LESSON 4.6 WORKBOOK. Designing an antiviral drug The challenge of HIV

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Anthony Maxwell
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LESSON 4.6 WORKBOOK Designing an antiviral drug The challenge of HIV In the last two lessons we discussed the how the viral life cycle causes host cell damage.

In this lesson, we will review the details of HIV life cycle, and will use that information to identify drug targets. As we discussed in Lesson 4.

Because of this, retroviruses remain in a host cells without making any viral proteins, and particles. This means that the virus can stay truly invisible to the immune system for a long time.

1 LESSON 4.6 WORKBOOK Designing an antiviral drug The challenge of HIV In the last two lessons we discussed the how the viral life cycle causes host cell damage. But is there anything we can do to prevent such damage? In order to answer this question, we first need to learn as much as possible about life cycle of that specific virus. In this lesson, we will review the details of HIV life cycle, and will use that information to identify drug targets. As we discussed in Lesson 4.4, retroviruses are RNA viruses that use their RNA as a template to make DNA. Then this viral DNA integrates into the host cell genome. Because of this, retroviruses remain in a host cells without making any viral proteins, and particles. This means that the virus can stay truly invisible to the immune system for a long time. This is why retroviruses often lead to disease long after initial infection. A couple of important disease-causing retroviruses include HIV as well as human T-cell lymphoma/leukemia virus 1 (HTLV- 1), which is associated with leukemia and lymphoma. In this lesson we are going to focus on the steps of the HIV life cycle to better understand how it damages host cells and to predict the parts of the virus that might make good drug targets. Figure 1: Structure of a mature HIV virus. Besides the typical viral components such as genome, capsid, envelope with receptors, the virus also carries key enzymes it needs inside the host such as reverse transcriptase, integrase, and protease. 1. Retroviruses, such as HIV, defy molecular dogma by making from and then inserting their into the host s genome. a. RNA; DNA; DNA b. DNA; DNA; DNA c. RNA; DNA, RNA d. DNA, RNA, DNA 182

DEFINITIONS OF TERMS Pandemic an outbreak of infectious disease that has spread through human populations across a large geographical region. For a complete list of defined terms, see the Glossary.

2 DEFINITIONS OF TERMS Pandemic an outbreak of infectious disease that has spread through human populations across a large geographical region. For a complete list of defined terms, see the Glossary. LESSON READINGS HIV infection is a global pandemic (Review from Lesson 1.2) One of the largest modern pandemic is due to HIV (human immunodeficiency virus). Over 30 million people worldwide are living with HIV/AIDS (acquired immune deficiency syndrome). The number of AIDS cases in the United States and Europe rose steadily through the mid-1990s, and then plateaued as a result of increasingly effective efforts at prevention and drug treatments. In the developing world the disease has continued to spread. Africa has just over 12% of the world s population but more than 60% of the AIDS cases worldwide. Figure 2: Statistics on HIV prevalence worldwide (2013). AIDS is a uniquely devastating disease: it kills all those who exhibit symptoms. It is a chronic illness, often appearing years after first infection with the virus and long after the individual has had the opportunity to transmit it. HIV inactivates a central key component of the immune system, the helper CD4 T cell (more about these cells in Unit 5), severely impairing its ability to fight infections. AIDS is lethal because its effects on the immune system cause the body to lose its defenses against opportunistic pathogens. Diseases that were under reasonable control, e.g., mycobacterial infections such as TB, have become common and highly dangerous among persons with AIDS. It has been particularly difficult to design a vaccine because the virus varies rapidly its surface antigens and other molecules. Designing drugs to control an existing infection is critical but to be successful, we must know the HIV life cycle really well. HIV's Life Cycle: Please note that there are a lot of steps and names here, but the idea is to look for the parts of the virus that might make a good drug target. Here is a hint, look for the steps and proteins that are not part of molecular dogma. 2. Reverse transcriptase and integrase are viral proteins that are unique to each virus. a. True b. False 183

DEFINITIONS OF TERMS Receptor a molecule, usually protein, on a cell or viral surface that can interact with specific molecules from the outside world.

