Lesson 2b: Antivirals and antiviral strategies

1. Antiviral drugs are used to treat infections caused by viruses other than HIV
2. Antiretroviral drugs are used to treat infections caused by HIV, the virus that causes AIDS
3. A good antiviral agent must selectively target the virus replication cycle while leaving the host cell unaffected

Key characteristics of antiviral drugs

• Able to enter the cells infected with a virus
• Interfere with viral nucleic acid synthesis and/or regulation
• Some drugs interfere with the ability of viruses to bind to cells
• Some drugs stimulate the body’s immune system
• Best responses to antiviral drugs are in patients with competent immune systems
• A healthy immune system works synergistically with the drug to eliminate or suppress viral activity

The strategies for developing antivirals are based on the virus replication cycle

A. Targets for antivirals

B. Targets for HIV

Principles and modes of action of antiviral agents

•  Antiviral drugs are medications specifically designed to treat viral infections by targeting the replication and spread of viruses within the body.
• Unlike antibiotics, which are effective against bacteria, antivirals are often more challenging to develop due to the fact that viruses use the host’s cellular machinery to replicate.

1. Attachment Inhibitors:

• Mode of Action: These inhibitors interfere with the initial attachment of the virus to the host cell surface. They may target viral envelope proteins or host cell receptors involved in the binding process. By preventing attachment, these inhibitors block the first step of viral entry.
• a) CCR5 Antagonists:

• Mode of Action: Some viruses, such as HIV, use specific chemokine receptors like CCR5 on the surface of host cells for entry. CCR5 antagonists, like maraviroc, block the binding of gp120 of HIV to host chemokine receptor 5 (CCR5), preventing viral entry into the cell.
• b) CD4 Attachment Inhibitors:

• Mode of Action: Certain viruses, including HIV, interact with the CD4 receptor on the surface of immune cells during the attachment phase. CD4 attachment inhibitors, like ibalizumab, interfere with this interaction, preventing viral entry into the host cell.

2. Entry Inhibitors:

• a) Fusion inhibitors:
• Fusion inhibitors are a class of antiviral drugs that specifically target the fusion process of a virus with the host cell membrane. This class of inhibitors is commonly used in the treatment of certain viral infections, including HIV and some forms of influenza. By preventing the fusion of the viral envelope with the host cell membrane, fusion inhibitors effectively block the entry of the virus into the host cell.
• Mode of Action: Fusion inhibitors act at the initial stage of viral entry, specifically during the fusion process. Viruses, especially enveloped viruses, use fusion proteins to merge their lipid envelope with the host cell membrane, facilitating the release of the viral genetic material into the host cell.
• Examples: enfuvirtide (ENF; T-20; Fuzeon) binds a gp41 subunit of the HIV envelope glycoprotein and prevents the conformational changes required for the fusion.
• b) Neuraminidase Inhibitors:

• Mode of Action: Neuraminidase is an enzyme that plays a role in the release of new influenza virus particles from infected cells. Drugs like oseltamivir and zanamivir inhibit neuraminidase, preventing the release of new virions and slowing down the spread of the influenza virus.

3. Uncoating Inhibitors:

• Uncoating inhibitors are a class of antiviral drugs that target the process of uncoating during the viral life cycle.
• a) Ion channel blockers:
• Mode of Action: Amantadine and rimantadine inhibit the uncoating of influenza A viruses by blocking the M2 ion channel protein, prevent the release of viral genetic material into the host cell. The M2 protein is involved in the acidification of the viral interior, a process necessary for uncoating.
• Principle: Ethyl group is added to the amantadine and they act by blocking the M2 channel and prevent the acidification of the virion in the endosome enclosing the virus. This blocks uncoating because the acid-induced dissociation of the matrix M1 protein and acid-induced hemagglutinin mediated fusion between the endosome and the viral envelope does not occur.
• b) Acidification inhibitors:

• Mode of Action: Acidification inhibitors are a class of antiviral drugs that target the acidification process within endosomes, cellular compartments involved in the entry of certain viruses into host cells. These inhibitors interfere with the acidification of endosomes, preventing the activation of viral proteins required for membrane fusion and subsequent release of the viral genome into the host cell cytoplasm.
• i) Chloroquine and Hydroxychloroquine: These drugs are traditionally used as antimalarials, but they also exhibit antiviral properties. They are weak bases that accumulate in acidic cellular compartments, including endosomes. By raising the pH in these compartments, chloroquine and hydroxychloroquine interfere with the acidification process, inhibiting the entry of viruses like SARS-CoV-2 (the virus that causes COVID-19) and others.
• ii) Bafilomycin A1 and Concanamycin A: These compounds are macrolide antibiotics that inhibit the activity of vacuolar-type H+-ATPase (V-ATPase), an enzyme responsible for pumping protons into endosomes, leading to their acidification. By blocking V-ATPase, bafilomycin A1 and concanamycin A prevent the acidification of endosomes and inhibit viral entry for certain viruses.
• iii) Ammonium Chloride: Ammonium chloride is a weak base that can raise the pH in endosomes. By doing so, it interferes with the acidification process and inhibits the entry of some viruses. However, its use is limited due to potential cytotoxic effects.

4. Nucleoside/Nucleotide Analog Reverse Transcriptase Inhibitors (NRTIs):
   • Mode of Action: Nucleoside/Nucleotide Reverse Transcriptase Inhibitors (NRTIs) are a class of antiretroviral drugs used in the treatment of human immunodeficiency virus (HIV) infection. They are nucleoside analogs that interfere with the reverse transcription process, a crucial step in the replication of the virus. NRTIs are incorporated into the growing viral DNA chain by the reverse transcriptase enzyme, causing premature termination and inhibiting viral replication.
   • a) Zidovudine (AZT): Zidovudine, also known as azidothymidine (AZT), is an antiviral medication used in the treatment of human immunodeficiency virus (HIV) infection. Zidovudine was one of the first antiretroviral drugs approved for the treatment of HIV, and it played a significant role in the early management of the HIV epidemic. Zidovudine works by inhibiting the activity of the HIV reverse transcriptase enzyme. Reverse transcriptase is responsible for converting viral RNA into DNA, a crucial step in the replication of the virus. Zidovudine is a nucleoside analog of thymidine and gets incorporated into the growing viral DNA chain, causing premature termination of the chain.
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     • b) Didanosine (ddI): Didanosine is an analog of adenosine. It undergoes phosphorylation and gets incorporated into the viral DNA chain, disrupting its synthesis.
     • c) Zalcitabine (ddC): Zalcitabine is a cytidine analog. Like other NRTIs, it interferes with viral DNA synthesis by being incorporated into the growing DNA chain.
     • d) Stavudine (d4T): Stavudine is a thymidine analog that is phosphorylated and subsequently incorporated into the viral DNA chain, leading to chain termination.
     • e) Lamivudine (3TC): Lamivudine is a cytidine analog that inhibits reverse transcriptase by being incorporated into the viral DNA chain. It is often used in combination with other antiretroviral drugs.
     • f) Abacavir (ABC): Abacavir is a guanosine analog that is converted into its active form within the host cell. It inhibits reverse transcriptase and terminates viral DNA chain synthesis.
     • g) Emtricitabine (FTC): Emtricitabine is a cytidine analog and is structurally similar to lamivudine. It is often used in combination with other antiretroviral drugs.
     • h) Tenofovir Disoproxil Fumarate (TDF) and Tenofovir Alafenamide (TAF): Tenofovir analogs (TDF and TAF) are adenine analogs. They undergo phosphorylation and inhibit reverse transcriptase, leading to chain termination. TDF and TAF are often used in combination with other antiretroviral drugs.

5. Protease Inhibitors (PIs):

• Mode of Action: Protease is an enzyme required for the final processing of viral proteins during the assembly of new virions. PIs block the activity of this enzyme, preventing the formation of functional viral particles. This class is commonly used in the treatment of HIV.
• a) HIV Protease Inhibitors:

• Mode of Action: These drugs specifically target the protease enzyme of HIV, inhibiting its activity. By doing so, they prevent the cleavage of viral polyproteins into functional proteins, disrupting the maturation process and production of infectious HIV particles.
• Examples: Saquinavir, Ritonavir, Indinavir, Nelfinavir, Amprenavir, Lopinavir, Atazanavir, Darunavir, Fosamprenavir.
• b) HCV Protease Inhibitors:
• Mode of Action: HCV protease inhibitors target the NS3/4A protease of hepatitis C virus. Inhibiting this protease disrupts the processing of viral polyproteins, hindering the production of mature and infectious HCV particles.
• Examples: Telaprevir, Boceprevir, Simeprevir, Grazoprevir, Paritaprevir.
• c) Other Viral Protease Inhibitors: Lopinavir/Ritonavir for Coronaviruses: Lopinavir, in combination with ritonavir, has been used in the treatment of certain coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). These drugs inhibit the protease activity of coronaviruses.

