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Chapter • Peptidomimetics
10
Peptides are open-chain polymers made up of amino
acids (. Fig.10.1). The main chain is constructed of
alternating amide groups –CONH– and aliphatic carbon atoms, which are labeled Cα. The side chains branch
from the main chain at the Cα atom. The amide group is
barely exible (Sect.14.1). In contrast, rotation around
the Cα–Cβ bond is possible. The side chains are exible
as well. Because of this, each amino acid can take on
multiple conformations. As aconsequence, peptides are
very exible molecules with many rotatable bonds and
a multitude of possibilities to adopt different spatial
congurations. Formally, there is no difference between
the construction of peptides and proteins. Nonetheless,
oligomers of amino acids up to asize of 30–50 monomer
building blocks are called peptides, and the term protein
is preferred for any members of this substance class that
are above this limit.
10.1 Therapeutic Relevance of Peptides
Peptides are responsible for numerous biological functions in humans, e.g., enzyme substrates and hormones.
A few important examples are summarized in . Table10.1. Accordingly, peptides are interesting for therapeutic purposes, and in fact, several important drugs are
peptides (. Fig.10.2).
The use of peptides as drugs is signicantly limited
by several factors:
Peptides are poorly absorbed after oral administra-
-
tion; this is mostly because of their high molecular
weight and pronounced polarity.
Peptides are easily degraded by proteases in the gas-
-
trointestinal tract and are, therefore, metabolically
unstable.
The body is able to very quickly excrete peptides via
-
the liver and kidneys.
. Table 10.1 Several important peptide hormones
Peptide Function
Leu-Enkephalin, Met-Enkephalin
Fibrinogen Platelet aggregation
AngiotensinII Increases blood pressure
Endothelin Increases blood pressure
NeuropeptideY Increases blood pressure
SubstanceP Bronchoconstriction and pain
Opiate receptor ligands,
analgesics
(among other actions)
(among other actions)
mediation
. Fig. 10.1 The pentapeptide Leu-enkephalin as an example of
apeptide structure. The left side with the free NH2 group is the N-ter-
minus, and the other is the C-terminus. Each amino acid contributes
three nonhydrogen atoms to the peptide chain. Nature almost exclusively uses the 20proteinogenic l-amino acids for the construction of
peptides (see pageIX). Depending on the functional groups in the side
chains, the distinction is made between hydrophilic acidic and basic
amino acids and those with hydrophobic aliphatic and aromatic side
chains. The amino acids are abbreviated with three letter codes. Aone
letter code is also used. The denition of the torsion anglesω, φ, ψ,
andχ is shown in the example of the amino acid phenylalanine. The
angleω is practically always close to 180°. The spatial course of the
peptide backbone is determined by the φ and ψangles (see Sect.14.2).
The tetrahedral carbon atom in the chain is called Cα, the rst atom in
the side chain is named Cβ, and the following atom is given the indexγ
. Fig. 10.2 Peptides applied as drugs: Oxytocin is used to induce
and strengthen contractions during labor. The immunosuppressive
cyclosporine prevents organ rejection after transplantation. Leuprolide (pGlu =pyro-glutamate) is an analogue of luteinizing hormone
releasing hormone (LHRH), one of the hypothalamic hormones that,
via luteinizing hormone (LH), controls the synthesis of male and female sexual hormones. Leuprolide is used to treat advanced-stage
prostate cancer
. • Designing Peptidomimetics
Because peptides are involved in so many biological functions in our bodies, there is tremendous interest in nding
active substances that do not have the above-mentioned
detrimental properties, but that bind to the same receptors analogously to peptides or block enzymes that transform peptide substrates. Astepwise approach is taken in
the search for such compounds. Peptide structures are
replaced with isosteric building blocks so that the molecular recognition properties of the peptide remain, but
the undesirable characteristics are reduced. Such peptid-
omimetics should have the following qualities:
Few or no cleavable amide bonds to improve meta-
-
bolic stability,
Reduced molecular weight to improve oral bioavail-
-
ability, and
The same spatial orientation of groups responsible
-
for strong binding to the receptor or enzyme as in the
peptide.
