Prof. Dr. Amani S. Awaad

Professor of PharmacognosyPharmacognosy Department,

College of Pharmacy Salman Bin Abdulaziz

University,

Al-Kharj. KSA.

Email: amaniawaad@hotmail.com

Pharmacognosy- 1

PHG 222

A Biosynthetic

Approach of

Medicinal Natural

Products

To know what is photosynthesis

To Recognize roll photosynthesis

To Identify types of natural products

To know the relationship between photosynthesis &

biosynthesis

To differentiate between all types of biosynthesis

bathways

Carbon dioxide + water + sunlight = sugar + oxygen

6CO2 + 6H2O (+ light energy) = C6H12O6 + 6O2.6CO2 + 6H2O

+ ENERGY)ATP)

photosynthesis, from the Greek, phōs, "light", and, synthesis, "putting together

Photosynthesis

light energy ------- absorbed by proteins called reaction centers

that contain green chlorophyll pigments

In plants, these proteins are held inside organelles called

chloroplasts, which are most abundant in leaf cells

in bacteria they are embedded in the plasma membrane.

In these light-dependent reactions, some energy is used to strip

electrons from suitable substances such as water, producing

oxygen gas

Furthermore, two further compounds are generated: reduced

nicotinamide adenine dinucleotide phosphate (NADPH) and

adenosine triphosphate (ATP), the "energy currency" of cells.

Plants metabolites

Primary

Important for plant vitality

sugars and polysaccharides; amino acids, peptides and proteins (including enzymes); fatty acids; and nucleotides. The starting materials are CO2, H2O and NH3

Secondary

not essential for growth, development or reproduction

arise from acetyl coenzyme A (acetyl-CoA), mevalonic acid (MVA) and methyl erythritolphosphate (MEP), shikimicacid, and the amino acids phenylalanine/tyrosine,

tryptophan, ornithine and lysine (Alkaloids, Terpens,

phenolic compounds)

Primary metabolism:

Biosynthesis, utilization and breakdown of

the essential compounds and structural

elements of the living organism, such as:

sugars and polysaccharides; amino acids,

peptides and proteins (including enzymes);

fatty acids; and nucleotides. The starting

materials are CO2, H2O and NH3.

All organisms possess similar primary

metabolic pathways and use similar primary

metabolites.

Metabolism: (Gr. metabole = change) the totality of the chemical

changes in living cells which involves the buildup and breakdown

of chemical compounds.

IntroductionPhotosynthesis

Plants metabolites

Primary

sugars and polysaccharides; amino acids, peptides and

proteins fatty acids

Secondary

Alkaloids, Terpens, phenolic compounds

IntroductionPhotosynthesis

Secondary metabolism:

Secondary metabolism, metabolic pathways

that are not essential for growth,

development or reproduction, but that

usually have ecological function.

refers to the biosynthesis, utilization and

breakdown of smaller organic compounds

found in the cell. These compounds, called

secondary metabolites, Secondary

metabolites are those chemical compounds

in organisms that are not directly involved in

the normal growth, development or

reproduction of an organism

Secondary metabolites, are found in only specific organisms, or groups of organisms, and are an expression

of the individuality of species.

Plants metabolites

Primary

sugars and polysaccharides; amino acids, peptides and

proteins fatty acids

Secondary

Alkaloids, Terpens, phenolic compounds

IntroductionPhotosynthesis

Secondary metabolism:

some important functions:

1. Hormones.

2. As coloring agents to attract or warn other species

3. Vitoalexan (As toxic materials) providing defense against predators.

4. Stimulate secretion of other compounds. Alkaloids, terpenoinds, phenolic compounds, glycosides, sugars & amino acids.

Primary and Secondary MetobolitsPhotosynthesis

Relationship between primary and secondary

metabolism

•The processes and products of primary metabolism are

similar in most organisms, while those of secondary

metabolism are more specific.

