for the strategy 2 linker was synthesized by
coupling of 9 with benzylamine, followed by a substitution of ethyl 2-bromoacetate to give 10. A
Boc to Fmoc protection group exchange of 10 was performed, and after ester hydrolysis orthogonal
to the Fmoc protection group,28 11 was formed in five steps with an overall yield of 79%, starting
from Boc-protected L-tyrosine. A set of solid-supported compounds were then synthesized on a
PEGA1900 resin (500-550 µm)29 and subjected to a maltose binding protein (MBP) fused DD,
which had been fluorescently labeled with the rhodamine-X fluorophore (MBP-DD-(ROX)). The
MBP was fused to the DD to prevent aggregation of the destabilized protein and to increase the
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overall polarity of the protein, hence reducing the non-specific binding. The unique swelling
properties of the porous PEGA1900 resin in aqueous media enabled the large fusion protein to gain
access to the bead interior.30 As a reference compound for the initial test screen, a solid-supported
version of the SLF* compound was synthesized by adapting known procedures (see supporting
information).18
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Strategy 1:
O
e, f, g
or
e, h
NH
NH
NR
NH
O
O
O
O
a, b, c, b,
d, b
N
O
O
O
N
O
N
H
N
H
H
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NH
H2N
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or
i
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R =
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= Gly-HMBA, PEGA1900 (500-550 µm)
O
O
O
Strategy 2:
BocHN
BocHN
FmocHN
OH
N
N
j, k
l, m, n
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H
OEt
OH
OH
O
O
O
O
9
10
11
O
NH
e, f, g
or
i
NR
O
O
O
O
N
H
N
H
N
o, b, d, b
N
HN
O
HN
O
O
N
H2N
N
O
O
N
H
O
R =
H
O
O
12
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= Gly-HMBA, PEGA1900 (500-550 µm)
O
Reference:
O
O
O
NFmoc
O
N
O
o, b, i
O
O
O
O
O
H2N
O
O
O
O
OH
N
H
O
17
18
= Gly-Rink, PEGA1900 (500-550 µm)
Scheme 1. Reagents and conditions: a) Fmoc-4-Amb-OH, TBTU, NEM, DMF, 2 h; b)
Piperidine/DMF (1:4), 20 min; c) Fmoc-L-Phe-OH, TBTU, NEM, DMF, 2 h; d) Fmoc-L-Pip-OH,
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TBTU, NEM, DMF, 2 h; e) Fmoc-D-Abu-OH, TBTU, NEM, DMF, 2 h; f) Imidazole-1-sulfonyl
azide hydrochloride, CuSO4, K2CO3, H2O, 16 h; g) Phenylacetylene, CuSO4, ascorbic acid, t-
BuOH/H2O (3:1), 16 h; h) Ac2O/Pyridine/DMF (1:1:8), 30 min; i) 2-(3,4,5-
Trimethoxyphenyl)butanoic acid, TBTU, NEM, DMF, 2 h; j) Benzylamine, PyBOP, NEM, DMF,
1 h, 99%; k) ethyl-2-bromoacetate, Cs2CO3, DMF, 3 h, 86%; l) TFA/CH2Cl2 (1:1), 0°C to rt, 60
min; m) Fmoc-Cl, Na2CO3, Dioxane/H2O (2:1), 0°C to rt, 1.5 h, 93% (2 steps); n) MgI2, THF, mw
120°C, 15 min., quant; o) TBTU, NEM, DMF, 2 h.
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The carboxylic acid part of the SLF* has been shown to have minor influence on the binding to
the DD protein and has previously been used as an anchor for solid-support while retaining its
interaction with the protein.31 To estimate any level of non-specific binding, three different control
tripeptides presenting negative, positive, and neutral charge (19-21, see Figure 3) were tested in
the on-bead binding assay. As presented in Figure 3, compounds from both attachment strategies
containing the 2-trimethoxyphenylbutyric acid building block showed significant binding, albeit
with lower affinity than the reference solid-supported SLF* (18) in the single concentration on-
bead screen. The acetylated compound 7 bound poorly to the protein, while the derivatives 6 and
15 containing a phenyltriazole presented good binding, as measured by the fluorescence due to the
resin bound MBP-DD-(ROX). With a relatively high effective ligand concentration of
approximately 3.4 mM, a situation of on-bead binding saturation is presumably observed for strong
binding ligands. Indeed, compound 6 provided the same if not more fluorescence intensity than
resin bound SLF*. However, these results indicated that the triazole based mimetics of the 2-
trimethoxyphenylbutyric acid would be a good starting point for development of a combinatorial
library.
