Viral Infection and HIV Flashcards
What are the 3 viral enzymes involved in HIV viral replication
Reverse transcriptase, integrase, protease
Describe the stages of HIV replication
- Surface proteins on HIV recognise specific receptor proteins on the surface of target cells, bind
- Fusion: HIV envelope and cell membrane fuse, allows HIV to enter the cell
- HIV replicates within the cell via translation and transcription, using reverse transcriptase
- Maturation of HIV cell - protease
- Budding of HIV cell - formation of the capsid and new HIV pushes out of host cell
What does protease do?
Protease is toxic to cells, chops us viral precursor proteins which go on the make viral proteins
What does intergrase do?
It is a critical enzyme, which takes viral DNA and inserts it into the Host DNA, leading to irreversible infection
What does reverse transcriptase do/which function does it not have?
Reverse transcriptase is used to produce complimentary DNA strands to produce viral proteins. It does not have a proof reading function
Discuss the structure-activity relationship of RNA
RNA’s sugar has 3 chiral centres, The 2’ and 3’ OH groups in RNA make it less stable. The sugar part of the nucleotide is responsible for orientating the base and triphosphate into the correct position.
What is the purpose of the sugar in a nucleotide and can it be changed?
The sugar is the scaffold, it holds the triphosphate in the correct orientation. You can change this configuration, as do chain terminators which stops rRNA polymerisation
What is the purpose of the base in a nucleic acid and can it be changed?
The base allows the nucleotide to make the complementary strand and bonds via hydrogen bonding, Changing this would lead to the wrong tautomer
what is the purpose of the triphosphate in a nucleic acid and can it be changed?
The triphosphate lacks an active site an cannot be changed as it is important for molecule recognition.
What changes can be made to sugars on nucelotides?
Remove the hydroxyl group, opportunities at the 2’ and 3’. Changing the sugar element is how nucleoside inhibitors work
Describe the process of HIV replication with reference to reverse transcriptase
- Reverse transcriptase reads RNA and makes complementary DNA strand.
- RT cuts RNA out and leaves a single strand of viral DNA
3) integrase inserts this viral DNA into the host cell DNA
4) Host cell replicates this viral DNA as part of it’s Genome
5) protease translates viral proteins
Describe the structure/function relationship of reverse transcriptase
Reverse transcriptase’s structure can be described as a right hand with palm, fingers and thumb. The active site sits in the crease between the fingers and thumb. This active site has aspartic acid residues, holding Mg2+ ions, which are lewis acids and would pair with lewis bases. Reverse transcriptase also has an allosteric binding site.
How are NRTIs able to bind to the active site of reverse transcriptase
o2 on the phosphate group of NRTIs are strong lewis bases and therefore can bind to the strong lewis acid Mg2+ in the active site of reverse transcriptase
Do NRTIs need to be phosphorylated to be active? Why?
Yes, to gain the phosphate groups in order to appear like the Nucleotides and prevent chain elongation
How do NRTIs work?
The 3 hydroxyl group on the sugar is replaced with an azido group, to prevent chain elongation. NRTIs are transported into the cell via soluble carrier transporters, are phosphorylated by kindases but it is not the correct sugar, and chain elongation is terminated, as there is no proof reading function
How can NRTIs have toxicity?
The phosphorylation inside cells can have toxic effects due to it’s effect on mitochondria
How are NRTIs used?
As part of Highly Actrive Antiretroviral Therapy (HAART).
2 nucleoside reverse transcriptase inhibitors are given with an NNRTI
2X NRTIs + boosted protease inhibitor
When is therapy with 2x rt inhibitors + protease inhibitors saved for?
Resistance to 1st line regimens and for patients that wish to become pregnant or have psychiatric illness
What are some key points to remember about tenofovir?
It doesnt inhibit mitochondrial DNA polymerases but there is no way to administer it orally
What does NNRTI stand for?
Non nucleoside reverse transcriptase inhibitor
Discuss common physiochemical propertires of NNRTIs
High logP in order to enable binding, high chemical diversity
Where do NNRTI’s bind?
At the allosteric binding site
How do NNRTIs work?
They bind to the allosteric binding site on reverse transcriptase, into the hydrophobic binding pocket. This binding leads to a conformational change in the aspartic acid residues in the active site, binding is inhibited. There is a change in the thumb position, which leads to decreased thumb mobility, and slowing or prevention of the primer strand
Discuss the key chemical aspects of NNRTI therapy
Resistance - as they bind to non-essential site on RT
Used as part of the HAART regimen to reduce risk of resistance
Very long t1/2
High logP:2.3 which gives it just the right amount of water solubility and hydrophobicity