Bacteria are the true masters of constructing peptide
structures that frequently achieve the desired metabolic
stability. They incorporate amino acids that do not belong
to the typical 20residues that are usually used for the construction of proteins. Stereochemically inverted amino acids are also employed, and many of these structures have
acyclic architecture. Due to an exceptional spatial structure, as e.g. in the lasso peptides, these peptides achieve
very good proteolytic stability. Microorganisms have even
evolved adedicated synthesis machinery for this: the non-
ribosomal peptide synthesis (Sect.32.7). This system of
modular, coupled enzymes works like an assembly line.
Depending on the desired product, different enzymatic
functional units are lined up, one after the other, to successively assemble the amino acids cyclizing the product
in the nal step. The exchange of an enzymatic synthesis
unit causes other amino acids to be incorporated into
the otherwise unchanged peptide. Even ester bonds can
be constructed with avery similar multienzyme complex.
Many lead structures all the way to complete drugs can
be derived from these original bacterial peptides, such as
cyclosporine in . Fig.10.1, which is avery important
immunosuppressant. Alarge number of macrolide antibiotics (Sect.32.7) are also synthesized in this way.
Recently, a so-called chemoenzymatic synthetic
strategy was developed for the construction of such
macrolides. As discussed in Sect.11.6, linear oligopeptides can easily be synthesized by using the Merrield
synthesis. Nonproteinogenic amino acids with l- and
d-congurations can also be used to generate high combinatorial diversity. It is very difcult to cyclize these
linear oligopeptides to the desired macrocycle by using
synthetic chemistry methods. Here, the nonribosomal
peptide synthetic machinery is of service. The synthetically prepared peptides are then funneled into the enzymatic process chain and the cyclization domain from
the bacteria catalyzes the ring closure of the peptide:
aperfect symbiosis between synthetic chemistry and
enzyme biology!
10.2 Designing Peptidomimetics
In the beginning of the 1980s, there was only one generally accepted example for alow-molecular-weight active
substance that takes over the function of an endogenous
peptide: the opiate. It is assumed that morphine 10.1 is
amimetic of the endogenous peptide β-endorphin 10.2
(. Fig.10.3). Acomparison of both structures makes
it immediately clear that morphine cannot possibly simulate all of the functional groups of the peptide. Obviously not all are necessary for the biological activity.
This underscores the suspicion that other peptides also
bind to receptors with only afew functional groups. If
this hypothesis is true, it should be possible to identify
the essential functional groups and nd asmall organic
molecule that has the necessary functional groups in the
correct relative orientation.
The starting point for the design of peptidomimetics is the identication of the biologically active peptide,
the function of which is to be imitated. In the rst step,
single amino acids are excluded to determine whether
aportion of the peptide retains sufcient activity. Next
the importance of the individual side chains is investigated. In aso-called alanine scan (Sect.10.7), each amino
acid is successively replaced with alanine. Asevere loss
of activity is an indication that the removed side chain
is important. Until now only peptides made up of the
20amino acids found in proteins have been investigated.
In the next step, structural elements are introduced that
do not occur in the 20proteinogenic amino acids. In principle, the following are possibilities for peptide structure
modication:
The use of d- instead of l-amino acids,
-
Modications of the side chain of amino acids,
-
Changes on the peptide main chain,
-
Cyclization to stabilize the conformation, and
-
The use of templates that enforce aparticular sec-
-
ondary structure, or that allow the attachment of side
chains in adened spatial orientation.
