Pharmacogenomics, venomous snakes, and targeted cancer therapy
- from phenotype to genotype
Centra dogma: a super-oversimplified view
Exercise(s)
- Your task, in each exercise, is to explain the physical basis of interaction between the genetic variants and pharmacological molecules.
- Suggested place of start: the PDB (Protein Data Bank) page related to the molecule of interest in the exercise.
- What does PDB have to say about the identifiers given at the beginning of each exercise?
- When using GnomAD, look at 'missense variants' only.
- In Pymol, the bioactive molecule, for example FLP, can be selected by "select somename, resn FLP", and residues, for example 132 and 345, by "select somename, resi 123+345."
Presentation sample
Pymol crash course
Today we will use PyMol (installed on the desktops in front of you) to visualize the protein structure and its interaction with bioactive molecules.
Variant frequencies in general (healthy) population can be found using gnomAD Browser.
Exercises
- Exercise 1: Aspirin - the mechanism of action and its breakdown
- Cyclooxygenase, the PDB molecule of the month
- PDB: 3pgh; bioactive molecule:FLP, heme: HEM; residues of interest 109, 346; note that the crystallized protein was extracted from sheep so the sheep 109 corresponds to human R108
- What types of residues are 109 and 346? What are their properties? (Wikipedia is your friend.)
- COX-1 and COX-2 on Wikipedia
- Aspirin prefers COX-2
- "Decreased cyclooxygenase inhibition by aspirin in polymorphic variants of human prostaglandin H synthase-1"
- Check the frequency of the mutations in R108 in COX1 in the general population. What is the corresponding location (and the variant) on the genome? (Keep in mind that the official gene name is not COX1 - see the Wikipedia entry.)
- Exercise 2: Genetic differences in drug metabolism - the example of NAT2
- Genetic Basis of Drug Metabolism , Medscape
- PDB: 2PFR; of special interest D122N (especially) and K268R; "cofactor" COA
- Variant effect on pharmacodynamics.
- NAT2 alleles
- Structural Basis of Substrate-binding Specificity of Human Arylamine N-Acetyltransferases. Check out Fig. 5 in particular.
- Check the frequency of the mutations in the general population. What is the corresponding location (and the variant) on the genome?
- Exercise 3: Osimertinib: targeted tumor therapy
- Osimertinib, briefly on Wikipedia
- Osimertinib making a breakthrough in lung cancer targeted therapy
- How osimertinib works
- PDB: 4ZAU; in particular, residue T790, and the molecule YY3.
- Check the frequency of the mutations in the general population. What is the corresponding location (and the variant) on the genome?
- Nicotinic acetylcholine receptor
- PDB: 6CNJ (you can delete chains F through K: "select deletable, chain F or chain G or chain H chain I or chain J or chain K", then action -> remove atoms), a brief look at the full receptor
- Alpha-bungarotoxin, briefly on Wikipedia
- Mutations in resistant species
- PDB: 5HBT (you can delete chains C and D by directly clicking on them and selecting "remove atoms"; do "action" -> "align to molecule" -> 6CNJ; do not delete chain A - that's the toxin) residues 187, 189, and 194 on chain B.
- Check out the intro of this paper . What is the role of the two cysteine residues (CC) at the positions 192 and 193?
- Do any humans carry the resistance conferring variants? (GnoMAD.. Note the change in consensus numbering since the Mutations in resistant species paper was published to 232, 234, 239).
- Wiki intro
- Pharmacogenomics (hint: search for the word "TPMT."); focus on TPMT*3A
- What exactly is TPMT*3A (again, search specifically for "TPMT*3A" in the text)
- PDB 3BGD, with the emphasis on residue ids 154 and 240 (But beware of the actual impact of these mutations!) See Pharmacogenomics above; a fun protein folding animation here.)
Collection of pharmacogenomic information PharmGKB