Lesson Plan: The Mould in the Rice

Overview

• Grade Level: AP Biology, AP Chemistry, IB Biology HL, AP US/World History (history of medicine), and first-year undergraduate biochemistry, pharmacology, and history of science. Suitable for grades 11-12.

• Time Required: Single 50-minute class with optional 25-minute extension. The 11-minute audio narration also works as a bell-ringer.

• Historical Period: 1971-2024, primarily Tokyo (Sankyo Company), with anchor moments in Akita prefecture, the Bronx (Albert Einstein College of Medicine), Kyoto, Paris (Necker-Enfants Malades Hospital), and Dallas (UT Southwestern).

• Modern Connection: Polypurine reverse Hoogsteen hairpin DNA molecules silencing PCSK9 transcription, published in Biochemical Pharmacology and reported in early May 2026.

Learning Objectives

Students will be able to:

1. Explain why HMG-CoA reductase is the rate-limiting enzyme of cholesterol biosynthesis and why blocking it lowers blood LDL.

1. Reconstruct the experimental logic of Akira Endo's 1971-73 fungal screen, including the assay design and the role of radioactive tracers.

1. Describe the role of the LDL receptor and PCSK9 in clearing LDL from the bloodstream and explain why a loss-of-function PCSK9 mutation is protective.

1. Compare three generations of cholesterol-lowering interventions (statins, PCSK9 antibodies, polypurine hairpin DNA) on the dimensions of mechanism, scale, manufacturability, and cost.

1. Articulate the difference between "discovering a molecule that nature already makes" and "designing a molecule from scratch", and identify which step in any drug pipeline each represents.

Before Reading

Anticipation Questions

1. If high blood cholesterol is dangerous, why doesn't the body simply turn down its own production?

1. Penicillin, one of the most consequential medicines in human history, was found in a contaminated Petri dish. What does that suggest about how to look for new drugs?

1. The University of Barcelona team have designed a synthetic DNA molecule that silences a single human gene. If this approach works in patients, which existing classes of drugs could it replace, and which it could not?

Key Vocabulary

• HMG-CoA reductase: The rate-limiting enzyme in cholesterol biosynthesis. Statins are competitive inhibitors of this enzyme.

• Statin: A class of drugs that lower blood cholesterol by inhibiting HMG-CoA reductase. Compactin (mevastatin) and lovastatin are the founding members.

• LDL receptor: A protein on the surface of liver cells that binds and clears LDL ("bad cholesterol") particles from blood.

• PCSK9: A protein that binds to the LDL receptor and targets it for degradation, reducing the number of LDL receptors on the cell surface.

• Loss-of-function mutation: A genetic change that reduces or eliminates the activity of a gene's protein product.

• Familial hypercholesterolaemia: An inherited condition causing very high LDL cholesterol from birth, leading to early heart disease.

• Polypurine reverse Hoogsteen hairpin (PPRH): A short single-stranded DNA molecule folded back on itself in a hairpin loop, designed to bind a specific gene sequence and block its transcription.

• Penicillium citrinum: The blue-green mould species, originally isolated from rice in a Kyoto grain shop, that produces compactin.

During Reading

Guided Questions

1. Why did Endo think a useful cholesterol-lowering molecule might come from a fungus, and not from chemical synthesis?

1. What did Endo measure in his screen, and how did he know when a fungus produced a hit?

1. Why was the loss-of-function PCSK9 finding so surprising, given what was already known about familial hypercholesterolaemia?

1. The Barcelona-Oregon team did not have to find their molecule in nature. What did they have to know in order to design it?

After Reading

Discussion Questions

1. Comprehension: List the three generations of cholesterol-lowering interventions discussed in the story, and the year each first reached patients (or was shown to work in mice).

1. Application: Why do statins remain effective for so many patients despite the existence of newer, more potent therapies?

1. Analysis: Endo's screen took two years and tested roughly six thousand fungal cultures. The Barcelona team designed a single molecule by computational analysis of the PCSK9 gene's regulatory region. Compare the cost and risk profiles of these two research strategies.

1. Synthesis: Identify another class of medicines whose first-generation member came from a natural product (e.g. penicillin, aspirin, taxol, artemisinin) and whose later generations are wholly synthetic. What pattern, if any, does this suggest?

1. Evaluation (debatable): Akira Endo received the Lasker Award and the Japan Prize but never the Nobel. Was that an oversight, or a coherent decision given how the prize selects discoveries?

The Parallel

1. Both Fleming's 1928 penicillin and Endo's 1973 compactin were "found" rather than "designed". What features of the early-twentieth-century life sciences made that approach productive, and what changed by 2026?

1. The story claims that "the body wants to do the right thing. You only have to remove the thing stopping it." Identify two other examples in physiology or medicine where a successful therapy works by removing an inhibitor rather than by adding a stimulus.

Activities

Bell-Ringer (7 minutes)

Play the audio narration as students enter. Distribute a card with one prompt: "What single sentence best summarises why Endo went looking for cholesterol-lowering molecules in fungi rather than in a chemical catalogue?"

