lecture 02 - natural products & biosynthesis, web

7/14/2019 Lecture 02 - Natural Products & Biosynthesis, Web

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Bratton, Heather

Bui, Steven

Chan, Hiu Fai

Doan, Chad

Ho, Joyce

Karimbabai Massihi, Anna

Krasner, Danielle

Loi, William

Malette, Jacqueline

Nguyen, Trang

Robles, Marisa

Tallorin, Lorillee

Truong, Daniel C

Udeh, Francis

Villalvazo, Adrianne

Yeh, Enrenn

Bautista, Candie

Chen, John

Chida, Odette

Cueva, Carla

Golanbar, Gelareh

Kashiwabara, Claudine

Kopilec, Jaimisyn

Lau, Jensen

Le, Giang-Tuong

Lee, Margaret

Mata, Francisca

Nguyen, Thuy Nhi

Phillips, Irving

Romero, Marcelo

Wang, Tony

Wittig, Michelle

Biol 444Chem 444



Primary (1°) Metabolism

- Construct common biological macromolecules from simple building blocks found within every cell

- Typically a process of polymerization, stringing monomers

together into a macromolecule that performs a cellular function

sugars polysaccharides

amino acids proteins

fats phospholipid bilayers

- Block production: cell dies (primary metabolites are essential)



Secondary (2°) Metabolism

- Synthesize compounds that are unique to a particular speciesor genus (unlike common proteins, lipids, etc.)

- Molecules may have extremely complex structures

- These molecules typically have no effect on the producingorganism, but are often highly biologically active against

other organisms (competitors, pathogens, predators)

- Often present at extraordinary concentrations, >10%of the dry weight of the organism

inference is, they must do something



Natural Products: Folk to Modern Medicines

- Humans have long used chemicals in plant and animal extractsfor many purposes: medicines, poisons, recreational stimulants

- Since the 1800’s, chemists have characterized and synthesized

such natural products, uncovering the basis for folk remedies

- Identifying the mechanism of action of natural products was

the genesis of modern drug discovery

-

-

- The active ingredients in many ancient curatives are still used

medicinally today



Natural Products 1: Toxins

Curare (Tubocurarine chloride)

- Derived from 2 South American plant genera

- Used as arrow-tip poison by native peoples

- Blocks transmission of acetylcholine signal to muscles, causing

instant paralysis

- 1st

drug used as muscle relaxant in surgery

Rotenone

- Natural fish + insect poison



Natural Products 1: Toxins

- Derived from plants: deadly nightshade (belladonna), mandrake

- In ancient Greece, mandrake was used as an anaesthetic

(or poison, in higher doses)

- ―Witches‖ smeared extracts on their armpits: avoided toxic oral route,

got maximum hallucinogenic effect = felt like they were flying

- Blocks certain acetylcholine receptors

- Modern use: prevention of motion sickness (patches behind the ear)

Hyoscine (= scopolamine)



Natural Products 2: Medicines

Salicin

COCH3

Acetyl-salicilic acid: aspirin

- From Willow tree bark, which was used in folk remedies

for treating fevers

- Led to synthetic analogue, modern aspirin




- From Ephedra plants, basis of ancient Chinese herbal remedy

―Ma Huang‖ (100 AD) for treating respiratory illness

- Used clinically since 1926 as bronchodilator to treat asthma- Similar to adrenaline, but also stimulates heart (not good in a drug)

- Stimulated research resulting in the non-stimulant drug Ventolin

Ephedrine

Ventolin




Quinine

- Found exclusively in the bark of the Chinona tree

- Used as a malaria treatment since 1600’s

- Now synthetic derivatives used, due to widespread resistance



Natural Products 3: Stimulants

- Caffeine-containing plant leaves + seeds have long been brewed to

produce stimulant drinks

- Such stimulants naturally act as feeding deterrents to repel insectherbivores that consume plants leaves

- Tobacco plant can up its production of nicotine 4-fold when under

attack by insects; nicotine by-products are used as insecticides

Caffeine Nicotine



Natural Products 3: Stimulants

- Coca leaves have been used as a source of cocaine for > 2,000 yrs

- Used by Incas in religious ceremonies

- Introduced to Europe by conquistadores

- Leaves chewed daily by >8 million native peoples in the Andes,

to alleviate feelings of hunger and fatigue

- Inhibits re-uptake of excitatory neurotransmitter dopamine

Cocaine



Natural Products 4: Halucinogens

Morphine (= opium) Heroin (synthetic derivative)

- Found in only 2 species of poppy flower ( Papaver )

- Milky exudate of seed capsules is 25% opiate

- Used as a baby calming treatment in ancient Egypt

- Binds to brain receptors for short peptides called enkephalins,

derived from endorphins




Morphine

Enkephalin

*

**

*

Similar spatial relationships of

(*)-marked atoms responsible for

similar pharmacological effects




- Lysergic acid is the parent compound from

which ergot alkaloids are derived, such as LSD

- Produced by fungus; often affected stored grain in Middle Ages

- Such compounds found in Aztec ―magical‖ preparation ololuiqui

- Structural mimics of human neurotransmitter 5-hydroxytryptamine

Lysergic acidTetrahydrocannabinol

Lysergic acid

Diethylamine

(LSD, synthetic)



Secondary Metabolites

- Produced from a small number of key intermediates, oftengenerated as by-products of primary metabolism

acetate (in the form of acetyl coA)

mevalonate

4-carbon sugars

- Perhaps arose as a means of dealing with excess metabolic

intermediary compounds

-2o metabolites then took on ecological roles as toxins, etc.



