A. M Kudal

Human Immunodeficiency Virus

HIV belongs to a special class of viruses called retroviruses. Within this
class, HIV is placed in the subgroup of lentiviruses. Other lentiviruses include
SIV, FIV, Visna and CAEV, which cause diseases in monkeys, cats, sheep and
goats. Outside of a human cell, HIV exists as roughly spherical particles
(sometimes called virions). The surface of each particle is studded with lots
of little spikes.

HIV particles are much too small to be seen
through an ordinary microscope. However they can be seen clearly with an
electron microscope.¹

A virus is a tiny organism (any
living thing is an organism). The average Human Immunodeficiency Virus (HIV),
the virus presumed responsible for AIDS, is about 0.000031 inches (120
Angstroms) long. Usually, a virus consists of a strand or strands of DNA
(deoxyribonucleic acid) or a strand or strands of RNA (ribonucleic acid),
coated with a layer of protein. Most known viruses have DNA cores. The Human
Immunodeficiency Virus (HIV), however, has an RNA core.

Schematic representation of the structure of HIV: ^2,3,4

 The virus is thought to contain 2 identical
copes of a positive sense (i.e. mRNA) single-stranded RNA strand about 9,500
nucleotides long. These may be linked to each other to form a genomic RNA dimer. The RNA dimer is in turn
associated with a basic nucleocapsid (NC)
protein (p9/6). By analogy with other RNA viruses, this nucleoprotein filament
may be helical, although this has not actually been determined in the case of
HIV. The ribonucleoprotein particle is encapsidated by a capsid made up
of a capsid  protein (CA),
p24. The capsid environment also contains other viral
proteins such as integrase and reverse
transcriptase. It also contains a wide variety of other macromolecules
derived from the cell including tRNAlys3, which serves as a primer for reverse
transcription. The capsid has an icosahedral
structure.

The capsid is in turn encapsidated by a layer of matrix protein (MA), p17.
This matrix protein is associated with a lipid bilayer
or envelope. The matrix protein may be:

• A
  continuous shell attached to the envelope as in HIV
• Noncontiguous
  but associated with envelope
• Separate
  from the envelope.

The HIV envelope is derived from the host
cell plasma membrane and is acquired when the virus buds through the cell membrane.
In addition it also contains viral proteins often forming spikes or peplomers.
The major HIV protein associated with the envelope is gp120/41. This
functions as the viral antireceptor or attachment protein. gp41
traverses the envelope, gp120 is present on the outer surface and is noncovalently attached to gp41. The precursor of gp120/41
(gp160) is synthesized in the endoplasmic reticulum and is transported via the golgi body to the cell
surface.              

Icosahedral Nucleocapsids:

Electron microscopy suggests that many viruses are roughly spherical. A detailed
examination shows that they are actually icosahedral. Icosahedral viruses
are very common plant and animal viruses. The HIV capsid layer is thought
to have an icosahedral structure. At the moment precise details of the HIV
capsid structure are not known but some general considerations are described
below:

The subunits of the capsid
are located around the vertices or face of an icosahedron.
An icosahedron has 20 equilateral triangles arranged
around the face of a sphere. It is defined by having 2, 3 and 5 fold axis of
symmetry.

HIV Genes

HIV has just nine genes (compared
to more than 500 genes in a bacterium, and around 20,000-25,000 in a human).
Three of the HIV genes, called gag, pol and env, contain information needed to make structural proteins
for new virus particles. The other six genes, known as tat, rev, nef, vif, vpr
and vpu, code for proteins that control the ability
of HIV to infect a cell, produce new copies of virus, or cause disease. At
either end of each strand of RNA is a sequence called the long terminal repeat,
which helps to control HIV replication.⁵

Replication of HIV

HIV can only replicate inside human cells. The
process typically begins when a virus particle bumps into a cell that carries
on its surface a special protein called CD4. The spikes on the surface of the
virus particle stick to the CD4 and allow the viral envelope to fuse with the
cell membrane. The contents of the HIV particle are then released into the
cell, leaving the envelope behind.

