organic chemistry iii...organic chemistry iii 後藤 佑樹 (yuki goto, bioorganic chemistry lab.)...
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![Page 1: Organic Chemistry III...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](https://reader030.vdocuments.mx/reader030/viewer/2022040917/5e90f2cd9ebb5605a77df518/html5/thumbnails/1.jpg)
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”
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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
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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
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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
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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
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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
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Structure of proteinsTertiary structures
hydrophobic interactions salt
bridge
H-bonds (backbone)
H-bonds (sidechain-backbone)
H-bonds (sidechains)
disulfide linkage
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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
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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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