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HIV (MCB3024S) notes
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  • Course
  • Defence and Disease (MCB3024S)
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  • University Of Cape Town (UCT)

Comprehensive lecture notes for the HIV: Molecular biology, drugs, mucosal immunity, hormonal effects module covered in MCB3024S. These notes cover all content taught in lectures as well as additional materials (powerpoints, textbooks) required to succeed. These notes were created by a student who...

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Document information

  • February 8, 2024
  • 54
  • 2022/2023
  • Class notes
  • Janet hapgood
  • All classes

Subjects

  • biochemistry

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  • University of Cape Town (UCT)
  • Defence and Disease (MCB3024S)
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MCB3024S

HIV, drugs and hormones

HIV structure, genome, lifecycle and current drugs for treatment
Introduction
Global and regional overview
- HIV continues to be a major global public health issue, having claimed more than 39 million lives so far
- the number of people become newly infected each year is very high, despite the ARVs and this is because they are not
taking their drugs or do not have access to the drugs
- huge death rates still and HIV is still a massive problem
- ARVs work and coverage is getting better, but there is still a large number that do not have access to the drugs
- Covid created a problem in that TB and HIV and basic vaccinations and ARVs were inaccessible
- HIV infection is usually diagnosed through blood tests detecting the presence or absence of HIV antibodies (CD4 cells)
- There is no cure for HIV infection. However, effective treatment with antiretroviral drugs can control the virus so that
people with HIV can enjoy healthy and productive lives

ARV therapy coverage and number of AIDS-related deaths globally
- illustrates one of the major advances which is the increased coverage of
the population of ARVs
- the greater the coverage, the lower the death (inverse relationship)
- massive increase in coverage and great drop in deaths
- blue is AIDS-related deaths (all ages)
- green is HIV treatment coverage (all ages)

HIV and AIDS in sub-Saharan Africa regional overview
- world-wide problem but more than 50% is in sub-Saharan Africa
- is a particularly south African problem, with over 7 million
- SA has the highest number of people living with HIV than any other country
(poverty, lack of health facilities, limited resource availability, access to
primary health care if very poor, education is poor with regards to disease and
presentation and importance of drugs, migrant labor and the history of
apartheid and violence contribute to HIV, government denied HIV existed, so
political factors)
- no genetic factor to the HIV distribution being greatest in South Africa

Gender disparity: more females infected than males
- males and females have different susceptibilities to HIV and this is due to biological dif-
ferences in their genital tract
- females are much more at risk, the purple is female, and green is male
- can see that in age group 20-24, there are 3 times more females than males being infected,
and these differences are greater in younger age groups
- females are more at risk, more infected

Introduction: HIV structure, genome and life cycle
Structure of the HIV particle
- the structure of the HIV particle is similar for both HIV-1 and HIV-2
- the gag gene encodes the structural proteins of the core and matric
- the env gene encodes the viral envelope glycoproteins gp120 and gp41 (which
recognize cell surface receptors)
- the pol gene encodes for the enzymes crucial for viral replication (reverse
transcriptase that converts viral RNA into DNA, the integrase that incorporates the
vial DNA into host chromosomal DNA and the protease that cleaves large Gag and
Pol protein precursors into their components)
- the HIV particle is surrounded by a lipoprotein-rich membrane

- this is a ss+ RNA retrovirus and integrates into the host genome via copying the RNA into ds DNA
- the viral particle has glycoprotein and in HIV, this is called gp120 and gp41
- there is a lipid membrane and under that is a protein boundary called matrix
- inside the particle is the nucleic acid surrounded by protein
- have 2 copies of ss RNA and have capsid which get ejected into the cell and is made up of a protein outer layer

,- 3 enzymes in the mature viral particle (Reverse transcriptase, integrase and protease viral proteins)
- in addition, are some accessory proteins, such as VPR
- note that the mature virus also contains virl integrase and protease proteins and some accessory proteins like Vpr