1. Reverse Transcription and Integration

Once inside the cell, the HIV enzyme reverse transciptase converts the viral RNA into DNA, which is
compatible with human genetic material. This DNA is transported to the cell's
nucleus, where it is spliced into the human DNA by the HIV enzyme integrase. Once integrated, the HIV DNA is known as
provirus.

2.Transcription and Translation

HIV provirus may lie dormant within a cell for a
long time. But when the cell becomes activated, it treats HIV genes in much the
same way as human genes. First it converts them into messenger RNA (using human
enzymes). Then the messenger RNA is transported outside the nucleus, and is
used as a blueprint for producing new HIV proteins and enzymes.

3. Assembly, Budding and Maturation

Among the strands of messenger RNA produced by
the cell are complete copies of HIV genetic material. These gather together
with newly made HIV proteins and enzymes to form new viral particles, which are
then released from the cell. The enzyme protease plays a vital role at this
stage of HIV's life cycle by chopping up long strands of protein into smaller
pieces, which are used to construct mature viral cores.

The newly matured HIV particles are ready to
infect another cell and begin the replication process all over again. In this
way the virus quickly spreads through the human body. And once a person is
infected, they can pass HIV on to others in their bodily fluids.

Transmission of HIV

In order for a
person to catch AIDS (HIV infection), the Human Immunodeficiency Virus (HIV)
must travel from the inside of one person to the inside of another person,
arriving with its RNA strand(s) intact. Then the virus or its intact RNA strand
must get into the new host's bloodstream and then successfully find and enter a
T-cell. Once inside a host cell, HIV can prepare for replication. After
replication, replica viruses infects other host cells, probably attaching to
new host cells when the infected host cell collides with other cells in the
bloodstream.

With AIDS, the
major infection sites are the bloodstream and the central nervous system. While
HIV-carrying macrophages (roving white blood cells that engulf invaders, but
are susceptible to HIV infection) are found in the connective tissues of the
lung and in oral and mucous membranes, the number of viruses present does not
seem great. Thus, HIV is present in low concentrations, if at all, in saliva
and sputum

In an infected
person, HIV is found in any body fluid or substance which contains lymphocytes
(T4-cell and company). Substances containing lymphocytes include: blood, semen,
vaginal and cervical secretions, mother's milk, saliva, tears, urine, and
feces.

 In HIV, an enzyme called reverse-transcriptase
(RT) performs the reverse-transcription process. Enzymes are chemical
workhorses. Human cells do not contain RT because they only write and have no
need to reverse-write. Thus, reverse transcriptase is virus-specific and an
important target for antiviral drug therapy.

As a group, retroviruses can live in their hosts
for a long period of time without causing any sign of illness. In most animals,
retrovirus infections last for life. Retroviruses are not very tough: they die
when exposed to heat, are killed by many common disinfectants, and usually do
not survive well if the tissue or blood they are in dries up. However,
retroviruses have high rates of mutation and, as a result, tend to evolve very
quickly into new strains (varieties). HIV seems to share this and other traits
with other known retroviruses.⁶

Types of HIV Infections (AIDS)

Basically, four loosely defined different stages
of HIV infection exist: I ) the healthy carrier state, 2) the lymphadenopathy syndrome (LAS), 3) AIDS-related complex
(ARC), and 4) AIDS or "frank AIDS," or "full-blown AIDS."
These forms or the symptoms of each may overlap the other.

Healthy Carrier State

A carrier is someone who is infected with a
disease and shows no clinical symptoms, but who is capable of infecting other
people with the disease. ("Clinical" means "seen in the doctors
office.")

HIV has been isolated (removed) and cultured
("grown" in a laboratory dish) from healthy people who show no
clinical signs of HIV infection. It is not yet clear when an HIV-infected
person becomes infectious. At this time, the only safe practice is to assume
that anyone carrying the virus is capable of transmitting it to others.

