Antiviral Drugs and the Viral Replication Cycle

Overview: why we study viral replication

• Before antiviral drugs, we need to understand how viruses replicate to identify where to intervene.
• Key idea: stopping replication prevents infection from spreading to new cells.

The viral replication cycle (steps in order)

• Step 1: Attachment to a host cell
  • Virus attaches to receptors on the outside of the host cell.
• Step 2: Entry (fusion or other entry mechanisms)
  • After attachment, the virus must get inside the cell.
  • For enveloped viruses, entry often occurs via membrane fusion; sometimes entry can involve pinocytosis.
• Step 3: Uncoating
  • The viral protein coat is removed so the genome is exposed and available for replication.
  • The genome is inside a protein shell called a capsid.
• Step 4: Integration into the host genome
  • The viral nucleic acid integrates into the host genome (host DNA for DNA viruses; proviral DNA for certain RNA viruses).
  • The process and enzymes differ depending on whether the virus is DNA or RNA, double- or single-stranded.
• Step 5: Replication of viral nucleic acids
  • Viral DNA or RNA is synthesized (genomic replication).
• Step 6: Production of viral proteins
  • Transcription and translation produce viral proteins (enzymes, capsid proteins, spike proteins, etc.).
• Step 7: Assembly of new virions
  • Viral components assemble into new virions (virions = complete virus particles).
• Step 8: Exit from the host cell
  • Virions exit the cell, either by lysis or budding, to infect new cells.

How antiviral drugs can stop replication (targets by step)

• Block step 1: Attachment to host cells
  • Interferons act on host cell receptors to prevent virus spread between cells by reducing attachment.
  • Interferons can shut down receptors on the outside of the cell to hinder initial infection.
• Block step 2: Entry or fusion
  • Entry inhibitors / fusion inhibitors prevent the virus from entering the host cell after attachment.
  • For enveloped viruses, entry often requires fusion with the cell membrane; inhibitors block this process.
• Block step 3: Uncoating
  • Uncoating inhibitors keep the genome inside the intact capsid, preventing genome exposure.
  • Without uncoating, the virus cannot proceed to integration or replication.
• Block step 4 (and step 5): Genome integration and replication of nucleic acids
  • Integration inhibitors prevent viral DNA/RNA from integrating into the host genome; this also blocks transcription/translation downstream.
  • Inhibitors of replication of viral nucleic acids (e.g., nucleoside/nucleotide analogs) prevent synthesis of viral genomes.
  • Example note: if the viral genome is very similar to human nucleic acids, this strategy may be more prone to toxicity or less effective, but some drugs still work (e.g., acyclovir).
• Block step 6: Viral protein production
  • Generally difficult, because viral proteins are produced by host ribosomes; targeted disruption risks harming host protein synthesis.
• Block step 7: Assembly of virions
  • Protease inhibitors block processing of viral structural proteins, preventing proper assembly of new virions.
  • The viral capsid proteins are often produced as a large polyprotein that must be cleaved into functional units by proteases; inhibitors halt this processing.
• Block step 8: Exit from the host cell
  • Exit inhibitors prevent budding or lysis, stopping the release of infectious particles.
• Important practical point
  • Not all antivirals are broad-spectrum. Viruses differ in genome type (DNA vs RNA, ds vs ss) and whether they are enveloped, which affects which drug targets are viable.

Examples of major antiviral targets and drugs (overview)