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On-Bead Screen
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4
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Figure 3. Single concentration binding tests of solid-supported ligands subjected to a fluorescently
labeled DD protein (550 nM) for 16 h. The three tripeptides 19 (Ac-Glu-Phe-Gly-OH), 20 (Ac-
Lys-Phe-Gly-OH), 21 (Ac-Ala-Phe-Gly-OH) were attached to the PEGA resin via the HMBA
linker and used as controls for non-specific binding.
The main advantage of this approach was that the azido acid could be generated on bead from
amino acid building blocks, hereby removing the need for introducing a stereocenter through
enantioselective alkylation of a range of phenylacetic acid derivatives.19, 20 Due to anticipation of
slightly better interaction, and ease of synthesis, strategy 1 was selected for the development of
the combinatorial library.
Library screening.
Using the split-and-mix approach, a library of in total 896 different compounds were synthesized
on PEGA1900 beads (500-550 µm) that were optically encoded by MicroParticleMatrix (MPM)-
encoding (Figure 4).32 Encoding of the immobilized peptides was performed by recording three
orthogonal images of every bead in each portion of the split process, to generate a microparticle
coordinate matrix used as a barcode for the individual beads. The images were recorded using a
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custom made MPM decoding instrument comprising a solid state laser, three CCD-cameras with
tele centric optics and a carousel for individual bead handling.21 Subsequently, the isolated hit-
beads were recorded and the 3-dimentional matrix represented by their microparticle coordinates
were determined, allowing tracking through the synthetic history of the immobilized compound.21
Pipecolic acid and 4-(aminomethyl) benzoic acid were maintained as structural features during the
library development. The remaining amino acid building blocks were varied and coupled using
either coupling reagents TBTU or HATU. Subsequently, a solid-phase diazotransfer to the N-
terminal amine was carried out to form the corresponding azide,33 which in turn was reacted by
the CuAAC click reaction using various alkynes (see supporting info Table S1 for the full list of
library building blocks).
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Figure 4. Development and screening of encoded one-bead one-compound library. (A) Using the
split-and-mix approach, an 896-member library was synthesized on encoded PEGA1900 beads
(500-550 µm) using the same conditions as presented in scheme 1. (B) and (C) bright field and
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fluorescence image, respectively, of library beads after being subjected to a 1 µM solution of shld1-
stabilized MBP-DD-(ROX) for 48 h. The images presents a clear hit bead among inactive beads.
(D) Typical encoded bead used in the present study. Three orthogonal images of the same bead
are recorded and used in construction of the 3-dimentional matrix represented by the microparticle
coordinates. These are used as a unique digital code to identify the structure of the compound
immobilized on the bead. The code of the bead is recorded at each synthetic step and used for hit
identification.
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51
52
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The structure variations of R, R1, and R2 were guided and chosen based on computational design
as described above. The moieties on the R-position were primarily aliphatic and aromatic cyclic
structures, whereas the R1-position consisted of small linear and branched alkyl groups.