Lymphadenopathy Syndrome (LAS)

Lymphadenopathy Syndrome (LAS) is a mild form of
HIV infection, generally characterized by some of the symptoms.  Lymphadenopathy means "disease of the
lymphatic system." The lymphatic system is the human body's second fluid
system which contains a clear fluid called lymph . The lymphatic system aids
the blood system by draining fluid out of the body' s tissues. The lymphatic
system is not a closed loop like the bloodstream, meaning it does not flow in a
circle, and it has no pump like the heart. Nevertheless, lymph flows from
smaller vessels into larger lymph ducts in the upper chest. In doing so,
lymphatic fluid passes through a series of filtering stations called lymph
nodes, or lymph glands. Lymph nodes filter bacteria (one-celled organisms),
foreign substances, and dead white blood cells out of the fluid.

The lymphatic system is a vital part of the
body's immune system. Lymph nodes store and mature lymphocytes and other white
blood cells and also manufacture antibodies. T-cells and macrophages can
migrate back and forth between the blood system and the lymphatic system,
perhaps exposing newly generating cells to HIV during their formative stages.

One of the key signs of lymphadenopathy
is swollen lymph glands. Of course, any infection, such as the flu, causes the
lymph nodes to swell; but, nodal swelling due to normal infections passes
quickly. With HIV infection, this nodal swelling may persist for months, with
no other signs of a temporary infectious disease. Consequently, lymphadenopathy is sometimes called persistent generalized lymphadenopathy (PGL).

Symptoms of Lymphadenopathy Syndrome (LAS)

• Unexplained
  fever
• Difficulty
  in swallowing
• Swollen
  glands
• Fatigue/Lethargy
• Night
  sweats and chills
• Apathy
• Gradual
  loss of weight
• Diarrhoea
• Sore
  throat
• Impotence
  AIDS-related Complex (ARC)

AIDS-related Complex is a more advanced level of
HIV infection. Symptoms generally include the symptoms of lymphadenopathy,
plus abnormal body conditions revealed by laboratory tests, and/or the presence
of one or more opportunistic infections.

A person with ARC has a discomforting illness.
His or her everyday activity may be restricted and he or she is probably
manifesting bouts of illness that require short-term or long-term medical
treatment in and out of the hospital.

Acquired Immune Deficiency Syndrome
(AIDS)

AIDS is the "full-blown" syndrome, also
called "frank" AIDS. Patients suffering from AIDS often have any
number of the opportunistic diseases listed below. These diseases develop
because of the widespread failure of the immune system. Drug treatments are
available for many of these infections; but, without the support of the immune
system, the drugs fail to cure the disease fully or are unable to keep the
disease from returning. These opportunistic infections, curable under other
circumstances, cause the death of most AIDS patients.

Symptoms and Conditions of ARC and AIDS

• Anergy: lack of skin allergic response
• Anemia:
  lack of red blood cells
• Autoimmune
  Disorders: immune system attacks own body
• Candidiasis/Oral Thrush.
• Hyperplasia:
  excessive growth of normal cells in organ
• Kidney
  Dysfunction: kidneys fail or function poorly
• Leukopenia: decreased number of
  leukocytes (white blood cells that engulf germs)
• Lymphomas:
  lymphatic system cancers
• Lymphopenia: decreased number of
  lymphocytes
• Nerve
  Damage: possible blindness, deafness, paralysis
• Oral
  Thrush: caused by Epstein-Barr Virus .
• Wasting:
  severe weight loss, perhaps death, from diarrhea and malnutrition .

Treatment:   Drugs
used  for the treatment of HIV can be divided into four
categories : (1) nucleoside reverse transcriptase inhibitors (NRTIs) Zidovudine, Lamivudine, Didanosine, Stavudine, Abacavir, Emtricitabine, Zalcitabine ; (2) nucleotide
reverse transcriptase inhibitors (NtRTIs) Tenofovir ; (3) Non-nucleoside reverse
transcriptase inhibitors (NNRTIs) Nevirapine, Delavirdine, Efavirenz ; (4) Protease inhibitors (PIs) Saquinavir, Ritonavir, Indinavir, Nelfinavir, Amprenavir, Lopinavir, Atazanavir. Information of some drugs is given below