3 DEFINITIONS OF TERMS Receptor a molecule, usually protein, on a cell or viral surface that can interact with specific molecules from the outside world. Conformational change a change in the shape of a molecule. Multimeric composed of multiple building units (monomers). For a complete list of defined terms, see the Glossary. LESSON READINGS Key steps of HIV's Life Cycle: 1. Attachment: HIV uses its receptor (gp120) to bind to CD4 receptor molecule on T helper cells, causing a conformational change in gp120. This change leads to two important moments: allows gp120 to bind to CCR5 on the host cell, and exposes gp41 (shown on Fig. 1) that allows the fusion of the viral envelope with the host cell membrane. 2. Entry: As the two membranes fuse, the viral capsid enters the host cell cytoplasm. Once in the cytoplasm, the viral capsid is degraded, releasing HIV s enzymes and genome. 3. Viral RNA converted to DNA: The viral reverse transcriptase uses host nucleotides to copy the viral RNA into DNA. While doing this, it makes a number of errors due to the lack of proofreading. 4. Integration in host genome: Viral integrase then carries the viral DNA into the nucleus and binds to the host chromosome. Following binding, integrase nicks the host DNA allowing host DNA repair enzymes to insert the viral DNA into the host chromosome. The HIV virus is now in a latent form in the T cell. Figure 2: HIV life cycle. 5. Making new viral particles: Under certain conditions, such as activation of the T cell by a different infectious agent, the HIV virus may become activated. The host s RNA polymerase transcribes the viral DNA into RNA, and the host ribosomes translate the RNA into multimeric viral proteins. The viral proteins migrate to the cell surface along with the new genomes. 6. Exit: At the cell surface, the viral proteins and RNA genomes come together, and bud off the host cell. 7. Maturation: Maturation may occur during budding or after its completion. During maturation, the multimeric viral protein chains are cleaved by the viral protease. This allows the capsid and viral enzymes to take their final, mature form. 3. Retroviruses are more advanced than most DNA and RNA viruses because a. they can permanently insert their genome into the genome of the host cell. b. they have an RNA genome that they make into DNA with a special enzyme called reverse transcriptase. c. it brings the gene for integrase when it infects the host cell. d. all of the above 184

4 STUDENT RESPONSES Would reverse transcriptase make a good drug target? Explain your answer. Remember to identify your sources Imagine a drug that targets a replication protein to prevent viral replication. Using symbols (circles, squares, pac-man shapes, etc.), draw a model to show how the drug works to prevent replication. _ 185

5 STUDENT RESPONSES Using the same symbols, draw two models to illustrate how that protein might change shape (structure) if there was a mutation in the DNA coding for the replication protein. In the first model, the protein loses function and can t bind the genome. In the second model, the protein can still replicate the genome but the drug no longer binds. This second model is the first step in drug resistance. Remember to identify your sources A person is infected with a virus that can be treated with an anti-viral drug. While taking the drug, inside the person s body a single virus gets a mutation that changes the shape of its replication protein like the second model above. Predict what happens to the population of viruses in the person s body. What happens to the person? _ 186

6 TERMS TERM DEFINITION Conformational change Multimeric Pandemic Receptor A change in the shape of a molecule. Composed of multiple building units (monomers). An outbreak of infectious disease that has spread through human populations across a large geographical region. A molecule, usually protein, on a cell or viral surface that can interact with specific molecules from the outside world. 187

LESSON 4.4 WORKBOOK. How viruses make us sick: Viral Replication

LESSON 4.4 WORKBOOK. How viruses make us sick: Viral Replication DEFINITIONS OF TERMS Eukaryotic: Non-bacterial cell type (bacteria are prokaryotes).. LESSON 4.4 WORKBOOK How viruses make us sick: Viral Replication This lesson extends the principles we learned in Unit