Natural Products 1

CHAPTER

1
NATURAL PRODUCTS
Amino Acid :
The amino acid is an organic acid containing both NH2 and COOH group called as amino-acid.
Basic structure of   amino-acid is R CH COOH
NH2
There are 20 amino acids in human body out of these two amino acids are -Imino - acid viz.
(1) Proline (2) Hydroxyproline

HO

COOH
N COOH
N
H
H

• All - amino acid are chiral except glycine.

• They are optically active

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• All amino-acid are L-Amino acid and their standard unit is serine.
• All amino-acid have S-configuration except cysteine which have R-configuration.
Classification on the basis of NH2 and COOH group:
1. Neutral Amino acid  –NH2 = – COOH
2. Acidic Amino acid  –COOH > – NH2
3. Basic Amino acid  –NH2 > – COOH

Amino Acid:
Name Three Letter Symbol Structure
H
H
Glycine Gly
H2N COOH
Me
H
Alanine Ala
H2N COOH
2 Natural Products
H3C CH3

Valine Val H

H2N COOH
Me

Me
Isoleucine ILe H

H2N COOH
Me

Me
Leucine Leu
H2N COOH

Phenylalanine Phe H

H2N COOH
H

Tryptophan Trp
H

H2N COOH
H

Proline Pro N COOH

H
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HO

H
Serine Ser
H2N COOH
HO Me

H
Threonine Thr
H2N COOH
HO

Tyrosine Tyr H

H2N COOH
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HS

H
Cysteine Cys
H2N COOH

H3C S
H
Methionine Met OH
H2N
O
H S S
H
Cystine Cys-cys H2N
HOOC NH2
CH2OOH
N

N H
Histidine His
H COOH
H2N

H2N
H
Lysine Lys
H2N COOH
H
H2N N
Arginine Arg H
NH
H2N COOH
H2N
H
Ornithine Orn
H2N COOH
Aspartic acid Asp HOOC
H

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H N COOH
2

O OH

Asparagine Asn H2N

H

H2N COOH

Glutamic acid Glu HOOC

H

H2N COOH

OH
H2N
Glutamine Gln H
O
H2N COOH
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• Amino acid with aromatic side chain: Phe, Tyr, Trp
Essential and Non - Essential Amino acid :
Those amino acid that can’t synthesised in the body and has to be provided from out side by food called as
essential amino acid. There are ten essential amino acid such as Phe, Val, Trp, Tyr, ILeu, Met, His, Arg, Leu
and Lys.
Synthesis of Amino ACid :
1. Gabriel Phthalimide Synthesis :
O O
C C
NaOH/H2O
NK + Cl CH2 COOEt N CH2COOEt
C C

O O

COONa COOH
HCl
+ NH2 CH2 COOH
CONH–CH2COOEt COOH

Synthesis of phenyl alanine by Gabriel phthalimide method:

O O
C C
H NaOH / H2O
NK + Cl CH COOEt N C COOEt
C CH2Ph C CH2Ph
O O
H
COONa HCl COOH NH2 C COOH
+ CH2Ph
CONH–CH2–COOEt COOH
Ph