. Fig. 10.3 Morphine 10.1 is a peptidomimetic for the endogenous
peptide β-endorphin 10.2 and the enkephalins (Sect.1.4). It binds as
an agonist to the opiate receptor
Chapter • Peptidomimetics
10
10.3 First Step to Variation: Modifying
Side Chains
An improvement in apeptide’s binding properties can often be achieved by using other side chains. For instance,
in . Fig.10.4 afew analogues of the amino acid phenyl-
alanine are shown that could be used as possible replacements. An increase in the binding afnity can be achieved
if nonproteinogenic amino acids ll the binding pocket
more completely. Rigid analogues will lead to improved
binding if the biologically active conformation, the one
that is adopted in or at the receptor site, is immobilized.
The introduction of nonproteinogenic amino acids
can increase the metabolic stability. The hydroxylation
of aromatic side chains can be suppressed by using
asubstitu ent, for example, auorine atom or amethoxy
group, especially in the para-position. Stability to cleavage
by the digestive enzyme chymotrypsin can be improved by
adding substituents to the Cβ-atom because the modied
side chain no longer ts into the active site of this protease. Apeptide’s proteolytic stability can also be improved
by exchanging l- for d-amino acids. As described above,
bacteria have already recognized this trick. Distributing
d
-amino acids randomly in the peptide can furnish active
substances with astonishing metabolic stability.
10.4 A More Courageous Step: Modifying
the Main Chain
An important step in the design of peptidomimetics is
the replacement of amide bonds in the main chain. Afew
commonly used groups are summarized in . Fig.10.5.
It can be difcult or even impossible to nd replacements
for amide bonds, which form hydrogen bonds to the protein with both the C═O and NH groups, that do not
signicantly reduce binding afnity. If the amides only
bridge functional groups to one another and do not form
hydrogen bonds to the protein, then a large palette of
different replacement groups is available. Substitution at
the amide nitrogen atom leads to metabolic stabilization
because proteases can hardly cleave N-methylated amide
bonds. If N-methylation of an amide group of the main
chain leads to aloss of afnity, several explanations are
possible. One is that the N-methylated compound can no
longer form hydrogen bonds, and an essential H-bond
involving the NH group is lost. It is also possible that
an undesired conformational change may have occurred
as aresult of the additional methyl group, or that the
methyl group may sterically block binding to the protein.
On the other hand, an improvement in binding as aresult
of N-methylation may indicate that the biologically active conformation is stabilized. At room temperature, an
amide bond is almost exclusively in the trans-geometry.
Therefore, it can be substituted by an ester bond that
assumes the same geometry. However, the H-bond-donating properties of the amide group are lost.
. Fig. 10.4 Sterically demanding,
conformationally xed, or metabolically stable analogues of the amino
acid phenylalanine; the structural
enhancements are indicated in red
. • Rigidifying the Backbone by Fixing Conformations
. Fig. 10.5 Different functional
groups that can serve as areplacement for amide bonds in peptidomimetics
An N-methyl substitution improves the stability of
the 180°-rotated conformation of the amide. In the case
of proline, the only proteinogenic amino acid with an
N-alkyl substitution, both the cis and trans amide conguration can be found. The exchange for a1,5-disubstituted tetrazole can replace the cis-orientation of aproline. In addition, trans-congured double bonds imitate
the geometry of an amide bond well. The polar characteristics, however, are lost. To acertain extent, this can
be compensated if the double bond is substituted with
uorine. The reduction of an amide or an isosteric ester
bond means the loss of the carbonyl group and leads to
increased exibility. If the carbonyl group is exchanged
for an –S═O, –SO2, or –PO2 group, the H-bond-accepting characteristics will be amplied; however, ageometry change comes with the bargain. The exchange of
an amide for athioamide results in aweakening of the
H-bond-accepting properties and can serve as atest of
the possible importance of H-bonds to carbonyl groups
in the peptide backbone. Nonetheless, a measure of
caution is warranted because the desolvation of athiocarbonyl group is less difcult than that of acarbonyl
group. This overlaps with the observed afnity and can
mask the effect of the loss of the H-bond. The retro–in-
verso exchange of an amide bond can lead to marked
improvement in the proteolytic stability without losing
the binding qualities (Sect.5.5).
