Natural Products Chemistry

Sources, Separations, and Structures

By
Mufti Dekamo (B Pharm, MSc)
PLANTS SECONDARY METABOLITES
1. Phenolic compounds from the willow bark
 The active ingredient in willow bark is salicin,
converted in the body into salicylic acid.
 Salicylic acid is more commonly known as aspirin.
 o

The presence of a phenol is recognized by the

attachment of an OH group to the benzene ring.
Substitutions on the phenolic group of various natural
products include, but are not limited to, methyl, acetyl,
and ether linkages.
2. Terpene camphor
Camphor: a terpenoid with the chemical formula
C10H16O.
It is found in the wood of the camphor laurel
(Cinnamomum camphora), a large evergreen tree.
It is a volatile oil and is often used for its scent.

O
3. Alkaloids & the presence of nitrogen
 N is present in alkaloids as part of cyclic ring.
E.g, nicotine which is found in tobacco.
 The compound contains two nitrogens, one in the
pyridine ring and the second as a reduced
(tetrahydro)–pyrrole ring.
N

N
4. A steroid from the garden
 Digitalis from foxglove (Latin name: Digitalis

purpurea).
 Foxglove roots & seeds, contains several deadly

physiological and chemically related cardiac and

steroidal glycosides.
 Used for the first time in 1785.

 Very toxic and must be very carefully administered

 O

O
HO

HO

HO
5. Sulfur in nature
 Garlic, known as Allium sativum, is a species in the
onion genus Allium.
 Has a history of use for over 7000 years and is used
for both culinary and medicinal purposes.
 There are a number of organosulfur compounds
present in garlic.
(a) Diallyldisulphide
(b) Ajoene
S
(a) S

S
S S
(b)

O
SOURCING OF NATURAL PRODUCTS

 Wrt sourcing of NPs from plants:

 1st, attention needs to be paid to the correct identification of the
species.
 2nd, identified species found in different geographical locations
might yield different metabolites or ratios of metabolites.
 Finally, the selection of the plant part is very important: flowers,
fruiting bodies, bark, seeds, or stems.
 Metabolites vary within the whole plant as fresh or dried
material, or from the roots or the aerial parts.
 Sources of Microbes

Bacteria and fungi:

• Have been an invaluable source for discovering
antimicrobial agents.

 Some remarkable discoveries:

o Penicillins.
o Cephalosporins.
o Tetracyclines.
 Marine Sources

 corals, sponges, fish, and other marine MOs have

provided a wealth of biologically potent chemicals with
interesting inflammatory, antiviral, and anticancer
activity.
E.g.,
o curacin A is obtained from a marine cyanobacterium

and shows potent antitumor activity.

o Other antitumor agents derived from marine sources

include the bryostatins.

 Animal Sources

 Interestingly, animals have yielded new natural

chemical entities.
E.g.,
o a series of antibiotic peptides was extracted from the skin
of the African clawed frog.
o a potent analgesic compound called epibatidine was
obtained from the poisonous skin extracts of the
Ecuadorian frog.
 Venoms and Toxins

 Discovered from plants, microbes, snakes, spiders,

scorpions & insects.
 Extremely potent because they often have very
specific interactions with a macromolecular target in
the body.
 As a result, they have provided researchers with
important tools in studying receptors, ion channels,
and enzymes.
 Many of them are polypeptides such as bungarotoxin
from cobras.
 However, nonpeptide toxins such as tetrodotoxin
from the puffer fish are also extremely potent.
 EXTRACTION
AND
SEPARATION
OF
NATURAL PRODUCTS
 NPs are found in a variety of sources and invariably
present as mixtures.
 It is the task of NPs chemist to isolate and purify
them, to homogeneity, to identify the chemical
structure.
 A variety of separation techniques is available.
 Generally,
 The first step is:
 Dissolving in (aqueous, organic, or liquid CO2, etc.), and
 Filtering from the marc (plant residue) or the mycelia
(fermentation).
 Then by concentrating the solvent an ideal outcome
would be crystallization!
 This is rare and generally other separation steps are
required.
1.Water-steam Distillation

1. Water is boiled
2. The water-steam vapors are passed over and
through the source material,
 Releasing and carrying the (volatile) chemicals
away from the residue.