2. Strecker Synthesis: www.careerendeavour.com

OH
CH3CHO + NH3 CH3–CH H2O
CH3–CH NH
NH2 H2O

CN
NH2
H+
CH3CH CH3CH(NH2)CO2H
CN
Natural Products 5

O NH2
O O O O
CH3 1. NH4Cl, NaOH CH3
Problem: HOOC
H CH3
O CH3 2. H3O+ O
BnO BnO

NHAc O O NH2 O O
AcO CH3 HO CH3 LiAlH4
CH3COOH
O CH3 O CH3

BnO BnO

3. Malonic Ester Synthesis :

COOEt COOEt COOH

COOEt H3C I HCl
EtONa CH H3C CH H3C CH
CH2 H2O COOH
COOEt COOEt COOEt

Br2 COOH NH3

H3C C CH3 CH COOH CH3 CH COOH
Reflux COOH
Br Br NH2
• By these methods we can prepare the following amino acids.
Phe, Pro, Tyr, Cys, Ser, Asp, Met and Lys.
4. Erlenmeyer Azalactone Synthesis :
OH
H
C6H5CHO + H2C COOH (CH3CO)2O C6H5 CH C COOH C6 H5 C C C O
CH3CO2Na N O
NH COPh NH COPh C
Ph
Azalactone
COOH
NaOH C6H5 CH C COOH Na–Hg C H CH CH HCl C6H5–CH2–CH–COOH
6 5 2
NH CO Ph NH2
NHCOPh
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This method is best for the synthesis of Phe, Tyr, Try and thyroxine.
5. Hydantoin Synthesis:

H
CHO N CH C NH Na–Hg
AC2O O
O
+ NH
N O
N O H N
H Hydantoin
H
H
CH2 CH NH CH2 C NH2
O HCl/H+
NH COOH
N O N
H H

This method may be used for the preparation of Phe, Tyr, Trp and Met.
6. Aromatic aldehydes may be condensed with diketonpiperazine, and the product converted into an amino acid
by heating with hydriodic acid and red phosphorus for example,
6 Natural Products

O O

CHC6H5
HN (CH3CO)2O HN
2C6H5CHO + HI
2C6H5CH2CH(NH2)CO2H
NH NH P
C6H5HC

O O

Physical Properties :
1. The amino acids are colourless crystalline compounds which are soluble in water and sparingly soluble in
organic solvent.
2. The acidity and basicity are very low.
3. They have very high melting point > 200oC.
4. They have high dipole moment.
The amino acids exist in Zwitter ion form such as

H2N CH COOH H3N CH COO

R R
The properties shown by amino acid suggest that they exist as dipolar ion by internal proton transfer known as
Zwitter ion because of the Zwitter ionic structure. The acidity in amino acid is due to NH3 group and basicity
is due to COO–.

NH3 CH COOH + OH– NH3 CH COO– + H2O NH2 CH COO + H3O

R Acid R (A) R (B)

(C)
 H 3O    B  C OH 
Ka   
, Kb 
 A  H2O  A H 2O
Isoelectric Point :

H+ H+
NH2 CH COO NH3 CH COO NH3 CH COOH
OH– OH–
R R R
Conjugate base (–ve charge)
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Zwitter ion Conjugate acid (+ ve charge)
(High pH) Don't migrate (Low pH)
migrate towards anode migrates towards cathode
in electric field in electric field
At high pH the amino acid migrates towards anode because of negative charge and at low pH they will migrate
to cathode because of +ve charge whereas at a particular pH the amino acid molecule will exist in zwitter ionic
form which has neutral structure and will not migrate to any of the electrode, this pH is known as isoelectric
point of that amino acid
Neutral Amino acid ~ 5.5 – 6.3
Acidic Amino acid ~3
Basic Amino acid ~ 9  10
Natural Products 7

SOLVED PROBLEMS

1. Arrange the following in increasing order of their isoelectric point (PI)

Arg, Tyr, Asp
Soln. Asp < Tyr < Arg
2. The pKa values for the three ionisable group X , Y and Z of aspartic acids are 2.09, 3.86 and 9.82 respectively.
The isoelectric point for the amino acid is:
HO2C CH2 CH CO2H

Y NH3 X
Z

Soln. NH3 CH OH– NH

COOH – OH– OH
3 CH COO NH3 CH COO– NH2 CH COO–
CH2 COOH H
+
H+ H+
CH2 COOH CH2COO– CH–COO
2.09 3.86 9.82
Low pH Zwitter ion High pH
Isoelectric point is the average of two pKa value of the right and left hand side of the zwitter ion .
p K  p K 2 2.09  3.86
pHi  1   2.97
2 2
3. The pKa value for the three ionisable groups x, y, z of glutamic acid are 4.3, 9.7 and 2.2 calculate the
isoelectric point.

