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Organic Chemistry III
後藤 佑樹 (Yuki Goto, Bioorganic Chemistry Lab.)
担当日：6/5 (Wed) 6/12 (Wed) 6/19 (Wed) 6/26 (Wed) 7/3 (Wed)
“Organic chemistry of biomolecules”
1
Topics
• structure of peptides- properties of amide bonds - secondary and tertiary structures of peptides
• synthesis of peptides- protection of amino group
- Boc group - Fmoc group
- activation of carboxyl group - condensation agents - additives
- solid phase peptide synthesis - condensation agents - additives
• reactions of peptides- Edman degradation - cleavage by CNBr
done
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Q and A
Fig. 19.61
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Q and A
Fig. 18.31
4
Q and A
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Activation of carboxyl groups in peptide synthesis Use of condensation agent (縮合剤)
N,N'-Dicyclohexylcarbodiimide (DCC)carbodiimide
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dicyclohexylurea
Activation of carboxyl groups in peptide synthesis Use of condensation agent (縮合剤)
N,N'-Dicyclohexylcarbodiimide (DCC)
easy to be crystalized
7
Activation of carboxyl groups in peptide synthesis other carbodiimides
NNC
N
NHN
O
HN
1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)
residual urearemovable by extraction
N,N'-Diisopropylcarbodiimide (DIC)
NC
N
HN
O
HN
residual ureasoluble in organic solvents
8
Activation of carboxyl groups in peptide synthesis Use of condensation agent (縮合剤)
BocHNO
O N
NHBocHN
O
O N
NH
racemization
prone to racemize
9
Activation of carboxyl groups in peptide synthesis Use of condensation agent (縮合剤) and additives to generate activated esters
NN
N
OH
R N
C
N RBocHN
OH
O
BocHNO
O
N
NN
hydroxybenzotriazole (HOBt)
carbodiimideBocHN
O
O N
NH
activated ester
prone to racemize suppressed racemization
2) TFA +H3N
O
NH
OH
OH-Ala-Leu-OH
H2NO
O
BocHN
O
NH
O
O
1) LiOH
pKa: 4.6
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Even if the yield of one cycle of coupling/deprotection is 90% …
yield of 10-mer peptide is 0.910 = 35% in 20 stepsyield of 20-mer peptide is 0.920 = 12% in 40 stepsyield of 30-mer peptide is 0.930 = 4% in 60 steps
Efficiency and facility are critical in peptide synthesis
Efficient and facile solid phase peptide synthesis（固相合成）
Robert Bruce Merrifield
"for his development of methodology for chemical synthesis on a solid matrix"Nobel Prize in Chemistry (1984)
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Loading an amino acid onto solid support (resin)
O
HO
O
HO
O
O
FmocHNO
O
FmocHNO
O
FmocHNOH
O
FmocHNO
Oresin
≡
Efficient and facile solid phase peptide synthesis（固相合成）
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FmocHN
R1
O
O
Elongation of peptide chain on solid support
resinpiperidine
H2N
R1
O
O
R1
O
ORn
NH
ORn+1HN
O
H2N
R1
OH
ORn
NH
ORn+1HN
O
H2N
resin
R1
O
O
FmocHN
R2
NH
O
resin
NH
DMF DMF
NC
N
NN
N
OH
FmocHN
R2
OH
ODIC
HOBt
(A) (B)
n-fold repetition of steps (A)/(B)
R1
O
ORn
NH
ORn+1HN
O
FmocHN resin
piperidine
DMF(A)
resinTFA
DCM
20% v/v 4–6 eq.
Efficient and facile solid phase peptide synthesis（固相合成）
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FmocHN
R1
O
Oresin
piperidineH2N
R1
O
O
resin
NH
DMF DMF
NC
N
NN
N
OH
FmocHN
R2
OH
ODIC
HOBt
(A) (B)
20% v/v 4–6 eq.
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FmocHN
R1
O
Oresin
piperidineH2N
R1
O
O
resin
NH
DMF DMF
NC
N
NN
N
OH
FmocHN
R2
OH
ODIC
HOBt
(A) (B)
20% v/v 4–6 eq.
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FmocHN
R1
O
Oresin
piperidineH2N
R1
O
O
resin
NH
DMF DMF
NC
N
NN
N
OH
FmocHN
R2
OH
ODIC
HOBt
(A) (B)
20% v/v 4–6 eq.
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FmocHN
R1
O
Oresin
piperidineH2N
R1
O
O
resin
NH
DMF DMF
NC
N
NN
N
OH
FmocHN
R2
OH
ODIC
HOBt
(A) (B)
20% v/v 4–6 eq.
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FmocHN
R1
O
O
Elongation of peptide chain on solid support
resinpiperidine
H2N
R1
O
O
R1
O
ORn
NH
ORn+1HN
O
H2N
R1
OH
ORn
NH
ORn+1HN
O
H2N
resin
R1
O
O
FmocHN
R2
NH
O
resin
NH
DMF DMF
NC
N
NN
N
OH
FmocHN
R2
OH
ODIC
HOBt
(A) (B)
n-fold repetition of steps (A)/(B)
R1
O
ORn
NH
ORn+1HN
O
FmocHN resin
piperidine
DMF(A)
resinTFA
DCM
20% v/v 4–6 eq.
Efficient and facile solid phase peptide synthesis（固相合成）
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Automated solid phase peptide synthesis
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Properties of backbone amide linkagesresonance structure of amide
R NR
O
H
Thus, • the C–N bond has a partial double bond character • the amide oxygen has (weak but significant) nucleophilicity
R NH
R
O
R NH
R
Oisomers of amide bond
s-trans s-cis
Review point conformation of conjugated dienes
rigidity of peptide chainR
OH
OR
NH
ORHN
O
H2N
fix and flat
φψ
only two rotatable bonds in each residue
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Structure of peptidesSecondary structures
β-sheet
R
O
N
R
OR
N
O
N
R
OR
N
O
N
R
O
N
H
H
H
H
H
H
R
O
N
R
O R
N
O
N
R
O R
N
O
N
R
O
N
H
H
H
H
H
H
R
O
N
R
OR
N
O
N
R
OR
N
O
N
R
O
N
H
H
H
H
H
H
polypeptide backbone is extended and flat
side chains alternately extend into opposite sides of the sheet
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Structure of peptidesSecondary structures
α-helix
hydrogen bondsbetween C=O of n th residue and N-H of (n+4) th residue
R
O
N
R
OR
N
O
N
R
OR
N
O
N
R
OR
N
O
N
R
OR
N
O
N
R
O
NH
H
H
H
H
H
H
H
H
H
top view
side chains extend into outside of the helix with various directions
22
Structure of proteinsTertiary structures
hydrophobic interactions salt
bridge
H-bonds (backbone)
H-bonds (sidechain-backbone)
H-bonds (sidechains)
disulfide linkage
23
Organic reactions of peptides
Edman degradation
Amide bonds are chemically stable, but there are some reactions to cleave them
Review point isocyanates generated by Curtius rearrangement
+
+
cleaved
overall reaction
24
Organic reactions of peptidesAmide bonds are chemically stable, but there are some reactions to cleave them
Intact peptide chain, one amino acid shorter, is here generated
Edman degradation
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Organic reactions of peptides
selective cleavage of Met sites by CNBr
Amide bonds are chemically stable, but there are some reactions to cleave them
overall reaction
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Organic reactions of peptidesselective cleavage of Met sites by CNBr
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