Indinavir sulphate C₃₆H₄₇N₅O₄,
H₂SO₄

HIV Protease inhibitors have been associated with a lipodystrophy syndrome
characterized by Peripheral fat wasting,central adiposity and the so called
‘ buffalo hump’, hyperlipidaemia and insulin resistance⁷.A Survey
of 113 HIV infected patients Receiving HIV Protease inhibitors found lipodystrophy
in 83% Patients and impaired glucose tolerance in 23% after a mean of 21 months
of therapy.⁸  

Interactions: Indinavir and similar HIV Protease inhibitors are metabolized
Principally by cytochrome P450 enzymes of the CYP3A family. Thus Concurrent
administration of a drug with a narrow therapeutic window, such as Cisapride
or terfenadine, is contraindicated, where as a drug with a wider,  therapeutic
window such as erythromycin, mayonly require dosage reduction at its highest
dose level.⁹

Mechanism of Action: These are antiretrovirals binding reversibly to
HIV Protease thereby preventing cleavage of the viral Precursor Polypeptides.
This results in formation of immature viral particles incapable of infecting
other cells. To avoid viral resistance combination of other drugs is used¹⁰.

Ritonavir: C₃₇H₄₈N₆O₅S₂

Ritonavir is a Protease inhibitor with antiviral activity
against HIV used in combination with other Protease inhibitors. Oral dose is
600mg twice daily with food . Children over the age of 2years may be given an
initial dose of 250mg/m² twice daily.¹¹ 

Structure

Star represents
C₁₄ atom.

Saquinavir: C₃₈H₅₀N₆O₅

Saquinavir is a Protease inhibitor with antiviral activity
against HIV used in combination with other Protease inhibitors.It
is available as Saquinavir mesilate.
Adult dose is 1gm twice daily given with 100mg ritonavir  in combination with other antiretrovirals.¹²

Structure

Stavudine: C₁₀H₁₂N₂O₄

Mechanism of Action: Stavudine is converted intracellularly in stages
to the triphosphate. This Prevents the DNA Synthesis of the retroviruses,
including HIV, through competitive inhibition of reverse transcriptase and
incorporation into viral DNA.

Dose: 40mg every
12 hours orally per 60kg bodyweight. Over 3 months of age weighing less than
30kg , 1mg/kg bodyweight.

Structure

Antiviral effect of Stavudine may be inhibited by zidovudine, doxorubin and
ribavirin.

Adverse effects
include motor weakness along with lactic acidosis.¹³

Zidovudine: C₁₀H₁₃N₅O₄

Zidovudine is structurally related to thymidine.

Structure

Mechanism of Action: Zidovudine is converted intracellularly in stages
to the triphosphate via thymidine kinase and other kinases which  Prevents
the DNA Synthesis of the retroviruses , including HIV, through competitive
inhibition of reverse transcriptase and incorporation into viral DNA.¹⁴

Adverse effects
commonly seen are anaemia and leucopenia within few
weeks of treatment so should be used with care in Patients with anaemia or bone marrow suppression and vitamin B₁₂
defficiency. Ribavirin and zidovudin should not be given in combination as they
inhibit each others activity.

Dose: 500-600mg
daily in divided doses.

CD4+ White blood cells:

The immune system’s
army of CD4+ T cells not only declines in overall size during the course of HIV
disease, but also becomes progressively less diverse, according to a recent
study by NIAID researchers. This produces "holes" in the immune
system that are not repaired, at least in the short term, by current anti-HIV
therapies.

 H. Clifford Lane, M.D., NIAID’s
clinical director and senior author of the study published in the May 1997
issue of the journal Nature Medicine says that drugs to prevent
opportunistic infections may remain important even for patients with CD4+ T
cell counts that are rapidly increasing in response to therapy, because these
individuals may be missing part of their CD4+ T cell repertoires."

Healthy people without
HIV infection typically have between 600 and 1500 CD4+ T cells per cubic
millimeter (cells/mm³) of blood. Normally, a diverse array of these
cells are present, each tailored to recognize one of a multitude of invaders.
Variations in T cell receptors (TCR), the cell surface molecules that bind to
these invaders, account for much of this diversity. Each TCR has an alpha and
beta chain, explains Dr. Lane, and each beta chain contains a variable region
belonging to one of at least 22 families. Immunologists often use these
"V-beta" families to classify T cells.