H OH OH OH
NH3 C COOH + NH3 CH COO + H3N CH COO H2N CH COO
H H H+
Soln. 2.2 (CH2)2COOH
(CH2)2COOH OOC(H2C)2 9.7 (CH2)2COO
Zwitter ion 4.3
2.2  4.3
pHi   3.25
2
Remark: Amino acid molecule show least solubility at its isoelectric point.
4. Find the isoelectric point of glycine whose pK1 and pK2 values are 2.4 and 9.6 respectively.
2.4  9.6
Soln. pHi   6.0
2

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 8 Natural Products
The values of isoelectric point for few important amino acids are listed below:
Acid Symbol Isoelectric point
Glycine Gly 6.0
Alanine Ala 6.1
Valine Val 6.0
Leucine Leu 6.0
Isoleucine Ileu 6.0
Phenylalanine Phe 5.9
Tyrosine Tyr 5.6
Serine Ser 5.7
Cysteine CySH 5.1
Cystine CySSCy 5.0
Threonine Thr 5.7
Methionine Met 5.7
Tryptophan Try 5.9
Proline Pr o 6.3
Hydroxyproline Hypro 5.8
Aspartic acid Asp 3.0
Asparagine AspNH 2 5.4
Glutamic acid Glu 3.1
Glutamine GluNH 2 5.7
Arginine Arg 10.8
Ly sin e Lys 9.5
Histidine His 7.6

5. Arrange the following amino acids in decreasing order of pI.

Asp, Tyr, Ala, Arg.
Soln. Arg > Ala > Tyr > Asp.

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Sorensen Formol Titration:
In order to titrate the carboxylic group with alkali, the amino group must be ‘masked’. Thus when a formalin
solution is added to glycine, methylene-glycine is formed. For example
H
– H2 O
C O + H2 NCH2COOH H2C NCH2COOH
H
Hence the carboxylic group is free which can be titrated by alkali. This method of titrating amino acid with
alkali is known as “Sorensen Formol Titration”.

Reaction of Amino Acid:

1. Reaction due to NH2 group :
(i) Salt formation:
HCl
R CH COOH R CH COOH
NH2 NH3Cl–
Natural Products 9
(ii) Acetylation of NH2 group: Amino acid may be acetylated of means of acetyl chloride or acetic anhydride
O
O O
Ph C Cl Ac2O
Ph C NH CH COOH NH2 CH COOH H3C C NH CH COOH
R R R
O O
O O O
Cl
+ H2N CH C OH H3C NH CH COOH
H3C O CH3 AlCl3
R R
–CH3COOH
O
O
H3C NH CH C OH
R
Reaction with Cbz-Cl: Cl O Ph (BnOCOCl)

O
O O O

OH Cl O Ph base OH OH
+
NH2 NH O Ph
O NHCbz

carboxy O benzyl

O O

(BOC)2O
O O O
Reaction with (BOC)2O: t-butyloxy BOC
carbonyl
or BOC

SMe
Me
S
O O O
OH
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+ H2N OH
O O O O N
O O
H

Fluorenyl

O Cl
methyl
oxy carbonyl

OH
+ H2 N
O O
O
OH
O N
O Cl
H O
 10 Natural Products
(iii) Reaction with Nitrous acid:
R CH COOH + HNO2 R CH COOH + N2 + H2O
NH2 OH
It is a quantitative method for the determination of number of amino acid in a mixture and the evolution of
nitrogen is the basis of “van Slyke method” for analysing mixtures of amino acid.
Number of N2 molecule released  Number of amino acid in the mixture.
(iv) Reaction with Hydriodic acid:
200oC
R CH COOH + HI R CH2 COOH + NH3
NH2
(v) Reaction with Sanger’s Reagent :
O2N O2N

R CH NH2 + F NO2 R CH NH NO2

COOH COOH
2, 4 - Dinitro fluoro
benzene (DNFB) Labelled amino acid
(Sanger Reagent) yellow coloured
2. Reaction due to carboxylic group:

C2H5OH
H+ R CH COOEt
NH2
PCl5
R CH COCl

R CH COOH NH2

NH2 Ba(OH)2
R CH2 NH2
Dry distill –CO2

LiAlH4
R CH CH2OH

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NH 2

SOLVED PROBLEMS

O O O
1. H3C CbzCl H3C H+ H3C
OH OH C2H5OH, OC2H5
NaOH
NH2 NHCbz NHCbz

H3C H3C Na|C2H5OH

1. NaH OH
OMEM
2. MEM–Cl NHCbz
NHCbz
Natural Products 11

O O O O

2. 1. H2SO4 NGP –H+

Ph OH Ph O Ph O Ph OH
2. NaNO2
NH2 OH
N2+Cl– H2O
CS2CO3 BnBr
O 1. TFA O O O
2. Pd/H2 NH2(BOC) TsCl, py
Ph OH Ph OBn Ph OBn Ph OBn
OH
NH2 NHBOC OTs

3. Reaction with both NH2 and COOH group :

(i) Dakin-West reaction:When the amino acid is heated with acetic anhydride in pyridine solution, it is
converted into methyl  -acetamidoketones, this reaction is known as Dakin-West reaction.
NH2 NHCOCH3
(CH3CO)2O
R CH R CH
Py COCH3
COOH
(ii) Chelate Complex : The copper salt of glycine is formed by heating copper oxide with an aqueous solution
of glyline.
H2
O N
O
2 NH2CH2COOH + Cu2+ Cu
NH2 O
O
Deep blue needles
The amino acid may be liberated from the alkali salts by treatment in ethanolic solution with
ethyloxyminocyanoacetate.

(iv) Action of Heat: When the  -amino acids are heated it forms 2, 5-diketopiperazines.
O
O
OEt H NH
NH
+ HN + 2 EtOH
NH H EtO
O O
(v) Test for amino acid (Ninhydrin Reaction) :

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O O

O + H2N CH COOH N H2 + O
R'
O O O

O O O O

N N

O O O O

Purple-coloured product

All   amino acid reacts with two molecule of ninhydrin to yield an intensely coloured product whereas with
proline and hydroxy proline it gives yellow colour.
 12 Natural Products
4. Synthesis of amino acids by reductive amination is illustrated by the following synthesis of leucine:
NaOC 2 H5
Ethyl isovalerate + ethyl oxalate  A  C11H18 O5 
boil
A  10%H 2SO 4   B  C6 H10O3   CO 2  C2 H 5OH
Pd. heat
B  NH3  H 2   leucine
O

H3C O H3C C OEt

Soln. CH CH2 C OEt CH CH H C2H5O
H3C H3C
O O
H3C COOEt O O
H3C C OEt C OEt
CH CH C C OEt
CH CH + O C OEt H3C
H3C

H3C O O H3C
10% H2SO4 NH3
CH CH2 C C OEt + CO2 + C2H5OH CH CH2 COOH
H2
H3C H3C

Peptide :
Amino acids are covalently linked by amide bonds the resulting molecules are called ‘Peptides’ and ‘Proteins’.
Peptide are the combination of minimum of two or more amino acid, connected by the peptide bond.

O O
NH2 CH C OH + NH2 CH COOH H2N CH C N CH COOH
R R1 R H R'
Dipeptide

The amino group of one amino acid combined with the –COOH group of the other amino acid and remove
one molecule of H2O to form the peptide bond. Peptides are condensation polymers.
Features of Peptide Bonds:
• The peptide bonds are usually inert.
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• There is a restricted rotation about the amide bond.
O H
H R1  
C C N
C N C
H
O H R2
• The atom in the group –CONH–, are planar and the O and H are trans.
• Since the peptide C–N bond length (1.32 Å) is shorter than the usual C–N bond length (~1.47Å), it means
that the peptide bond has some double bond character.
Synthesis of peptide
O
O
OH
N OH
OH + H2N
NH2 H O
NH2 O
Natural Products 13
Possibilities-1:
O
OH
OH + H2N
Leu-Gly
NH2 O

