ALS 6: Anti-Viral Agents

Question 1

What are some key features of a virus (in comparison to bacteria) and how do they function?

Answer 1

A moving piece of genomic materia
Very small - hundreds of nanometers
Obligate intracellular parasites
Completely inert on the outside 
They can only replicate inside host cells - insert their DNA / RNA genome, replicate it and use the host cell machinery to make more viral proteins (then package the viral proteins and copied genome to make more copies of itself)

Question 2

Why is it so difficult to develop drugs specific to viruses?

Answer 2

Some of the mechanisms of the virus once inside the host cell, such as DNA replication or protein synthesis is the same as what a healthy cell would be doing
Therefore attacking those mechanisms would damage healthy cells, making the person more ill
Many of the viral components are those of the host cell - i.e. eukaryotic mRNA, eukaryotic amino acids

Question 3

How should anti-viral drugs be developed?

Answer 3

To attack features / mechanisms that are specific to viruses only, as opposed to parts of the virus that have been borrowed from the host

Question 4

What is the generic viral replication cycle?

Answer 4

Virus outside the host is held together by something e.g. a capsule
Virus attaches to host cell membrane and enters the host cell
Whatever was holding the virus together in the environment falls apart so that the important viral genome is exposed to the machinery inside the cell that it needs to borrow
Transcribe mRNA which encodes viral proteins
Manufacture viral proteins, capsids, replicate their genome
These all put together and assembled into new viruses, which burst out of the cell to infect more host cells

Question 5

How quickly can a viral infection spread?

Answer 5

For one virus entering a host cell, up to 1000 can be manufactured and exits it

Question 6

What is a common way for new versions of viruses to arise?

Answer 6

Replication inside the host cell is error prone - make mistakes as their genome is copied
Many different versions of the virus can come out
Increases diversity - better survival during application of selective pressures

Question 7

What are the 2 broad categories / main ways to control viruses?

Answer 7

1. Prophylaxis

2. Therapy

Question 8

What is prophylaxis?

Answer 8

Prevent disease by taking action before the virus has met the host e.g. condoms, vaccines (building own immune response and herd immunity before encountering virus), drugs (before / during an epidemic - host cells have anti-viral drug in them before encountering the virus)

Question 9

What is therapy?

Answer 9

Patient presents symptoms
Diagnosis given
Anti-viral drugs administered

Question 10

Why must the patient be diagnosed before given the anti-viral drug?

Answer 10

The anti-viral drugs are highly specific so it is important to know which type of virus it is

Question 11

Which is more commonly used?

Answer 11

Mainly therapy / therapeutics as its not possible to give everyone drugs from before in case they encounter a virus, and cannot vaccine against every type of virus

Question 12

What are the 2 broad ways to discover anti-viral drugs?

Answer 12

1. Setup screens to look for chemicals that are going to work
2. Rational design (more hypothesis driven) - look at the structure of the viral components to manufacture molecules that target specific parts of the virus

Question 13

What is easiest for anti-viral drugs to target?

Answer 13

Enzymes - make a substrate analog, which is a chemical that looks like the real substrate to the enzyme but it has chemical modifications on it, so when picked up by the enzyme, the enzyme gets locked

Question 14

What is the most common substrate analog?

Answer 14

Nucleoside analogs - things that look like the building blocks of the DNA or the RNA as all viruses have a genome that must be copied

Question 15

Why are nucleoside analogs effective?

Answer 15

If one part of the genome replication cycle is stopped, it clogs up the process so the cirus is unable to replicate, allowing the host’s immune system to clear up the viral infection

Question 16

Why are nucleoside analogs difficult to discover / manufacture?

Answer 16

Host cells are also copying RNA and DNA, and our own machinery must not be clogged as it will cause damage to healthy cells
Therefore, the drugs must be modified to only target the virus’ ability to replicate

Question 17

How can enzyme structure be deduced in a lab?

Answer 17

Using crystallography to look at the 3D structure of the enzyme

Question 18

How can the structure of the enzyme be used for rational design?

Answer 18

Design small molecules that fit into pockets of the enzyme and stop it from working

Question 19

What is an example of an anti-viral drug that is a nucleoside analog and how does it function?