*In plants, primary metabolism is made up of

photosynthesis, respiration, etc., using CO2, H2O, and NH3

as starting materials, and forming products such as glucose,

amino acids, nucleic acids. These are similar among

different species

* In secondary metabolism, the biosynthetic steps, substrates

and products are characteristic of families and species.

Species which are taxonomically close display greater

similarities (and metabolites); those which are distant have

greater differences

Classification of natural products

According to physic-chemical

structure

according to biogenetic origins or biosynthetic

pathways

According to pharmacological activity

There are three approaches to the study of natural products:

Classification of natural products

Why study the biosynthetic pathway?

• The determination of the biosynthetic pathway enables us to

understand the relationships and dynamic flow of the compounds that

are present in a living cell.

• The objective of the study of a biochemical sequence is to be able to

identify the “intermediates” and the “product”. However, there are

cases when this is not so obvious. During the chemical extraction

process, we obtain many of these compounds and the problem is to

determine the sequence of their formation.

• An understanding of a biosynthetic sequence can help us identify

the enzymes and genes, understand the relationships among different

organisms (such as symbiosis, plant-insect interactions, etc). An

understanding of biosynthesis is part of a complete understanding of

plant biology, ecology and biodiversity.

Biosynthesis

• It enables us to classify the diversity and

complexity of natural products structures.

• It reveals the functional relationships among

natural products in a dynamic context.

• It provides essential information which enables

us to control or manipulate the formation of

desired metabolites.

• It opens up possible directions in biotechnology

and molecular biology through the study of

enzymes (proteomics) and genomics:

Genomics + Proteomics + Biosynthesis =

Metabolonomics

Why study the biosynthetic pathway?

Biosynthesis

A biosynthesis pathway, or biosynthetic pathway:

is a description of the steps of the chemical reactions that occur

when a living organism creates a new complex molecule out of

simpler, smaller precursors.

The word "biosynthesis" comes from two root words:

"bio," which indicates that the reaction is taking place within a

living organism as opposed to within a laboratory;

"synthesis," which indicates that simple starting materials are

being combined to form larger products.

A biosynthesis pathway is a summary of these chemical

reactions, broken down by each step.

To describe a pathway completely, extra relevant information is

often included, such as which enzymes, coenzymes and cofactors

are used in each reaction.

Biosynthesis

Biogenesis: overview of the origin of compounds starting

from the set of intermediate building blocks: acetyl-CoA, MVA

and MEP, shikimic acid, and the amino acids phenylalanine and

tyrosine, tryptophan, ornithine and lysine.

SCoA

O

CO2H

CH3HO

OH

CO2H

OH

OH

HO

NH2R

CO2H

NNH2

CO2H

HH2N CO2H

NH2

H2NCO2H

NH2

Biosynthesis: detailed study of the step-wise

formation of secondary metabolites. At more detailed

levels, the specific enzymes, genes and signals are also

identified.

HO

CH3HO

OP

OH

Biosynthesis

PRIMARY METABOLITES INTERMEDIATE METABOLITES SECONDARY METABOLITES

CO2 + H2O Glucose

Polysaccharides

Pentose phosphateErythrose-4-phosphate

Phosphoenol pyruvate

Shikimate

Aromatic compounds

(C6-C1; C6

-C2)

Phenylpropanoids (C 6-C3)

Lignans

Pyruvate

Citric acidcycle

Aromaticamino acids

Aliphaticamino acids

Aromatic alkaloids

Mixed alkaloids

Aliphatic alkaloids

Acetyl-CoA Polyketides Polyphenols

Phenylpropanoids

Flavonoids

Fatty acidsPolyacetylenesProstaglandins

Mevalonic acidTerpenesSteroidsCarotenoids

+NH3

Iridoids

Aliphaticamino acids

Alkaloids

Overview of

Secondary

Metabolism

* Metabolites found in

higher organisms only

*

*

*SCoA

O

CO2H

CH3HO

OH

CO2H

OH

OH

HO

NH2R

CO2H

NNH2

CO2H

H

H2N CO2H

NH2H2NCO2H

NH2

Biosynthesis

• The building blocks for secondary metabolites are derived from primary metabolism.

