This document provides an overview of peptidomimetics. It begins with the evolution of peptidomimetics and how they were developed to overcome limitations of peptides as drugs. It then covers classification of peptidomimetics, design strategies like modifying amino acids and imposing structural constraints, and examples of peptidomimetic drugs that inhibit enzymes like ACE, thrombin, and HIV protease. The document concludes by stating peptidomimetics are an important area of drug design for developing small molecule mimics of peptide functions.

1. PEPTIDOMIMETICS
PRESENTED BY:
MAHENDRAG. S
M.Pharm
Pharmaceutical
Chemistry,JSSCP. MYSURE

2. CONTENT:
• Evolution of peptidomimetics
• Introduction to peptidomimetics
• Classification
• Design of peptidomimetics
• Examples of peptidomimetic drug
• Conclusion
• Reference

3. EVOLUTION OF PEPTIDOMIMETICS
• Proteins control all functions in living organisms either enzyme catalysis, cell
signalling, ligand binding and many other functions.
• The function of protein is largely controlled by protein-protein interactions the
disruption of which forms the basis of many diseases either the loss of essential
interactions or by undesirable interaction or through host pathogen interaction.
• These protein-protein interactions can be mediated through the use of peptides.
• It is estimated that 15% and 40% of all cellular interactions are controlled by protein
–peptide interactions.
• Insulin was the first peptide discovered and administered therapeutically since 1922.

4. Contd….
• Peptides as a class of drugs cover a broad range of pathologies, used in treatment of
diabetes, gastro intestinal disorders, osteoporosis, cancers, bacterial and fungal
infections.
• These peptides generally cannot be used as good drugs due to their unfavourable
physicochemical properties and also due to poor bioavailability, low solubility, low
stability towards hydrolysis and poor membrane permeability.
• however research is ongoing to improve bioavailability of these peptides primarily
to enhance absorption and bioavailability through a novel delivery system.
•Even after several works their use was limited due to their flexibility.

5. • These requirements are all matched in the development of peptidomimetics. In this
approach, peptides and proteins are considered as tools for the discovery of other
classes of compounds.

6. INTRODUCTION:
• Since the early 1990s the goal of finding small drug like molecules that mimic peptide
function has emerged as leading area of drug design.
• A peptidomimetic compound may be defined as a substance having a secondary
structure, besides other structural features, similar to native peptide, such that it binds
to enzymes or receptors with higher affinity than the starting peptide.
• Peptidomimetics are the non peptide structures which replace portions of peptide in
order to increase the efficacy of the peptide.
• As an overall result, the native peptide effects are inhibited (antagonist or inhibitor) or
increased (agonist).

7. The development of peptidomimetics is based on knowledge of the electronic and
conformational features of the native peptide and its receptor or active site of an enzyme.
Thus, the development of peptidomimetics as compounds with potential biological activity
must take account of some basic principles:
• Replacement of peptide back bone with a non-peptide framework
• Preservation of side-chains involved in biological activity, as they constitute the
pharmacophore.
• In the development of second-generation mimetics, several modifications may be
introduced to improve biological activity, including chain length modification, introduction
of constraints, cyclopeptide bond replacement with a covalent one and introduction of
isosteric replacements.
• Maintenance of flexibility in first-generation peptidomimetics.
• Selection of proper targets based on pharmacophore hypothesis

8. Classification of peptidomimetics
Peptidomimetics may be divided into four different classes depending on their
structural and functional characteristics:
Type I mimetics or structural mimetics: These show an analogy of a local topography
with the native substrate, and they carry all the functionalities responsible for the
interaction with an enzyme or a receptor in a well-defined spatial orientation. Some
units mimic short portions of secondary structure (e.g., p-turns) and have been used to
generate lead compounds. Many early protease inhibitors were designed from
transition state analog mimetics or from collected substrate/product mimetics. These
are mimics of the peptide bond in a transition state or product state and will be classified as
pseudo peptidomimetics

9. • Type II mimetics, or functional mimetics:
Here the analogy with the native compound is based on the interaction with the target
receptor or enzyme, without apparent structural analogies which is a small non-peptide
molecule that binds to a peptide receptor. Morphine was the first well-characterized example
of this type of peptidomimetic.
• Type III mimetics or functional-structural mimetics:
These are synthesized by structure based drug design which represents that they possess
novel templates which are unrelated to native peptide but contain essential groups on a novel
non peptide scaffold to serve as topographical mimetics. Several type III peptidomimetic
protease inhibitors have been characterized.
• Recently, a fourth type of peptidomimetic called a GRAB-peptidomimetic (group
replacement-assisted binding) has been identified. These structures might share structural-
functional features of type I peptidomimetics, but they bind to an enzyme form not
accessible with type I peptidomimetics.