6. Integrase Inhibitors:

• Mode of Action: Integrase inhibitors are a class of antiretroviral drugs used in the treatment of human immunodeficiency virus (HIV) infection. They target the viral integrase enzyme, which plays a crucial role in the integration of viral DNA into the host cell’s genome. By inhibiting this step, integrase inhibitors prevent the establishment of a permanent viral reservoir within the host cell, thereby hindering the replication of the virus.
• a) Raltegravir: Raltegravir inhibits the integrase enzyme by binding to its active site. This prevents the integration of viral DNA into the host cell genome. Raltegravir is usually prescribed as part of combination therapy for the treatment of HIV.
• b) Elvitegravir: Elvitegravir is another integrase inhibitor that works by blocking the activity of the integrase enzyme. It is often co-formulated with cobicistat, a pharmacokinetic enhancer, and other antiretroviral drugs as a single-tablet regimen.
• c) Dolutegravir: Dolutegravir is a second-generation integrase inhibitor that is highly potent and has a high barrier to resistance. Like other integrase inhibitors, it blocks the integration of viral DNA into the host cell genome. Dolutegravir is commonly used in HIV treatment regimens.
• d) Bictegravir: Bictegravir is a newer integrase inhibitor that is co-formulated with emtricitabine and tenofovir alafenamide as a single-tablet regimen. It is used for the treatment of HIV infection in certain populations.

7. RNA Polymerase Inhibitors:

• Mode of Action: RNA polymerase inhibitors are a class of antiviral drugs that target the activity of viral RNA polymerase, an enzyme essential for the replication of viral RNA. By inhibiting RNA polymerase, these drugs interfere with the synthesis of viral RNA, ultimately hindering the replication of the virus. RNA polymerase inhibitors are used to treat viral infections caused by RNA viruses.
• a) Remdesivir: Remdesivir is a nucleotide analog that is initially metabolized to its active form, a nucleoside triphosphate, within the host cell. It is then incorporated into the growing viral RNA chain by the viral RNA-dependent RNA polymerase (RdRp). Remdesivir acts as a delayed chain terminator, leading to premature termination of viral RNA synthesis. It has been used in the treatment of RNA viruses such as Ebola virus and SARS-CoV-2 (the virus that causes COVID-19).
• b) Sofosbuvir: Sofosbuvir is a nucleotide analog that undergoes activation to its active form within the host cell. It inhibits the activity of the viral RNA polymerase of hepatitis C virus (HCV). Sofosbuvir is used as part of combination therapy for the treatment of chronic HCV infection.
• c) Ribavirin: Ribavirin is a nucleoside analog that has a broad spectrum of antiviral activity. It is phosphorylated within the host cell and inhibits the viral RNA polymerase, leading to chain termination. Ribavirin is used to treat infections caused by various RNA viruses, including respiratory syncytial virus (RSV), HCV, and certain viruses causing hemorrhagic fevers.
• d) Baloxavir Marboxil: Baloxavir marboxil is an influenza polymerase inhibitor that specifically targets the endonuclease activity of the influenza A and B viral polymerases. By inhibiting this activity, the drug prevents the initiation of viral mRNA transcription. It is used for the treatment of influenza.

