Chemical Biology
A few important points
To understand chemical biology, you also need to know these subjects:organic chemistry, biochemistry, molecule biologyorganic chemistry, biochemistry, molecule biology
Learning method
Performance during the lectures (question & answer) will be incorporatedinto 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 Peptide and ProteinChapter 1. Peptide and Protein
Outline
1. Chemical biology of polypeptidea. basic conceptsb. chemical synthesis of polypeptidec. peptide mimicsd. application of polypeptide and peptide drugs
2. Chemical synthesis of proteina. total synthesis of proteinb. semi-synthesis of protein
3. Protein modification and protein drugsa. protein modificationb protein drugsb. protein drugs
Basic Concepts
PolypeptideProtein Amino acid
amino acid-amino acidL-formR: side chain
Natural polypeptide and proteins consist by 20 kinds of L-form -amino acids
Chemical Biology of Polypeptide
Peptide and amino acid
polypeptideAmino acid
Polypeptide is the polymer of amino acids through amide bonds(peptide bonds)Polypeptide is the polymer of amino acids, through amide bonds(peptide 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: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
OHN
O
ONH
OHN
Boc Fmoc
tert-butoxycarbonyl 9-fluorenylmethoxycarbonyl
Solution-phase peptide synthesis
Chemical Biology of Polypeptide
F ti f tid b d f i idFormation of peptide bond from amino acids
selectiveselective protection activation
amide bond formation
selective deprotection
Chemical Biology of Peptide
S lid h tid th i1963 Merrifield: solid phase peptide synthesis (SPPS) 1984 Nobel Prize
Solid-phase peptide synthesis:
Xdeproection
Xresin
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 Deprotectioncondition
Cleavage condition
Auto synthesis
strong acid
week acid
seldom
convenientWang Trt Rink HMPA
Merrifield, Pam, MBHA
Wang, Trt, Rink, HMPA
Chemical Synthesis of Protein
Cyclic peptide:
Ciclosporin
Peptide Mimics
Can polypeptide be used as drugs?
Easy to be hydrolyzed by enzymes so have lower stability, cant be taken orally.
seldom
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 proteing p Target identification and confirmation Ligand in high throughput screening Drug deliver system
Chemical Synthesis of Protein
Usually contain only natural amino acid, hard to introduce unnatural amino acid.
Main way to get a protein: biological expression
y y , 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) Native chemical ligation (NCL) Protein semisynthesis (eg. EPL)
Chemical Synthesis of Protein
Native Chemical Ligation :
1. Transthioesterification2. Thioester intermediate3. S N acyl shift
Catalyst if necessary
HSS
O
O ONa
2-mercaptoethanesulfonate
Chemical Synthesis of Protein
Semisynthesis of protein:
protein splicing
Chemical Synthesis of Protein
Semisynthesis of protein:
Thioester preparation by protein splicing p p y p p g
Chemical Synthesis of Protein
Express protein ligation (EPL)
Semisynthesis of protein:
p p g ( )
Chemical Synthesis of ProteinApplication of EPL:Application of EPL:
Synthesis of Ub-Histone H2B
Protein Modification and Protein Drugs
Protein Modification
Change the chemical structure of protein through chemical methods introduceChange the chemical structure of protein through chemical 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 specificityfunction and change the structure and function of protein with specificity
High requirement for organic reaction
ReactivityChemo selectivityFunctional group compatibility
Protein Modification and Protein Drugs
Tyrosine modification
Protein Modification: Modification of protein residues
Tyrosine modification
good selectivityaromatic electrophilic substitution
OHprotein
aromatic electrophilic substitution (iodonation, nitration, )
J. Am. Chem. Soc., 2004, 126 (49), pp 1594215943
Protein Modification and Protein DrugsProtein Modification: Modification of protein residuesProtein Modification:
Lysine modification
Modification of protein residues
Protein Modification and Protein Drugs
Cysteine modification
Protein Modification:
t i
Modification of protein residues
Cysteine modification protein SH
1. C-S bond formation: alkylationy
R-X
2. S-S bond formation: reaction with disulfide
maleimidealkyl halide
2,2'-Dithiodipyridine
Protein Modification and Protein Drugs
N-terminal selective modification
Protein Modification: Modification of protein residues
C-terminal selective modification
Protein Modification and Protein Drugs
Modification of special sequence
Protein Modification: Modification of protein residues
Modification of special sequenceFLAsH
Protein Modification and Protein Drugs
Protein Modification:
Bio-orthogonal modifications
Ketone modification
g
Ketone modificationStaudinger ligationClick reaction
Protein Modification and Protein Drugs
Bio-orthogonal modifications
Staudinger azide-phosphine reaction
Protein Modification and Protein Drugs
Protein Modification: Bio-orthogonal modifications
Staudinger ligationStaudinger ligation traceless for chemoselective synthesis of amide bonds
Carolyn R. Bertozziy
Protein Modification and Protein Drugs
Protein Modification:
Bio-orthogonal modificationsgClick reaction
3+2 cycloaddition of azide and alkyney y
Protein Modification and Protein Drugs
Protein Modification:
Bio-orthogonal modificationsgClick reaction
Protein Modification and Protein Drugs
Protein Drugs:
Sources of protein drugs: IsolationDNA recombination and cell engineeringp g DNA recombination and cell engineering
Protein drugs as therapeutics:Protein drugs as therapeutics:
Peptide vaccine natural immune peptidep p synthetic peptide vaccine
Mono-cloned antibody (mAb)
Multifunctional protein drugs
Outline of Todays Lecture
1. Chemical biology of polypeptidebasic 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 proteintotal synthesis of proteinsemi-synthesis of protein (NCL, EPL)
3. Protein modification and protein drugsprotein modification (side chain modification, bio-orthogonal modification)protein drugsprotein drugs
Homework
Get aware of natural amino acids:
1. Name and structure of natural amino acids.
2 Classification of the amino acids by side chain2. Classification of the amino acids by side chain.