An entirely different concept is the incorporation of
β-amino acids (Sect.31.7). In contrast to the proteino-
genic α-amino acids, these residues have four chain members per monomer unit. The amide bonds are separated
by two aliphatic carbon atoms. Peptides that are made
from these amino acids also show secondary structural
characteristics (Sects.10.5 and14.2). They have already
successfully been incorporated into naturally occurring
peptides as mimetics and can simulate peptide–protein
interactions. Because of the altered sequence of amide
bonds, they are stable to proteolytic degradation (for an
example, see . Fig.31.23).
If the cleavable bond of aprotease substrate is replaced with an isosteric, noncleavable group, asubstrate
can be converted to an inhibitor (Sect.6.6). If the newly
introduced group forms particularly favorable interactions with the active site of an enzyme, an exceedingly
potent enzyme inhibitor can result. An example is found
in the ketomethylene group in serine and cysteine protease inhibitors as apossible replacement for the amide bond that is destined for cleavage (Chap.23). The
hydroxyethylene group is especially suitable for aspartic
protease inhibitors (Chap.24). Phosphonamides, phosphonates, and phosphinates are often strong inhibitors
of metalloproteases (Chap.25).
10.5 Rigidifying the Backbone by Fixing
Conformations
An important aspect in the design of peptidomimetics is
the peptide conformation. Peptides are exible molecules
and can take on different conformations. It is known,
however, that certain conformations are preferably adopted in proteins and in some peptides. Among these are
the two most important secondary structural elements:
the α-helix and the β-sheet (Sect.14.2). Furthermore,
there are loops and turns at the ends of these secondary
structural elements that also adopt preferred patterns,
particularly the β-turn (. Fig.10.6).
Aβ-turn is formed when ahydrogen bond exists between the carbonyl group of the amino acidi and the NH
group of the amino acid i + 3. It is obvious that such hydrogen bonds can only form for certain combinations of
the torsion anglesφ andψ, which are determined by the
amino acids in the i + 1 and i + 2positions (. Fig.14.6,
Sect.14.2).
β-Turns are especially interesting because many pep-
tides bind to proteins in aβ-turn conformation. Let us
assume that the backbone of the peptide only serves to
position the side chains for optimal receptor interactions.
Then it should be possible to replace the peptide chain
with acompletely different scaffold to which functional
groups are attached that assume the same spatial orientation as the amino acid side chains.
10
Chapter • Peptidomimetics
. Fig. 10.6 Aβ-turn is apeptide conformation in which ahydrogen
bond is formed between the amino acidsi and i + 3. Particular ranges
for the values of the torsion angles φ
acteristic for the β-turn
i+1
, ψ
i+1
, φ
i+2
, and ψ
are char-
i+2
If aβ-turn-congured peptide binds to areceptor,
then arigid analogue that “freezes” the β-turn conformation should lead to improved binding. The simplest
way to x aβ-turn is the incorporation of the necessary
sequence in asmall cyclic peptide. It is known from experimental structure determination that cyclic penta- and
hexapeptides almost always contain aβ-turn. The conformation of these peptides were investigated at length in
the research group of Horst Kessler at the Universities of
Frankfurt and Munich, Germany. It could be shown that
the position of aβ-turn in asequence can be controlled.
Proline as well as d-amino acids prefer the i + 1 position in these loops. The introduction of d-amino acids
supports the formation of aβ-turn above other possible
conformations (cf. Sect.31.2).
Aβ-turn can also be forced by anonpeptide template.
Numerous β-turn mimetics have been proposed for this
(. Fig.10.7). Apart of the structures serves as atemplate on which two peptide chains can be forced in an antiparallel orientation. However, substitution by introduction of the R2 and R3 side chains is synthetically difcult.
Benzodiazepines are interesting scaffolds onto which all
four side chains R1–R4 can be coupled. Other peptide
conformations can also be xed by the introduction of
rigid groups. Afew examples of conformation-stabilizing
ring systems are displayed in . Fig.10.8.
