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Me
OH
Ph
R1 O R3 R1 O R3 O O
Me H H
N N HN
N N N N Me
H H H H SO2
O R2 O O R2 O
N
CF3
Overview
1. Background
2. Primary structure modifications
3. Secondary structure modifications
4. Applications to drug design and development
Gretchen Peterson
04/13/01
01-title 4/11/01 7:03 PM
Definitions
Peptidomimetic: A molecule bearing identifiable resemblance to a peptide that,
as a ligand of a biological receptor, can imitate or inhibit the effect of a natural peptide
Isostere: Surrogate functionalities that are isosteric and/or isoelectronic with a peptide amide bond
Agonist: A molecule (natural or synthetic) which imitates the function of a ligand of a biological receptor
Antagonist: A molecule (natural or synthetic) which inhibits the function of a ligand of a biological receptor
Peptide analog: A peptidomimetic where one or more sidechains have been modified
Psuedopeptides: A peptidomimetic where one or more peptide bonds have been replaced with an isostere
Retro-inverso peptide: A linear peptide whose amino acid sequence is reversed and the α-center chirality is inverted
Exo-peptidase: A non-specific enzyme that degrades peptides by sequential hydrolysis of peptide bonds
from either the amino (aminopeptidase) or carboxylic acid (carboxypeptidase) end of an amino acid
Pharmacophore: Structural region of a peptide responsible for interaction with its biological target
Isostere R1 O
H R1 O
R1 O H
N
N N
H N N
N R2 H H
H O
R2 O
F R2
R1 O R3 OH R3
H
N N
N N N N
H H H H
O R2 O O R2 O
2. Poor transport properties from the intestines 2. Addition of hydrophobic residues and/or
to the blood and across the blood-brain barrier replacement of amide bonds results in better
due to high MW and lack of specific transport systems transport properties through cellular membranes.
3. Rapid excretion through the liver and/or kidneys 3. Isosteres, retro-inverso peptides, cyclic
peptides and non-peptidomimetics all reduce the
4. Inherent flexibility enables interaction with multiple rate of degradation by peptidases and other
receptors besides the target, and could result in undesired enzymes.
side-effects
conformational analysis
physical studies
ω: Ni+1 - Ci
• Sequentially substitute D-amino acids and conformationally
α
constrained amino acids for the natural residues in the target. ψ: Ci - C i
• Conformationally restricted amino acids must retain the crucial φ: C αi - Ni
side-chain interactions with the receptor.
α β
χ: C i - C i
• Constrained amino acids can be categorized by the
torsional angles that they restrict in the peptide.
ω: Ni+1 - Ci
α
ψ: Ci - C i
φ: C αi - Ni
α β
χ: C i - C i
β-turns φ2 ψ2 φ3 ψ3
β-sheet
φ = -139 °, ψ = +135 °
R R
H-Tyr-Gly-Gly-Phe-Leu-OH
Enkephalin
Me OH Me OH • When incorporated in a
Me SH
peptidomimetic, these constrained
H 2N amino acids have the potential for
H2N COOH COOH H2N COOH
Me disulfide bond formation or other
cyclizations to furthur rigidify the
α-Methylcysteine α-Methylthreonine D-allo-threonines structure.
Sharpless
Asymmetric OH 1. RuCl3•H2O,
Epoxidation O NaIO4 O CO2Bn
OH
Me 2. DCC, DMAP, BnOH Me
Me 71% y.
> 95% ee 63% y. (2 steps)
1. NaN3, 99% y.
2. PPh3, 83% y.
BF3•OEt2
SAr CO2Bn
Me
HN Me
R= H2N CO2Bn RSH
78% y.
Protected
OMe α-Methylcysteine
Sharpless
Me Asymmetric O Me
HO Me
Dihydroxylation 1. SOCl2
Me OBn Me OBn O 2S
OBn
O
AD-Mix-α OH O 2. RuCl3•H2O, Me
O O
91% y., >98% ee NaIO4, 94% y.
