Possible Outline for the Capstone Presentation

1. Biological Target Background
   1. When was it discovered?
   2. Why is it important?
   3. What role does general role does it play in physiology?
   4. What diseases does it affect?
2. Where is your biological target expressed?
   1. What organs is it expressed in?
   2. What type of cells is it expressed in?
   3. Where in the cell is it expressed?
3. How does your biological function?
4. Describe the structure of the biological target?
   1. What is the two dimensional topology?
   2. X-ray crystal structure, Cryo-em, or homology model.
5. Describe a detailed mechanism of the biological target?
6. Describe how your drug is synthesized or extracted from a plant source?
7. Mass spectra of your drug with fragmentation assignments (experimental and simulated).
   1. https://webbook.nist.gov/chemistry/name-ser/
   2. https://spectrabase.com/
   3. https://fluorine.ch.man.ac.uk/research/mstool.php
   4. https://www.protpi.ch/Calculator/MassSpecSimulator
   5. https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:mspepsearch
   6. https://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi
   7. Search online for articles for experimental information.
8. NMR spectrum of your drug with assignments (experimental and simulated).
   1. https://webbook.nist.gov/chemistry/name-ser/
   2. https://spectrabase.com/
   3. https://www.nmrdb.org/
   4. https://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi
   5. Search online for articles for experimental information.
   6. If you picked a drug that is too difficult to simulate by NMR such as large biologic, describe how you would determine it by NMR.
9. Describe known drug/substrate/ligand binding sites.
10. If you did Assignment #6, describe drug binding site to your target protein after docking.
    1. If your is a large protein biologic, then you dock it with ClusPro. A description of the interactions of a biologic with its target will be a lot broader than for a small molecule drug.
    2. For all other drugs, then dock it with SwissDock.
    3. For either Be sure to show all your parameters and explain your rational.
11. d.    Compare to the known drug binding sites.
12. 12. Describe the properties of your drug
13. a.     If your drug is a small molecule, chemoinformatics.
14. b.    If your drug is a large protein biologic like an antibody, bioinformatics.
15. 13. Develop a pharmacophore of your drug based on drugs in the same class and explain your rational.
16. a.     If your drug is a large protein biologic like an antibody, you might pick a different site of the drug to bind to. You might pick a different peptide fragment of the target protein to serve as an antigen. Explain the rational of picking that peptide fragment to target.
17. b.    If your drug is a small molecule, then design a pharmacophore based on similar drugs within the drug class.
18. 14. Based on your analysis describe how you would find a new drug lead.
19. a.     See http://zincpharmer.csb.pitt.edu/
20.                     i.     Only show the top 10.
21. b.    If you picked a large biologic like an antibody, describe how you make new biologics against your biologic target.