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Rational Drug Rational Drug DesignDesign

Using the 3D Shape of Proteins to Design Drugs that Inhibit

Protein Function

Download Cn3d from this siteBefore you start this activity, make sure you have the program Cn3D installed on your computer.

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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

Source: http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/page2.htmlhttp://www.cbp.pitt.edu/bradbury/projects.htmhttp://www.abc.net.au/cgi-bin/common/printfriendly.pl?/science/news/enviro/EnviroRepublish_1191825.htmhttp://www.umass.edu/microbio/chime/

TransportHaemoglobin (far right) in red blood cells transports oxygen to cells around the body

Examples of Protein Function

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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!

Source: http://accad.osu.edu/~ibutterf/ibp/molecule/http://folding.stanford.edu/education/water.htmhttp://www.opti-balance.com/hyperox.htm

Add ferric ions (Fe 3+)

Rate increases 30 000-fold

Add Catalase

Rate increases 100 000 000-fold

Reactants

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Products

Hydrogen peroxide

oxygen

water

Location of active site where

Hydrogen peroxide binds

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How enzymes do it!• Enzyme proteins have specific sites where all the action Enzyme proteins have specific sites where all the action

happens. We call this the happens. We call this the active siteactive site. Molecules that . Molecules that need to be ripped apart or put together enter the active need to be ripped apart or put together enter the active site. site.

• Each protein has a specific shape so it will only perform Each protein has a specific shape so it will only perform a specific job. a specific job.

http://chsweb.lr.k12.nj.us/mstanley/outlines/enzymesap/Enzymesap.htmlhttp://academic.brooklyn.cuny.edu/biology/bio4fv/page/active_.html

Joining things togetherRipping things apart

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Many toxins are proteins

Source: http://www.wiley.com/legacy/college/boyer/0470003790/cutting_edge/molecular_recognition/molecular_recognition.htmhttp://science-univers.qc.ca/image/ricin061.jpghttp://www.staabstudios.com/Spider.htm

Funnel web spider toxin: blocks movement of calcium ions.

Ricin from the seeds of the

castor oil plant destroys

ribosomes

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Protein molecules are polymers• Proteins are very large polymer molecules. Polymers are made by Proteins are very large polymer molecules. Polymers are made by

linking smaller molecules, monomers, together to make a long chain. linking smaller molecules, monomers, together to make a long chain.

• In the case of proteins, the monomers are amino acids. There are 20 In the case of proteins, the monomers are amino acids. There are 20 different amino acids.different amino acids.

AA

AAAA

AAAA

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 chainsEach protein has a specific sequence of amino Each protein has a specific sequence of amino

acids that are linked together, forming a acids that are linked together, forming a polypeptidepolypeptide

http://www.mywiseowl.com/articles/Image:Protein-primary-structure.png

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The protein chain foldsInteractions between amino acids in the chain form:Interactions between amino acids in the chain form:

alpha helicesalpha helices beta sheetsbeta sheets Random coils Random coils

Source: http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/prot.htm#I

Together usually form the binding and active sites of proteins

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And folds again!

• After folding, amino After folding, amino acids that were acids that were distant can become distant can become closeclose

• Now the protein Now the protein chain has a 3D chain has a 3D shape that is shape that is required for it to required for it to function correctlyfunction 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 The final protein may be made up of more than one polypeptide chain. polypeptide chain.

The polypeptide chains may be the same type or different The polypeptide chains may be the same type or different types.types.

Source: http://fig.cox.miami.edu/~cmallery/150/chemistry/hemoglobin.jpg

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Designing a Drug to Block Designing a Drug to Block Amylase ActionAmylase Action

Amylase is a protein that cuts small maltose Amylase is a protein that cuts small maltose sugar molecules off starch molecules. sugar molecules off starch molecules.

Another enzyme, maltase, is responsible for Another enzyme, maltase, is responsible for breaking down the maltose molecules into breaking down the maltose molecules into

two simple sugars known as glucose.two simple sugars known as glucose.

Glucose is absorbed into the blood and Glucose is absorbed into the blood and transported to cells around the body to transported to cells around the body to

provide them with energy.provide them with energy.

STARCH

MALTOSE

STARCH

AMYLASE

GLUCOSE

GLUCOSE

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Block the active site of Block the active site of amylaseamylase

Pig

Active Site

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Your turn…Your turn…

Designing a diet pillDesigning a diet pill

Amylase in Cn3DClick on the button on the right to start exploring amylase with its active site blocked by a drug.