Using a specialized
polymerase chain reaction (PCR) technique, Dr. Lane and his colleagues examined
TCR V-beta regions in CD4+ T cells taken from both HIV-infected and HIV-uninfected
people. Among those studied were five sets of twins in which one sibling was
HIV-positive, the other HIV-negative. V-beta regions of cells from the
uninfected twins were virtually all normal. Cells from infected twins, on the
other hand, had molecular disruptions in as many as 11 different V-beta
families. In another group of persons without HIV infection, fewer than 5
percent of all V-beta families were disrupted. By comparison, disruptions were
noted in approximately 15 percent of all V-beta families in cells from a group
of HIV-infected people with CD4+ T cell counts above 200 cells/mm³.

Among infected
individuals with CD4+ T cell counts below 200/mm³, nearly 40 percent
of V-beta families had disruptions. Even when treatment with antiretroviral
drugs and interleukin-2 (IL-2) boosted a person’s CD4+ T cell count to 200/mm³
or higher, CD4+ T cell diversity was not restored, the researchers observed.

"The loss of CD4+
T cells is a qualitative phenomenon as well as a quantitative one," says
co-lead author Mark Connors, M.D., of the NIAID Laboratory of Immunoregulation (LIR). "In other words, a CD4+ T cell
count of 200/mm³ of blood during the natural history of HIV
infection may be very different from a CD4+ T cell count of 200/mm³
in the context of therapy.

The current findings
shed light on an observation reported by Dr. Lane and his colleagues in the
mid-1980s. They noted that HIV-infected people often lose their ability to
respond to "remote recall antigens," substances to which one was
exposed in the past such as the antigens in a tetanus vaccine. The new data
suggest that this decreased responsiveness is due to a loss of specific CD4+ T
cell types, which scientists refer to as "clones."

"Most likely, the
increase in a patient’s CD4+ T cell count after initiating therapy represents
expansion of the existing repertoire in a patient’s bloodstream and lymph nodes
rather than the generation of "new" CD4+ T cells by the thymus,"
says Dr. Kovacs. "This view is supported by our observation that many of the
patients in the study had minimal thymic
tissue." However, Dr. Lane suggests that even patients with advanced
disease may be able to mount adequate immune responses if antiretroviral
therapy reduces HIV replication to very low levels. With potent suppression of
HIV, other clones may be able to proliferate to sufficient levels to perform
the job normally done by the missing clones.¹⁵

"In the future,
modifications of the techniques used in this study may prove useful clinically
for better defining the predictive value of a CD4+ T cell count," he adds.
"Knowing a person’s specific T cell repertoire might allow one to better
predict the susceptibility of a person to opportunistic infections, and may one
day help guide treatment decisions."

Gene Therapy May Restore Immune Systems:

As an NIAID-funded
National Cooperative Drug Discovery Group for the Treatment of HIV Infection,
Dr. Zaia and his COH colleague John J. Ross, Ph.D.,
were the first to propose the use of ribozymes in HIV
gene therapy

Researchers have initiated
a study in humans to determine whether gene therapy can be used to attack HIV
and possibly rebuild patients’ immune systems

The experimental
treatment uses ribozymes, ribonucleic acid (RNA)
molecules capable of enzymatically cleaving other RNA
molecules. Researchers led by John Zaia, M.D., of the
City of Hope (COH) National Medical Center in Duarte, Calif., seek to fortify
the immune cells of HIV-infected patients with ribozymes
designed to inactivate HIV RNA. Strategy involves shuttling genes encoding
anti-HIV ribozymes into immune cells aboard vector
molecules. Cells that have been genetically modified, or transduced,
in this way would produce ribozymes, available to
attack HIV RNA as soon as the virus enters the cell. To guard against the
development of resistance, Dr. Zaia and his
colleagues insert two ribozyme genes, each targeting
a different piece of HIV RNA, into each cell. If resistance develops against
one ribozyme, the second one should still interfere
with HIV replication . In laboratory experiments, the scientists have shown
that HIV replication is inhibited in human T cells containing anti-HIV ribozyme genesscientists remove
blood-producing "stem cells" from HIV-infected patients, insert ribozyme genes into the cells, then re-infuse the modified
stem cells back into the patients. Found primarily in bone marrow, stem cells
are the ancestors from which all immune system cells (and other blood cells)
are derived. Theoretically, stem cells endowed with anti-HIV ribozyme genes could repopulate a damaged immune system
with cells genetically resistant to HIV infection.The
purpose of this trial  was  to see whether the transduced
stem cells would produce daughter cells.

