pharmacognosy- 1 phg 222 - faculty.psau.edu.sa department, ... email: [email protected]...
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Prof. Dr. Amani S. Awaad
Professor of PharmacognosyPharmacognosy Department,
College of Pharmacy Salman Bin Abdulaziz
University,
Al-Kharj. KSA.
Email: [email protected]
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