11. PEPTIDE SECONDARY STRUCTURE
An important goal in the development of mimics is to restrict the backbone and side
chain moiety into a bioactive conformation while reducing the affinity for proteolytic
enzyme. Such secondary protein structures are defined by their ɸ(phi), Ψ(psi) and
ω(omega) angles, while side chain geometry is defined by Χ(chi) space.
• The angle Phi φ is present at the C alpha to
Nitrogen of amino group in the
polypeptide
• The angle Psi ψ is present at the C alpha
to carbon of carboxylic group in the
polypeptide.
• The angle ω is present at the nitrogen and
carbonyl group.

12. • α-helix is the most common peptide secondary structure. α-helices are characterised by the
presence of hydrogen bond between the first residue carbonyl oxygen and fifth residue NH
hydrogen.
• β-turns are a class of reverse turn and change the orientation of peptide by 180 degrees.
β-turns are characterised by the presence of hydrogen bond between carbonyl oxygen and
amide protein residues and form a ring structure.
β-helix α-helix

13. DESIGN OF PEPTIDOMIMETICS
• A major effort in peptidomimetic chemistry is connected to the development of
compounds capable of replacing one or more amino acids in a peptide sequence
without altering the biological activity of the native peptide.
• Access to novel amino acids as peptide isosteres has been pursued by:
o either modifying the atoms involved in backbone formation of a peptide or in
manipulating the side-chain moiety, for example by introducing chemical tethers as
rigidifying elements.
o Moreover, peptidomimetic chemistry has been oriented to the development of higher
isosteres, taking into account di-, tri- or tetrapeptides motifs to be replaced by more
complex molecular architectures.
o Finally, the approach to intervening in terms of the overall peptide structure has been
accessed by working on global restrictions of the native peptide conformation.

14. Modification of Amino Acids
• Manipulation of the peptide structure with aim of reducing molecular recognition by
proteases and of introducing conformational restrictions is achieved locally by
intervening on either backbone or side-chains by introduction of modified amino acids.
• Accordingly, a well-established approach is to replace proteinogenic amino acids locally
and systematically with their corresponding d-variants, Cα-alkylated, Cβ-alkylated or
Nα-alkylated amino acids.
For example, substitution of α- aminocycloalkane carboxylic acids varying in ring size
into various positions of enkephalin (H-Tyr-Gly-Gly-Phe-Leu-OH),a peptide responsible
for modulating pain response, resulted in a peptidomimetic with greater in vivo activity.

15. Amino acid mimemtics

16. • β-Methylamino acids have been reported for restricting the conformations of a bioactive
peptide through the insertion of stereocenter at theβ-position. Indeed, four configurations
are accessible by varying the two stereocenters;
an example to this approach, the systematic incorporation of β-Me Phe into somatostatin
peptidomimetics has resulted in a model for the ligand–receptor interaction, based on the
changes in activity induced by different configurations at the β centre.
• Proline analogues have been proposed with the aim of orienting the equilibrium towards
preferred geometry, generally the cis form owing to its importance in peptide folding. This
has been approached by varying the ring size, the substitution pattern around the cyclic
backbone and introducing heteroatoms.
For example, the substitution of 5,5-dimethylthiazolidine-4-carboxylic acid(Dtc) for Pro
in angiotensinII, resulted in a peptidomimetic with 39% greater agonist activity than the
natural peptide.

17. • More complex local modifications have considered the introduction of dipeptide isosteres,
with aim of mimicking amide bond and side-chains with suitable chemical moieties. The
dipeptide fragment is commonly addressed with cyclic compounds possessing chemical
tethers for imposing restricted conformations. In addition, retro-inverso isomeric moieties,
double bond fragments and cyclic cis-amide bond isosteres have been proposed with aim of
replacing the amide bond without altering the topology of the adjacent side chains of the
corresponding dipeptide.

18. Mimicking the peptide backbone:
• Although there are quite a number of amide bond replacements reported, the most
widely used surrogates, namely aminomethylene, oxomethylene, thiomethylene,
ketomethylene, ester, sulfoxide, sulfonamide, thioamide, (E)-alkene, tetrazole, other
heterocycles, and surrogates such as beta-amino acids, aaminophosphinicacids, and
phosphonamidates.
• These surrogates has its own unique physicochemical properties that need to be
considered before incorporation into a peptide chain.