• The number of building blocks needed is surprisingly few

The building blocks

• The most important building blocks employed in the biosynthesis of secondary metabolites are derived from:

1. Acetyl coenzyme A (acetyl-CoA)

2. Shikimic acid

3. Mevalonic acid

4. 1-deoxyxylulose 5-phosphate

5. Amino acids

• The form in which acetate is used in most of its important biochemical reactions is acetyl coenzyme A (acetyl-CoA).

• Acetyl-CoA is formed by oxidative decarboxylation of the glycolytic pathway product pyruvic acid.

• Important secondary metabolites formed from the acetate pathway includes:

1. Phenols (Synthesis of plumbagin )

2. Prostaglandins

3. Macrolide antibiotics

1. Acetate pathwayBiosynthesis cont….

Coenzyme A: present in all living cells that functions as an acyl

group carrier

P

N

N

N

NH2

OP

O

O O

OH OH

NH

NH

RS

OH

OO

O

O OH

O

P

O

HOHO

CH3H3C N

2. Shikimate pathwayBiosynthesis cont….

• Shikimic acid is produced from a combination of phosphoenolpyruvate, a glycolytic pathway intermediate, and erythrose 4-phosphate from the pentose phosphate pathway.

• The shikimate pathway leads to a variety of:

1. Phenols

2. Cinnamic acid derivatives

3. Lignans

4. Alkaloids

3.Mevalonate pathwayBiosynthesis cont….

• Mevalonic acid is itself formed from three molecules of acetyl-CoA, but the mevalonate pathway channels acetate into a different series of compounds than does the acetate pathway.

Mevalonic acid is a precursor to biosynthesis of

terpenoid. The biosynthesis which is started from

acetylCoA until formation of the mevalonic acid is called

as Mevalonate Pathway

This pathway starts with production of acetoacetyl-CoA through

Claisen-like condensation mechanism which was catalyzed by

thiolase. The third acetyl-CoA is then condensed with a

acetoacetyl-CoA through aldol reaction to form (S)-3-hydroxy-

3-methylglutaryl- CoA (HMG-CoA) by HMG-CoA synthase.

The NAdph-dependent HMG-CoA reductase then converts to

CoA derivative to (R)-Mevalonate acid (MVA).

4. 1-Deoxyxylulose phosphate pathway

Biosynthesis cont….

• Deoxyxylulose phosphate arises from a combination of two glycolytic pathway intermediates, namely pyruvic acid and glyceraldehyde 3-phosphate.

• The mevalonate and deoxyxylulosephosphate pathways are together responsible for the biosynthesis of a vast array of terpenoid and steroid metabolites

Biosynthesis cont….

5. Amino acids pathway

• Peptides, proteins, alkaloids and many antibiotics are derived from amino acids.

• Intermediates from the glycolytic pathway and the Krebs cycle are used in constructing many of them.

• The aromatic amino acids phenylalanine, tyrosine, and tryptophan are themselves products from the shikimatepathway.

• Secondary metabolites can be synthesized by combining several building blocks of the same type, or by using a mixture of different building blocks.

• Many of secondary metabolites also contain one or more sugar units in their structure.

• To appreciate how a natural product is elaborated, it is of value to be able:

1. To dissect its structure into the basic building blocks from which it is made up.

2. To propose how these are mechanistically joined together.

• Oxygen atoms can be introduced and removed by a variety of processes, and so are not considered in the initial analysis, except as a pointer to an acetate or shikimate origin.

• Relatively few building blocks are routinely employed, and the following list includes those most frequently encountered in producing the carbon and nitrogen skeleton of a natural product

Biosynthesis

• Indole.C2N: the third of the aromatic amino acids is L-tryptophan.

• C4N: the C4N unit is usually found as a heterocyclic pyrrolidine system and is produced from L-ornithine (non-protein amino acid).