Genome organization




- HIV isolates are currently grouped into two types, HIV-type 1 and HYV-type 2
- HIV1 is the one that causes severe disease (AIDS) and HIV 2 is mild
- HIV-1 is the main agent of world-wide AIDS and HIV-2 is restricted to some regions of western and central Africa
- HIV is genetically related member of the Lentivirus genus of the Retroviridae family
- at the DNA level, they have the same genes
- the retrovirus genome is composed of two identical copies of single-stranded RNA molecules and is characterized by the
presence of structural genes gag, pol and env
- HIV-1 and HIV-2 viruses differ in the organization of their genome, although the basic structure (present of the 3
structural genes) is the same as for all retroviruses
- in addition, HIV-1 and HIV-2 genomes present a complex combination of other regulatory and accessory genes
- the virus only encodes 9 genes (very small genome) yet incredibly efficient
- it is able to exert all its function because it co-opts the hosts machinery (protein and enzymes) to carry out its life cycle

The critical genes
- LTR (long terminal repeat) and this is a promoter which contains all the binding sites for host transcription factors and for
some viral proteins and is necessary to initiate transcription once it has been integrated into the hosts genome
- GAG, Pol and Env are the main genes
- other genes are accessory proteins, are not essential for infection but essential for replication and disease (important for
the functions)
- TAT accessory protein: is essential for efficient viral transcription and is involved in transcription elongation in the
nucleus

Function of these genes- the gag gene encodes the capsid proteins (the structures)
- p24 is one of the most abundant proteins in the virus
- the pol gene encodes the enzymes
- an initial polypeptide gets cleaved to generate the
individual genes for gag and pol
- env gene encodes the envelope proteins
- gp120 recognizes the target host cell by binding to host
cell surface receptor (CD4 and chemokine receptors)
- gp41 facilitates viral fusion between the viral and cell
membrane
Accessory proteins
- HIV viruses are characterised by other accessory/ regulatory genes that
play key roles in modulating virus replication
- TAT is the most important accessory protein and is only expressed after
infection and is essential for efficient for gene expression at the level of
transcription, so the virus can replicate without it but does not replicate well
- these are regulatory and increase the efficiency of infection and disease
progression
- VPU is well known for being involved in budding (release)
-VPR is important in helping to cause cell cycle arrest and apoptosis of host
target cell
- do not know accessory proteins other than TAT

HIV replication cycle
- It can be summarised in six steps; 1) binding and entry; 2) uncoating; 3) reverse transcription; 4) provirus integration; 5)
virus protein synthesis and assembly and 6) budding
- The entry pathway can be divided into three major events: virus binding to the cell, activation and fusion
- The viral envelope, composed of gp120 and gp41, is essential for virus recognition and entry into target cells

, - step 1: binding, fusion and entry: virus recognizes target cell, binds and
viral membrane fuses with host cell membrane and capsid injected into
the cell (this involves gp120)
- step 2: uncoating
- step 3: ss RNA gets reverse transcribed into dsDNA for integration into
the host genome (as host is dsDNA genome) and the enzyme is reverse
transcriptase that does this
- RT is a big target for drugs
- step 4: dsDNA enters the nucleus via pores and an active transport
mechanism to traffic the DNA into the nucleus, and integrates into the
host genome using the enzyme integrase which cuts the dsDNA and
inserts the cassette into the host genome

- transcription via the host genome and enzyme (DNA dependent RNA polymerase) and need many copies of the mRNA (to
make proteins and to make the viral genetic material)
- mRNA gets translated into viral proteins using host ribosomes in the cytoplasm (same as host)
- step 5: self-assembly of the particle and viral genome and a precursor viral particle formed
- step 6: budding off and the host membrane becomes the viral membrane
- after the particle has budded off, proteolysis takes place to get mature proteins to get the mature infectious HIV particle

Anti-HIV drugs can target different stages of the HIV life cycle
- You need to know the mechanisms of action of some of them i.e. AZT,
tenofovir, enfirvitide, maraviroc and protease inhibitors

