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
Examples of NRTIs
Abacavir
Emtricitabine
Tenofovir
Discuss the pharmacodynamic and physiochemical properties of Nevirapine (NRTI)
pKa 2.8 strong base poor water solubility High CSF/CNS penetration Efavirenz preffered NNRTI in pregnant women
Discuss the pharmacodynamic and physiochemical properties of delvaridine (NRTI)
pKa 4.5, weak base poorly water soluble at physiological pH low CNS penetration Teratogenic in rats hepatic metabolism
Discuss the pharmacodynamic and physiochemical properties of etravine (NRTI)
pKa 3.5, weak base
insoluble in water
highly lipid soluble
taken with food to increase gastric residence time
elimination in faeces
limited cross-resistance with other NNRTIs
Discuss the pharmacodynamic and physiochemical properties of Efavirenz (NRTI)
practically insoluble high membrane permeability (40-50% bioavailability) hepatic metabolism Induces CYP enzymes Effects in CNS
Discuss the pharmacodynamic and physiochemical properties of doravine (NRTI)
Pka 3.5
quickly absorbed after oral administration
pharmacodynamics not affected by age/gender/ethnicity
metabolised by cyp3a4
Discuss the pharmacodynamic and physiochemical properties of ripilvirine (NRTI)
pka 5.6 - weak base poorly water soluble administered with food metabolised by cyp3a4 lower incidence of cns effects not recommended in breast feeding women
Discuss the pharmacodynamic and physiochemical properties of elsufarazine (NRTI)
oral formulation
t 1/2 9 days, once weekly dosing?
active against isolates from NNRTI experienced patients
higher barrier to genetic resistance
In simple terms, what do NRTIs do?
Chain Terminators
In simple terms, what do NNRTIs do?
Bind to reverse transcriptase and denatures it
Which drugs block entry of HIV?
Fusion inhibitors - block gp41 (fuzeon)
Post attachment inhibitors - (ibalizumab, temsavir)
Entry inhibitors CCR5 co recepotor antagonists (maraviroc)
What is membrane fusion?
The fusion of enveloped vriuses and host cell membranes. It is mediated by viral glycopeptides.
How does membrane fusion occur?
- Binding of gp120 to target cell surface on CD4 changes the confirmation of GP120, enabling the protein to bind to another receptor on the cell surface (CCR5/CXCR4)
- binding of GP120 leads to a confirmational change in GP120 which exposes GP41 and allows it to insert itself into the membrane, which leads to fusion of the two membranes
What is the function of gp41?
Gp41 drives final fusion step - a transmembrane protein
What is the function of gp120?
It is a surface protein responsible for host cell recognition. Gets the HIV particle into the correct place
What does fuzeon do?
Binds to gp41 and blocks the fusion of membranes
Discuss the clinical use of fuzeon
- fuzeon is a polypeptide not orally absorbed
- salvage therapy
- administered s/c
- hypersensitivity reactions are common
What is albivuirtide?
- fusion inhibitor
- links to serum albumin which increases t 1/2 whilst maintaining activity
- chemically modified peptide derived from HIV-1 protein GP41
How do drugs inhibit HIV entry?
Virus attaches to the cell via very few, specific high affinity molecular interactions, mediated by viral glycoproteins, blocking these (gp120, gp41)
Inhibit co-receptors CXCR4 and ccr5
Which drugs act on post-attachment?
Idalizumab
What is idalizumab used for?
For treatment of heavily experienced patients with multi-drug resistance. Antibody binds to CD4 receptor. Requires loading dose
Which drug acts on the CCR5 co-receptor? How does it work?
Maravirol. The only drug in it’s class. Binds to allosteric binding site on CCR5 receptor, causes a conformational change and disrupts binding of the virus
What is integrase?
An essential viral enzyme. Binds to doubled stranded viral DNA generated by reverse transcriptase and mediates it’s integration into the cellular genome
What is integration?
The final step before irreversible and productive HIV infection of the target cell
What is an active reservoir?
Untreated person
What is a latent reservoir?
Virus lies dormant
Describe the structure of integrase
It has 3 functional domains: N-terminal, catalytic core and the c-terminal
Why is LEDGF-p75 Significant?
It manages chromatin. If you disrupt this, defective viral proteins are produced
How does intergrase interact with LEDGF-P75?
Intergrased and LEDGF P75 bind and form a tetramer intasome.
What is the N-terminal domain and what is its purpose?
Domain that is part of integrase structure, contains a zinc ion which stabilises the enzyme and is critical for it’s function
What is the catalytic core domain and what is its purpose?
Part of the structure of integrase and binds to DNA non-specifically
What is the C-terminal domain and what is its purpose?
Part of integrase’s structure. Contains 3 negatively charged amino acids, which coordinate the mg2+ divalent metal ions, which is essential for catalysing the reactions that lead to 3’ strand transfer of DNA
Describe the process of strand transfer and integrase’s involvement
3’ processing occurs in the cytoplasm. Integrase cuts DNA and produces sticky ends, preparing DNA to be inserted into the nucleus of the host cell. Integrase cuts cellular DNA and inserts viral DNA, leading to permanent infection
What is the stable synaptic complex?
A tetramer of intasome engages two viral dna forming the stable synaptic complex
What happens to form the CDC?
3’ processing of the intasome and 2 vdna. Liable phosphodiester bond is cleaved, mg2+ is key for activity
What is the cleaved donor complex?
It is partly in the cytpolasm and the nucleus of the host cell
What happens after the CDC is formed?
tDNA binding to the CDC forms the TARGET CAPTURE COMPLEX
What happens and is formed after the TCC?
Cleavage of the phosphodiester bond, 3’ processing and the joining of v DNA of to cellular DNA
What is the strand transfer complex?
Where bonds form between vDNA and cellular DNA