The
researchers will infuse a total of five patients with ribozyme-transduced
stem cells and then periodically look for ribozyme-producing
immune cells in the patients’ blood. They also will monitor the patients for
signs of side effects of the treatment.

"To get a
significant proportion of genetically protected cells in the blood, a
significant proportion of a patient’s stem cells must carry the ribozyme genes. In this study, however, we basically have a
competition between a small number of transduced stem
cells and a large number of the patient’s resident (non-transduced)
stem cells." Future studies, says Dr. Zaia, may
involve ablating, or destroying, patients’ resident stem cells prior to
infusing them with transduced cells as a means of
increasing the proportion of protected daughter cells in the bloodstream.

1. Overview of T cell epitope prediction algorithms:

Several computer-driven algorithms search the amino acid sequence of a given
protein for characteristics believed to be common to immunogenic peptides,
locating regions that are likely to induce cellular immune response in
vitro. Computer-driven algorithms can identify regions of HIV proteins
that contain epitopes and are less variable among geographic isolates; alternatively,
computer-driven algorithms can rapidly identify regions of each geographic
isolate's more variable proteins that should be included in a multi-clade
vaccine.

Peptides presented in conjunction with class I
MHC molecules are derived from foreign or self protein antigens that have been
synthesized in the cytoplasm. ^16,17,18.Peptides presented in the
context of class II MHC molecules are usually derived from exogenous protein
antigens.^19,20,21 Peptides
binding to class I molecules are generally shorter (8-10 amino acid residues)
than those that bind to class II molecules (8 to greater than 20 residues).           The identification of T cell epitopes within protein antigens has traditionally been
accomplished using a variety of methods, including the use of whole and
fragmented native or recombinant antigenic protein, as well as the more
commonly employed "overlapping peptide" method. The latter method for
the identification of T cell epitopes within protein
antigens involves the synthesis of overlapping peptides which span the entire
sequence of a given protein antigen. These peptides are then tested for their
capacity to stimulate T cell cytotoxic or proliferative responses in vitro.

MHC binding motifs are patterns
of amino acids that appear to be common to most of the peptides that bind to a
specific MHC molecule. For example, a lysine might be required in position N+1
(one amino acid from the amino terminus), and a valine
in position N+8, while any amino acid may occur at any of the other positions

Most of the novel computer-driven algorithms depend on published information
on MHC binding motifs. One methodological concern when designing a multiple
binding motif-based predictive algorithm is the accuracy of the MHC binding
motifs used to predict putative epitopes, and thus the overall validity of
the motif database.

2. Applications of T cell epitope algorithms to HIV research:

 Searching for T cell epitopes

Identification of T cell epitopes
that stimulate cell-mediated immunity is essential to HIV vaccine development.
The identification of HIV peptide epitopes that
contain clusters of MHC binding motifs representing multiple HLA alleles from
HIV protein sequences may be useful for HIV vaccine development.

There appear to be more stringent
binding criteria for class I-restricted binding peptides, and few
multi-determinant class I epitopes have been identified
for any pathogen. However, several HIV protein regions that contain multiple
overlapping class-II restricted epitopes, also known
as "multi-determinant" or multi-determinant peptides, have been
identified in mice and humans. Such regions might be important to include in
the synthesis of multiple antigenic peptides (MAPS) for HIV vaccine
development, particularly if a multi-determinant T cell epitope
is required for boosting immune response to B cell epitopes.

The EpiMer algorithm is readily applied to HIV protein sequences. In a recent
comparison of EpiMer predictions to published HIV protein T cell epitopes,
the EpiMer algorithm was shown to be 2.4 fold more sensitive than the overlapping
method for detecting published T cell epitopes for four HIV proteins, gp160,
nef, tat, and gag (CGP Roberts et al., manuscript submitted²²).
A summary of these comparisons of the overlapping method to the EpiMer prediction
method is shown in Table
1.