Answer 19

Acyclovir - similar to guanine but missing the 3’ hydroxy group
Acyvlovir instead of guanine gets incorporated into a growing chain of DNA as the viral genome is copied
As it lacks this three prime hydroxy group, the next base is unable to attach (no phosphodiester bond created), stopping DNA replication and producing a much shorter genome than usual

Question 20

How is Acyclovir specific to viruses only and does not affect human host cells?

Answer 20

The triphosphate version of a nucleotide is incorporated into the growing strand of DNA
Acyclovir is a produrg, administered in the unphosphorylated version - must be triphosphorylated in the cell
The enzyme in human cells that carry out the first phosphorylation of a nucleotide does not work on avyclovir
Thymidine kinase, encoded by viruses and so only present in infected cell, can put the first phosphate onto acyclovir
After, cellular kinase enzymes can place the second and the third phosphate, activating acyclovir (only inside infected cells)
Active form also has a better affinity for viral DNA polymerase than human DNA polymerase

Question 21

How common is resistance and what is the most common reason for resistance to acyclovir?

Answer 21

Quite rare
Usually mutation in the thymidine kinase enzyme so monophosphorylated acyclovir is not formed - but simultaneously is compromising the efficiency of thimidine kinase to work, which is not useful under selective pressure

Question 22

What would be the features of an ideal anti-viral drug for e.g. the influenza virus?

Answer 22

Effective
Targets something specific to the virus only 
Works for majority / all strains
Easy to take
Few side effects

Question 23

What are the 3 classes of drugs licensed to target the influenza virus?

Answer 23

1. Amantadine
2. Neuraminidase inhibitor
3. Baloxavir

Question 24

What are amantadines?

Answer 24

They are byproducts of the petroleum industry
Contain cyclic amines
Blocks replication in the influenza A virus only

Question 25

What is an endosome?

Answer 25

An acidic structure that surrounds a virus when it is entering the host cell

Question 26

How do amantadines function?

Answer 26

Normally, viruses have a tetramic ion channel made of M2 protein
This tetramic ion channel allows for the passing of H+ ions from the endosome to inside the viral core, necessary to unlock the viral core to release its contents
Amantadines sat in and blocked these channels so the viral core could not be unlocked and the virus remained trapped within the endosome

Question 27

How can viruses develop a resistance to amantadines?

Answer 27

Even a single point mutation in the gene coding for the M2 protein could change it’s structure, so the drug can no longer sit in the tetramic channel to block the H+ ions from entering

Question 28

Why is the single point mutation in the S31N gene coding for the M2 protein more common and not selected against?

Answer 28

There is little / no cost of fitness to the virus
It is strongly selected for when selective pressures are applied e.g. amantadines, and the next person is them infected with this resistant version
Resistance can spread very quickly
This class of drugs is pretty useless now

Question 29

What is neuraminidase and how does it function?

Answer 29

A tetramer enzyme that binds to its substrate, sialic acid, and slices it
Important for the release of viral particles at the very end of the replication cycle as sialic acid binds the virus back down onto the cell

Question 30

What are and how do the anti-viral drugs that work as neurominidase inhibitors work?

Answer 30

Two drugs using rational design were created to resemble sialic acid - Relenza and Tamiflu
They both stick to the enzyme pocket more avidly than sialic acid, locking the enzyme in by not coming out (‘plug drug’)
Viruses made are bound to the old host cell, and cannot leave to infect new ones - reduces spread of viral infection

Question 31

What is baloxavir and how does it function?

Answer 31

Structural rational design
Molecule that fits into the pocket of the viral polymerase to stop it from carrying out its endonuclease function (hydrolysing phosphodiester bonds)

Question 32

How does resistance arise against baloxavir?

Answer 32

A single point mutation in the PA target of the polymerase

Question 33

How quickly do the Tamiflu and baloxavir drugs work?

Answer 33

Reasonably slow but do make people better quicker than if the drug was not administered

Question 34

What is unique about HIV and how are these features used to create anti-viral drugs that specifically target HIV?

Answer 34

Retrovirus - contains its genome in RNA
Converts the RNA into DNA using reverse transcriptase, and integrates it into the host cell’s DNA using integrase
During assembling, a protein needs to be sliced into smaller pieces using a viral protease
Drugs can inhibit the enzymes reverse transcriptase, integrase and viral protease

Question 35

HIV is a chronic condition, so how is HIV treated for long periods of time successfully?

Answer 35

Combination therapy - using multiple HIV specific anti-viral drugs at once, unlikely for HIV to mutate enough to be resistant to all the drugs simultaneously