1. NaN3 1. LiBr, 93% y.
• Use of AD-mix-β allows access to all 2. 20% H2SO4 2. 20% H2SO4, 87% y.
the 3R threonine and allo-threonine 87% y.
stereoisomers.
Me OH 1. H2, Pd/C Me OH Me OH
96% y.
Me OBn Me OBn Me OBn
BocHN 2. Boc2O N3 Br
O BuOH, 63% y. O O
α-Methyl Threonine
1. PPh3 1. NaN3
2. Cbz-OSu, 2. H2, Pd/C
DMAP, Pyr. 3. Boc2O
82% y.
Me Me OH
H
BF3•Et2O
Me N Me Cbz N BocHN OBn
OBn
Me Me
BnO Me O
O
NHCbz
O N α-Methyl Allo-threonine
Me
Alkylated Tryptophan
45-70% y. Goodman J. Org. Chem. 1998, 63, 5240-5244
09-a-me synth 2 4/12/01 10:38 AM
α-Methyl Amino Acids and Dipeptides From β-Lactams
1. LiHMDS S-α-Methyldopa
2. BnBr
90% y., >99% ds
i+2 i+3
Ri+2
O
C terminus Ri+1 O
N
i+1 H
HN O HN Ri+3
χ = 0°C
Ri NH O
i
Boc-Val-∆Phe-Phe-Ala-Phe-∆Phe-Val-∆Phe-Gly-OMe
X-Ray Structure Chuhan J. Am. Chem. Soc. 1992, 114, 9225-9226
11-dehydro aa 4/12/01 10:38 AM
β-Methylamino Acids
Me R Me R Me R Me R
NH NH NH NH
Me H R Me Me R H Me
OC H H CO OC H H CO
R H H R
t g– g+ t
H
H
N N • φ is constrained to –65 ± 15°, preventing α-helix
N N formation, and encourages formation of β-turns.
φ R O
O O
O (trans isomer) • Barrier to proline cis-trans isomerism is ~ 2
R (cis isomer) kcal/mol, whereas 2° amide barrier is 10 kcal/mol.
NH
HN
• 2,4-MePro prefers the trans isomer by 6-8 kcal/mol.
2,4-Methanoproline
Proline (Pro) (2,4-MePro)
H-Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-OH
Angiotensin II
OH
PPh3, DEAD
84% y.
O
• Spirolactam combines O
the conformational N O
1. 4N HCl/dioxane
restraints of both proline N N CO2Me
H 2N
and the lactam to fix the 2. Boc-Pro-OH, N
tripeptide in a Type II O DCC, HOBt
β-turn. Boc
N 3. NH3/MeOH
Boc 48% y. (3 steps)
ψ2 O φ3 ψ3
φ2 ψ2 φ3 ψ3
φ2 N O
N
H 2N X-ray structure –50.9 128.7 91.1 –5.4
O ideal Type II β-turn –60 120 80 0
N
Boc
O R S R X R X R
H H H H
N N N N
N N
H H
R O R O R O R O
O R R O R O R
H H H H
N N N N N N
X N
H
R X Y O R O R O R O
N-Methyl amides
• The cis-amide is only 0.6 kcal/mol higher in energy
than the trans isomer.
Me O R3
O N OH
• The increase in flexibility is tempered by the steric
N restrictions imposed by the Me group. ψi-1 is restricted
ψi-1 H to 60<ψ<180 in both the cis- and trans-amide.
R2 O
H 2N R1
Tetrazoles
• The tetrazole locks the amide in a cis configuration,
and is more easily synthesized than a cis-olefin isostere.
N
N N
• Similar or enhanced activity of a tetrazole
R1 N R2 peptidomimetic indicates a cis-amide bond is favorable
for receptor binding.
NH
O • Absence of activity can be due to the increased steric
bulk of the tetrazole, not necessarily that a cis-amide
bond is not the bioactive conformation.
