Lecture 14 - HIV protease inhibitors Flashcards
Designing a drug
Drugs work best when they target a non-human factor
– Drugs that bind or inactive common or multiple targets cause numerous side effects
– HIV is difficult because it integrates its viral DNA (via RNA) into human cells meaning there are fewer possible drug targets - virus becomes a part of you so need to find a part of HIV that is different to us
• But, enzymes and proteins help the HIV develop and mature to spread to other cells, perhaps we could target this?
• One enzyme of interest is HIV protease
The more specific the less the adverse effect, the adverse effect is not a function of the drug that is intended
Background research of HIV protease
It is a protease therefore it chops up protein
Aim is to hinder maturation so that it can’t spread and to hinder proteins without shutting down other processes in the body
The HIV protease enzyme is homo-dimeric
– It contains two amino acid chains, both identical
HIV Protease is an aspartate (aspartyl) protease
– There are multiple types of protease with different mechanisms; serine, aspartate (aspartyl), metalloprotein, cysteine. Information about aspartyl proteases will be relevant to HIV.
HIV Protease cleaves a long protein into fragments, mammalian cells do not have enzymes that do this specific reaction.
The HIV enzyme works on bonds between the amino acids phenylalanine- proline or tyrosine-proline, mammalian cells do not have enzymes that do this.
– Proteases cleave proteins, they break peptide bonds between two amino acids. – There are many different proteases but the HIV protease is specific to the virus.
HIV PROTEASES MIGHT BE A GOOD DRUG TARGET
HIV is a RNA retrovirus
Changes its RNA to DNA and can integrate into human DNA which causes problems in treatment as you have to target your own cells
Enzyme features of HIV protease that can be used
They are proteins –
– Not very useful, many ways to inactivate but would inactivate everything
• They catalyse reactions –
– Useful, if we can find a specific reaction
• They have an active site –
– Useful, likely to be specific to a specific enzyme
• They have preferred substrates –
– Useful, gives us an idea of structure of molecules that fit in the active site
• They can be inhibited, competitive/non-competitive –
– Very useful, competitive inhibition could be used to develop a virus specific drug
Aspartate residues in the active site
HIV proteases are a type of aspartate (aspartyl) protease - have this residue in their active site
Two (protein formed by 2 subunits coming together, homodimer) aspartate residues use water to cleave the peptide bond in a one step reaction
HIV protease
HIV Protease is a homodimer formed of two identical amino acid chains and there are aspartate residues in the active site.
Active site of HIV protease
HIV protease cleaves bonds between Phenylalanine and Proline or Tyrosine and Proline.
All of these amino acids have rings on them, they are all big and bulky amino acids therefore drugs need these to prevent targeting mammals
As well as the key aspartate residues, other residues help position the amino acid chain (substrate, S) by forming hydrophobic pockets for the side chains
These are named S1, S2, S3 (on one chain)
and S1’, S2’, S3’ (on the other chain)
What is the substrate?
Normally the HIV protease is cleaving a long amino acid chain that then forms multiple smaller proteins that the HIV virus uses to replicate and infect other cells
What bond do you need to cut to cleave a protein?
Peptide bond
How to make a drug?
Make it look like the substrate but don’t let it act like the original substrate
1-Build a peptide-like backbone
2-Add some bulky side groups so it firs the active sites (hydrophobic pockets in the original)
3- Design the rest of the drug so that it can be absorbed from a tablet
Downsides
Even though the HIV Protease is only found in viruses, protease inhibitors cause effects on other systems (side effects) including
• Nausea, vomiting, diarrhea
• Heart problems, increased blood lipids and liver
toxicity
• Interactions with other medications and drugs
The HIV protease can also mutate and become resistant to the inhibitor
Saquinavir
Three-dimensional structure of the HIV protease dimer in complex with the protease inhibitor saquinavir bound at the active site therefore it can’t spread around the body
Has bulky side groups - just changed configurations of side chains and/or extra molecules
How does specifically inhibiting certain enzymes lead to a therapeutic effect?
The binding of an inhibitor can stop a substrate from entering the enzyme’s active site and/or hinder the enzyme from catalyzing its reaction.
HIV protease inhibitors
From kinetic studies we can see that saquinavir is acting as a competitive inhibitor (same Vmax, Km is increased).
There are now different variants of HIV inhibitors
Even though the protease is specific to HIV it can have bad side effects
HIV protease can also mutate and become resistant to the inhibitor - RNA to DNA to RNA so there is a high error rate and viruses reproduce very quickly so mistakes can easily occur
