Lecture 3 TYJ Flashcards
how does the viral proteins get produced
They use the host machinery (ribosome) to translate their mRNA into viral proteins
By default mRNA is a?
(+) sense single stranded sequence
Explain the mechanism of viral protein production for DNA viruses (dsDNA and ssDNA)
in general, DNA viruses heavily relies on the host polymerase II for DNA transcription into mRNA and the host ribosome for mRNA translation into viral protein
for dsDNA
- follows the host normal transcription and translation mechanism.
- use the host polymerase II to transcribe the template strand into (+) mRNA
- use host ribosome to translate the mRNA into protein
- dsDNA > (+) mRNA > protein
for ssDNA
- virus self replicate their ssDNA to become dsDNA
- use the host polymerase II to transcribe the template strand into (+) mRNA
- use host ribosome to translate the mRNA into protein
- ssDNA > dsDNA > (+) mRNA > protein
Explain the mechanism of viral protein production for RNA viruses ( (+) ssRNA and (-) ssRNA)
for (+) ssRNA
- use host ribosome to directly translate their viral genome to proteins
- alternatively, after they have infected the cells, they can synthesize RdRP.
- RdRP can help to convert the (+) sense to (-) sense which generates a template sequence, after which using the template strand to generate more copies of the complementary strand which can be serve as the mRNA to be translated
for (-) ssRNA
- their RdRP is incorporated within their viral genome, after decoating their nucleocapsid in the cytoplasm, the RdRP would convert the (-) sense genome to a (+) sense ssRNA = (+) mRNA sequence
- which can then be used for translation into protein
- the RdRP is a structural protein to them
What is RNA dependent RNA polymerase (RdRP)?
it is a virus encoded enzyme that is incorporated in (-) sense ssRNA virus but not in (+) sense ssRNA, thought they can synthesized it later in their life cycle
RdRP is only found in RNA viruses and they heavily rely on them during synthesis and replication of their genome and proteins
in normal human cells, there is no RdRP, hence antiviral drugs can be designed to inhibit the activity of of this virus encoded enzyme
What is the 3 mechanism of antiviral drugs that can interrupt with the synthesis process in the virus life cycle
1) inhibit RdRP activity
2) inhibit new virus genome formation
3) preventing mRNA translation into protein
There is a higher mutation rate for RNA viruses than DNA viruses, why is that so?
This is because, the RdRP that RNA viruses utilizes during their replication process lack proof reading capabilities, which means that during the synthesis process the enzyme does not detect any form of mutation leading to accumulation of mutated viral RNA genome
However, since DNA viruses heavily relies on the DNA polymerase II from the host, this enzyme has proof reading capabilities and this DNA viruses are less likely to mutate
RdRP in influenza virus
Influenza viruses:
In IAV, the RdRP is made up of 3 subunits, PA, PB1 and PB2
polymerase acidic protein, polymerase basic protein 1 and 2
Drugs can be used to block all 3 subunits which would inhibit the activities of the RdRP preventing the (-) sense to become (+) sense
What is the drug name that inhibits the formation of new genome?
MOA of the drug?
Rabivirin
rabivirin is a nucleoside drug and it is structurally similar to guanine and adenosine nucleotides present in the sequence of the genome.
During viral genome replication, the virus can incorporate rabivirin into the sequence which results in mutation that can be lethal to the virus. As rabivirin is a decoy nucleotide, no proteins can be translated from the mRNA
However, this drug is not selective as the host replication system can also end up utilizing rabivirin into their sequence which damages the host cell proteins and genome. but the rate at which this is happening is slower than the virus
What is the drug used to stop the translation process from mRNA to protein
antisense oligonucleotide (ASO)
ASO is a short single stranded DNA sequence that is specific to binding to the mRNA sequences transcribed by the virus protein. The binding of ASO results in degradation of the mRNA sequence or it can block cellular factors from binding to the mRNA sequence to prevent translation from occurring.
What happens during assembly?
The viral genome and the protein gets transported by the microtubules dependent trafficking pathway to a common site for assembly.
enveloped virus can acquire their envelop during assembly by budding intracellularly with organelles like ER and golgi.
what is the MOA of drugs that interrupts assembly?
- inhibiting the functions of the structural protein (so that packaging of the genome is disrupted)
- formation of a wrong type of virion
antiviral drug: capsid assembly modulator (CAM), not approved yet
During nuclear transportation pathway, what are the viral proteins involved?
NLS (nuclear localisation signal)
NES (nuclear export signal)
NLS requires importin alpha and beta to assist in the transportation of the cargo (import)
NES responsible for exporting cargo out of nucleus
3 methods that virus can use during the release from host cell to extracellular space
1) budding
- for envelope virus, they can acquire their envelop through budding from the cell membrane
eg: influenza
2) cell lysis and apoptosis
- for naked virus, resulting in cell lysis and apoptosis of the host cell, essentially damaging the cellular membrane to allow for release
3) exocytosis via the host mediated vacuole
- for enveloped viruses that has already acquire an envelope during assembly, they would utilize the host specialized vacuoles to transport the virion progeny and exit the cell via exocytosis
- eg: SARS-COv-2 viruses
What is the function of neuraminidase (NA) of the influenza virus?
NA spike protein helps to break the bonds between the sialic acid binding domain in the HA protein from the sialic acid receptor found on the host cell to allow for release of the virion progeny
What is the drug used to inhibit the NA from breaking the bond to allow for the release?
Tamiflu aka osteltamivir
osteltamivir binds to pockets present in the NA protein inhibiting its acitivity
what are the 4 requirements of antiviral therapy?
1) they should target the viral components (DNA and viral protein)
2) have to inhibit 1/5 of the steps in the life cycle
3) should not result in drastic side effects in the host
4) should not affect the host proteins
Drug resistance
drug resistance is developed due to mutations that occur during replication of the viral genome. The rate of mutation is higher for RNA virus due to its RdRP lacking proof reading mechanism resulting in accumulation of mutations, generating mutated spike proteins that makes the antiviral therapy ineffective when it was previously.
How to overcome/ prevent drug resistance
1) use combination therapy (for HIV)
2) constant update of current vaccines (for influenza and covid19)
3) design new drugs that targets the host and virus interaction