• C5N: it is produced by using L-lysine and the unit tends to be found as a piperidine ring system.

C1: the simplest of the building blocks is composed of a single carbon atom, usually in

the form of a methyl group, and most frequently it is attached to oxygen or nitrogen, but

occasionally to carbon. It is derived from the S-methyl of L-methionine.

C2: A two-carbon unit may be supplied by acetyl-CoA. Acetyl-CoA is first converted into

the more reactive malonyl-CoA before its incorporation.

C5: the branched-chain C5 “isoprene” unit is a feature of compounds formed from

mevalonate or deoxyxylulose phosphate.

C6C3: this refers to a phenylpropyl unit and is obtained from the carbon skeleton of either

L-phenylalanine or L-tyrosine.

C6C2N: again, this building block is formed from either L-phenylalanine or L-tyrosine

Biosynthesis

• Natural product molecules are biosynthesized by a sequence of reactions which are catalyzed by enzymes.

• Enzymes have the power to effect these transformations:

1. More efficiently and more rapidly than the chemical analogy.

2. Under very much milder conditions.

3. Carry out reactions in a stereospecific manner.

The construction mechanisms

Biosynthesis

Biogenetic classification of natural products.

Biogenesis

Intermediate

Structural Types

Acetogenins (n x C2)

acetyl CoA

fats and lipids,

macrolides, phenols

Terpenoids (n x C5)

mevalonic acid,

methyl erythritol phosphate

monoterpenes, sesquiterpenes, diterpenes, triterpenes, steroids

carotenoids

Shikimates

shikimic acid, prephenic acid

phenylpropanoids, phenols

flavonoids

Aliphatic alkaloids

lysine, ornithine

aliphatic alkaloids

Aromatic alkaloids

phenylalanine, tyrosine,

tryptophan

aromatic alkaloids

Most of the biosynthetic reactions are mediated by specific enzymes.

Enzymes have five fundamental properties:

Enzymes in biosynthesis

1. increase in reaction rate - enzymes are catalysts which increase the

forward and reverse rates of a chemical step.

2. kinetic control - Enzymes are subject to various types of control, such as

pH and feedback.

3. chemoselectivity - Enzymes can distinguish functional groups. For

example, in an oxidation reaction: C-H C-OH, chemoselectivity

allows the differentiation between various types of C-H, such as primary,

secondary and tertiary alkyl, olefinic and aromatic positions.

4. regioselectivity - Regioselectivity is the ability of select only one site of

reaction from a number of possibilities of the same functional group. For

example, in a long chain saturated fatty acid, the initial site of

dehydrogenation is typically 9,10. In a sugar, or a compound with many

-OH groups, the position of methylation is specific.

5. stereoselectivity - This refers to the chiral recognition of substrates

(compare with chemoselectivity).

1- All secondary metabolites, no matter how complex, are biosynthesized via discrete

chemically-reasonable steps. The biosynthetic transformations are classified as

follows:

1. hydrolysis

2. esterification

3. oxidation: hydroxylation, epoxidation or oxygenation of alkene,

dehydrogenation, halogenation

4. reduction: hydrogenation, deoxygenation

5. carbon-carbon bond formation: aromatic radical coupling, Claisen

condensation, aldol condensation

6. Cationic rearrangement: 1,2-migration, Wagner-Meerwein

7. Rearrangement under control of orbital symmetry

8. Sn2 displacement

9. E2 elimination

10. carboxylation / decarboxylation

Biosynthesis

3. The enzymes are located in specific parts of the cell, and in some cases may be immobilized on a membrane.

4, The enzymes are coded for in the plant’s genome whose expression can be controlled at the level of the gene.

Biosynthesis2. Each step is presumed to be mediated by a specific enzyme. All chemical transformations are accounted

for by the system of six enzyme classes:

1-oxidoreductase2-transferase 3-isomerase

4- ligase 5-lyase 6-hydrolase