Presumably, the enlargement of the hydrophobic cavity formed upon F36V mutation of FKBP12
could allow binding of longer alkyl groups, particularly in combination with the less bulky triazole
moiety, as comparison to the reference trimethoxy phenylbutyric acid residue of SLF*. In order to
induce the correct folding of the protein, the MBP-DD-(ROX) was preincubated for 30 minutes
with a stoichiometric amount of Shld1 prior to the incubation of the library beads. A final
concentration of 1 µM MBP-DD-(ROX) was used and the beads were incubated for 48 hours to
establish equilibrium between the individual compounds in a binding-competition assay. As
presented in Figure 4, a clear difference in interaction with the protein among the solid-supported
ligands was observed, which was visualized by recording the fluorescence intensity of the bead
collections. The binding was quite selective and provided a number of bright beads on a
background of many inactive beads. The identified hit-beads were manually sorted based on their
apparent fluorescence intensity. The structures attached to the isolated encoded hit-beads were
decoded giving a total of 16 different hit-structures out of 17 isolated beads (see supporting info
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for all the hit structures).21 Nine of the hit compounds contained a 4-trifluoromethyl phenylalanine
derivative as the second amino acid. In addition, 12 compounds had an ethyl group on the R1-
position, and primarily either a 4-methoxy phenyl or a cyclopropyl on the R2-position.
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On-bead assay and structure evaluation.
In order to distinguish and verify the potency among the structures of the solid-supported hit
compounds, a well-based on-bead binding assay was employed.34 Guided by the results from the
library screen, a set of immobilized substrates were resynthesized on PEGA1900 beads (125-200
µm). The beads were singly sorted into a 96-well plate using a COMPAS bead sorter (Union
Biometrica) and subjected to a dilution series of MBP-DD-(ROX). After 16 hours of incubation,
the fluorescence intensity was measured on wide-field fluorescence microscope. The individual
binding profile of the resynthesized peptide mimetics was compared to the solid-supported SLF*
and graded in a scale from 1-4 (Table 1). In general, it was found that the most abundant
substituents from the hits in the library screen, also proved to be the most potent in the bead assays.
Compounds containing a 4-trifluoromethyl phenylalanine as the second amino acid, and an ethyl
group on the R1-position displayed the most promising binding profile. On the R2-position, neither
the phenyl group of 23 of nor the 3-benzoic acid of 24, were identified as hits during the screening,
but were selected for comparison with the binding of 25. These two compounds displayed a
comparable binding profile to the anisole of 25, which indicated that aromatic moieties on this
position was preferred. Resynthesis of the peptide mimetics in the solid-supported screening
format was realized on a low micromolar scale, requiring a minimal amount of the unnatural amino
acid building-blocks, which in combination with the library screening gave an efficient and rapid
structure evaluation.
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Table 1. On-bead screening of compounds derived from the hits identified through optically
5
6
encoded split-and-mix library technology.
7
8
9
R2
N
N
N
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
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45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
R1
O
O
O
R
NH
N
H
H
N
O
O
H
O
N
=
O
O HMBA PEGA1900
Cmp.
R
-
R1
R2 Potencya
18b
-
-
++++
F3C
23
++++
(R)
HO
O
F3C
F3C
24
++++
++++
(R)
(R)
O
25
F3C
F3C
F3C
F3C
F3C
F3C
26
27
28
29
30
31
+++
+++
++
(R)
(R)
(R)
(R)
(R)
H2N
HO
+++
++
-
(S,S)
(S,S)
(R)
HO
O
F3C
32
-
O
33
34
+
HO
-
(R)
(R)
O2N
35
a
++
Binding profile of the peptide mimetics was
compared to the solid-supported SLF* and their
potency was graded in a scale from 1-4.
b
Immobilized SLF* (see scheme 1).
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Off-bead peptide resynthesis and screening.
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The next step was to survey the non-linked scaffold for binding to the MBP-DD in solution.
Based on the results obtained from the well-based on-bead assay, a set of 19 unnatural peptides
were synthesized in solution or from solid-support (see supporting info). Using the same synthetic
approach as presented in Scheme 1, the compounds containing a primary amide or a benzoic acid
on the C-terminal of the peptides were synthesized from the Rink-amide linker and the 2-chloro
trityl linker, respectively. The solid-supported compounds were cleaved upon acid treatment to
yield the desired peptide mimetics in modest to excellent yields. The compounds with no handle
for solid-support were synthesized in 3-4 steps in solution. For this, primary and secondary amines
were coupled with a substituted Boc-protected L-phenylalanine derivative. Subsequently, the Boc-
group was removed under acid treatment and the Boc-pipecolic acid was coupled using HBTU. In
a subsequent one-pot protecting group removal and coupling procedure, an azido modified D-α-
aminobutyric acid was introduced, and the final triazole was formed in a CuAAC reaction.