An especially convincing example of a scaffold
mimic is the design of athyrotropin-releasing hormone
(TRH) mimetic by Gary Olson and his colleagues at
Roche in Nutley, New Jersey, USA. TRH is the tripeptide pGlu–His–Pro–NH2 10.3. The approach is shown
in . Fig.10.9. After deducing apharmacophore hypothesis, arigid scaffold molecule was sought upon
which the side chains could be appended in the correct
relative orientation. Cyclohexane was chosen as ascaffold. Compound 10.4 is apotent TRH receptor ligand.
The substance acts as an agonist and elicits the same
effects as TRH. An improvement in cognitive function
could be seen in animal experiments after the administration of 10.4.
. Fig. 10.7 Typical β-turn mimics. The
amino acids are added onto the template
at the red-colored positions
. Fig. 10.8 The illustrated rings replace
one or two amino acids and force aparticular conformation
. • Peptidomimetics to Interfere with Protein–Protein Interactions
. Fig. 10.9 By starting with the structure of tripeptide TRH 10.3
and ahypothesis for the functional groups that are essential for binding, the nonpeptidic molecule 10.4 was designed, which also binds to
the TRH receptor
10.6 Peptidomimetics to Interfere with
Protein–Protein Interactions
Proteins communicate with one another and transmit
information and signals by forming complexes with
each other via commonly shared surfaces. The area of
the shared contact surface usually extends over more
than athousand square Ångstroms (Å2). This is alarge
value when compared to the surface that asmall organic
molecule of typical drug size occupies upon binding.
Furthermore, the contact area between two proteins is,
as ageneral rule, not very jagged. It hardly resembles
the deep binding pockets in enzymes that can host
small ligands. Nevertheless, it would open entirely new
perspectives for drug therapy if such protein–protein
contact surfaces could be blocked with low molecu
lar weight compounds. At rst glance, this task seems
almost impossible. How can asmall molecule bind to
aat, barely structured protein surface with an interaction that is strong enough not to be “washed away” when
the protein–protein contact forms? Furthermore, there
is the problem that amino acid residues on the convex
surface of aprotein have in general much more space
to exibly adapt their conformation. Astatistical analysis of the amino acid composition across the contact
surfaces in protein complexes showed apreference for
aromatic residues, aspartate, arginine and the aliphatic
residues proline and isoleucine. The selective exchange
of amino acids in the contact surface also showed that
there are afew protruding residues that dominate the interaction (so-called “hot spots,” Sect.17.10). The search
for possible binding sites of asmall molecule that can
compete with the formation of the protein–protein interface starts with adetailed analysis of the complementary
geometry to the contacting surfaces. Are there clustered
areas with charged residues or does astructural element
such as aβ-turn or α-helix penetrate alittle more deeply
into the opposite contact surface? Next, the peptide sequence that corresponds to the contact surface is synthesized. This can be portions that preferably adopt
ahelical structure or that can be xed in aturn pattern
such as acyclopeptide. If an active peptide is found, it
must be structurally characterized in complex with the
opposite contact surface.
The complex of the BCL-XL (B-cell lymphoma)
protein with a16-residue peptide that was cut from
the BAK protein is shown in . Fig.10.10. BCL-XL
belongs to the proteins that prevent programmed cell
death (apoptosis). Its function is regulated by binding to
pro- and antiapoptotic factors such as BAK. Inhibitors
of this contact formation might, therefore, deliver potential drugs for an anticancer therapy. The binding of
the helical peptide takes place in astretched-out groove.