- diagram shows the different targets currently being used in the context of the
life cycle
- pink boxes are targets that are currently used in antiviral combinational therapy
- 2 drugs target different steps, and the less likely that the virus will be able to
evade the therapy through mutating a gene and develop resistance
- HIV mutated very quickly and the RT has low fidelity (makes many mistakes)
which is a mechanism to introduce mutations and many variants which is
mechanisms whereby the virus can escape drugs
- the first step that is targeted is the attachment step using co-receptor antagonist:
binds to CD4 receptor and has to also bind to a co-receptor (CCR4and CCR5)
and there are some drugs that prevent the binding of the virus to the co receptor
(called co-receptor antagonists)
- can also target the fusion step using fusion inhibitors in the market (process w
here viral and host membrane fuse to insert the capsid)
- reveres transcription step involved RT enzyme which is a target of most
antiretroviral drugs (it is not a common host protein and secondly, it is essential
for the viral life cycle and there are multiple ways in which you can target the
enzyme)
- are integrase inhibitors and they prevent the integration step
- proteins that have to be cleaved to make infectious particles and there are
protease inhibitors to prevent this, they target the viral protease mainly
- potential new targets: the uncoating step, the budding step


Summary: Current types anti-HV drugs
- RT inhibitors have 3 types: nucleoside, nucleotide and non-nucleoside
inhibitors (use nucleotide or nucleoside analogues or non that bind
somewhere else and act allosterically)
- protease inhibitors
- co-receptor (antagonists)
- fusion inhibitors (target gp41)
- integrase inhibitors



Mechanism of action of some current anti-HIV drugs
- You need to know the mechanisms of action of some of them i.e. AZT, tenofovir, enfirvitide, maraviroc and protease
inhibitors

, Drugs targeting Attachment of virus to host cell (co-receptor inhibitors or CRIs)
HIV tropism
- the differential expression of chemokine receptors on cell targets has
been shown to be a major determinant of the HIV-1 tropism
- tropism is whether the virus favors one of the other co-receptors
- there are mainly 2 receptors: the CXCR-5 and CCR-4 and the relative
distribution of these cell receptors is different in different cell types
- some HIV-1 strains preferentially bind to CXCR-4 which are referred
to as X4 viruses
- some preferentially bind to CCR-5 and are referred to as R5 viruses
- can also get dual tropic X4R5 but this is unusual
- the virus that first infects you is usually R5

- later, once you have infection and replication and disease progression, then you get X4 virus strains becoming more
prominent
- both co-receptors are found on T-cells but CCR-5 is also found on macrophages (no CXCR-4 on macrophages)
- CCR-5 preferential virus is usually called m-trophic and the others are called t-tropic
- trophism is a property of the virus itself
- both need CD4, so the initial contact is with CD4 (receptor on the cell surface), and once it contacts CD4, it undergoes a
conformational change and can recognize a co-receptor (G-protein coupled receptor which can be XCX4 or CCR5)
- co-receptors function as receptors for natural ligands and are involved in immune function but have now been co-opted by
the virus as a means of getting into the cell

Attachment: HIV-1 gp120 binds to host cell CD4 receptor
- diagram shows an M-tropic virus on a macrophage and a T-
tropic virus on a T4-lymphocyte

M-tropic HIV example from diagram:
- gp120 protein (part of the envelope protein) binds to the CD4
molecule, undergoes conformational change and binds to the co-
receptor (chemokine receptor), this exposes gp41 which darts
out and pi erces the host cell membrane and anchors the virus
and get fusion of the membranes

Another view of binding and entry




Figure above. Overview of HIV attachment and entry. To deliver the viral payload into cells, HIV Env, comprised of gp120
and gp41 subunits (1), first attaches to the host cell, binding CD4 (2). This causes conformational changes in Env, allowing
coreceptor binding, which is mediated in part by the V3 loop of Env (3). This initiates the membrane fusion process as the
fusion peptide of gp41 inserts into the target membrane, followed by six-helix bundle formation and complete membrane
fusion (4)

- gp120 is shown here as a trimer and gp41 is also a trimer
- gp120 has a variable loop (loop 3) which recognizes the CD4 receptor
- firstly, gp120 recognizes the CD4 receptor and it undergoes a conformational change in such a way that allows it to
interact with the co-receptor
- this conformational change also results in gp41 fusion peptide piercing into the membrane
- and get formation of a 6-helix bundle which then allows membrane fusion and entry

Attachment inhibitors: HIV Co-Receptor Inhibitors (CRIs) e.g. maraviroc
- co-receptor antagonists inhibit attachment by binding the co-receptor and changing its shape such that gp120 cannot
recognize it
- the diagram: in the absence of maraviroc, the CD4 receptor binds to gp120

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