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The Strategy of Peptide The Strategy of Peptide Synthesis Synthesis

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Page 1: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Strategy of Peptide SynthesisThe Strategy of Peptide Synthesis

Page 2: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

General ConsiderationsGeneral Considerations

Making peptide bonds between amino acids is Making peptide bonds between amino acids is not difficult.not difficult.

The challenge is connecting amino acids in the The challenge is connecting amino acids in the correct sequence.correct sequence.

Random peptide bond formation in a mixture of Random peptide bond formation in a mixture of phenylalaninephenylalanine and and glycineglycine, for example, will give , for example, will give four dipeptides.four dipeptides.

PhePhe——PhePhe GlyGly——GlyGly PhePhe——Gly Gly GlyGly——Phe Phe

Page 3: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

General StrategyGeneral Strategy

1.1. Limit the number of possibilities by Limit the number of possibilities by "protecting" the nitrogen of one amino acid "protecting" the nitrogen of one amino acid and the carboxyl group of the other.and the carboxyl group of the other.

N-ProtectedN-Protectedphenylalaninephenylalanine

C-ProtectedC-Protectedglycineglycine

NNHCHCOHHCHCOH

CHCH22CC66HH55

OO

XX HH22NNCHCH22CC

OO

YY

Page 4: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

General StrategyGeneral Strategy

2.2. Couple the two protected amino acids.Couple the two protected amino acids.

NNHCHHCH22CC

OO

YYNNHCHCHCHC

CHCH22CC66HH55

OO

XX

NNHCHCOHHCHCOH

CHCH22CC66HH55

OO

XX HH22NNCHCH22CC

OO

YY

Page 5: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

General StrategyGeneral Strategy

3.3. Deprotect the amino group at the N-terminus Deprotect the amino group at the N-terminus and the carboxyl group at the C-terminus.and the carboxyl group at the C-terminus.

NNHCHHCH22COCO

OO

HH33NNCHCCHC

CHCH22CC66HH55

OO++ ––

Phe-GlyPhe-Gly

NNHCHHCH22CC

OO

YYNNHCHCHCHC

CHCH22CC66HH55

OO

XX

Page 6: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Amino Group ProtectionAmino Group Protection

Page 7: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Amino groups are normally protected by Amino groups are normally protected by converting them to amides.converting them to amides.

Benzyloxycarbonyl (CBenzyloxycarbonyl (C66HH55CHCH22O—) is a common O—) is a common

protecting group. It is abbreviated as protecting group. It is abbreviated as ZZ..

ZZ-protection is carried out by treating an amino -protection is carried out by treating an amino acid with benzyloxycarbonyl chloride.acid with benzyloxycarbonyl chloride.

Protect Amino Groups as AmidesProtect Amino Groups as Amides

Page 8: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Protect Amino Groups as AmidesProtect Amino Groups as Amides

CHCH22OCClOCCl

OO

++ HH33NNCHCOCHCO

CHCH22CC66HH55

OO

––++

1. NaOH, H1. NaOH, H22OO

2. H2. H++

NNHCHCOHHCHCOH

CHCH22CC66HH55

OO

CHCH22OCOC

OO

(82-87%)(82-87%)

Page 9: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Protect Amino Groups as AmidesProtect Amino Groups as Amides

NNHCHCOHHCHCOH

CHCH22CC66HH55

OO

CHCH22OCOC

OO

is abbreviated as: is abbreviated as:

ZZNNHCHCOHHCHCOH

CHCH22CC66HH55

OO

or Z-Pheor Z-Phe

Page 10: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

An advantage of the benzyloxycarbonyl An advantage of the benzyloxycarbonyl protecting group is that it is easily removed by:protecting group is that it is easily removed by:

a) hydrogenolysisa) hydrogenolysis

b) cleavage with HBr in acetic acidb) cleavage with HBr in acetic acid

Removing Z-ProtectionRemoving Z-Protection

Page 11: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Hydrogenolysis of Z-Protecting GroupHydrogenolysis of Z-Protecting Group

NNHCHCHCHCNNHCHHCH22COCO22CHCH22CHCH33

CHCH22CC66HH55

OO

CHCH22OCOC

OO

HH22, Pd, Pd

HH22NNCHCCHCNNHCHHCH22COCO22CHCH22CHCH33

CHCH22CC66HH55

OO

CHCH33 COCO22

(100%)(100%)

Page 12: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

HBr Cleavage of Z-Protecting GroupHBr Cleavage of Z-Protecting Group

NNHCHCHCHCNNHCHHCH22COCO22CHCH22CHCH33

CHCH22CC66HH55

OO

CHCH22OCOC

OO

HBrHBr

HH33NNCHCCHCNNHCHHCH22COCO22CHCH22CHCH33

CHCH22CC66HH55

OO

CHCH22BrBr COCO22

(82%)(82%)

++

BrBr ––

Page 13: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The The tert-tert-Butoxycarbonyl Protecting GroupButoxycarbonyl Protecting Group