Small molecules have been discovered that ll this crevice (. Fig.10.11). The group of Andrew Hamilton at
Yale University, New Haven, USA has been searching
for abasic scaffold that can imitate the characteristics of
ahelix and simultaneously hold the side chains on one
side. Terphenyl derivatives 10.5–10.7 were found that
can arrange the side chains in astaggered conformation
analogous to ahelix. An alanine scan along the BAK
peptide showed that four hydrophobic residues (Val74,
Leu78, Ile81, and Ile85) are essential for binding. In
addition, Asp83 forms asalt bridge to BCL-XL. The terphenyl scaffold was, therefore, furnished with an acidic
group at the end and decorated with alkyl and aryl residues in the ortho-positions. Compound 10.6 binds to the
BCL-XL protein with an afnity of 114 nM.
Adifferent approach was taken at AbbVie. Small
molecules that interact with the BCL protein were
sought by NMR spectroscopy (Sect.7.8). The millimo-
-
lar inhibitors para-uorobiphenylcarboxylic acid 10.8
(. Fig.10.11) and 1-hydroxytetraline 10.9 were discovered. Both bind to distinct but neighboring positions.
They replace Asp83 and Leu78 of the binding domain
of the BAK peptide, and 10.9 occupies the Ile85 position. From the two discovered fragments, the scientists at AbbVie developed compound 10.10, which had
two-digit nanomolar afnity for the protein. Further
optimization led to 10.11, ahighly potent antagonist
that blocks the entire family of antiapoptotic BCL-2
proteins. The synergistic effect of ABT-737 together
with radiation and chemotherapy was demonstrated in
animal experiments. Unfortunately, the bioavailability
of ABT-737 was insufcient. Nevertheless, the clinical
trials were also discontinued for the structurally similar
follow-up compound navitoclax (ABT-263) due to severe side effects.
Chapter • Peptidomimetics
10
. Fig. 10.10 The NMR spectroscopic structure of the BCL-XL pro-
tein with the α-helical, 16-membered peptide fragment from the BAK
protein (blue–gray). The peptide binds in adeep groove with the amino
acids Ile85, Ile81, Leu78, Val74 (from left to right, side chains are
in magenta). The surface of the BCL protein is shown in white, the
An analogous case was studied with the MDM2 protein at Roche. MDM2 is overexpressed in many tumors.
It binds to the tumor-suppressor protein p53, which
protects cells from converting to amalignant state. It
is, therefore, the protein that is most often inactivated
during carcinogenesis. Inhibition of complex formation
between the overexpressed MDM2 protein and p53
could, thus, represent an approach to apossible cancer therapy. Here too, an α-helical p53 peptide stretch
binds to ahydrophobic groove on the MDM2 protein.
Acis-imidazoline with an afnity of 100–300 nM was
found in screening. The cocrystal structure was accomplished with 10.12 (. Fig.10.11). The imidazoline scaffold imitates the side of an α-helix of the peptide from
contact surface of the hydrophobic amino acids of the peptide all protrude into the cleft. (7 https://sn.pub/ooSzpg)
the p53 protein. The two p-bromophenyl rings replace
aTrp and aLeu. The ethyl ether group on the third aromatic ring orients in the pocket that is lled with aphenylalanine in the peptide. The MDM2 protein is blocked
through this competitive binding, and the level of free
p53 increases. Through this, the p53 pathway in cancer
cells is activated, and the cell cycle comes to acomplete
stop. The cell may go into programmed cell death. The
tumor growth inhibition has already been demonstrated
in animal models.
Another large class of proteins that is controlled by
contacts with other proteins is the integrins. Numerous
low molecular weight inhibitors have been discovered
for this class. An example for the successful design of
. • Tracing Selective NK Receptor Antagonists by Ala Scan
. Fig. 10.11 Different inhibitors of protein–protein contacts that
imitate the α-helical structural building blocks in the contact surface.