H Rn+3 Rn+1
O NH O
N3
Me O
O
O
ring 3 ring 2 ring 1 stereocenter 4
N3 NH2
H N
• A β-turn is defined as a tetrapeptide sequence where the O
H
CO2H
distance between α-Ci and α-Ci+3 is ≤ 7Å. The turn can be N
H2N CN 1. Hg(OAc)2
CN 2. NaBH4
H CN
H
1. H2, Pd/C 1. O3 H 56% y.
N
N 2. H2, Rh/Al2O3
2. O N
78% y. (4 steps)
O P CN
O
EtO O
1 CN OEt
NH2
Kahn Tetrahedron Lett. 1986, 27, 4841-4844
21-b-turn 2 4/12/01 10:47 AM
β-Turn Mimetics for Solid Phase Synthesis
1. SOCl2, HO
HO • The peptide sequence -Asn-Pro-Asn-Ala- has been
MeOH, 93% y. CO2Me identified as a key target to mimic for developing an
COOH effective malaria vaccine. It is present on the surface of
2. BnOCOCl N H Plasmodium falciparum parasite which is recognized
N H
H Na2CO3, 84% y. Cbz by the human immune system.
PhthN HO
1. PPh3, DEAD O
CO2Me PhthNH, 74% y. CO2Me O
O O
N N
2. H2, Pd/C; NH O
H Ot-Bu separation, 47% y. Cbz Ot-Bu H2N
N
(mixture) OAllyl
1. Fmoc-Asp(OAllyl)-OH, O
DCC, HOAt
2. 5% DBU, 64% y. (2 steps) 1. Tentagel-SAC,
pyridine
O O 2. piperidine, DMF
O O
t-BuO HO
1. MeNHNH2
NH O NH O
PhthN FmocN
N 2. Fmoc-Succ, imidazole N
OAllyl OAllyl
DMAP, 58% y. (2 steps)
O 3. 60% TFA, CH2Cl2, 97% y. O
N O
N H
O
MttHN O HN
O 1. peptide coupling: Me
O HBTU, HOBt, Fmoc-aa, NH O
DIEA, DMF O NH
NH O Me Me
H2N FmocHN
N 2. Fmoc removal:
OAllyl O O
piperidine, DMF O
HN
O 3. repeat sequence N
AllylO HN
O
O
N O
H 1. Pd(PPh3)4, NMM, AcOH, DMF
O N
O 2. piperidine, DMF
H2N HN 3. BOP, DIEA, NMP
• Attachment of this peptidomimetic
to a carrier protein and injection into Me 4. TFA
NH
mice resulted in production of anti- O (Mtt = methyltrityl)
sera to malaria sporozoites. O
Me NH
HN Me
• NMR studies of the macrocycle
indicate the illustrated φ and ψ were ψ
O
O O
in close agreement with a Type I β-turn. HN
H N φ
HN
O
O
OH Robinson Synlett. 1999, 429-441
23-b-turn 4 4/12/01 10:54 AM
Morphine: a Non-peptidomimetic For Enkephalin
Me Ph
R N O O O
N H H
H2N N N
N N OH
OH H H
O O Me
Enkephalin Me
O O HO
HO HO OH
O
OH
• Morphine, one of the oldest known analgesics, binds to the opiate
receptors. Three receptors have been identified: κ, µ, and δ.
Enkephalin is specific for δ, while dynorphin binds to the κ receptor.
O N An endongenous µ peptide ligand has not been identified yet.
HO
H
• Exact nature of the binding interaction between either natural or
Naltrindole synthetic ligand and a receptor has yet to be elucidated.
