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ANTHRAX
Aim
To select a disease and to do a complete study on it.

Description
Anthrax is an acute disease in humans and animals caused by the bacterium Bacillus anthraces which is highly
lethal in some forms, there are effective vaccines against anthrax and some forms of the disease respond well to
the antibiotic treatment.
Bacillus anthraces is a gram positive, facultatively anaerobic, rod shaped bacterium of the genus bacillus, an
endospore forming bacterium, Bacillus anthraces is a natural soil dwelling organism, as well as the causative
agent of anthrax, under conditions of environmental stress, Bacillus anthraces bacteria naturally produce
endospores which rest in the soil and can survive for thousands of years in this state. Bacillus anthraces may be
inoculated into a wound, inhaled or ingested. In ruminants, the bacterium causes sudden death from septicaemia.
For this reason any ruminants found to have died suddenly and without obvious reason should be treated as a
suspected anthrax case. In these events, a blood sample is taken, by a qualified veterinary surgeon, from a
superficial vein and subjected to the MacFaydean polychrome methylene blue staining procedure which screens
for Bacillus anthraces. Confirmational diagnosis is achieved through PCR and Immunofluorescence
Horses respond variably to Bacillus anthraces depending on the site of entry. Ingestion tends to lead to a severe
enteritis and septicaemia. Inoculation in the skin tends to result in a local swelling and associated lymphadenitis.
Bacillus anthraces again causes an acute necrotising tonsillitis, or a subacute pharyngeal swelling, or the
intestinal disease described in horses. The intestinal disease carries a higher mortality. Dogs and cats seem less
susceptible to Bacillus anthraces and require a relative large dose of infectious agent before they begin to show
clinical signs.
Anthrax is an acute infectious disease caused by the spore-forming bacterium Bacillus anthraces. Anthrax most
commonly occurs in wild and domestic lower vertebrates (cattle, sheep, goats, camels, antelopes, and other
herbivores), but it can also occur in humans when they are exposed to infected animals or tissue from infected
animals
Transmission of Anthrax
Anthrax infection can occur in three forms: cutaneous (skin), inhalation, and gastrointestinal. Bacillus anthraces
spores can live in the soil for many years, and humans can become infected with anthrax by handling products
from infected animals or by inhaling anthrax spores from contaminated animal products. Anthrax can also be

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spread by eating undercooked meat from infected animals. It is rare to find infected animals in the United States.
Symptoms of disease vary depending on how the disease was contracted, but symptoms usually occur within 7
days.
Cutaneous: Most (about 95%) anthrax infections occur, when the bacterial spore enters a cut or abrasion on the
skin, such as when handling contaminated wool, hides, leather or hair products of infected animals. Skin infection
begins as a raised itchy bump that resembles an insect bite but within 1-2 days develops into a vesicle and then a
painless ulcer, usually 1-3 cm in diameter, with a characteristic black necrotic (dying) area in the center. Edema
or swelling of the surrounding tissues may develop and lymph glands in the adjacent area may swell. About 20%
of untreated cases of cutaneous anthrax will result in death. Deaths are rare with appropriate antimicrobial
therapy.
Inhalation: Initial symptoms may resemble a common cold. After several days, the symptoms may progress to
severe breathing problems and shock. Inhalation anthrax is usually fatal, and even with aggressive antibiotic and
supportive therapy 45% of inhalation anthrax cases were fatal in the bioterrorist attack in the fall of 2001.
Intestinal: The intestinal disease form of anthrax may follow the consumption of contaminated meat and is
characterized by an acute inflammation of the intestinal tract. Initial signs include nausea, loss of appetite,
vomiting, fever are followed by abdominal pain, vomiting of blood, and severe diarrhea. Symptoms may also
include lesions and soreness in the throat, difficulty swallowing, marked swelling of the neck and regional lymph
glands. Intestinal anthrax results in death in 25% to 60% of cases.
Structure and Targets of the Anthrax
The identification of [the receptor for the anthrax protein] now allows for a more detailed investigation of the
mechanism of uptake by cells of anthrax toxin, write John A. T. Young, of the University of Wisconsin-Madison,
and colleagues. In the second paper, researchers report the three-dimensional structure of another part of the
toxin, called lethal factor. This enzyme disrupts communication within immune cells, inhibiting a response. Cells
eventually rupture, which causes shock, a loss of blood pressure, and death. Anthrax toxin has three parts:
protective antigen (PA), a protein that binds to a receptor on the target cell surface; and two enzymes that must be
transported into the cell to cause damage. The enzymatic portions of the toxin enter the cell through a pore
created for them by PA after it binds to the cell's outer surface. PA can be seen as a bundle of seven cigar-shaped
parts, a molecular arrangement referred to as "polyvalent," meaning it displays multiple binding sites.
The inhibitor designed by Dr. Kane and his colleagues is also polyvalent. Just as a glove matches the shape of a
hand more closely than a mitten, and so fits more snugly, the polyvalent inhibitor binds the toxin at multiple sites
and is orders of magnitude more potent than an inhibitor that binds at a single site. The multiple peptides on the