Possibilities-2:

+ Leu-leu
H2N COOH H2N COOH
Possibilities-3:

OH
H2N
+ Gly–leu
O H2N COOH
So, one can use protecting group strategy.
O O

CbzCl
OH OH
NaOH
NH2 NHCbz (A)
OH C2H5OH, H+ OC2H5
H 2N H 2N
O
O
(B)
Now, coupling between (A) and (B)
O
O
OC2H5 OC2H5
OH H2N N
+ H
NHCbz O NHCbz O

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N
H
OH H+

NH2 O

Problem: HOOC HOOC

H H2N COOH
N COOH
H2N OH +
H2N
O Ph
Ph O Phe
Asp

O O

H2N H2N
OH C2H5OH, H+ OC2H5

Ph Ph
(A)
 14 Natural Products

O COOH
COOH O
Ph O Cl PhCH2OH, H+
Ph O N COOH
H2N COOH NaOH
H
CO2CH2Ph
O
CO2CH2Ph
O
1. LiOH, H2O, acetone
Ph O N CO2CH2Ph
Ph O N COOH 2. H+
H
(B) H

Coupling between (A) and (B).

CO2CH2Ph
O O
H2N
OC2H5 + Ph O N COOH

Ph H
(A) (B)

O CO2CH2Ph COOH
O O
H
N H2, Pd–C
Ph O NH NH
OEt H2N OH
Deprotection
O
Ph O
Ph
Structure of Peptide:
1. Ala – Gly – Phe
NH2 CH CONH CH2 CO NH CH COOH
CH3 CH2Ph
2. Tyr – Met - Gly - Ser

H2N CH CO NH CH CONH CH CO NH CH COOH

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H2C CH2CH2SCH3 H CH2OH

OH

Determination of Sequence of amino acid in Peptide :

1. Enzymatic Hydrolysis :
(a) Carboxypeptidase: It cut at C-terminal of peptide with one amino acid at once.
CBA
A—B—C—D A—B—C+D CBA = Carboxypeptidase
CBA
For example: Phe – Gly – Lys  ?
Natural Products 15

Soln. Phe – Gly  Lys

2. Leucine - aminopeptidase (or Aminopeptidase) : Cut at N- terminal at once
LAP
A—B—C—D A+B—C—D LAP = Leucine-aminopeptidase

For example
LAP
Gly-Arg-Phe-Ala   Gly + Arg – Phe – Ala

3. Trypsin : It cut at the C-terminal / or right side of basic amino acid : Lys, Arg.
Trypsin
Ala – Gly–Lys Asp Met Ala – Gly – Lys + Asp – Met
4. Chymotrypsin : It cut at the C-terminal / or right side of amino acid having aromatic side chain: Trp, Tyr, Phe.
Chymotrypsin
ALa  Gly  Phe  Met  ALa   ALa – Gly – Phe  Met – ALa
5. Pepsin : N–side of Leu, Asp, Glu
6. Papain : C– side of Gly , Lys, Arg
7. Cyanogen Bromide : It is a chemical method and cut at the C-terminal / or right side of methionine.
For example:
CNBr
Gly — Arg — Met — Ala Gly — Arg — Met + Ala

PROBLEMS
1. Phe - Gly – Lys – Glu – Met – Tyr – Leu – Asp – Arg – Trp – Ala
Trypsin: Phe – Gly – Lys + Glu – Met – Tyr – Leu – Asp – Arg + Trp – Ala
Chymotrypsin : Phe + Gly – Lys – Glu – Met – Tyr + Leu – Asp – Arg – Trp + Ala
Pepsin : Phe  Gly  Lys  Glu  Met  Tyr  leu  Asp  Arg  Trp  Ala
CNBr + HCOOH : Phe –Gly–Lys–Glu – Met + Tyr – Leu – Asp – Arg – Trp – Ala
2. The peptide has been treated with trypsin to give fragments A and B. Which are respectively re-
acted with chymotrypsin & CNBr + HCOOH. Deduce the ultimate fragment.