NNHCHCOHHCHCOH

CHCH22CC66HH55

OO

(CH(CH33))33COCCOC

OO

is abbreviated as: is abbreviated as:

BocBocNNHCHCOHHCHCOH

CHCH22CC66HH55

OO

or Boc-Pheor Boc-Phe

Page 14: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

HBr Cleavage of Boc-Protecting GroupHBr Cleavage of Boc-Protecting Group

NNHCHCHCHCNNHCHHCH22COCO22CHCH22CHCH33

CHCH22CC66HH55

OO

(CH(CH33))33CCOCOC

OO

HBrHBr

HH33NNCHCCHCNNHCHHCH22COCO22CHCH22CHCH33

CHCH22CC66HH55

OO

COCO22

(86%)(86%)

++

BrBr ––CHCH22CC

HH33CC

HH33CC

Page 15: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Carboxyl Group ProtectionCarboxyl Group Protection

Page 16: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Carboxyl groups are normally protected as Carboxyl groups are normally protected as esters.esters.

Deprotection of methyl and ethyl esters isDeprotection of methyl and ethyl esters isby hydrolysis in base.by hydrolysis in base.

Benzyl esters can be cleaved byBenzyl esters can be cleaved byhydrogenolysis.hydrogenolysis.

Protect Carboxyl Groups as EstersProtect Carboxyl Groups as Esters

Page 17: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Hydrogenolysis of Benzyl EstersHydrogenolysis of Benzyl Esters

HH22, Pd, Pd

HH33NNCHCCHCNNHCHHCH22COCO

CHCH22CC66HH55

OO

CC66HH55CHCH33 COCO22

(87%)(87%)

NNHCHCHCHCNNHCHHCH22COCOCHCH22CC66HH55

CHCH22CC66HH55

OO

CC66HH55CHCH22OCOC

OO OO

++ ––CHCH33CC66HH55

Page 18: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Peptide Bond FormationPeptide Bond Formation

Page 19: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The two major methods are:The two major methods are:

1. coupling of suitably protected amino acids 1. coupling of suitably protected amino acids using using NN,,N'N'-dicyclohexylcarbodiimide (DCCI)-dicyclohexylcarbodiimide (DCCI)

2. via an 2. via an active esteractive ester of the N-terminal amino of the N-terminal amino acid.acid.

Forming Peptide BondsForming Peptide Bonds

Page 20: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

DCCI-Promoted CouplingDCCI-Promoted Coupling

ZZNNHCHCOHHCHCOH

CHCH22CC66HH55

OO

++ HH22NNCHCH22COCHCOCH22CHCH33

OO

DCCI, chloroformDCCI, chloroform

ZZNNHCHCHCHC

CHCH22CC66HH55

OO

NNHCHHCH22COCHCOCH22CHCH33

OO

(83%)(83%)

Page 21: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Mechanism of DCCI-Promoted CouplingMechanism of DCCI-Promoted Coupling

ZZNNHCHCOHHCHCOH

CHCH22CC66HH55

OO

++ CC66HH1111NN CC NCNC66HH1111

CHCH22CC66HH55

OO

CC66HH1111NN CC

CC66HH1111NN

HH

OCCHOCCHNNHZHZ

Page 22: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Mechanism of DCCI-Promoted CouplingMechanism of DCCI-Promoted Coupling

CHCH22CC66HH55

OO

CC66HH1111NN CC

CC66HH1111NN

HH

OCCHOCCHNNHZHZ

The species formed by addition of the Z-The species formed by addition of the Z-protected amino acid to DCCI is similar in protected amino acid to DCCI is similar in structure to an acid anhydride and acts as an structure to an acid anhydride and acts as an acylating agent.acylating agent.

Attack by the amine function of the carboxyl-Attack by the amine function of the carboxyl-protected amino acid on the carbonyl group protected amino acid on the carbonyl group leads to nucleophilic acyl substitution.leads to nucleophilic acyl substitution.

Page 23: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Mechanism of DCCI-Promoted CouplingMechanism of DCCI-Promoted Coupling

HH22NNCHCH22COCHCOCH22CHCH33

OO

CC66HH1111NN CC

CC66HH1111NHNH

HH

OO ++ ZZNNHCHCHCHC

CHCH22CC66HH55

OO

NNHCHHCH22COCHCOCH22CHCH33

OO

CHCH22CC66HH55

OO

CC66HH1111NN CC

CC66HH1111NN

HH

OCCHOCCHNNHZHZ

Page 24: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

A A pp-nitrophenyl ester is an example of an "active -nitrophenyl ester is an example of an "active ester."ester."

pp-Nitrophenyl is a better leaving group than -Nitrophenyl is a better leaving group than methyl or ethyl, and methyl or ethyl, and pp-nitrophenyl esters are -nitrophenyl esters are more reactive in nucleophilic acyl substitution.more reactive in nucleophilic acyl substitution.

