T04-Tutorial_4_Instructions
T04-Tutorial_4_Instructions
Always be Prepared
To prepare for the quiz in this tutorial you should review the topic of enzyme
inhibition. And now is the time to know your amino acids.
Acetaminophen Toxicity
For example, the common drug acetaminophen, is mostly disposed of in our
bodies by conjugation with sugars in reactions catalyzed by several versions
of glucuronosyltransferase (EC 2.4.1.17).1 This makes the acetaminophen more 1
“The UDP-glucuronosyltransferases:
soluble in water and easily disposed of in urine. However, high concentrations Their role in drug metabolism and
detoxification”, A. Rowland, J.O. Miners,
of acetaminophen can be substrates for two versions of cyp450 – 2E1 and P.I. Mackenzie, J. Biochem. Cell. Biol.,
3A4. Both are fairly non-specific and act on small hydrophobic molecules. 2013, 45, 1121-32. https://doi.org/10.
1016/j.biocel.2013.02.019.
The site of oxidation is at the nitrogen. This leads to the production of
N-acetyl-p-benzoquinone imine (NAPQI), a toxic molecule.2 You can kill 2
“Pathways of acetaminophen metabolism
yourself with Tylenol, however you are more likely to just damage your liver at the therapeutic versus toxic doses”, L.L.
Mazaleuskaya, K. Sangkuhl, C.F. Thorn,
and suffer for the rest of your life. G.A. FitzGerald, R.B. Altman, T.E. Klein,
Today, we will consider an exercise calculating relative rates of these two Pharmacogenet. Genomics, 2015, 25, 416-
426. https://dx.doi.org/10.1097/FPC.
pathways at various concentrations of acetaminophen. 0000000000000150
tutorial #4: enzyme kinetic and medicine 2
Resources
Please share any useful resources that you find on the moodle forum.
tutorial #4: enzyme kinetic and medicine 3
Tutorial #4 Plan
The Exercises
Today in tutorial we will enjoy a quiz that focuses on enzyme inhibition and
then explore enzyme kinetics as described above.
The Report
You are an employee of a major international pharma concern. Your job is to
evaluate a new drug for possible interactions with a common blood thinner.
If the concentrations of blood thinner increases unexpectedly the patient may
die of internal bleeding before they even know anything is wrong. We want
to know if our drug interferes with the action of cyp450 on warfarin.
For the report you will interpret the results of an enzyme experiment. Use
the data set that matches your student number. The data will include a series
of enzyme kinetics experiments with a drug being oxidized with catalysis by
cyp450. Then there will be a second set of data with the addition of a second
drug that acts as an inhibitor (we will assume that this second drug is oxidized
very slowly by ctyP450 and that process does not matter in the time frame
of or experiment).
• Present the structures of warfarin and your drug. Use your favourite
chemical drawing program. All drugs in the data sets are shown in figure 2
of this document.
• Using the conc. vs. time data from each experiment calculate the rate of
oxidation. Present a plot that shows all conc. vs. time plots in a single
graph.
• Plot rate vs. substrate concentration and report the KM and Vmax values
for warfarin with the version of cyp450 that you are investigating. Present
the Michaelis-Menten plot and any plots that you used to determine the
parameters.
• You will know the concentration of cyp450, so calculate and report kcat
and kcat / KM .
• Repeat the first two steps with the experimental data that includes the
presence of your new drug. Report the apparent KM and Vmax values for
warfarin in the presence of the new drug.
The report should have a clear and well-organized appearance. All figures
should have legends (just look at the legends in this document for guidelines).
You might choose to present your final data in a table so that the executives
who make decisions don’t have to search through the report to quickly evaluate
app app
the conclusions. KM , Vmax , KM , Vmax , and Ki should be reported. Also
report the kcat and kcat /KM values for the uninhibited system.
The higher-ups at your behemoth corporation now have all the information
that they need to make a decision. Congratulations, you won’t be fired. . . at
least not today.
Python Challenges
We have had our first taste of using Python in the last tutorial. This time
we can type in all the data again and use the linear() function from the
previous tutorial to plot and curve fit each line. With the recorded slopes of
each run, you can calculate the rates (look at the units of the slopes – do you
need to change them?). Then you can type the numbers back in and use the
MMfit() function.
That seems tedious. Can we import the data from a text file? Can all this
be automated? Examine and steal the code provided in tutorial and change
it to work with your data set. Automate yourself out of your job and then
continue to be paid for it while you do other things. Computers are not
going to take your job – they are going to enable you to be paid for three
jobs at once. Stay on top of technology and you will stay on top of the heap.
tutorial #4: enzyme kinetic and medicine 6
Data Tables
Below are the data tables. All data sets are available as text files in csv format.
Note: Look carefully to units. Mole, mmol, μmol, and nmol span orders
of magnitude that could describe the difference between you and the whole
solar system.
Data Set #0
Testing for the effect of amitriptyline on warfarin oxidation by cytochrome
P450. In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #1
Testing for the effect of diclofenac on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #2
Testing for the effect of fluoxetine on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #3
Testing for the effect of mefenamic acid on warfarin oxidation by cytochrome
P450. In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #4
Testing for the effect of piroxicam on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #5
Testing for the effect of phenytoin on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #6
Testing for the effect of seratrodast on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #7
Testing for the effect of tenoxicam on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #8
Testing for the effect of tolbutamide on warfarin oxidation by cytochrome
P450. In all experiments the concentration of the enzyme was set to 1.0 nM
Data Set #9
Testing for the effect of torsemide on warfarin oxidation by cytochrome P450.
In all experiments the concentration of the enzyme was set to 1.0 nM