Variation on the R1-position (Table 2) included moieties of different size, polarity, and charge.
The nineteen peptide mimetics were screened towards the MBP-DD using a recently described
fluorescence polarization competition assay.13 Directed by the results from the on-bead assay, the
unbound versions of 24 and 25 were synthesized and tested. The most promising of these
compounds was the aminomethyl benzamide 37, which showed a Ki of 21.5 µM. It was found that
omitting a R1-substituent (38) reduced the activity fivefold, whereas enhancing the lipophilicity
by changing the carboxylic acid to an ester or omitting the amide on the R1-substituent led to loss
of activity. Many of the resynthesized ligands showed poor solubility under the conditions of the
assay, which is a crucial property for biological activity. This influenced the outcome of the
fluorescence polarization competition assay and complicated the accurate assessment binding
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constants. Reducing the lipophilicity of 36 revealed that changing to an aliphatic amide substituent
(40), some activity could be achieved and that this was lost when switching to a lipophilic
substituent (49). However, the effect appeared not only to be enhanced solubility, since benzoic
acid derivatives (45-47) or shorter aliphatic amide substituent (42-44) in the R1-position only led
to inactive derivatives. Compound 40 exhibited a Ki of 33.9 µM and has a primary amide
positioned in a similar distance from the pipecolic core as compound 37, suggesting that a
hydrogen bond donor in this position may be advantageous to the binding of the protein. Testing
rather small moieties on the R1-position in combination with or without changing the R- and R2-
substituents (50-54) interestingly revealed the two most potent compounds in the series (51 and
53) with Ki-values of 5.13 µM and 11.2 µM, respectively. Both compounds are among the most
hydrophilic, but again this effect is not the only determining factor, as introducing the aliphatic
amide substituent found the active derivative 40 in the R1-position of 51 led to loss of activity (41).
This underlines that further optimization of the scaffold has to be multi-dimensional, which exactly
is the strength of combinatorial screening. However, the presented data demonstrates that the
combination of computational design and combinatorial synthesis and screening is a powerful
concept for developing new active scaffolds towards a given biological target.
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51
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Table 2. Ki values of resynthesized peptide mimetics 36-54
O
R1
N
HN
O
R2
N
N
N
R
Cmp
Shld1
SLF*
R
-
-
R1
-
-
R2 Ki (µM)a
13
-
0.0075
13
-
0.0187
O
O
NH2
H
CF3
>200
36
N
O
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O
4
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6
NH2
HO
H
CF3 21.5 ± 4.0
37
N
O
O
7
8
9
HO
O
H
H
CF3 110 ± 109
38
39
O
O
10
11
12
13
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24
25
26
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37
38
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40
41
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45
46
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49
50
51
52
53
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CF3
>200
O
H
N
NH2
NH2
CF3 33.9 ± 7.6
40
41
42
43
O
O
O
O
H
N
CF3
CF3
CF3
>200
>200
>200
H
N
NH2
NH2
O
O
O
O
H
N
O
O
H
N
NH2
O
O
CF3
CF3
>200
>200
44
45
O
O
O
OH
H
N
O
O
O
O
O
OH
OH
H
N
CF3
>200
>200
46
47
O
O
O
H
N
NO2
HO
N
CF3
CF3
CF3
>200
>200
>200
48
49
50
51
O
O
O
O
H
N
O
O
O
O
N
N
O
O
O
CF3 5.13 ± 0.4
CF3 >200
NO2 11.2 ± 9.3
>200
O
O
O
NH2
52
53
54
O
O
O
O
F
O
a
A competitive fluorescence polarization assay was used to
obtain the reported Ki values ± SD from three independent
experiments.
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Binding evaluation of peptide ligands.