The Active Ester MethodThe Active Ester Method

Page 25: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Active Ester MethodThe Active Ester Method

ZZNNHCHCHCHCOO

CHCH22CC66HH55

OO

++ HH22NNCHCH22COCHCOCH22CHCH33

OO

NONO22

Page 26: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Active Ester MethodThe Active Ester Method

ZZNNHCHCHCHCOO

CHCH22CC66HH55

OO

++ HH22NNCHCH22COCHCOCH22CHCH33

OO

chloroformchloroform

ZZNNHCHCHCHC

CHCH22CC66HH55

OO

NNHCHHCH22COCHCOCH22CHCH33

OO

(78%)(78%)

++ HHOO

NONO22

NONO22

Page 27: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Solid-Phase Peptide Synthesis:Solid-Phase Peptide Synthesis:The Merrifield MethodThe Merrifield Method

Page 28: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Solid-Phase Peptide SynthesisSolid-Phase Peptide Synthesis

In solid-phase synthesis, the starting material is In solid-phase synthesis, the starting material is bonded to an inert solid support.bonded to an inert solid support.

Reactants are added in solution.Reactants are added in solution.

Reaction occurs at the interface between the Reaction occurs at the interface between the solid and the solution. Because the starting solid and the solution. Because the starting material is bonded to the solid, any product from material is bonded to the solid, any product from the starting material remains bonded as well.the starting material remains bonded as well.

Purification involves simply washing the Purification involves simply washing the byproducts from the solid support.byproducts from the solid support.

Page 29: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Solid SupportThe Solid Support

The solid support is a copolymer of styrene and The solid support is a copolymer of styrene and divinylbenzene. It is represented above as if it divinylbenzene. It is represented above as if it were polystyrene. Cross-linking with were polystyrene. Cross-linking with divinylbenzene simply provides a more rigid divinylbenzene simply provides a more rigid polymer.polymer.

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

Page 30: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Solid SupportThe Solid Support

Treating the polymeric support with Treating the polymeric support with chloromethyl methyl ether (ClCHchloromethyl methyl ether (ClCH22OCHOCH33) and ) and

SnClSnCl44 places places ClCHClCH22 side chains on some of the side chains on some of the

benzene rings.benzene rings.

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

Page 31: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Solid SupportThe Solid Support

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22ClCl

The side chain chloromethyl group is a benzylic The side chain chloromethyl group is a benzylic halide, reactive toward nucleophilic substitution halide, reactive toward nucleophilic substitution (S(SNN2).2).

Page 32: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Solid SupportThe Solid Support

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22ClCl

The chloromethylated resin is treated with the Boc-The chloromethylated resin is treated with the Boc-protected C-terminal amino acid. Nucleophilic protected C-terminal amino acid. Nucleophilic substitution occurs, and the Boc-protected amino substitution occurs, and the Boc-protected amino acid is bound to the resin as an ester.acid is bound to the resin as an ester.

Page 33: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22ClCl

BocBocNNHCHCOHCHCO

RR

OO––

Page 34: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

BocBocNNHCHCOHCHCO

RR

OO

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22

Next, the Boc Next, the Boc protecting group is protecting group is removed with HCl.removed with HCl.

Page 35: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

HH22NNCHCOCHCO

RR

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22OO

DCCI-promoted DCCI-promoted coupling adds the coupling adds the second amino acidsecond amino acid

Page 36: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

NNHCHCOHCHCO

RR

OO

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22

BocBocNNHCHCHCHC

R'R'

OO

Remove the Boc Remove the Boc protecting group.protecting group.

Page 37: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22

NNHCHCOHCHCO

RR

OO

HH22NNCHCCHC

R'R'

OO

Add the next amino Add the next amino acid and repeat.acid and repeat.

Page 38: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

Remove the peptide Remove the peptide from the resin with from the resin with HBr in CFHBr in CF33COCO22HH

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22

NNHCHCOHCHCO

RR

OO

NNHCHCHCHC

R'R'

OO

CC

OO++

HH33NN peptide

Page 39: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield ProcedureThe Merrifield Procedure

CHCH22 CHCH22 CHCH22 CHCH22CHCH CHCH CHCH CHCH

CHCH22BrBr

NNHCHCOHCHCO

RR

OO

NNHCHCHCHC

R'R'

OO

CC

OO++

HH33NN peptide––

Page 40: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

Peptide SynthesisPeptide Synthesis

Page 41: The Strategy of Peptide Synthesis. General Considerations Making peptide bonds between amino acids is not difficult. The challenge is connecting amino

The Merrifield MethodThe Merrifield Method

Merrifield also automated his solid-phase Merrifield also automated his solid-phase method.method.

Synthesized a nonapeptide (bradykinin) in 1962 Synthesized a nonapeptide (bradykinin) in 1962 in 8 days in 68% yield.in 8 days in 68% yield.

Synthesized ribonuclease (124 amino acids) in Synthesized ribonuclease (124 amino acids) in 1969.1969.

369 reactions; 11,391 steps369 reactions; 11,391 steps

Nobel Prize in chemistry: 1984Nobel Prize in chemistry: 1984


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