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functionalized liposome are arranged with the same average spacing as the binding sites of the PA molecule,
which permits a firmer bond between the two, explains Dr. Kane. When the inhibitor is bound tightly to PA, the
subsequent steps of enzyme entry cannot occur and the toxin is effectively neutralized.
Anthrax Bacterium Genome
Genes are the instructions for making proteins, which in turn build components of the cell or carry out its
biochemical processes. The instructions that dictate how a microbe works are encoded within its genes. Bacteria
keep most of their genes in a chromosome, a very long stretch of DNA. Smaller circular pieces of DNA called
plasmids also carry genes that bacteria may exchange with each other. Because plasmids often contain genes for
toxins and antibiotic resistance, knowing the DNA sequence of such plasmids is important. Scientists have
sequenced plasmids carrying the toxin genes of B. anthraces. In addition, researchers have sequenced the
complete chromosomal DNA sequence of several Bacillus anthraces strains, including one that killed a Florida
man in the 2001 anthrax
Bioterrorism attack by comparing the DNA blueprints of different Bacillus anthraces strains, researchers are
learning why some strains are more virulent than others. Variations between strains might also point to
differences in antibiotic susceptibility, permitting doctors to immediately determine the appropriate treatment.
Scientists are now analyzing the Bacillus anthraces genome sequence to determine the function of each of its
genes and to learn how those genes interact with each other or with host-cell components to cause disease.
Knowing the sequence of Bacillus anthraces genes will help scientists discover key bacterial proteins that can
then be targeted by new drugs or vaccines.
Spore Biology
Bacillus anthraces spores are essentially dormant and must “wake up,” or germinate, to become reproductive,
disease-causing bacteria. Researchers are studying the germination process to learn more about the signals that
cause spores to become active once inside an animal or person. Efforts are under way to develop models of spore
germination in laboratory animals. Scientists hope those models will enable discoveries leading to drugs that
block the germination process in Bacillus anthraces spores.
Host Immunity
People who contract anthrax produce antibodies to protective antigen protein. Similar antibodies appear to block
infection in animals. Recent studies also suggest that some animals can produce antibodies to components of
Bacillus anthraces spores. Those antibodies, when studied in a test tube, prevent spores from germinating and
increase their uptake by the immune system’s microbe-eating cells. These discoveries suggest that scientists
might be able to develop a vaccine to fight both Bacillus anthraces cells and spores. Researchers also are studying

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how the immune system responds to Bacillus anthraces infection. Part of the immune system response, known as
adaptive immunity, consists of B and T cells that specifically recognize components of the anthrax bacterium.
The other type of immune response,innate immunity-aims more generally to combat a wide range of microbial
invaders and likely plays a key role in the body’s front-line defenses. Scientists are conducting studies of how
those two arms of the immune system act to counter infection, including how Bacillus anthraces spore
germination affects individual immune responses.
In another study, NIAID-supported scientists have discovered a potential target for developing new measures to
prevent and treat anthrax toxicity. Their study shows that a human gene called LRP6 plays a role in the delivery
of anthrax toxins into cells. Antibodies directed against LRP6 protected cell cultures from anthrax lethal toxin.
These results suggest that targeting LRP6 may prove useful in developing ways to protect against the effects of
accumulated toxin.

Result
The disease anthrax was selected as of the interest and their characteristics, symptoms,
gene information, treatments were determined.

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Bacillus Anthraces
Aim
To study the organism responsible for the disease anthrax – Bacillus anthraces.

Description
Anthrax is an acute disease in humans and animals caused by the bacterium bacillus anthraces which is highly
lethal in some forms, there are effective vaccines against anthrax and some forms of the disease respond well to
the antibiotic treatment.
Classification