(A) (B)
Cyanogen
Chymotrypsin
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bromide

Asp – Phe + Val – Ser – Lys Met + Gly – Ala

1. End Group Analysis: C – Terminal determination

(i) Carboxypeptidase : It cut at C-terminal of peptide with one amino acid at once.
CBA
A—B—C—D A—B—C+D

(ii) Hydrazenolysis: The peptides (or protein) is heated with anhydrous hydrazine at 100ºC. This converts all
amino acids residues except the C-terminal one into amino acid hydrazides. The mixture of products is
subjected to chromatography on a column of a strong cation exchange resin. On elution the strongly b asic
hydrazides are retained, but the free amino acid is eluted and can be identified.
 16 Natural Products

NH CH CONH CH CONH CH COOH

R1 R2 R3
NH2 NH2

–NH CH CONH NH2 + NH2 CH CONHNH2 + H2N CH COOH

1 2
R R R3
Ion exchange
Strongly basic
Resin (cation exchange resin) Less basic

Strongly basic fragments will be retained and less basic amino acid will come out first.
(ii) Reduction by Lithium borohydride or lithium aluminium hydride:
The lithium borohydride converts the free terminal carboxyl group to a primary alcoholic group. The hydrolysis
produces a mixture of amino acids and amino alcohol, the amino alcohol being separated and identified by
paper chromatography.
NH CH CONH CH CONH CH COOH

R1 R2 R3
LiAlH4

NH CH CONH CH CONH CH CH2OH

R1 R2 R3
aq HCl/H2O

NH CH COOH + NH2 CH COOH + NH2 CH CH2OH

R1 R2 R3
Basic
cation exchange resin
Less basic
Free amine alcohol will come out last
2. N- Terminal Determination :
(i) Edman Method / Degradation : It is based on reaction between the peptide and phenyl isothio cyanate
 Ph  N  C  S  to form phenyl thio carbamyl (PTC) peptide in the presence of dilute
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terminal end react with phenyl isothio cyanate.
On treatment with acid the N-terminal end gets converted to phenyl thio hydantoin (PTH) and the
peptide is degraded by one unit from N–terminal site. PTH is separated by paper chromatography.
Advantage :
(i) It breaks only one amino acid from N-terminal side and keeps the rest of the peptide intact. So the process
can be repeated again.
(ii) This process is automatic and less time consuming
C6H5 N C S + NH2 CH CONH CH CONH CH COOH
R1 R2 R3
H2O
O

C6H5 NH C NH CH C NH CH CONH CH COOH

S R1 R2 R3
Natural Products 17
R1
HN
aq. HCl
C O + H2N CH CONH CH COOH
N
S R2 R3
Ph
Intact - Peptide
Separated by paper
chromatography
Labelled peptide Repeated the process
2. Amino Peptidase : Cut one amino acid from N-Side.
LAP
A—B—C—D A+B—C—D

3. Sanger’s Method :

O2 N F + NH2 CH CONH CH CONH CH COOH

R1 R2 R3
–HF
NO2

O2 N N CH CONH CH CONH CH COOH

H R1 R2 R3
Labelled peptide or DNFB peptide
Acid hydrolysis

O2 N N CH COOH + NH2 CH COOH + NH2 CH COOH

H R1 R2 R3
NO2
Yellow complex
DNFB derivatives are formed with any free NH2 group the basic amino acid like Lys and Arg will react with
DNFB even if it is not N-terminal acid. Besides NH2 the –OH group of Tyr, SH group of Cys and OH group
of Ser and imidazole nucleus of Histidine also react with DNFB slowly.
If the basic amino acid is not in the N terminal it will form mono DNFB derivative. If it is N-terminal it will form
di DNFB derivatives. The DNFB derivatives are isolated and identified by TLC (thin layer chromatography)
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For example: If Lys is in N-Terminal
NO2
R1
H2N CH CONH CH COOH DNFB
O2N N CH2 (CH2)4 + H2N CH COOH
aq. HCl
(CH2)4 1 H
R
HN NO2
NH2
O2N
Di-DNFB derivatives
4. Dansyl Method: A recent modification of DNP method is use of 5-dimethylaminonaphthalene-1-
sulphonylchloride ‘dansyl’ chloride (DNS-Cl), in place of DNFB. This modificication is called Dansyl
method. The Dansyl method is being used because the dansyl group is highly fluorescent permits the
detection and estimation of dansyl amino acids in minute amount by fluorometric methods.
18 Natural Products