The terphenyl derivatives 10.5–10.7 bind to the BCL-XL protein in
apronounced crevice and block the binding site of ahelix. The small
antagonists by starting from cyclic peptides is presented in Sect.31.2. Many G-protein-coupled receptors
(Sect.29.1) are controlled by endogenous peptides or
proteins. For this, the peptide or protein bind to the
receptor. The replacement of the peptide sequences with
an organic molecule that imitates the binding of the
natural ligand has also been attempted. An example
of the design of such an active compound is given in
Sects.29.5 and29.6. An example of how small fragments can lead the way to ligands that interfere with
the formation of protein–protein interfaces is shown in
Sect.21.15.
fragments 10.8 and 10.9, which led to the development of inhibitors
10.10 and 10.11 were discovered in the same area during NMR spectroscopic screening. Compound 10.12 is adifferent helix mimetic that
prevents the interaction between the MDM2 and p53 proteins
10.7 Tracing Selective NK Receptor
Antagonists by Ala Scan
Tachykinins are neuropeptides that all contain the same
lipophilic C-terminus: –Phe–X–Gly–Leu–Met–NH2.
A well-investigated representative of the tachykinins
is substanceP, Arg–Pro–Lys–Pro–Gln–Gln–Phe–Phe–
Gly–Leu–Met–NH2 (10.13, . Table10.2). Tachykinins
bind to at least three different tachykinin receptors, the
NK1, NK2, and NK3 receptors. All three belong to the
class of G-protein-coupled receptors (Sect.29.1). They
mediate avariety of biological effects, for example, bron-
Chapter • Peptidomimetics
. Table 10.2 The rational design of NK2 receptor ligands
No. Structure
10
SubstanceP 10.13 Arg–Pro–Lys–Pro–Gln–Gln–Phe–Phe–Gly–Leu–Met–NH
Minimal fragment 10.14 Leu–Gln–Met–Trp–Phe–Gly–NH
Ala scan 10.15 Ala–Gln–Met–Trp–Phe–Gly–NH
10.16 Leu–Ala–Met–Trp–Phe–Gly–NH
10.17 Leu–Gln–Ala–Trp–Phe–Gly–NH
10.18 Leu–Gln–Met–Ala–Phe–Gly–NH
10.19 Leu–Gln–Met–Trp–Ala–Gly–NH
10.20 Leu–Gln–Met–Trp–Phe–Ala–NH
10.21 Leu–Gln–Met–Trp–Phe–NH
Dipeptide 10.22 Z–Trp–Phe–NH
Immobilization of the biologically active conformation
N-Terminal optimization 10.24
Stereochemical optimization 10.25
Addition of amino acid 10.27
Z=benzyloxycarbonyl group
10.23
10.26
Z–Trp–(R,S)–(α–Me)Phe–NH
(2,3-di-OCH3)C6H3CH2OCO-Trp-(R,S)-(α-Me)Phe-NH
(2,3-di-OCH3)C6H3CH2OCO-Trp-(R)-(α-Me)Phe-NH
(2,3-di-OCH3)C6H3CH2OCO-Trp-(S)-(α-Me)Phe-NH
(2,3-di-OCH3)C6H3CH2OCO-Trp-(S)-(α-Me)Phe-Gly-NH
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
295
11.7
40
138
156
> 10,000
8300
28
200
2700
327
37.6
10,000
17.2
1.4
. Fig. 10.12 Important in-
termediates on the way from
the dipeptide 10.22 to the potent NK2 receptor antagonists
10.27
choconstriction or pain transmission. Consequently,
areceptor antagonist could be helpful for the treatment
of asthma as well as to ght pain.
The study conducted at Parke-Davis in Cambridge,
UK, to develop an NK2 receptor antagonist is aclassic
example of the conversion of apeptide into apeptido
mimetic (. Table10.2 and. Fig.10.12). Acompound
was sought that would bind to the same receptor as substanceP. The starting point of the work was ahexapeptide, Leu–Gln–Met–Trp–Phe–Gly–NH
(10.14), known
2
from the literature to bind to the NK2 receptor with
an afnity of 11.7 nM. In arst step, each amino acid
was systematically replaced by alanine (10.15–10.20).
