2. Couple the two protected amino acids.

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1 General Considerations The Strategy of Peptide Synthesis Making peptide bonds between amino acids is not difficult. The challenge is connecting amino acids in the correct sequence. andom peptide bond formation in a mixture of phenylalanine and glycine,, for example, will give four dipeptides. Phe Phe Gly Gly Phe Gly Gly Phe General Strategy 1. Limit the number of possibilities by "protecting" the nitrogen of one amino acid and the carboxyl group of the other. N-Protected phenylalanine C-Protected glycine General Strategy 2. Couple the two protected amino acids. NC C 6 5 N N 2 N N 2 N C 6 5 C 6 5 General Strategy 3. Deprotect the amino group at the N-terminus and the carboxyl group at the C-terminus. NC C 6 5 N Amino Group Protection 3 NC N C 6 5 Phe-Gly

2 Protect Amino Groups as Amides Protect Amino Groups as Amides Amino groups are normally protected by converting them to amides. Benzyloxycarbonyl (C 6 5 ) ) is a common protecting group. It is abbreviated as Z. Z-protection is carried out by treating an amino acid with benzyloxycarbonyl chloride. CCl C 3 NC C Na, 2 2. N C 6 5 (82-87%) Protect Amino Groups as Amides emoving Z-Protection C is abbreviated as: ZN C 6 5 N C 6 5 or Z-Phe An advantage of the benzyloxycarbonyl protecting group is that it is easily removed by: a) hydrogenolysis b) cleavage with Br in acetic acid ydrogenolysis of Z-Protecting Group Br Cleavage of Z-Protecting Group C NCN C 2 3 C NCN C 2 3 C 6 5 C 6 5 2, Pd Br 3 C 2 2 NCN C 2 3 C 6 5 (100%) Br C 2 3 NCN C 2 3 C 6 5 Br (82%)

3 The tert-butoxycarbonyl Protecting Group Br Cleavage of Boc-Protecting Group ( 3 ) 3 CC N C 6 5 ( 3 ) 3 CC NCN C 2 3 C 6 5 is abbreviated as: Br BocN C 6 5 or Boc-Phe 3 C 3 C C C 2 3 NCN C 2 3 C 6 5 Br (86%) Protect Carboxyl Groups as Esters Carboxyl Group Protection Carboxyl groups are normally protected as esters. Deprotection of methyl and ethyl esters is by hydrolysis in base. Benzyl esters can be cleaved by hydrogenolysis. ydrogenolysis of Benzyl Esters C 6 5 C NCN C C 6 5 C 6 5 2, Pd Peptide Bond Formation C C 2 3 NCN C C 6 5 (87%) 3 C 6 5

4 Forming Peptide Bonds DCCI-Promoted Coupling The two major methods are: 1. coupling of suitably protected amino acids using N,N' N'-dicyclohexylcarbodiimide (DCCI) 2. via an active ester of the N-terminal amino acid. ZN C N 3 DCCI, chloroform ZNC C 6 5 N 3 (83%) Mechanism of DCCI-Promoted Coupling ZN C 6 5 C 6 11 N NC 6 11 CNZ Z C 6 5 Mechanism of DCCI-Promoted Coupling The species formed by addition of the Z- protected amino acid to DCCI is similar in structure to an acid anhydride and acts as an acylating agent. Attack by the amine function of the carboxyl- protected amino acid on the carbonyl group leads to nucleophilic acyl substitution. C 6 11 N CNZ Z C 6 5 Mechanism of DCCI-Promoted Coupling C 6 11 N ZNC C 6 5 N 3 2 N 3 The Active Ester Method A p-nitrophenyl ester is an example of an "active ester." p-nitrophenyl is a better leaving group than methyl or ethyl, and p-nitrophenyl esters are more reactive in nucleophilic acyl substitution. C 6 11 N CNZ Z C 6 5

5 The Active Ester Method The Active Ester Method ZNC N 2 2 N 3 ZNC N 2 2 N 3 C 6 5 C 6 5 chloroform ZNC C 6 5 N 3 (78%) N 2 Solid-Phase Peptide Synthesis Solid-Phase Peptide Synthesis: The Merrifield Method In solid-phase synthesis, the starting material is bonded to an inert solid support. eactants are added in solution. eaction occurs at the interface between the solid and the solution. Because the starting material is bonded to the solid, any product from the starting material remains bonded as well. Purification involves simply washing the byproducts from the solid support. The Solid Support The Solid Support The solid support is a copolymer of styrene and divinylbenzene.. It is represented above as if it were polystyrene. Cross-linking with divinylbenzene simply provides a more rigid polymer. Treating the polymeric support with chloromethyl methyl ether (Cl 3 ) and SnCl 4 places Cl side chains on some of the benzene rings.

6 The Solid Support The Solid Support Cl The side chain chloromethyl group is a benzylic halide, reactive toward nucleophilic substitution (S N 2). Cl The chloromethylated resin is treated with the Boc- protected C-terminal amino acid. Nucleophilic substitution occurs, and the Boc-protected amino acid is bound to the resin as an ester. BocNC Cl Next, the Boc protecting group is removed with Cl. BocNC 2 NC BocNC NC DCCI-promoted coupling adds the second amino acid ' emove the Boc protecting group.

7 2 NC ' NC Add the next amino acid and repeat. 3 N peptide C NC ' NC emove the peptide from the resin with Br in CF 3 C 2 Peptide Synthesis 3 N peptide C NC NC Br ' The Merrifield Method Merrifield also automated his solid-phase method. Synthesized a nonapeptide (bradykinin)) in 1962 in 8 days in 68% yield. Synthesized ribonuclease (124 amino acids) in reactions; 11,391 steps Nobel Prize in chemistry: 1984

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