SO2Cl
H3C
N
H3C
Dansyl group (Highly fluorescent) chloride

S Cl + H NH CH CONHCH COOH
H3C R2
O R1
N
–HCl
H3C
O

S NH CH CONHCH COOH
H3C
O R1 R2
N
HCl / H2O
H3C

S NH CH COOH + H2N CH COOH

H3C R2
O R1
N
H3C

Synthesis of Peptides:
1. Glycyl - Glycine : H 2 N  CH 2  CONH  CH 2  COOH
2. Glycyl alanine : H2N CH2 CONH CH COOH
CH3
3. Alanyl alanine : H2N CH CONH CH COOH
CH3 CH3
Protection Method:
Protecting group – For NH2 group.
1. Benzyl oxy carbonyl : Ph CH2 O C Cl
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O
(carbobenzyloxy)

2. t - butyl oxy carbonyl : t-Bu O C Cl

O
(BOC)

3. Trityl : (C6H5)3C –
(Triphenyl methyl)
O

O
4. Phthaloyl
O
Natural Products 19
CH3

5. Tosyl
O S Cl
O
Protecting group for COOH : Esterification
Activation group for COOH: Acid choride, acid azide, p-nitrophenyl ester.
DCC (Dehydrating agent): Direct combination of NH2 and COOH.
Dicyclo hexyl carbo-di-imide C6H11N C N C6H11
1. From Benzyl –Oxy Carbonyl :
O O
OH– H PCl5
Ph CH2 O C Cl + NH2 CH COOH Ph CH2 O C N CH COOH
–HCl
R' R'
NH2 CH COOH
H R2 H
Ph CH2 O C N CH COCl Ph CH2 O C N CH CONH CH COOH
O R' O R2
R'
HBr H2 – Pd
or, AcOH

Ph CH2Br + CO2 + Peptide Ph CH3 + Peptide

Alanyl Phenylaline :

O O
NH2 CH COOH – HCl H
Ph CH2 O C Cl + Ph CH2 O C N CH COOH
CH3 CH3
NH2 CH COOH
H CH2Ph H
Ph CH2 O C N CH COCl Ph CH2 O C N CH CONH CH COOH
O CH3 O CH3 CH2Ph
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H2–Pd

Ph CH3 + CO2 + Peptide

Activation of – COOH :

HO NO2
Z–N–CH–C–O NO2
R O
Z–NH–CH–COOH
R HNO2
NH2–NH2
Z–NH–CH CONHNH2 Z–NH–CH–CON3
R R
 20 Natural Products
2. FROM BOC METHOD :
(t-BuOCO)2O + NH2 CH COOH t-BuOCOCl
t-BuO C NH CH COOH
R' O R''
1. PCl5 H H + HBr
t-BuO C N CH CONH C COOH
– HOAc
2.NH2 CH COOH O R' R"
R"

CH2 + CO2 + NH2 CH

(CH3)2C CONH CH COOH
R' R"
3. FROM TRITYL CHLORIDE:
H
(C6H5)3C Cl H NH CH COOH –HCl (C6H5)3C N CH COOH
R' R'
O O
–H2O
4. From Phthalayl : O H2N CH COOH N CH COOH