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The interactions between ligand 37 and F36V-FKBP12, involve two hydrophobic pockets (see
Figure 5A). One for the ethyl group which interact with Ile-91,Gly-28, Val-36, Phe-99, Tyr 26
and Leu-97 of F36V-FKBP12, and one for the pipercolic acid, which is lined by Phe-46, Phe-99,
Tyr-26, Ile-56 and Val-55, with Trp-59 positioned at the bottom of the pocket. In addition, the 4-
trifluoromethyl-L-phenylalanine interact with Phe-46, and the aromatic ring of the
amidomethylbenzamide residue interact with Ile-56. The bound 37 show a set of crucial hydrogen
bonds. The C-terminal amide binds to the carbonyl group of Val-55 while the NH of the
amidomethylbenzamide binds internally to the carbonyl of the pipecolic amide. This in turn binds
amide NH of Ile-56. Tyr-82 forms a hydrogen bond to the deeply buried carbonyl of the triazole
modified butyric acid, while the triazole forms a hydrogen bond to the NH of the Phe(CF3) residue.
Overall the fit of 37 is not as tight as that of SLF*.5, 13 The optimized interaction of the three
peripheral aromatic rings seem to lift the core pipecolic amide and α-aminobutyric acid residue
slightly from their binding pockets, since it cannot reach over the rim of the binding pocket.
Hereby, interaction with the protein is compromised, and as visualized in Figure 5C, the SLF* is
in significant closer contact with the protein in the deep hydrophobic binding pocket. The complex
of F36V-FKBP12 with compound 51 presents an alternative binding mode in which the
cyclopropane ring interacts with Ile-90, His-97, and Tyr-82 and the triazole binds perpendicularly
to the NH of the Phe(CF3). This redirects Tyr-82 to form a hydrogen bond to the carbonyl of
Phe(CF3), allowing optimal interaction of the morpholine residue with Ile-56. Surprisingly, the
smaller compound 51 showed the highest binding affinity. However, since all peripheral residues
of 51 are relatively small, they may allow optimal interaction of the core pipecolic amide and α-
aminobutyric acid residues with the F36V-FKBP12. These observations suggest that the scaffold
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could be even further improved by extending the core framework to position the peripheral
aromatic residues at more favorable regions of the interaction interface, thus providing a better
match of binding to the active site of the DD.
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Figure 5. (A), (B), and (C) the binding modes of compound 37 and compound 51 (D) to the crystal
structure of F36V-FKBP12 in the SLF*-stabilized complex presented by computational modeling.
(A) Contact residues of interaction between 37 with F36V-FKBP12. (B) Hydrogen bond network
of interacting residues between the complex 37 and F36V-FKBP12. C) The overlay of SLF* of
the crystal structure (Green) and ligand 37 (grey) in the binding pocket of F36V-FKBP12. D) The
alternate binding mode presented by compound 51.
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In summary, an 896 member one-bead one-compound library was synthesized on microparticle
encoded PEGA1900 beads using the split-and-mix approach. The library was screened towards a
fluorescently labeled version of the DD-protein and the screen resulted in 16 different structures,
which were identified as hits and deconvoluted using in-house developed decoder equipment.
General trends among the hits included the presence of a 4-trifluoromethyl-L-phenylalanine as
the second amino acid and an ethyl-group on the R1-position (Figure 4) originating from an α-D-
aminobutyric acid. Guided by the library hits, solid supported peptide mimetics were
resynthesized on small scale and screened in a novel on-bead binding format to confirm and
distinguish the potency among the library hits. The structure information was then used for the
synthesis of 19 peptide mimetics. By exploiting the fixed stereochemistry of the unnatural amino
acids, the small peptide-like compounds were synthesized in few steps using either solution- or
solid-phase synthesis. The peptide mimetics were tested in a competition fluorescence
polarization assay and one compound with a low micromolar binding affinity towards the DD
was identified. Analysis of the identified low potency ligand (37) indicates that binding may be
partly compromised by the small displacement of the pipecolic and butyric acids caused by rim
interaction of the peripheral residues. This may also add to the explaination, why a small
compound like 51 bind better than 37, while displaying less interaction. Our high-throughput
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screening approach to identify a novel peptide-like structure scaffold for the DD has involved the
combination of computational modeling, combinatorial library screening, and on-bead structure
evaluation.