20. Compounds with Global Restrictions
•The introduction of global restrictions into the peptide by cyclization of the peptide strand
typically results in a higher in vivo stability of the cyclic peptidomimetics compared to their
linear analogues.
• The introduction of rigid bridges of varying lengths in different parts of peptide can improve
potency by fixing torsion angles or side chain orientation, locking the ligand into the preferred
bioactive conformation.
•The cyclization strategies can be classified with respect to backbone and side-chains according
to the chemical moieties used for the introduction of the constraint. Cyclization between
backbone elements is approached in several ways:

21. • by tethering two amide nitrogen atoms with a linker (backbone to backbone);
• by introducing a chemical junction between a Cα and a nitrogen atom (backbone to
backbone);
• by linking a N-terminal amino group with an amide nitrogen atom with a spacer (head to
backbone);
• by cyclizing the two N- and C- terminal ends of a peptidomimetic structure with an
amide bond (head-to-tail);
The latter is by far the most popular approach for the generation of acyclic
peptidomimetics.
Specifically, cyclization is achieved by exploiting basic amino acid residues for the
formation of an amide bond or by taking advantage of cysteine amino acids for the
development of cyclic peptidomimetics through disulfide bridges between the two side-
chains.

22. GRB2 Cyclic analogue
Peptidomimetic was designed as a ligand for growth factor receptor bound protein 2
(GRB2) by ring closing metathesis. The macrocycle stabilises the bent conformation
required for binding to increase the affinity by 140 fold.

23. Examples of Peptidomimetic Drugs
The most successful application of the concept of peptidomimetics in drug discovery is
in the development of enzyme inhibitors. In this field, proteases have been found as an
attractive therapeutic target for several pathologies, as they are crucial for a number of
processes, including the regulation of peptide hormones and neuromodulators through
proteolytic activation of inactive precursors.
The most representative entries to peptidomimetic drugs acting as protease inhibitors
are illustrated by angiotensin-converting enzyme (ACE) inhibitors, thrombin inhibitors
and human immunodeficiency virus (HIV) protease inhibitors and many others.

24. ACE Inhibitors
ACE inhibitors are an important class of drugs that are used in the treatment of
hypertension. Specifically, renin, an endoprotease of the aspartic acid proteases family,
cleaves the angiotensinogen peptide to produce the biologically inactive decapeptide
angiotensin I. Such a peptide is successively cleaved at the C-terminal by ACE, which
removes a dipeptide fragment to give the bioactive octapeptide angiotensin II, which
has strong hypertensive properties by inducing vasoconstriction and augmenting the
levels of aldosterone, which in turn promotes the retention of water and sodium ion,
ultimately resulting in the increase of blood pressure.
ACE is a metalloprotease possessing a Zn ion in the active site, and has been the starting
point for the identification of ACE inhibitors. Subsequent studies to identify the
fragments responsible of the inhibition allowed for the identification of the Ala-Pro
dipeptide unit as the pharmacophore. Two different elaborations of this dipeptide
resulted in two different ACE inhibitors, namely, captopril and enapril.

25. • Captopril resulted from matching the structure of the Ala-Pro unit with that of alkyl-
succinic acids. Thus, replacement of the amino group of Ala with an acetyl group resulted
in the corresponding α-methylsuccinylproline, which demonstrated major inhibition with
respect to Ala by a factor of 100 due to improved coordination of the second carboxylic
group with the zinc ion. Indeed, further improvement of such interaction resulted in the
development of captopril, which has a SH group in place of the carboxy unit, thereby
possessing stronger coordinating activity towards the metal ion.
• Enapril resulted from the addition of a carboxyalkyl group to the nitrogen atom of Ala. In
this case, the improved inhibition was due to a hydrophobic interaction between the
phenylethyl group at the nitrogen atom of Ala with active site.

27. THROMBIN INHIBITORS
Thrombin and Factor Xa are both serine proteases involved in the blood coagulation
cascade. Inhibition of these two enzymes provides novel anticoagulants.
The peptidomimetic approach resulted in the design and synthesis of a large array of
compounds mimicking the fibrinogen sequence that interacts with the thrombin active
site. Specifically, starting from the tripeptide fragment Phe-Pro-Arg of fibrinogen, which
is recognized by the catalytic triad within the site of thrombin, several compounds have
been developed with varying degree of mimetism. Replacement of the carboxylic end at
the Arg amino acid with boronic acid resulted in a marked improvement in inhibition,
taking advantage of the tetrahedral intermediate. The observation that the simple N-
tosyl-arginine methyl-ester retained inhibition activity allowed development of the
highly potent peptidomimetic drug argatroban by replacing the methyl ester with a
pipecolic acid moiety. Other thrombin inhibitors are ximelagtaran, dabigatran.