O R O R

3. ANHYDRIDE METHOD :
H
Ph CH2 O C Cl + H2N CH COOH Ph CH2 O C N CH COOH
O R' O R'
(BOC) Benzyloxy carbonyl
PCl5
R O
C Heat O
Ph CH2 Cl + O H
PhCH2 O C N CH C Cl
HN C 70oc
O O R'
Anhydride
R O
C O
OH–
H
O NH2 CH COOH OOC NH CH C N CH COOH
HN C 1 2

O
R2
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R R
H+
CO2 + NH2 CH CONH CH COOH
R1 R2
4. DCC METHOD :
(i)
–H2O O
R C OH + NH2R' + C6H11N C N C6H11
R C NH R' + C6H11NH C NH C6H11
O
O
(ii)
Z NH CH COOH + NH2 CH COOH DCC Z NH CH CONH CH COOH + (C6H11NH)2CO
R' R' R' R"

SOLID PHASE SYNTHESIS :

Given by Bruce Merryfield. In this method amino acid or a peptide is bound chemically to a insoluble synthetic
resin and the peptide chain is build up by adding one amino acid at a time at the free end. When the required
peptide is synthesised it is liberated and removed from the solid support. The resin which is commonly used is
a co-polymer of styrene and divinylbenzene.
Natural Products 21
The biggest advantage of this method is that the purification of product is not neccessory because of the use of
insoluble solid support. Excess reagent or side product are simply removed by washing with suitable solvent.
The process is less time consuming & give excellent yield. The process is now automated that is each addition
of appropriate amino acid is carried out automatically at the predetermined time.

ClCH2 H
Resin + H2N CH COOH BOC N CH COOCH2 Resin
R' R'

i) HCl – AcOH DCC

NH2 CH COO CH2 Resin + (CH3)2C CH2
ii) Et3N H
R1 BOC N CH COOH
R2

Repeat
BOC NH CH CONH CH COOCH2 Resin above process
R2 R1
HBr
NH2 A3 CONH A2 CONH A1 COOCH2 Resin
CF3COOH

NH2 A3 CONH A2 CONH A1 COOH + H3C Resin

SOLVED PROBLEMS
NO2
Ph
O O2N F , H+
+ O
H (B)
LAH
C D
(A)
1. NaHCO3
H2N N COOH +
Leucine
H

Find, A  D

NO2 NO2 Ph
Ph O
O
O2N F + O2N NH N COOH
Soln. H2N N COOH
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H
H

Ph
NO2
O
+
aq, H
O2N NH OH + H2N COOH

LAH

NO2 Ph NO2 Ph
+
,H
O
O2N NH OH O2N NH OTHP
Protection of
–OH group
 22 Natural Products
NO2

O 2N F
N H+
2. H2N A B
NaHCO3
O COOH
NO2 NO2

N N
Soln. O2N F + H2N O2N NH
COOH COOH
O O
NO2

OH H+
O2N NH + N
O H
COOH
Nucleic Acid :
Nucleic acids are colourless solids which contain: Carbon, hydrogen, oxygen, nitrogen and phosphorus.
There are three components of the nucleic acid such as
(1) Nitrogenous Base (2) Sugar/Carbohydrate (3) Phosphate group PO34  H3PO 4  .
1. There are two types of bases which occurs in nucleic acids: purines and pyrimidines. The most common purine
bases are adenine and guanine whereas the most common pyrimidine bases are uracil, thymine and cytosine.

Nitrogenous Base

Purines Pyrimidine

Adenine Guanine Cytosine Uracil Thymine

NH2 H NH2 O O
6 1 4
1N N7 N
N 3
HN 5
HN CH3
8
2 6
2 N 4 N N N
O N1 O N
9
3 H H H
Adenine Uracil Thymine

O H
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O NH2 NH2
N CH3
HN N N
N
HN
H2N N N O N O N
H2N N N H
H H
guanine Cytosine 5-methylcytosine
2. Sugars: The sugar present in the nucleic acids are pentoses: D(–)-ribose and 2-deoxy-D-(–)-ribose.
CHO CHO
H OH H H
H OH H OH
H OH H OH
CH2OH CH2OH
D(–)-ribose 2-deoxy-D-(–)-ribose