8. DNA polymerase inhibitors:

• Mode of Action: DNA polymerase inhibitors are a class of antiviral drugs that interfere with the activity of viral DNA polymerase, an enzyme essential for the replication of viral DNA. By inhibiting DNA polymerase, these drugs prevent the synthesis of new viral DNA strands, ultimately hindering the replication of the virus. DNA polymerase inhibitors are used to treat viral infections caused by DNA viruses.
• a) Acyclovir (and its prodrugs Valacyclovir and Famciclovir): Acyclovir is a nucleoside analog that is selectively activated by viral thymidine kinase. Once phosphorylated, it competes with deoxyguanosine triphosphate (dGTP) for incorporation into the growing viral DNA chain by viral DNA polymerase. This incorporation results in chain termination and inhibits viral DNA synthesis. Acyclovir is commonly used to treat herpes simplex virus (HSV) and varicella-zoster virus (VZV) infections.
• b) Ganciclovir (and its prodrugs Valganciclovir): Similar to acyclovir, ganciclovir is a nucleoside analog activated by viral kinase. It is used to treat cytomegalovirus (CMV) infections, particularly in immunocompromised individuals. Ganciclovir is incorporated into the viral DNA, leading to chain termination and inhibition of viral replication.
• c) Foscarnet: Foscarnet is a pyrophosphate analog that directly inhibits the activity of viral DNA polymerase. It does not require activation by viral kinases. Foscarnet is active against a broad spectrum of DNA viruses, including CMV and herpesviruses. It competes with pyrophosphate for binding to the pyrophosphate-binding site on the DNA polymerase.
• d) Cidofovir: Cidofovir is a nucleotide analog that, once phosphorylated, inhibits viral DNA polymerase. It is active against a variety of DNA viruses, including CMV, HSV, and adenoviruses. Cidofovir does not require viral kinase activation, and its active form competes with deoxycytidine triphosphate (dCTP) for incorporation into the viral DNA chain.

9. Non-nucleoside DNA polymerase inhibitors:

• Mode of action: They bind to an allosteric site that regulates the polymerase activity rather than to the enzyme’s active site itself as other nucleoside analogs
• a) AICAR (Acadesine): AICAR (5-aminoimidazole-4-carboxamide ribonucleotide) is a non-nucleoside inhibitor that interferes with the activity of DNA polymerase. It has been studied for its potential antiviral activity.
• b) Nevirapine: Nevirapine is a non-nucleoside reverse transcriptase inhibitor (NNRTI) used in the treatment of HIV. While it primarily targets reverse transcriptase, which is an RNA-dependent DNA polymerase, it can indirectly affect DNA polymerase activity.

10. Inhibitors of viral exit:

• Mode of action: Inhibitors of viral exit are antiviral drugs that target the final stages of the viral life cycle, specifically the process by which new virions are released from infected host cells. The viral exit process involves the assembly and release of fully formed viral particles, allowing them to infect new cells and propagate the infection. Here are some examples of inhibitors targeting viral exit:
• a) Neuraminidase Inhibitors: Neuraminidase is an enzyme that plays a crucial role in the release of influenza viruses from infected cells. Neuraminidase inhibitors block the activity of this enzyme, preventing the release of newly formed virions from the surface of infected cells. These drugs are commonly used to treat and prevent influenza infections. Examples: Oseltamivir (Tamiflu), Zanamivir (Relenza), Peramivir.
• b) Protease Inhibitors (HIV): Protease inhibitors for HIV primarily target the viral protease enzyme, which is essential for the maturation of new virions. By inhibiting protease activity, these drugs disrupt the cleavage of viral polyproteins, preventing the formation of infectious viral particles. Examples: Saquinavir, Ritonavir, Atazanavir, Darunavir.
• c) Fusion Inhibitors (HIV): While fusion inhibitors primarily act during viral entry, they indirectly affect viral exit by inhibiting the fusion of the viral envelope with host cell membranes. Enfuvirtide, for example, interferes with the fusion process, preventing the release of viral contents into the host cell. Examples: Enfuvirtide, Maraviroc.
• d) Budding Inhibitors (HCV): In the context of hepatitis C virus (HCV), inhibitors like velpatasvir interfere with the process of viral particle assembly and release. They target viral proteins involved in the budding process, preventing the release of new HCV virions from infected cells. Example: Velpatasvir.
• e) Maturation Inhibitors (HIV): Maturation inhibitors interfere with the final steps of HIV assembly by blocking the processing of the Gag polyprotein, which is necessary for the formation of mature and infectious virions. Bevirimat is an example, although it is still under investigation. Example: Bevirimat (Investigational).

Mechanisms of Antiviral Resistance

• Antiviral resistance refers to the ability of viruses to evolve and develop mechanisms that render antiviral drugs less effective or completely ineffective.
• The emergence of resistance can occur due to various genetic and evolutionary processes.