Kingdom: Bacteria

Phylum: Firmicutes

Class: Bacilli

Order: Bacillales

Family: Bacillaceae

Genus: Bacillus

Species: B. anthraces

Table: Classification of Bacillus anthraces

Bacillus anthraces is a gram positive, facultatively anaerobic, rod shaped bacterium of the genus bacillus, an
endospore forming bacterium, Bacillus anthraces is a natural soil dwelling organism, as well as the causative
agent of anthrax, under conditions of environmental stress, Bacillus anthraces bacteria naturally produce
endospores which rest in the soil and can survive for thousands of years in this state. Bacillus anthraces may be
inoculated into a wound, inhaled or ingested. In ruminants, the bacterium causes sudden death from septicemia.
For this reason any ruminants found to have died suddenly and without obvious reason should be treated as a
suspected anthrax case. In these events, a blood sample is taken, by a qualified veterinary surgeon, from a
superficial vein and subjected to the MacFaydean polychrome methylene blue staining procedure which screens
for Bacillus anthraces. Conformational diagnosis is achieved through PCR and Immunofluorescence. Horses
respond variably to Bacillus anthraces depending on the site of entry. Ingestion tends to lead to a severe enteritis

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and septicemia. Inoculation in the skin tends to result in a local swelling and associated lymphadenitis. In pigs,
Bacillus anthraces again causes acute necrotising tonsillitis, or a subacute pharyngeal swelling, or the intestinal
disease described in horses. The intestinal disease carries a higher mortality. Dogs and cats seem less susceptible
to Bacillus anthraces and require a relative large dose of infectious agent before they begin to show clinical signs

Bacillus anthraces
Bacillus anthraces is typically a disease of herbivores (plant-eating mammals), although it can affect other
animals as well. Among domestic animals, cattle, sheep, and goats have been the most frequent victims. In most
industrialized countries, livestock are routinely vaccinated, and cases of anthrax are rare. In developing countries,
however, where animal vaccination is not regularly practiced, anthrax in animals is a problem. This is especially
so in tropical and sub-tropical environments. In the USA, anthrax cases among animals have been generally
limited to the western plains.
Endospores can survive in the soil for years. Animals consume the spores along with grass as they graze. After
the spores enter an animal, they germinate, changing from the resistant form into the growing and dividing
vegetative form. The sporangium lyses, the spore germinates, and the bacilli multiply rapidly.
Anthrax is a very serious disease in animals, culminating in a fatal septicemia. The carcass of the animal should
be burned where it lies. The carcass should never be opened, since doing this will cause the vegetative forms,
which can be destroyed relatively easily, to form into the resistant spores that can survive for years.
Infection in humans traditionally has been much rarer than infection in animals. Anthrax occurred in people who
came in contact with animals or animal products. It was frequently an occupational disease, affecting
veterinarians, people who raised livestock, and people who prepared products from wool, hide, and hair of
animals. The ordinary citizen in the USA is most likely to encounter anthrax from imported products that have not
been treated sufficiently to destroy spores. In humans there are three possible forms of the disease anthrax.
Historically, the most common form has been cutaneous anthrax, in which the organism enters through a break in
the skin. The cutaneous form begins as a papule at the entry site that progresses over several days to a vesicle and
then ulcerates. Edema, sometimes massive, surrounds the lesions, which then develop a characteristic black
eschar. The patient may have fever, malaise and headache. A small percentage of cutaneous infections become
systemic, and these can be fatal.

A more serious form is inhalation anthrax. Here the victim breathes in the organism and develops a severe
respiratory disease. Systemic infection resulting from inhalation of Bacillus anthraces has a mortality rate
approaching 100%. Initial symptoms are vague and flu-like, progressing to hypotension, shock and massive

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bacteremia and toxemia. The severe symptoms are believed to be the result of the bacillis exotoxins. Early
antibiotic treatment is an absolute necessity and should be started during the incubation period if a person has
been exposed.

The third form, intestinal anthrax, is contracted from the consumption of contaminated meat. In industrialized
countries this is not usually a risk, although rare exceptions have been described. In August 2000, the Minnesota
Department of Health was notified that Bacillus anthraces had been isolated from a steer on a farm in Roseau
County. The infected steer was one of five dead cattle found in a pasture. On the basis of identification of the
bacteria by phage typing of isolates cultured from tissues and blood samples by the North Dakota State University
Veterinary Diagnostic Laboratory, anthrax was confirmed. A report of this incident described the management of
and public health response to human exposure to meat contaminated with anthrax.
Genes Involved
In order to cause the disease anthrax, Bacillus anthraces requires two plasmids, pX01 and pX02, which carry toxin
and capsule genes, respectively, that are used as genetic targets in the laboratory detection of the bacterium
presence of 10 genes (acpA, capA, capB, CapC, capR, capD, IS1627, ORF 48, ORF 61, and repA)