29. Other type lll peptidomimetic inhibitors of thrombin have been developed from screening
leads such as inhibitors(1). SAR led to the design of (2) Inhibitor (3) was derived from
docking studies with the 5-amidino indole nucleus, followed by addition of a lipophilic side-
chain to interact with the important S , subsite of thrombin. The crystal structures of both
(2) and (3) in the active site of thrombin shows that the aromatic core, binds in the S, site as
expected, but does not pick up hydrogen bonding from the important active site sequence
Ser214- Gly216. Both crystal structures showed a similar binding mode; where interaction
was between C-2 side-chain with Trp which explain the high thrombin selectivity.
1 2 3

30. HIV PROTEASE INHIBITORS
Type-I HIV protease inhibitors, Saquinavir, ritonavir, Indinavir, Amprenavir, Viracept and
Lopinavir are established drugs for the treatment AIDS. All these inhibitors employ the
centraI hydroxyl transition state mimetic as a scaffold on which varying functionality
was systematically added until the required balance between potency, in vivo activity
and oral orption was achieved. In general, the binding interactions were optimized
through synthesis and co-crystallization of inhibitor with enzyme, molecular modeling,
and redesigning the inhibitor side-chains.

32. Another approach to achieve greater in vivo activity is to start with a molecular template
with proven useful pharmacokinetics and oral bioavailability and to selectively modify it to
achieve the desired activity. Identification of the orally active anticoagulant warfarin as a
weak inhibitor of HIV protease was followed by two reports of 4-hydroxycoumarins as
possible type lll HIV inhibitors. Subsequent SAR studies led to the more potent 5,6-dihydro-
4-hydroxy-3-pyrone inhibitior, which has good anti-viral activity and is orally bioavailable.

33. Ras-Farnesyltransferase Inhibitors
Inhibitors of Ras-farnesyltransferase have been developed by mimicking the C-terminal
CAAX motif (where C is a cysteine residue, A is any aliphatic amino acid, and X is usually
Met, Ser, or Ala). This tetrapeptide is the signal for farnesylation of Ras proteins. Ras-
farnesyltransferase is one of the most promising targets for novel anti-cancer drugs,
because at least 30% of the human cancers contain mutated Ras.
Two types of peptidomimetic structures have been used to develop inhibitors. Some
typical type I inhibitors were generated by replacing the amide backbone with different
isosteres like the oxymethylene amide bond in (1). The central dipeptide segment of
CA,A,X has been replaced with rigid linkers like the 3-aminomethylbenzoic acid (AMBA)
in (2). This novel inhibitor was not farnesylated, showing that the two amino acids in
the middle of the CAAX tetrapeptide are required for farnesylation. An imidazole group
has been used to replace the thiol group of the CAM motif to produce compound (3).

34. 1 2
3

35. Intrduction of conformational restriction of a reduced isostere of the parent peptide
substrate, followed by systematic replacement of the peptide like side-chains provided the
potent non- peptidic inhibitor.

36. Type lll peptidomimetic inhibiyors

37. CONCLUSION
Several decades after the introduction of the concept of peptidomimetics, this
approach in drug discovery is still timely, owing to the never-ending interest in new
compounds based on peptides and proteins. Besides the development of
biotechnological therapeutics based on antibody-derived compounds, the field of small
molecules encompassing the whole region of peptide drugs is still covered by the
generation of peptidomimetics, with the aim of obtaining hit compounds that possess
optimal bioactivity and pharmacokinetics profile. During recent decades the basic
concepts and approaches to peptidomimetic compounds have evolved to cover diverse
compounds and synthetic strategies spanning from combinatorial chemistry to solid-
phase synthesis and heterocyclic chemistry.

38. REFERENCE
 Burger’s drug discovery and medicinal chemistry 6th edition vol-1 pg.no-633-686
 Peptidomimetics in Organic and Medicinal Chemistry: The Art of Transforming
Peptides in Drugs, First Edition. Andrea Trabocchi and Antonio Guarna. © 2014 John
Wiley & Sons, Ltd. Published 2014 by John Wiley & Sons, Ltd.
Peptidomimetics for drug design by M.Angels estiarate Daniel H.Rich.
Peptidomimetics and pro drug design by Hugo Kubinyi Germany
Peptidomimetics and peptide backbone modifications:Jung-MOAhn, Nicholas A. Boyle,
Mary T. MacDonald and Kim D. Janda.S