Table 1. Efficiency and sensitivity of the Overlapping method, compared
to EpiMer, for the HIV proteins nef, gag, gp160, and tat.

	Overlapping	EpiMer
Per Cent Efficiency	60%	62%
Range	43%-100%	61%-64%
Per Cent Sensitivity	100%	59%
Range	100%-100%	22%-86%
Average Sensitivity per amino acid	2.7	4.9
Range	0.6-6.4	1.3-8.1
Average Æ sensitivity per AA	(ref)	2.4

Efficiency, =
(total length, in amino acid residues, of the peptides that overlap by at least
eight or eleven amino acid residues with Class I or Class II published epitopes, respectively)/(total length, in amino acid
residues, of all putative epitopes identified by the
algorithm in question).
Sensitivity, S, (number of published epitopes
that were predicted by the algorithm in question)/(total number of published epitopes for the protein).
Sensitivity per amino acid (SAA), = 1000 x (Sensitivity)/(total length, in
amino acids, of peptides to be synthesized). Æ Sensitivity/AA, (ÆSAA) =
(Sensitivity per amino acid residue for a given method)/(Sensitivity per amino
acid residue of the overlapping peptide method).

Application of MHC binding motifs
to HIV vaccine development may be restricted by the amount of sequence
variation in individual quasi-species, HIV strains, and HIV clades,
as well as by the MHC background of the target populations. One might consider
evaluating regions of MHC clustering that occur in sites of low HIV sequence
variability, as shown in Figure 5. The region 130 to 160, which
has a great deal of inter-strain variation described by the variability plot,
might best be avoided for subunit HIV vaccine development. HIV peptide epitopes which contain multiple MHC binding motifs, either
conserved across HIV strains or derived from several different HIV strains, may
be ideal candidates for inclusion in a multi-subunit vaccine.

Figure 5. gp160 (variability plot)

The mean variability of the 11-residue segments of known gp160 sequences
(Los Alamos HIV Sequence Database) are
shown as well. Variability = (number of different amino acids at a given position)/(frequency
of the most common amino acid at that position).

Conclusion:

Apart from the recently available drugs used individually e.g zidovudine,lamivudine,efavirenz,nevirapine,Stavudine
and their combinations as acyclovir along with lamivudine and zidovudine for
the management of HIV infection, gene therapy may prove beneficial. The changes
in the gene sequence of lymphocytes prior to HIV infection in the high risk
groups will definitely be useful in the near future for the prevention and
treatment of AIDS. Futhermore considering the studies including gene insertion 
of a right sequence at a  particular site of  T lymphocytes may lead to development
of  a  vaccine against  the dreaded disease.

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About Authors

Dr. S. R. Parakh

Working as Principal and Professor in Pharmaceutics at MAEER’s, Maharastra
Institute of Pharmacy, MIT Campus, Pune-411038

Email:srparakh@rediffmail.com

Mr.Anand M. Kudal*

Working as
Lecturer at MAEER’s,Maharastra Institute of Pharmacy, MIT Campus, Pune. He has
completed M.Pharm in Medicinal and Pharmaceutical Chemistry from Department of
Pharmacy, SGSITS, Indore, RGPV, Bhopal. He is a Life
member of APTI.

Email:anand_kudal@yahoo.com, Cell-09371182099

Mr. Satish A. Polshettiwar

Working
as Lecturer at MAEER’s, Maharashtra Institute of Pharmacy, MIT Campus, Pune. He
has done his M.Pharm in Quality Assurance from Nagpur University. He is a Life
member of APTI. He has published and presented several research articles in
national level.

E.Mail:contact_psatish@yahoo.co.in, Cell No. 09422842838

V.P. Chaudhari

Working as
Assistant Professor at MAEER’s, Maharashtra Institute of Pharmacy, MIT Campus,
Pune. He is a Life member of APTI and IPA.

E.mail:
viraj1404@rediffmail.com