Chapter 35 — Quiz

Twenty-five questions on drug design, mechanism, and medicinal chemistry. ∗ marks questions answered in the answer key.

Multiple choice

1.∗ Aspirin's molecular target is: (a) cyclooxygenase (COX) (b) histamine receptor (c) acetylcholine receptor (d) NMDA receptor

2.∗ Aspirin's inhibition of COX is: (a) reversible (b) irreversible (covalent acetylation of Ser530) (c) competitive only (d) allosteric

3.∗ Ibuprofen's mechanism of COX inhibition is: (a) covalent acetylation (b) reversible competitive inhibition (mimics arachidonic acid binding) (c) allosteric (d) Michael addition to a cysteine

4.∗ The pharmacologically active enantiomer of ibuprofen is: (a) (R) (b) (S) (c) racemic equally active (d) neither

5.∗ Acetaminophen's toxic metabolite is: (a) NAPQI (a Michael acceptor that depletes glutathione) (b) glutathione (c) salicylic acid (d) NAC

6.∗ Lipinski's rule of 5: a drug-like molecule should have molecular weight: (a) ≤ 500 (b) ≤ 100 (c) any (d) ≥ 1000

7.∗ Lipinski's rule of 5: H-bond donors should be: (a) ≤ 5 (like the OH and NH groups) (b) ≥ 10 (c) any (d) zero

8.∗ A bioisostere is: (a) a structural replacement that preserves biological activity but changes chemistry (b) the identical molecule (c) a metabolite (d) a prodrug

9.∗ A prodrug is: (a) active when administered (no metabolism needed) (b) inactive when administered, activated by metabolism (c) only used in animal studies (d) the same as a drug

10.∗ A PROTAC is: (a) a targeted protein degrader (b) a proton pump inhibitor (c) a kinase inhibitor (d) an antibody

11.∗ Why is low-dose aspirin (81 mg/day) used for cardiovascular prevention? (a) the irreversible inhibition of platelet COX gives long-lasting effect (the platelet's lifetime, ~10 days) (b) it kills platelets directly (c) it's the active dose (d) all of the above

12.∗ Why do COX-2-selective inhibitors (Vioxx, Celebrex) have cardiovascular concerns? (a) they disrupt the COX-1/COX-2 balance, particularly affecting prostacyclin production (b) they increase blood viscosity (c) they cause aspirin allergy (d) they're only for cancer

13.∗ Acetaminophen overdose causes: (a) liver damage via NAPQI Michael acceptor + glutathione depletion + protein modification (b) brain damage (c) kidney damage primarily (d) immediate death

14.∗ Why is N-acetylcysteine (NAC) the antidote to acetaminophen overdose? (a) NAC replenishes glutathione, which detoxifies NAPQI (b) NAC inhibits CYP2E1 (c) NAC binds NAPQI directly (d) all of the above (especially the first)

15.∗ Atorvastatin (Lipitor) works by: (a) inhibiting HMG-CoA reductase, blocking cholesterol biosynthesis (b) blocking dietary cholesterol absorption (c) increasing cholesterol excretion (d) all of the above

16.∗ Ibrutinib (BTK kinase inhibitor for CLL) works by: (a) covalent thia-Michael addition of an acrylamide warhead to Cys481 of BTK (b) reversible competitive inhibition (c) allosteric inhibition (d) DNA modification

17.∗ Sotorasib (LUMAKRAS, K-Ras G12C inhibitor) is uniquely targeted to which mutation? (a) the K-Ras G12C mutation, which introduces a reactive cysteine at position 12 (b) any K-Ras mutation (c) only normal K-Ras (d) only inactive K-Ras

18.∗ Why is thalidomide the foundation of PROTAC drugs? (a) thalidomide binds cereblon, an E3 ubiquitin ligase, which can be recruited to ubiquitinate any target protein (b) thalidomide is itself an effective drug (c) thalidomide is achiral (d) thalidomide is non-toxic

19.∗ AlphaFold and AI tools are used in drug discovery for: (a) target structure prediction, virtual screening, retrosynthesis, ADME prediction (b) only synthesis (c) only target identification (d) only clinical trials

20.∗ A drug-discovery program typically takes: (a) ~10-15 years and ~$1-3 billion (b) 1-2 years and $10K (c) months (d) immediately on demand

Short answer

21. Sketch the chemistry of aspirin's COX inhibition. Identify the active site residue, the nucleophile, and the leaving group.

22. Compare ibuprofen and aspirin's mechanism: reversible vs. irreversible. Why does this distinction matter clinically?

23. Explain how acetaminophen overdose leads to liver damage. Identify the toxic metabolite and the chemistry of liver protein modification.

24. Apply Lipinski's rule of 5 to evaluate atorvastatin (MW 558, logP 5.7, H-bond donors 4, acceptors 6). Is it drug-like? Why is it still a major drug despite some violations?