δ antagonist
H-Tyr-Gly-Gly-Phe-Leu-OH
Enkephalin
R2 R2 Ph
O O O
HN R3 O Me
R1 R3 Me
N R1
O N N
H N
NH NH CO2H
O H-Tyr-Gly-Gly NH
γ-turn 1
Factors affecting binding: ring conformation, dipole, steric fit, hydrogen bonding, hydrophobicity
H-D-Phe-Cys-Phe-D-Trp
Thr(ol)-Cys-Thr-Lys
Octreotide
β-turn
• Octreotide has similar biological activity to
3.2 Å
somatostatin and is a drug of first choice for the
treatment of several carcinoid syndromes.
Thr(ol) = L-threoninol
X-ray Structure
of Octreotide
Synthesis: Pless Life Sci. 1982, 31, 1133-1140
X-ray: Sheldrick Acta. Cryst. D 1995, 48-59
a
a NH
O
H 8 (D) O O
N
N 7
NH
b
H
N OO R2 O
O
H NH b
O 11 10 N 9 O O
N NHR1
d H
c
O d
Me OH
c 1: R1 = R2 = H
NH2
2: R1 = CH3CO, R2 = OCH2Ph
L-363,301
G-Protein
Coupled
Receptor Distance (Å)
Biological Activity (IC50, µM)
a-b a-c a-d b-c b-d c-d
L-363,301 1 2
L-363,301 7.1 11.3 9.2 7.3 9.2 14.1
somatostatin 0.001 15 1.3 2 5.6 10.6 8.0 6.6 10.3 13.5
low conc.: agonist agonist
high conc.: antagonist (all conc.) • Computer modeling, combined with previous
___ biological studies of somatostain peptidomimetics, led
β2-adrenergic 3 to the design of a glucose-based non-peptidomimetic.
antagonist
• Glucose shows promise in development of
NK1 0.18 0.06 non-peptidomimetics for several G-protein coupled
agonist antagonist receptors, but selectivity must be fine-tuned for the
desired activity.
Ph
• Thrombin is a serine protease that promotes blood
N H O coagulation by cleavage of fibrinogen to the active protein fibrin.
N N Contraction and dilation of blood vessels are also affected.
H
O Antagonists could be theraputic in treating arteriosclerosis and
O
thrombosis.
Fibrinogen • Early antagonist design focused on non-hydrolyzable
target sequence
transition state mimetics of the -Phe-Pro-Arg- sequence
NH adjacent to the substrate cleavage site.
HN
NH2
Ph Ph Ph
N H OH Ph O 2S N H
H 2N N N N
B H
O O OH O O
A Ki = 3.6 pM B Ki = 2.5 pM
NH
H2N
HN
NH2
O
NH O O H
O S N
B H N N
N H
S N O
O O
HO2C Me
HN
C Ki = 39 nM HN D Ki = 6.6 nM
HN NH2
NH2
Me O O
O H H
• Can you assume D is binding in the same
S N N
pocket as the fibrinogen substrate does? N N
H
Me O
• X-ray structural studies indicate C and D
bind to a different site in the enzyme through O Me
Me
their hydrophobic residues,which causes Me
collapse of the active site pocket. Enzymatic
activity is thereby inhibited.
E HN
NH2
more potent than D
• developed by using a
H bioactive template (glucose)
N
O and altering the periphery to Ki = 13 nM
NH give desired activity. Angew. Selectivity
N Chem. Int. Ed. Eng. 1997, 36, Me Me over trypsin:
NH2 751-752. >760:1
H
O
N
O
N
Ki = 0.5 µM
O H
• HCl
OH
H-Ala-Ala-NH Val-Val-OMe
Me
OH
OH Ph
S Optimization
Ph O O
Me HN
Ph O O SO2
Lead Structure
PNU-140690 N
IC50 = 3 µM IC50 = 2.7 nM
CF3
• Lead found in a high volume library screen
at Pharmacia & Upjohn in 1994. The pyrone
inhibits HIV-1 protease but has no anti-viral activity.