Single Class (50 minutes)

| Time | Segment | Activity | |------|---------|----------| | 0-7 | Hook | Audio narration plays. Students take notes on Endo's experimental setup. | | 7-15 | Vocabulary | Quick review of HMG-CoA reductase, statin, LDL receptor, PCSK9, hairpin DNA. | | 15-25 | Diagram task | In pairs, students draw three diagrams: (a) Endo's 1971-73 fungal screen as he would have schematised it; (b) the LDL clearance loop showing LDL receptor + PCSK9; (c) a polypurine hairpin DNA molecule binding the PCSK9 gene's regulatory region and blocking transcription. Each diagram labels what is being measured or perturbed. | | 25-35 | Discussion | Whole-class discussion of the After Reading questions, focused on the trade-off between "find a molecule in nature" and "design a molecule against the gene". | | 35-45 | Application | Each pair selects one near-term decision a clinician might face: which patients should get a statin, which should also get a PCSK9 antibody, which (if the Barcelona approach succeeds in trials) might benefit from a hairpin therapy. They write a one-paragraph clinical decision rule and explain their reasoning. | | 45-50 | Exit ticket | One sentence: "Why is it scientifically meaningful that Endo's molecule and the Barcelona team's molecule act on different proteins in the same regulatory loop?" |

Extension Activity

Choose one.

• Research paper (1500 words): Trace the path from Endo's 1973 compactin to lovastatin (Merck 1987) and on to atorvastatin (Pfizer/Lipitor). What scientific, regulatory, and commercial decisions shaped each step?

• Numerical exercise: Given a healthy LDL receptor recycling rate of approximately one round per 20 minutes, calculate how many LDL particles a single hepatocyte's full complement of LDL receptors could clear per day. Estimate, qualitatively, how reducing PCSK9 by 80% might shift this number, given that PCSK9 normally targets receptors for degradation.

• History of science essay: Compare Akira Endo's 1973 isolation of compactin with Alexander Fleming's 1928 isolation of penicillin. What features of the two stories are alike, and what features differ? What does the Endo story add to the Fleming archetype?

Primary Source Connections

1. Endo, A., Kuroda, M., and Tsujita, Y. (1976). "ML-236A, ML-236B, and ML-236C, new inhibitors of cholesterogenesis produced by Penicillium citrinum", The Journal of Antibiotics, 29(12), 1346-1348. The original paper.

1. Endo, A. (2017). "Discovery and Development of Statins", a retrospective review by the original investigator, freely available in Natural Product Communications via SAGE Journals.

1. Abifadel, M., Boileau, C., et al. (2003). "Mutations in PCSK9 cause autosomal dominant hypercholesterolemia", Nature Genetics, 34, 154-156. The PCSK9 discovery paper.

1. Cohen, J., Hobbs, H., et al. (2006). "Sequence variations in PCSK9, low LDL, and protection against coronary heart disease", New England Journal of Medicine, 354(12), 1264-1272. The Dallas Heart Study finding.

1. López-Aguilar, E., Pacheco-Velázquez, S., Busquets, M., Hay, J., Mueller, P., Fazio, S., Ciudad, C., Noé, V., Pamir, N. (2025/2026). "Inhibition of PCSK9 with polypurine reverse Hoogsteen hairpins: A novel gene therapy approach", Biochemical Pharmacology, vol. 238, art. 116976. The 2026 study at the centre of this episode.

1. Scandinavian Simvastatin Survival Study Group (1994). "Randomised trial of cholesterol lowering in 4444 patients with coronary heart disease: the Scandinavian Simvastatin Survival Study (4S)", The Lancet, 344(8934), 1383-1389.

Standards Alignment

C3 Framework

• Dimension 1 (Developing Questions): Students develop testable scientific and historical questions about how a screen design choice shapes which discoveries are possible.

• Dimension 2 (Applying Concepts): Students apply concepts from biochemistry (enzyme kinetics, rate-limiting steps), molecular biology (gene transcription, regulatory regions), pharmacology (mechanism of action, off-target effects), and history of science (industrial vs academic research).

• Dimension 3 (Evaluating Sources): Students compare a peer-reviewed primary paper, an institutional press release, and a secondary narrative as evidence for the same scientific claim. The Time Rhymes evidence manifest is itself a model of explicit source evaluation.

• Dimension 4 (Communicating Conclusions): Students must write or present a clinical decision rule that integrates evidence from at least two distinct sources, using appropriate biochemical and clinical vocabulary.

AP Alignment

• AP Biology Unit 3 (Cellular Energetics) and Unit 6 (Gene Expression and Regulation): Enzyme kinetics, rate-limiting steps, transcription regulation. PCSK9 silencing is a clean classroom example of transcription blockage at a regulatory region.

• AP Chemistry Unit 7 (Equilibrium): Competitive inhibition (compactin / statins fit the active site of HMG-CoA reductase as substrate analogues).

• AP US History (Period 9): The post-1980 globalisation of pharmaceutical R&D, with Japanese, American, French, and Spanish/American teams each playing a key role.

• AP World History: Modern (Unit 9, Globalization): International scientific cooperation across language and political systems; the Lasker as an "American Nobel" and the Japan Prize as an analogue.