Rational Drug Design

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Rational Drug Design
Using the 3D Shape of Proteins to Design Drugs
that Inhibit Protein Function
Before you start this activity, make sure you
have the program Cn3D installed on your computer.
Download Cn3d from this site
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Examples of Protein Function

• Hormones
• Insulin binds to receptors on cell membranes
  signalling cells to take up glucose from the blood

Protein ChannelsRegulate movement of substances
across the plasma membrane. E.g. The CFTR
protein pumps ions across membranes
Transport Haemoglobin (far right) in red blood
cells transports oxygen to cells around the body
Source http//www.biology.arizona.edu/biochemistr
y/tutorials/chemistry/page2.html http//www.cbp.pi
tt.edu/bradbury/projects.htm http//www.abc.net.au
/cgi-bin/common/printfriendly.pl?/science/news/env
iro/EnviroRepublish_1191825.htm http//www.umass.e
du/microbio/chime/
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Catalase - enzyme power!

• Hydrogen peroxide, a natural product of
  metabolism in your cells, is highly toxic in high
  concentrations and must be removed quickly!

Products
Reactants
oxygen
Add ferric ions (Fe 3) Rate increases 30 000-fold
2
2
water
Hydrogen peroxide
Add Catalase Rate increases 100 000 000-fold
Location of active site where Hydrogen peroxide
binds
Source http//accad.osu.edu/ibutterf/ibp/molecul
e/ http//folding.stanford.edu/education/water.htm
http//www.opti-balance.com/hyperox.htm
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How enzymes do it!

• Enzyme proteins have specific sites where all the
  action happens. We call this the active site.
  Molecules that need to be ripped apart or put
  together enter the active site.
• Each protein has a specific shape so it will only
  perform a specific job.

Ripping things apart
Joining things together
http//chsweb.lr.k12.nj.us/mstanley/outlines/enzym
esap/Enzymesap.html http//academic.brooklyn.cuny.
edu/biology/bio4fv/page/active_.html
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Many toxins are proteins
Ricin from the seeds of the castor oil plant
destroys ribosomes
Funnel web spider toxin blocks movement of
calcium ions.
Source http//www.wiley.com/legacy/college/boyer/
0470003790/cutting_edge/molecular_recognition/mole
cular_recognition.htm http//science-univers.qc.ca
/image/ricin061.jpg http//www.staabstudios.com/Sp
ider.htm
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Protein molecules are polymers

• Proteins are very large polymer molecules.
  Polymers are made by linking smaller molecules,
  monomers, together to make a long chain.
• In the case of proteins, the monomers are amino
  acids. There are 20 different amino acids.

AA
AA
AA
AA
AA
AA
AA
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Why is protein structure important?

• Each protein molecule has a characteristic 3D
  shape that results from coiling and folding of
  the polymer chain.
• The function of a protein depends upon the shape
  of the molecule.

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Protein chains

• Each protein has a specific sequence of amino
  acids that are linked together, forming a
  polypeptide

http//www.mywiseowl.com/articles/ImageProtein-pr
imary-structure.png
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The protein chain folds

• Interactions between amino acids in the chain
  form
• alpha helices
• beta sheets
• Random coils

Together usually form the binding and active
sites of proteins
Source http//www.rothamsted.bbsrc.ac.uk/noteboo
k/courses/guide/prot.htmI
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And folds again!

• After folding, amino acids that were distant can
  become close
• Now the protein chain has a 3D shape that is
  required for it to function correctly

Source io.uwinnipeg.ca/simmons/
cm1503/proteins.htm
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The final protein

• The final protein may be made up of more than one
  polypeptide chain.
• The polypeptide chains may be the same type or
  different types.

Source http//fig.cox.miami.edu/cmallery/150/ch
emistry/hemoglobin.jpg
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Designing a Drug to Block Amylase Action

• Amylase is a protein that cuts small maltose
  sugar molecules off starch molecules.
• Another enzyme, maltase, is responsible for
  breaking down the maltose molecules into two
  simple sugars known as glucose.
• Glucose is absorbed into the blood and
  transported to cells around the body to provide
  them with energy.

