This method can help answer key questions in systems biology such as how combinations of multiple drugs or agents affect shorten The main advantage of this technique is that its efficiency and ease of interpretability allows the study of interactions between more than two agents. Begin this procedure with preparation of antibiotic aliquots and the bacterial culture as detailed in the text protocol. Take one aliquot of each drug from minus 20 degrees Celsius and leave the aliquots to thaw at room temperature for 10 minutes.
To prepare for serial dilutions of these drugs, mix 990 microliters of LB media, and 110 microliters of DMSO to make LB 10%sol. Then, prepare 500 microliters of LB 10%LEV by mixing 450 microliters of LB media and 50 microliters of LEV. Vortex the LB 10%sol for five seconds at the highest setting.
Add 20 micro liters of LB 10%sol to the top four rows of the wells in the 96-well micro plate. Now, vortex the LB 10%LEV in the same way. Add 20 microliters of LB 10%LEV to the first well in row A.Next, prepare a twofold serial dilution for LB 10%LEV by aspirating 20 microliters from the first well, adding it to the second well, and pipetting up and down five times.
Repeat this for all wells sequentially until the 11th well which ends up with 40 microliters. Remove and discard 20 microliters of the content from the 11th well using a micro pipette. Repeat these steps for NAL using the second row of the micro plate.
And for PNG using the third row. Then, repeat these steps for the drug LEV again on the fourth row as an internal positive control. Using a spectrophotometer, measure the optical density at 600 nanometers or OD600 of a one to 10 dilution of the culture.
Dilute the cells in five milliliters of LB media to an OD600 of 0.01. Then, pour the diluted cells into a reservoir. Using a multichannel micro pipette, add 80 microliters of the diluted cells to the drug serial dilutions.
Seal the plate to prevent evaporation. Incubate the plate for 16 hours at 37 degrees Celsius. Then, start a new bacterial culture to use for the dose-response experiment.
Measure the OD600 for the serial dilution dose-response plate using a plate reader and normalize the growth as described in the text protocol. For each drug, locate the wells that have approximately 50%growth inhibition or IC50. Assign the concentration in these wells as serial IC50 for each drug.
Next, thaw fresh drug aliquots. Prepare one milliliter of LB 10%drug by mixing LB media and drug in a nine to one ratio. Here, the drug's concentration is 100 times each drug serial IC50, before adding the LB media.
Also, prepare one milliliter of LB 10%sol as before. Also, prepare one milliliter of LB 10%sol as before. Prepare a linearly increasing doses of LEV, NAL, and PNG in 11 concentrations by mixing LB 10%drug and LB 10%sol in volumes as shown here.
Also, prepare linearly increasing doses of LEV on fourth row as an internal positive control. Now, measure the OD600 of the one to 10 dilution of the culture that has been growing. Dilute the cells in five milliliters of LB media to an OD600 of 0.01.
And pour the diluted culture into a reservoir. Add 80 microliters of the diluted cells to the drug linear dilutions using a multichannel micro pipette. Then, incubate the plate for 16 hours at 37 degrees Celsius.
Also, start two fresh bacterial cultures for the interaction experiment. Measure the OD600 for the linear dilution dose-response. For each drug, choose the concentration that resulted in IC50 and prepare the drug in 100 times IC50 concentrations.
Next, use freshly thawed drugs to prepare 100 times IC50 for each drug. From these, formulate one to one drug mixtures by volume of LEV plus NAL, LEV plus PNG, and NAL plus PNG. Also, prepare a one to one to one drug mixture of LEV plus NAL plus PNG.
Now, prepare two plates for drug interaction experiments, similar to before, except that a one to one or one to one to one mixture of drugs is used. Measure the OD600 of the one to 10 dilution of the culture started earlier. Prepare two dilutions with an OD600 of 0.01 in five milliliters of LB media.
Add 80 microliters of the cells from culture one onto plate one and add 80 microliters of the cells from culture two onto plate two. After sealing the plates to prevent evaporation, incubate them for 16 hours at 37 degrees Celsius. Following incubation, measure the OD600 absorbance for the diagonal drug interaction experiment plates.
For each row, locate the column that has growth inhibition closest to the IC50. Assign the IC50 based on the relative concentration of drug in this well. Shown here is one plate of a duplicate drug interaction experiment.
All single drugs have their IC50 which is defined as an absorbance of 0.25 at one times concentration. The expected IC50 for the pairwise or three way combination is calculated by the arithmetic mean of constituent drugs making the expected IC50 for all combinations also one times concentration. The drug interaction score or FIC for each combination is calculated by dividing the observed IC50 by the expected IC50.
Inspection of the FIC scores demonstrates that LEV plus NAL, and LEV plus NAL plus PNG are synergistic, while LEV plus PNG, and NAL plus PNG are antagonistic. The FIC scores obtained from the second duplicate plate are in agreement, supporting the reliability of the protocol. Generally, individuals new to this method will struggle because reproduce all the results will require minute attention to detail and day to day consistency.
While attempting this procedure, it's important to remember to be extremely careful with drug and cell concentrations to ensure reproducible dose-response relationships. Although the method presented here is optimized for bacteria, it can also be applied to other biological systems such as mammalians cell lines. The implications of this technique extend towards therapy of infectious diseases or cancer, because these diseases often require treatment by multiple drugs.
After its development, this technique paved the way for researchers to explore synergies among many agents in tuberculosis and colorectal cancer.