O O O
n-BuLi, THF, -78 °C Me
O NH O N
O
Ph Me Ph
Cl
MgBr
2. Na2CO3, BnBr,
H2O, CH2Cl2
78% y. (2 steps)
Me
Me 1. TiCl4; O O
O
Hunig's Base;
N(Bn)2 O N
Me
MeO Ph
O Xa OMe
O N(Bn)2
O
2. Aq. HClO4
95% y. (2 steps)
Ti(On-Bu)Cl3,
Me Me
CH2Cl2, -78 °C; Me
O Hunig's Base; OH O
N(Bn)2
Me N(Bn)2
Ph
O
O Xa
O Xa
Ph
Me 62% y.
dr = 25:1
Ph Me
OH
O O 1. H2, Pd/C Ph N(Bn)2
Me HN
SO2
O O
2. SO2Cl
N
PNU-140690 Me
N
9 steps, 24% overall y. F 3C
CF3
pyr., CH2Cl2
81% y.
Gammill J. Am. Chem. Soc. 1997, 119, 3627-3628
Et Et Et
isoprenyl
acetate
Amano P30 1. MsCl EtO2C
HO HO
50% y. 2. EtO R
>98% ee CO2Et
NO2 NO2 ONa NO2
(separated
86% R = CO2Et
by chromatography) 6N HCl
R = H (2) 87% y.
(2 crystallized as the
cyclohexamine salt)
Me O Et
OH
O
2, NaHMDS, THF, -80 °C
Ph Ph
CO2Me
90% y. OPOM
Me NO2
(unpurified)
1. PCC, 99% y.
2. H2SO4, 84% y.
Me 3. NaOH, MeOH, 75% y.
OH
Ph
Et
OH
O O 1. H2, Pd/C, quant.
Me HN Ph
(precipitation) SO2
2. SO2Cl O O
N NO2
Me
N
F 3C (recrystallized)
Tapranavir
CF3 pyr., CH2Cl2
13 steps, 4% overall y. 78% y.
HO OH 1. Set of likely O
O Biological Dock analogs
assays inhibitors
of structure
HN NH
N N
2. Prediction of how
stereocenters will R R
affect binding, and into HIV protease
Ph Ph thereby activity. dimer X-ray structure OH
HO OH HO
IC50 = 36 nM
4. Biologically active mimetics support the existence of the desired element being
present in the receptor-bound conformation of the peptide. However, the binding
site of an antagonist may be different than active site, where the native peptide is
bound.
5. Mimetics are usually designed based on analogy to the native peptide structure,
then optimized to give the best possible pharmacokinetic properties.
Giannis, A.; Rubsam, F. Adv. Drug. Res. 1997, 29, 1-78 Excellent coverage of design principles
and recent examples of the major classes of
non-peptidomimetics
Gante, J. Angew. Chem. Int. Ed. Eng. 1994, 33, 1699-1720 Overview of peptide isosteres and review of
Giannis, A.; Kolter, T. Angew. Chem. Int. Ed. Eng. 1993, 32, 1244-1267 peptidomimetics designed for specific biological receptors
Goodman, M.; Ro, S. Burger's Medicinal Chemistry and Drug Comprehensive coverage of constrained
Discovery. Ed. M. E. Wolff. New York, John Wiley & Sons, Inc.; amino acids and peptide isosteres
1995, 803-861.
Liskamp, R. M. J. Recl. Trav. Chim. Pays-Bas 1994, 113, 1-19 Thorough compliation of constrained amino acid
syntheses and secondary structure mimetics
Ripka, A. S.; Rich, D. H. Curr. Opin. Chem. Bio. 1998, 2, 441-452 Most recent coverage of biologically
active peptidomimetics
Fauchere, J.-L.; Thurieau, C. Adv. Drug. Res. 1992, 23, 127-159 Review of peptidomimetic biological stability
Marshall, G. R. Tetrahedron 1993, 49, 3547-3558 Concise explanation of peptidomimetic design process
Hirshmann, R. Angew. Chem. Int. Ed. Eng. 1991, 30, 1278-1301 Overview of medicinal chemistry with a section on the
beginning of peptidomimetics