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Influenza Influenza PandemicsPandemics

The Hong Kong Flu in 1968 evolved into H3N2. 750,000 people died of the virus worldwide

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.

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Influenza Influenza epidemicsepidemics

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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There are two types of protein = N and H.

N and H have special shapes to perform specific jobs for the virus.

Influenza viruses are named according to the proteins sticking out of

their virus coat.(H)

(N)

Designing a Flu Drug Designing a Flu Drug Step 1: looking for Step 1: looking for

protein targetsprotein targets

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Human Lung Cell

Virus Proteins on cell

surface

H attaches to cell surface proteins so virus can enter cell

Virus genes are released into the cell.

The lung cell is ‘tricked’ into using these genes to make new virus particles.

N cuts the links between the viruses and the cell surface so virus particles are free to go and infect more cells.

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Your turn…Your turn…Explore the research of an Explore the research of an

Australian team of scientists Australian team of scientists headed by Prof Peter Coleman. headed by Prof Peter Coleman.

They designed the flu drug, They designed the flu drug, Relenza.Relenza.

Source: http://www.vnn.vn/dataimages/original/images126851_relenza.jpghttp://www.omedon.co.uk/influenza/beans/relenza%20binding.jpg

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Blocking the active siteBlocking the active site

Neuraminidase in Cn3D

This link will open a Cn3D file of Neuraminidase with the drug relenza blocking

its active site

RELENZA

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Venoms to Venoms to drugsdrugs

Source: http://www.unimelb.edu.au/ExtRels/Media/02media/02july08.html

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!

Link to watch movie

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Some facts…Some facts…

Calcium, sodium and potassium ions control essential Calcium, sodium and potassium ions control essential functions inside cells: calcium, for example, helps functions inside cells: calcium, for example, helps regulate the contraction of muscle cells. regulate the contraction of muscle cells.

Ion channels control the entry and exit of ions into and Ion channels control the entry and exit of ions into and out of cells. out of cells.

Some conotoxins act as analgesics, interacting with ion Some conotoxins act as analgesics, interacting with ion channel receptors in nerves so the ion channel cannot channel receptors in nerves so the ion channel cannot open. Blocking ion channels stops ions from entering a open. Blocking ion channels stops ions from entering a neighbouring nerve fibre. No electrical impulse is set off neighbouring nerve fibre. No electrical impulse is set off so the ‘pain’ message is switched off! Phew!so the ‘pain’ message is switched off! Phew!

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The nerve impulseThe nerve impulse

++

++

- -

- -

Synaptic Junction

Sodium ion

Calcium ion

Acetylcholine

Ca2+Na+

4. Acetylcholine binds with receptor proteins changing 4. Acetylcholine binds with receptor proteins changing the shape of the ion channel. the shape of the ion channel. 5. This opens the sodium ion channel to let in sodium. 5. This opens the sodium ion channel to let in sodium. 6. Sodium ions set off an electrical impulse along the 6. Sodium ions set off an electrical impulse along the next nerve cell. next nerve cell. 7. The pain message is working. 7. The pain message is working.

To block pain we can try to target the ion channels.To block pain we can try to target the ion channels.

1. Electrical impulse generated along axon – sodium 1. Electrical impulse generated along axon – sodium ions (red) rush in and Potassium ions (green) rush outions (red) rush in and Potassium ions (green) rush out

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

3.3. Influx of Calcium Influx of Calcium causes acetylcholine to causes acetylcholine to be released into be released into synaptic junction.synaptic junction.

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Acetylcholine at workAcetylcholine at work

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!

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. Let’s slice through an ion channel to show its

inner workings..

Inside Cell

Outside Cell

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Na+ ion channelNa+ ion channel

Cell membrane (Phospholipid bylayer)

Inside neuronal cell

Outside neuronal cell

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.

Some conotoxins block acetylcholine (nACh) receptors that stud the surface of neurons. Let’s eplore this ion channel in Cn3D

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Your turn…Your turn…

Explore the action of a Explore the action of a natural Pain Killernatural Pain Killer

Source: http://www.theage.com.au/news/creative--media/painkiller-comes-out-of-its-shell/2005/07/24/1122143728598.html

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