Question

You are the resident biochemical scientist at a pharmaceutical company and you are part of a research group working on drug development targeting pancreatic cancer. You come across the attached review (Murthy et al. 2018) on the role of PI3K signaling in PDAC, the most aggressive form of pancreatic cancer. Your company has access to a pancreatic cancer cell line and a healthy pancreatic cell line that you can grow and manipulate. Your company also has access to a 2 million compound library to screen for small molecule drugs against any protein of interest. Your job is to read the above-mentioned review carefully and propose two sets of experiments (as explained in 2A.-2C. below) based on the assays available at your company. Available protein-based assays: a. Ability to delete a protein of choice from these cell lines. b. Ability to overexpress or introduce a protein of choice into these cell lines. c. Ability to measure cell growth and death. d. Ability to measure ligand-protein binding on-rate (kon) and off-rate (koff) constants. e. Ability to measure protein function for any protein of interest (a tall order in practice!). Target identification experimental design: 2A. Use the review to hypothesize about two of the proteins that can serve as promising therapeutic targets for PDAC. Then design experiments that will test your hypothesis. Drug discovery experimental design: 2B. We will now assume that you have identified those two proteins as potential targets to inhibit for PDAC. Now create an experimental design using the above-mentioned protein-based assays to find small molecule drugs that will serve as inhibitors for those proteins. 2C. Will these drugs work in cancer patients who have mutations in those proteins? If not, what is a potential work-around? What are the potential benefits or drawbacks of using these two drug candidates together in a drug combination?

Answer 1

A cancer biologist can investigate PI3K and RAS as therapeutic targets for PDAC by deleting or overexpressing these proteins in cell lines and measuring changes in growth and death. A high-throughput drug screening against these targets can identify potential inhibitors. The effectiveness of these inhibitors can be impacted by genetic mutations, which can be addressed through personalized medicine and combination therapy.

Step-by-step explanation:

Experimental Design for Therapeutic Target Identification in Pancreatic Cancer

Given the review by Murthy et al. (2018) on PI3K signaling in PDAC (pancreatic ductal adenocarcinoma), one can hypothesize that proteins such as PI3K and RAS, which are known to be involved in cell growth and survival signaling, are promising therapeutic targets. To test this hypothesis, the cancer biologist can design experiments to delete these proteins from a pancreatic cancer cell line while monitoring for changes in cell growth and death. Additionally, a healthy pancreatic cell line can be used as a control. Overexpression experiments can similarly be performed by introducing these proteins into both cell lines to assess the effect on cellular proliferation and survival, thereby validating the target. Furthermore, the function of these proteins in regulating signaling can be measured using the available assays.

Development of Small Molecule Inhibitors for Pancreatic Cancer

Identifying potential drug candidates involves screening the 2 million compound library for molecules that inhibit the function of PI3K and RAS. Assays measuring ligand-protein binding (kon and koff) constants can lead to the discovery of compounds with high affinity for these targets, while functional assays evaluate their inhibitory effects on protein activity. If mutations in the targeted proteins are present, inhibitor efficacy could be compromised. A workaround could involve using high-throughput screening to find molecules that are effective against multiple variants of the protein or combination therapy to overcome resistance. The combination therapy could synergize the effects of individual drugs but may also result in increased toxicity or drug-drug interactions.

Implications in Personalized Medicine

Using these developed inhibitors in a personalized medicine approach, where treatment is tailored according to an individual's specific cancer profile, can lead to improved therapeutic outcomes with fewer side effects. However, extensive clinical trials would be necessary to establish efficacy and safety profiles for these new drug candidates in the context of diverse genetic backgrounds among pancreatic cancer patients.