At a few positions, alanine substitution resulted in
only asmall decrease in binding afnity. For example,
the N-terminal leucine could be replaced by an alanine
(10.15). It was concluded that the Leu side chain may be
-
of minor importance for receptor binding. However, the
compound in which tryptophan or phenylalanine was replaced by alanine showed very little afnity for the NK2
receptor. This was clear evidence that these two amino
acids are essential for binding. Removal of the C-ter-
minal amino acid glycine (10.21) decreased the afnity
by afactor of 7. Apparently, this amino acid also has
. • CAVEAT: Idea Generator for the Design of Peptidomimetics
. Fig. 10.13 The optimization of lead structure
10.28, which was found by screening, to selective
NK1 receptor antagonists 10.32 and 10.33. In
contrast to the metabolically labile benzyl esters
10.28–10.32, ketone 10.33 is also active in animal
experiments. The rst NK1 receptor antagonist
aprepitant 10.34 was successfully brought to
the market by MSD for the prevention of acute
emesis
some importance for receptor binding. Testing of several
N-terminal protected dipeptides led to Z–Trp–Phe–NH2
(10.22, Ki = 2700 nM, Z = benzyloxycarbonyl-) as the
lead structure for further work. This completed the rst
phase of the project. As adipeptide, 10.22 was an inter-
esting lead structure for subsequent work.
In the next step, additional methyl groups were introduced at different positions of the molecule. This
restricted the number of possible conformations. Adecrease in binding afnity was observed for many of
the conformationally restricted compounds. Amethyl
group on the Cα-atom of phenylalanine increased the
binding afnity by afactor of8 (10.23, Ki = 327 nM).
Apossible explanation for this nding is that the conformation adopted at the receptor site is stabilized by
the additional methyl group. The N-terminal part of
the molecule was then varied. Replacement of the terminal phenyl ring with a2,3-dimethoxyphenyl group
further increased the binding afnity by afactor of10
(10.24, Ki = 37.6 nM). This value corresponds to racemic α-methylphenylalanine. The enantiomerically pure
compound 10.26 with this moiety in the S-conguration
binds with aKi of 17.2 nM. The reintroduction of the
C-terminal glycine nally led to the highly potent com-
pound 10.27 (Ki = 1.4 nM).
Independent of the work at Parke-Davis, lead structure 10.28 was optimized to the NK1-specic receptor
antagonists 10.32 and 10.33 at Merck Sharp & Dohme
(MSD). Although 10.28–10.32 were only effective in
vitro, 10.33 is also active in vivo because of its higher
metabolic stability (. Fig.10.13). MSD was nally successful with the structurally related aprepitant 10.34.
The compound was introduced as amedicine to prevent
acute emesis (vomiting) during highly nausea-inducing
chemotherapy.
10.8 CAVEAT: Idea Generator for the
Design of Peptidomimetics
In the previous sections, it was often highlighted that
the side chains of the amino acids are responsible for
the binding to receptors. Usually the main chain merely
plays the role of ascaffold that serves to bring the side
chains into the necessary spatial alignment for binding.
Thus, arigid, nonpeptidic scaffold to which the side
chains could be attached in the same spatial orientation
should be suitable for designing molecules with properties similar to those of peptides. This idea has been
implemented in acomputer program in Paul Bartlett’s
group at the University of California at Berkeley, USA.
The program, CAVEAT, allows the search for rigid mol-
ecules that mimic aparticular segment of apeptide backbone. To do this, the bonds on the peptide backbone are
described by vectors (. Fig.10.14). The 3D structure of
the peptide for the peptidomimetic being sought must
be known as aprerequisite. The orientation of the side
chains is determined by the binding vectors Cα–Cβ. The
relative orientation of, for instance, three amino acid side
chains is found by the position of the relevant Cα–Cβ
binding vectors. This spatial pattern of vectors is used
to search a3D database of molecular scaffolds containing three substitutable bonds oriented analogously to the
three Cα–Cβ vectors. The result is alist of rigid, usually
cyclic molecular scaffolds, the free positions of which can
be coupled to the amino acid side chains.