• Interferons
  • Mechanism: reduce attachment/spread by acting on host cell receptors.
  • Clinical use: hepatitis viruses (e.g., hepatitis B and C in some regimens historically; hepatitis examples in lecture context).
• Entry/fusion inhibitors
  • Target: block viral entry into the host cell.
  • Used for enveloped viruses like influenza and HIV.
• Nucleoside/nucleotide analogs that inhibit reverse transcription (RT inhibitors)
  • Tenofovir (a nucleotide reverse transcriptase inhibitor): blocks reverse transcription in retroviruses like HIV, preventing RNA from being copied into DNA.
• Acyclovir (a deoxyguanosine analog)
  • Structure analogy: resembles guanine; activated selectively in infected cells by viral thymidine kinase (TK).
  • Activation pathway (in infected cells):
  • Viral TK adds a phosphate group to acyclovir, forming acyclovir monophosphate.
  • Cellular kinases convert to di- and triphosphate forms.
  • Mechanism: acyclovir triphosphate competes with deoxyguanosine triphosphate (dGTP) for incorporation by DNA polymerase; it lacks a proper 3′-hydroxyl group, causing chain termination when incorporated into viral DNA.
  • Clinical note: widely used for herpes infections (herpes simplex virus types 1 and 2), varicella-zoster virus (chickenpox and shingles), especially important for immunocompromised patients.
  • Analogy used in lecture: a barrel of monkeys – an analogy to how normal nucleotides connect; acyclovir disrupts the chain because it creates a broken linkage when the next nucleotide tries to attach.
• Antiretrovirals (for retroviruses like HIV)
  • Key concept: retroviruses carry reverse transcriptase (RT), an enzyme not normally present in healthy human cells.
  • Normal cell gene expression pathway: DNA -> transcription by RNA polymerase -> mRNA -> translation by ribosomes -> proteins.
  • Retroviral process: RNA genome is reverse-transcribed into DNA by reverse transcriptase, which then integrates into the host genome and is transcribed/translated to produce viral proteins.
  • Drugs commonly target RT or other steps in the retroviral life cycle:
  • RT inhibitors (reverse transcriptase inhibitors): block reverse transcription, preventing viral DNA synthesis.
  • Integrase inhibitors: prevent integration of viral DNA into the host genome.
  • Protease inhibitors: block processing of viral polyproteins into mature, functional viral proteins, hindering virion assembly.
  • Fusion inhibitors or entry inhibitors: block the virus from entering host cells.
  • Rationale for combination therapy (to avoid resistance): combine an RT inhibitor with another drug such as a protease inhibitor, an integrase inhibitor, or a fusion/entry inhibitor.
• Practical considerations about antiviral specificity
  • Antiviral drugs are usually not broad-spectrum due to life-cycle differences among viruses and the presence of viral vs host enzymes.
  • The most effective targets are steps that are unique or significantly different in viruses compared with healthy host cells (e.g., reverse transcription, specific viral proteases, viral genome integration).

Key biological concepts tied to drug action

• Nucleic acids and base pairing (DNA vs RNA)
  • Base-pairing rules (in DNA): A
    ightleftharpoons T and C
    ightleftharpoons G.
  • In RNA, thymine (T) is replaced by uracil (U); pairs with adenine (A).
• Viral genome types influence drug targeting
  • DNA viruses vs RNA viruses; single-stranded vs double-stranded genomes; enveloped vs non-enveloped viruses
  • These differences affect which steps can be targeted safely and effectively.
• Enzymes mentioned and their roles
  • Thymidine kinase (TK): activates certain nucleoside analogs (e.g., acyclovir) preferentially in infected cells.
  • DNA polymerase: extends DNA strands; targeted by acyclovir triphosphate in infected cells.
  • RNA polymerase (host): transcribes viral DNA to mRNA (in general, host transcription machinery is used for viral gene expression after integration).
  • Reverse transcriptase (RT): viral enzyme in retroviruses that copy RNA into DNA; target of RT inhibitors.
  • Integrase: viral enzyme that inserts viral DNA into the host genome; target of integrase inhibitors.
  • Protease: viral enzyme that processes viral polyproteins into mature proteins; target of protease inhibitors.

Specific, practical takeaways for exams and clinical context

• Antiviral strategies are most effective when they interrupt a distinct virus-specific step without severely harming host cell functions.
• Combination therapy is common in HIV to reduce resistance development and target multiple life-cycle stages.
• Acyclovir is a cornerstone in treating herpesvirus infections due to selective activation in infected cells and chain-termination mechanism.
• Not all antivirals work across many viruses; most are tailored to specific viruses due to differences in genome type, replication, and enclosure.
• The stages of the replication cycle provide clear targets for different drug classes, and understanding these stages helps explain why a drug would be chosen for a given infection.