3. In many cases, as the steam condenses and cools,

the oils float to the top and are easily removed.
 commonly used to extract volatile plant oils.
 2. Supercritical Fluid Extraction

 Separating a component from the matrix using SFs

(CO2, most used) as a solvent.
 Extraction is usually from a solid matrix, but can also
be from liquids.
 Extraction conditions for supercritical CO2 require a T°
around 31°C and a critical pressure of 74 bar.
 3. Solvent Partitioning

The most common 2nd step of solid extraction.

Taking advantage of 2 or 3 immiscible solvents (e.g.,

Water and ether)

The common rule of thumb is:
1. Polar compounds go into polar solvents
o e.g., amino acids, sugars, and proteins remain in water,

2. Nonpolar remain in the organic phase

o e.g., steroids, terpenes, waxes, and carotenoids are extracted ethyl

acetate.
 EXTRACT FLOW

1. Source the natural material (fresh or in dried form)

2. Grind material to powder

3. Extract with an organic solvent (liquid­extraction)

4. Filter, remove marc

5. Retain the elute

6. Separate between two immiscible solvents (solvent

partition)

7. Retain organic layer and concentrate

 4. Refined Isolation Techniques & Chromatography
4.1. Separation of Nonpolar Compounds
ⅰ. TLC: the simplest, cheapest, and most rapid.
 Mixtures are applied to precoated silica gel plates, which are
then immersed in a chamber containing a sufficient amount of
the eluting solvent, to allow for solvent migration.
 As the solvent migrates up the plate the mixture is separated on
the coated plate due to each component having a different
retention time.
 Used mostly for small quantities of material and is a very
versatile technique for nonpolar compounds.
ⅱ. Silica gel column chromatography
 Often referred to as normal phase.

 Commonly used for separation of larger quantities of nonpolar

materials.
 In this case, an eluent is passed through a column packed with

silica gel.
 The mixtures of compounds are separated and are eluted off

the silica gel column in the eluting solvent.

ⅲ. GC is used for more volatile and nonpolar compounds.
 In this case, a carrier gas (e.g., nitrogen/ helium) is passed
over a coated and heated column.
 This method has been successfully used for the separation of
oils, volatiles, terpenes, and esters of fatty acids.
 Polar stationary phase may be used for the chromatographic
separation.
4.2 Separations of Polar Compounds
Ion exchange chromatography is used.
 The resin is often made from polymeric material, coated or bound
with a resin.
 There are 4 main types of ion exchange resin differing in their
functional group:
1. Strongly acidic
2. Strongly basic
3. Weakly acidic
4. Weakly basic
 5. Charcoal
 Black, refined and of fine mesh or macroporous.
 Advantages: very cheap, plentiful, and can be used with either
aqueous or organic solvents or a combination of both
 The exact mechanism by which charcoal interacts with solutes is
not well understood, however, it is often used to “decolorize”
and remove impurities.
 6. Reverse Phase Resins
 Can be used to separate compounds that are much more polar.
 The more polar compounds elute first.
 7. HPLC
 Using modern macroporous resins as the stationary phase, the
beads can be as small as 2.5 to 3.0 microns.
 Popular resin-based packing material is made from the
copolymerization of polystyrene and divinylbenzene.
 Advantages: fast separations using high pressure and small
volumes of solvent.
 Good resolution can be achieved with baseline separation using
ultra high-performance technology.
 8. Capillary Electrophoresis (CE)
 Used to separate ionic species by charge, frictional forces, and
hydrodynamic radius.
 Separates species based on size: charge ratio in the interior of a
small capillary, filled with an electrolyte.
 In traditional electrophoresis, electrically charged analytes move
in a conductive liquid medium under the influence of an electric
field.
 9. Polyamide gel Chromatography
 Porous polyamide resin possesses H-bond acceptor properties &
is a very good medium for separation of polyphenolic solutes
such as phenolic acids, flavonols, and flavonoids.
 Typical solvent mixtures include aqueous acetic acid and
ethanolic solutions.
 10. Size- exclusion Chromatography
 In SEC, molecules in solution are separated according to their
size (i.e., molecular weight).
 Well adapted to separation of large molecules, particularly
proteins and industrial polymers.
 Gel filtration chromatography when aqueous sln is used to
transport sample through column.
 Gel- permeation chromatography occurs when organic solvent is
chosen as the mobile phase.