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With a focus on improving the solubility of the peptide mimetics, the identified ligand 51 could
serve as a starting point for development of unnatural peptides that mimic the Shld1-DD
interaction. We envision that the present methodology can be applied to the synthesis and
screening of larger peptide and non-peptide libraries, where the screening and initial structure
refinement can be accomplished routinely and rapidly using small quantities of library building
blocks in a high throughput manner using the MPM-encoding technology.
SUPPORTING INFORMATION
A full description of the materials and methods, including HPLC, NMR, and MS data can be found
in the supporting info.
AUTHOR INFORMATION
Corresponding Authors. Professor Morten Meldal and Associate Professor Frederik Diness,
CECB, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100
Copenhagen, Denmark. Email: Meldal@nano.ku.dk, fdi@chem.ku.dk
Author Contributions. The manuscript was written through contributions of all authors. All
authors have given approval to the final version of the manuscript.
Funding Sources. University of Copenhagen – CECB-Lighthouse Grant 2013. Danish Council
for Independent Research (DFF-4184-00019).
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ACKNOWLEDGMENT
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The University of Copenhagen has supported the present research through the UCPH –
lighthouse program (CECB) and the free Research Council of Denmark.
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ABBREVIATIONS
Ac: acetyl; Abu: α-aminobutyric acid; Amb: aminomethylbenzoic acid; Boc: tert-butoxycarbonyl;
Comp: compound; DD: destabilizing domain; DMF: N,N-dimethylformamide; FKBP: FK506-
binding protein; Fmoc: 9-fluorenylmethyloxycarbonyl; HATU: 1-[Bis(dimethylamino)methylene]-
1N-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate; HMBA: hydroxymethylbenzoic
acid; MBP: maltose-binding protein; NEM: N-ethylmorpholine; NSB: non-specific binding; PEGA:
polyethylene glycol dimethyl acrylamide; Pip: pipecolic acid; POI: protein of interest; PyBOP:
benzotriazole-1-yl-oxy-tripyrrolidinophosphonium hexafluorophosphate; ROX: 5(6)-rhodamine-
X; rt: room temperature; Shld1: Shield-1; SPPS: solid phase peptide synthesis; SPS: solid phase
synthesis;
TBTU:
N-[(1H-benzotriazol-1-yl)(dimethylamino)methylene]-N-methyl
methanaminium tetrafluoroborate; TFA: trifluoroacetic acid; THF: tetrahydrofuran.
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Figure 1. Illustration of the development process for small molecule peptide mimetics and their respectively
attachment strategies. Originating from the natural product FK506, compounds such as SLF* and Shield-1
(Shld1) were derived from structure based design. Strategy 1 of the peptide mimetics is based on solid-
phase synthesis in the C- to N-direction, whereas strategy 2 is anchored via a carboxylate linker attached to
a tyrosine OH.
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Scheme 1. Reagents and conditions: a) Fmoc-4-Amb-OH, TBTU, NEM, DMF, 2 h; b) Piperidine/DMF (1:4), 20
min; c) Fmoc-L-Phe-OH, TBTU, NEM, DMF, 2 h; d) Fmoc-L-Pip-OH, TBTU, NEM, DMF, 2 h; e) Fmoc-D-Abu-
OH, TBTU, NEM, DMF, 2 h; f) Imidazole-1-sulfonyl azide hydrochloride, CuSO4, K2CO3, H2O, 16 h; g)
Phenylacetylene, CuSO4, ascorbic acid, t-BuOH/H2O (3:1), 16 h; h) Ac2O/Pyridine/DMF (1:1:8), 30 min; i)
2-(3,4,5-Trimethoxyphenyl)butanoic acid, TBTU, NEM, DMF, 2 h; j) Benzylamine, PyBOP, NEM, DMF, 1 h,
99%; k) ethyl-2-bromoacetate, Cs2CO3, DMF, 3 h, 86%; l) TFA/CH2Cl2 (1:1), 0°C to rt, 60 min; m) Fmoc-
Cl, Na2CO3, Dioxane/H2O (2:1), 0°C to rt, 1.5 h, 93% (2 steps); n) MgI2, THF, mw 120°C, 15 min., quant;
o) TBTU, NEM, DMF, 2 h.
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