STARCH
AMYLASE
MALTASE
GLUCOSE
MALTOSE
STARCH
GLUCOSE
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Block the active site of amylase
Active Site
Pig
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Your turnDesigning a diet pill
Click on the button on the right to start
exploring amylase with its active site blocked by
a drug.
Amylase in Cn3D
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Influenza Pandemics
The Spanish Flu in 1918, killed approximately 50
million people. It was caused by the H1N1 strain
of influenza A.
The Asian Flu in 1957 was the H2N2 influenza A
strain. Worldwide it is estimated that at least
one million people died from this virus.
The Hong Kong Flu in 1968 evolved into H3N2.
750,000 people died of the virus worldwide
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Influenza epidemics

• Economic Effects
• Days away from work
• Providing medical advise and treatment
• Mortalities

Figure 1. Weekly number of influenza and
pneumonia deaths per 10 000 000 population in the
United States, France, and Australia (black
line).
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Designing a Flu Drug Step 1 looking for protein
targets
Influenza viruses are named according to the
proteins sticking out of their virus coat.
(H)
There are two types of protein N and H. N and
H have special shapes to perform specific jobs
for the virus.
(N)
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H attaches to cell surface proteins so virus can
enter cell
N cuts the links between the viruses and the cell
surface so virus particles are free to go and
infect more cells.
Virus
Proteins on cell surface
Virus genes are released into the cell. The lung
cell is tricked into using these genes to make
new virus particles.
Human Lung Cell
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Your turnExplore the research of an Australian
team of scientists headed by Prof Peter Coleman.
They designed the flu drug, Relenza.
Source http//www.vnn.vn/dataimages/original/imag
es126851_relenza.jpg http//www.omedon.co.uk/influ
enza/beans/relenza20binding.jpg
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Blocking the active site
Neuraminidase in Cn3D
RELENZA
This link will open a Cn3D file of Neuraminidase
with the drug relenza blocking its active site
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Venoms to drugs
Link to watch movie
A team of scientists from Melbourne University
have patented a toxic chemical from the venom of
an Australian Cone Shell. The chemical, called
ACV1, is an analgesic that will help relieve
chronic pain. It is more powerful than morphine
and is not addictive. This analgesic will be
used to treat pain resulting from nerve injury,
post-surgical pain, phantom limb pain in
amputees, leg ulcers in diabetics or the pain of
terminal AIDS or cancer. ACV1 treats pain by
blocking the transmission of pain along our
peripheral nervous system This drug could
generate an annual profit of greater than1
billion dollars to the company that develops it!
Source http//www.unimelb.edu.au/ExtRels/Media/02
media/02july08.html
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Some facts

• Calcium, sodium and potassium ions control
  essential functions inside cells calcium, for
  example, helps regulate the contraction of muscle
  cells.
• Ion channels control the entry and exit of ions
  into and out of cells.
• Some conotoxins act as analgesics, interacting
  with ion channel receptors in nerves so the ion
  channel cannot open. Blocking ion channels stops
  ions from entering a neighbouring nerve fibre. No
  electrical impulse is set off so the pain
  message is switched off! Phew!

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The nerve impulse
Sodium ion Calcium ion Acetylcholine
Synaptic Junction
3. Influx of Calcium causes acetylcholine to be
released into synaptic junction.
Na
Ca2


-
-
2. Sodium ions accumulate causing Calcium ion
channels to open.
-
-


4. Acetylcholine binds with receptor proteins
changing the shape of the ion channel. 5. This
opens the sodium ion channel to let in sodium.
6. Sodium ions set off an electrical impulse
along the next nerve cell. 7. The pain message
is working.
1. Electrical impulse generated along axon
sodium ions (red) rush in and Potassium ions
(green) rush out
To block pain we can try to target the ion
channels.
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Acetylcholine at work
Below is an image of a section of a nerve cell
cut open to reveal one of the Sodium Ion channels
that studs its surface. Lets slice through an
ion channel to show its inner workings..
2 Acetylcholine molecules bind to Receptor
binding protein on an ion channel. The shape of
the ion channel protein changes so the Na gate
opens.
Ions move into the neuron setting off an impulse.
The message is passed on!
Outside Cell
Inside Cell
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Na ion channel
You will explore this part of the ion channel.
This is the section that binds acetylcholine
/or drug molecules causing the ion channel to
change its shape.
Outside neuronal cell
Cell membrane (Phospholipid bylayer)
Inside neuronal cell
Some conotoxins block acetylcholine (nACh)
receptors that stud the surface of neurons. Lets
eplore this ion channel in Cn3D
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Your turnExplore the action of a natural Pain
Killer
Follow in the footsteps of Associate Professor
Bruce Livett and his team to explore how
conotoxins can block nerve impulses, stopping
pain.
Ion Channel with Neurotransmitter
Ion Channel with Drug
alpha conotoxin A
Alpha conotoxin B
Source http//www.theage.com.au/news/creative--me
dia/painkiller-comes-out-of-its-shell/2005/07/24/1
122143728598.html