25. Outline the principle of a PROTAC drug. How does it use thalidomide-derived chemistry to degrade a disease-causing protein?

Answer key

  1. a — Aspirin targets COX.
  2. b — Aspirin irreversibly acetylates Ser530.
  3. b — Ibuprofen is reversible competitive.
  4. b — (S)-ibuprofen is active.
  5. a — NAPQI is acetaminophen's toxic metabolite.
  6. a — Lipinski MW ≤ 500.
  7. a — H-bond donors ≤ 5.
  8. a — Bioisostere description.
  9. b — Prodrug description.
  10. a — PROTAC = targeted protein degrader.
  11. a — Irreversible platelet COX inhibition.
  12. a — Disrupting COX-1/COX-2 balance.
  13. a — NAPQI mechanism for liver damage.
  14. a — NAC replenishes glutathione (also some direct binding to NAPQI).
  15. a — Statins inhibit HMG-CoA reductase.
  16. a — Ibrutinib's covalent thia-Michael mechanism.
  17. a — K-Ras G12C-specific cysteine.
  18. a — Thalidomide-cereblon binding for PROTAC.
  19. a — AI in drug discovery (multiple aspects).
  20. a — 10-15 years, $1-3 billion.

21. Aspirin's chemistry on COX: - Aspirin has an ester group: $\text{CH}_3-CO-O-\text{Ar (salicylate)}$. - Ser530-OH of COX is the nucleophile. - The Ser530-OH attacks the acetyl C=O of aspirin (nucleophilic acyl substitution, Ch 26). - Tetrahedral intermediate forms. - Salicylate leaves (-O-Ar is the leaving group). - The acetyl group is now covalently attached to Ser530 as an ester: Ser530-O-CO-CH₃. - COX is permanently inactivated. The whole reaction is acyl transfer of the acetyl group from aspirin to the enzyme.

22. Aspirin: irreversible inhibition. Once attached to COX, it stays. The COX must be replaced by new protein synthesis (~12 hours for COX-2; ~10 days for platelet COX-1). Clinical: low-dose aspirin (81 mg/day) is uniquely effective for cardiovascular prevention because of the long-lasting platelet COX inhibition. Ibuprofen: reversible competitive inhibition. Ibuprofen binds COX, blocking arachidonic acid; when ibuprofen is metabolized and cleared (~2-4 hours), COX activity returns. Clinical: ibuprofen is a good anti-inflammatory + analgesic, but doesn't give the cardiovascular protection of low-dose aspirin.

23. Acetaminophen overdose: - At normal dose, acetaminophen is mostly conjugated (glucuronidation, sulfation) and excreted. - ~5% is metabolized by CYP2E1 to NAPQI (N-acetyl-p-benzoquinoneimine), an α,β-unsaturated quinone imine. - NAPQI is a Michael acceptor (Ch 29 chemistry). It rapidly reacts with glutathione (a tripeptide thiol, abundant in liver) via thia-Michael addition, depleting glutathione. - Once glutathione is depleted, NAPQI then attacks cellular proteins (cysteines and lysines), forming covalent adducts. - The covalent damage disrupts liver cell function → cell death → acute liver failure. - Treatment: N-acetylcysteine (NAC), which replenishes glutathione. Must be given within ~10 hours.

24. Atorvastatin: - MW 558: violates Lipinski (>500). - logP 5.7: violates Lipinski (>5). - H-bond donors 4: passes (≤5). - H-bond acceptors 6: passes (≤10). Two violations. By Lipinski's strict rule, atorvastatin is not "drug-like." Yet it was the top-selling drug in history. Why? Because Lipinski is a heuristic, not absolute. Atorvastatin's high lipophilicity is offset by efficient hepatic uptake (it's selectively transported into liver by OATP transporters). And its high MW comes from features needed for potency (the dihydroxyheptanoic acid mimics HMG-CoA's transition state). The drug works despite Lipinski violations. Lesson: Lipinski's rules are guides, not laws.

25. A PROTAC has three components: 1. E3 ligase ligand (often thalidomide or a derivative): binds cereblon, an E3 ubiquitin ligase. 2. Linker: connects the two ends; controls geometry of ternary complex. 3. Target ligand: binds a disease-causing protein (e.g., a cancer-driving kinase).

When the PROTAC binds both targets simultaneously, cereblon ubiquitinates the disease protein. The ubiquitinated protein is degraded by the proteasome.

Thalidomide-derived: thalidomide binds cereblon's substrate-binding pocket. By replacing thalidomide's "substrate" with a designed PROTAC linker + a target ligand, we can recruit cereblon to ubiquitinate a chosen target. This is targeted protein degradation.

The thalidomide arc: from teratogen (1957-1961) → multiple myeloma drug (1990s) → PROTAC ligand (2015+). The molecule's history is one of chemical rehabilitation.