Chemical Biology

A few important points

To understand chemical biology, you also need to know these subjects:

organic chemistry, biochemistry, molecule biology

Learning method
Performance during the lectures (question & answer) will be incorporated
into your final grade . Everybody is required to come to the class on time.
Any excuse for absence has to be reported before the class.

Chapter 1
1. Peptide and Protein

Outline
1. Chemical biology of polypeptide
a. basic concepts
b. chemical synthesis of polypeptide
c. peptide mimics
d. application of polypeptide and peptide drugs
2.

Chemical synthesis of protein

a. total synthesis of protein
b. semi-synthesis of protein

3. Protein modification and protein drugs

a. protein modification
b protein drugs
b.

Basic Concepts
Protein

Amino acid

Polypeptide

-amino

amino acid
L-form
R: side chain
Natural polypeptide and proteins consist by 20 kinds of L-form amino acids

Chemical Biology of Polypeptide

Peptide and amino acid

Amino acid

polypeptide

Polypeptide is the polymer of amino acids

acids, through amide bonds(peptide bonds)
bonds).
Polypeptides usually contain less than 50 amino acids

Chemical Biology of Polypeptide

Classification of Peptide

By original: ribosomal peptide, non-ribosomal peptide, synthetic peptide

By backbone: linear peptide, cyclic peptide
By amino acid numbers: oligopeptide, polypeptide(>15 amino acid)

Chemical Biology of Peptide

Chemical synthesis of peptide:
Amide bond formation

Chemical Biology of Peptide

Choosing a protecting groups for amino acids:
avoid of racemization
solubility
orthogonal
O

O
HN

N
H

tert-butoxycarbonyl

Boc
Solution-phase peptide synthesis

9-fluorenylmethoxycarbonyl

Fmoc

Chemical Biology of Polypeptide

F
Formation
ti
off peptide
tid bond
b d from
f
amino
i acids
id
selective
protection

activation

amide bond formation

selective
deprotection

Chemical Biology of Peptide

S lid h
Solid-phase
peptide
tid synthesis:
th i
1963 Merrifield: solid phase peptide synthesis (SPPS) 1984 Nobel Prize

deproection

X
resin
deproection

REPEATED
deproection

Chemical Synthesis of Protein

Steps for solid-phase peptide synthesis:
1. Connect the C-terminal of N-protected amino acid to resin.
2. Deprotection of N-protecting group.
3. Amide bond formation with another N-protected amino acid.
4. Repeat N-deprotection and amide coupling

Comparison of protecting groups in SPPS:

Type

Resin

Merrifield, Pam, MBHA

Wang Trt,
Wang,
Trt Rink,
Rink HMPA

Deprotection
condition

Cleavage
condition
strong acid
week acid

Auto
synthesis
seldom
convenient

Chemical Synthesis of Protein

Cyclic peptide:

Ciclosporin

Peptide Mimics
Can polypeptide be used as drugs?

seldom

Easy to be hydrolyzed by enzymes so have lower stability, cant be taken orally.

Hydrophilic, make it hard to go through cell membrane.

Peptide Mimics: valuable for drug discovery and development

Peptoid

Peptide

Peptoid

Peptide Mimics
-peptide :

Peptide Mimics
Application of polypeptide and peptide mimics :

Functional site of target

g p
protein
Target identification and confirmation
Ligand in high throughput screening
Drug deliver system

Chemical Synthesis of Protein

Main way to get a protein: biological expression
Usuallyy contain only
y natural amino acid,, hard to introduce unnatural amino acid.
Hard to control post-translational modification precisely
Difficulties for biological expression of protein larger than 30kDa
Difficult to express membrane protein or toxic proteins

Alternative: Chemical synthesis

Native chemical ligation (NCL)
Protein semisynthesis (eg. EPL)

Chemical Synthesis of Protein

Native Chemical Ligation :
1. Transthioesterification
2. Thioester intermediate
3. S N acyl shift
Catalyst if necessary

HS

O
S
ONa
O

2-mercaptoethanesulfonate

Chemical Synthesis of Protein

Semisynthesis of protein:
protein splicing

Chemical Synthesis of Protein

Semisynthesis of protein:
Thioester p
preparation
p
by
yp
protein splicing
p
g

Chemical Synthesis of Protein

Semisynthesis of protein:
Express
p
p
protein ligation
g
((EPL))

Chemical Synthesis of Protein

Application of EPL:
Synthesis of Ub-Histone H2B

Protein Modification and Protein Drugs

Protein Modification
Change the chemical structure of protein through chemical methods
methods, introduce
specific functional group and change its chemical function and biological
properties, to study the relationship between protein structure and protein
function and change the structure and function of protein with specificity

High requirement
for organic reaction

Reactivity
Chemo selectivity
Functional group compatibility

Protein Modification and Protein Drugs

Protein Modification: Modification of protein residues
Tyrosine modification
protein

good selectivity
aromatic
aromatic electrophilic substitution
(iodonation, nitration, )

OH

J. Am. Chem. Soc., 2004, 126 (49), pp 1594215943

Protein Modification and Protein Drugs

Protein Modification: Modification of protein residues
Lysine modification

Protein Modification and Protein Drugs

Protein Modification: Modification of protein residues
Cysteine modification

protein
t i

SH

1. C-S bond formation: alkylation

y
R-X
alkyl halide

maleimide

2. S-S bond formation: reaction with disulfide

2,2'-Dithiodipyridine

Protein Modification and Protein Drugs

Protein Modification: Modification of protein residues
N-terminal selective modification

C-terminal selective modification

Protein Modification and Protein Drugs

Protein Modification: Modification of protein residues
Modification of special sequence
FLAsH

Protein Modification and Protein Drugs

Protein Modification:
Bio-orthogonal
g
modifications

Ketone modification
Staudinger ligation
Click reaction

Protein Modification and Protein Drugs

Bio-orthogonal modifications
Staudinger azide-phosphine reaction

Protein Modification and Protein Drugs

Protein Modification: Bio-orthogonal modifications
Staudinger ligation
traceless for chemoselective synthesis of amide bonds

Carolyn
y R. Bertozzi

Protein Modification and Protein Drugs

Protein Modification:
Bio-orthogonal
g
modifications
Click reaction
y
of azide and alkyne
y
3+2 cycloaddition

Protein Modification and Protein Drugs

Protein Modification:
Bio-orthogonal
g
modifications
Click reaction

Protein Modification and Protein Drugs

Protein Drugs:
Sources of p
protein drugs:
g

Isolation
DNA recombination and cell engineering

Protein drugs as therapeutics:

Peptide vaccine
natural immune peptide
p p
synthetic peptide vaccine
Mono-cloned antibody (mAb)
Multifunctional protein drugs

Outline of Todays Lecture

1. Chemical biology of polypeptide
basic concepts
(amino acid, peptide)
chemical synthesis of polypeptide
(amide bond formation, protecting groups, SPPS)
peptidomimetics
(peptoid, -peptide)
application of polypeptide and peptide drugs
2.

Chemical synthesis of protein

total synthesis of protein
semi-synthesis of protein (NCL, EPL)

3. Protein modification and protein drugs

protein modification
(side chain modification, bio-orthogonal modification)
protein drugs

Homework
Get aware of natural amino acids:

1. Name and structure of natural amino acids.

2 Classification of the amino acids by side chain
2.
chain.