Secondary Metabolites

- Typically play ecological roles in nature, deterring would-be pests, predators or pathogens

- Affect humans due to structural resemblance to innate

neurotransmitters, or by binding to proteins in a way thatdisrupts normal cellular function

- Natural products are the basis for a big % of pharmaceutical

drugs currently on the market

-



Simple building blocks serve as the basis for each major

pathway of secondary metabolism:

(1) Shikimate Aromatics (ring - C3 chain)

(2) Amino acids Alkaloids, Penicillins

(N-containing)

(3) Mevalonate Terpenes, Steroids

(4) Acetate Polyketides

(aromatics, macrocycles)



Polysaccharides

Glycosides

Nucleic Acids

Shikimate pathwayAromatic Compounds

Lignans

aromatic amino acids

aliphatic amino acids

CH3COSCoA

CH3COSCoA

(photosynthesis)

phosphoenol

pyruvate

pyruvate

acetyl

CoA CH3COSCoA

-O2CCH2COSCoA

CH3COSCoA

Polyketides, Fatty Acids Prostaglandins, Macrocyclic Antibiotics

Shikimate

CH3COCH2COSCoA

mevalonate

Isoprenoids (terpenes, steroids,

carotenoids)

AlkaloidsPeptides

Penicillins

Cyclic Peptides

CITRIC

ACID

CYCLE

(1)

(2)

(3) (4)



from the Japanese flower shikimi (シキミ

, Illicium anisatum)

(A) Biosynthesis of aromatic amino acids (tyrosine,

phenylalanine, and tryptophan) lead to alkaloids

(B) Build aromatic secondary metabolites

Podophyllotoxin

(1) Shikimate pathway

Shikimate



Shikimate biosynthesisChorismateShikimate + PEP

Prephenate

+ NH3

Tyrosine,

Phenylalanine

- NH3Cinnamic

acid

Other

shikimate

metabolites:

ring-C3

...ring-C2

...ring-C1



Biosynthesis of phenyl compounds

vanillin vanillic acid salicin salicylic acid

- In plants, many shikimate metabolites are allelopathic:

they inhibit growth of competitors- Insoluble forms often linked to sugars in plant tissue

- Soluble acidic forms leach out into surrounding soil in rain

ring-C1 type



Lignans & Lignins

Podophyllotoxin

Polymerization:

complex lignins

Cinnamyl

alcohol

Large % of

woody plant

biomass

Enzymatic coupling:

dimeric lignans

phenylalanine

Cinnamicacid



Podophyllotoxin

- An important shikimate compound

- Used by native Americans to cure warts

- Powerful inhibitor of mitosis; found to

block enzyme tubulin polymerase

-

-

-



Flavanoid Biosynthesis

Shikimate + 3 acetates = flavanones

Cause bitter tastes in plants,

especially polymerized tannins;deter feeding by herbivores

Derived compounds are

responsible for much of plant

color



(2) Amino acids Alkaloids, Peptides, Penicillins

Penicillin

Cyclosporin A

(cyclic peptide)

Strychnine(alkaloid)

(2) Alkaloids



Alkaloid characteristics

- Non-(normal)-peptide, non-nucleic acid compounds thatcontain nitrogen

- Common in fungi, plants, insects + amphibians

- Derived from amino acid precursors



Tyrosine

Tyramine

Dopamine

Mescaline

- potent hallucinogen from the peyote cactus

- competitively binds to dopamine receptors



a-adipate

+

cysteine

+

valine

Penicillin Biosynthesis

- start with peptide made of 3 amino acids

(including a non-standard a.a., a-adipate)



a-adipate+

cysteine+

valine

isopenicillin synthase

epimerase penicillin Nisopenicillin N

penicillins

cephalosporins



Penicillins: Mechanism of Action

This class of antibiotics interferes with synthesis of the cell wall

of Gram-positive bacteria (Staphylococci, Streptococci)

Cell wall is a repeating polymer of disaccharide, tetrapeptide

repeats cross-linked into a 3D matrix

sugar - sugar - phospholipid

L-ala — D-glu — L-lys — D-ala — D-ala

(glycine)5

(1) cleave here(transpeptidase)

(2) cross-link here



Penicillins: Mechanism of Action

Penicillins inhibit the bacterial transpeptidase enzyme by

mimicking its natural substrate, the terminal D-ala — D-ala

Transpeptidase attacks the b-lactam ring of penicillin, forms a

covalent bond; enzyme is now out of business



(1) NO CLASS next Monday

(2) For NEXT WEDNESDAY –

- bring to class a small amount of some spice, seeds, leaves,

fruit, or medicinal herb

- pick something with a strong taste/smell, or that you

know is used in a folk remedy

- at Wednesday’s lecture, you will put your material in a tube

and label it; I will then add solvent and extract the natural

products from it over the weekend

- in the next lab, you will bioassay the extracts of your material

for antibiotic activity and cytotoxicity

lecture 02 - natural products & biosynthesis, web

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