Diagonisation
Anthrax is diagnosed by culture and isolation of the causative bacterium, B. anthraces- by detecting the bacterial
DNA or antigens; or by measuring specific antibodies in the blood of persons with suspected cases. The bacteria
can be cultured from the blood, skin lesions, fluid from the lungs or respiratory secretions, spinal fluid, or other
affected tissues prior to the start of antibiotic treatment. Detection of the DNA or antigens of the bacteria, and
detection of antibodies in the blood of suspected cases, is important tools for diagnosis because positive culture is
unlikely after antibiotic treatment has been started.
Treatment
The antibiotics ciprofloxacin, doxycycline and penicillin can be given in high doses to treat the condition.
Ciprofloxacin and doxycyline are also used as prophylaxis (prevention) for people who have been exposed. Early
treatment is needed if inhalational anthrax is suspected. There is an immunisation against anthrax but it takes five
doses of vaccine over the course of a year to get immunity. This makes immunisation too slow to deal with
accidental or deliberate exposure. It is normally offered to those who handle infected animals, and laboratory staff
who work with the bacteria. It would be recommended for a person who had been exposed, in conjunction with
antibiotics, because of uncertainty about when the spores may germinate. The armed forces in the USA are
currently being given immunisation, but concerns have been expressed about how safe, and effective, it is for the

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general public. In the UK, the Public Health Laboratory Service controls supply of the vaccine. Their advice, as
of 15 October 2001, is that immunisation is not recommended pre-exposure to anyone except people who are in
the relevant occupational groups mentioned above. PHLS is monitoring the situation and will act according to any
outbreaks or events

Result
The organism responsible for anthrax was found to be Bacillus anthraces. The structure was described and also
the causes, diagnosis, and the treatment of the disease were determined.

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DOXYCYCLINE
Aim
To find the protein responsible for the anthrax disease this is the binding sites for the human.

Description
Doxycycline is a tetracycline antibiotic. It works by slowing the growth of bacteria in the body. Doxycycline is

used to treat many different bacterial infections, such as urinary tract infections, acne, gonorrhea, and chlamydia,

periodontitis (gum disease), and others. It may be used in combination with other medicines to treat certain

amoeba infections.

Doxycycline comes as a regular and a coated capsule, a tablet, syrup, and a suspension (liquid), all to take by
mouth. Doxycycline is usually taken once or twice a day. Drink a full glass of water with each dose of the capsule
or tablet.

CAS Number 10597-92-9

(2Z,4S,4aR,5S,5aS,6R,12aS)-2-(amino-hydroxy-
Chemical IUPAC methylidene)-4-dimethylamino-5, 10,11,12a-tetrahydroxy-6-
methyl-4a,5,5a,6-tetrahydro-4H-tetracene-1,3,12-t rione
PubChem Drug Bank KEGG
154560 APRD00597 C06973

Table: Details of Doxycycline

The structure of doxycycline has positive changes represented in the SAR. The north western portion of
Doxycycline has subsistent on R2 thru R4 which increases activity and pharmacokinetic properties compared to
older tetracycline agents. Improvements include longer half life due to slower elimination, better stability and
tissue penetration, and good oral availability due to higher lipophilicity. There is no R1 substitute, R2 is H, R3 is
a methyl, and R4 is a hydroxyl subsistent. Typical tetracycline form nephrotoxic anhydrotetracycline in prolonged
acidic medium. Also, epimerization at C4 amine from beta position to alpha causes inactivation. In basic medium,
ring opening inactivates the antibiotic. However, the removal of C6 hydroxyl group improves acid and basic

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stability. Doxycycline is less susceptible to chelation thus has less GI disturbance, such as cramps which is
usually most common.

Fig.: Structure of Doxycycline

Interactions
Doxycycline interacts with many types of medications. It can increase the absorption of digoxin, which may lead
to digoxin toxicity. The gastrointestinal side effects (nausea, vomiting, stomach upset) of theophylline may be
increased by doxycycline. The dosage of oral anticoagulants (blood thinners, such as warfarin) may need to be
adjusted when this medication is started. Doxycycline may decrease the effectiveness of oral contraceptives (birth
control pills), and pregnancy could result. Barbiturates, carbamazepine, phenytoin, and antacids can lower the
levels of doxycycline in the blood, thus decreasing its effectiveness. Iron and antacid containing aluminum,
calcium and magnesium can chelate doxycycline in the gastrointestinal tract and form an insoluble complex,
which can decrease its absorption and, therefore, its effectiveness.
Resistance
Doxycycline resistance occurs via two mechanisms. First, bacteria can produce proteins that bind to ribosome and
can inhibit drug binding or allow protein biosynthesis to continue in the presence of bound doxycycline. The
second mechanism is through active efflux of doxycycline to the outside of the cell. Because doxycycline was
once very widely used, the popularity has decreased considerably due to wide spread resistance and the
introduction of newer broad spectrum agents.
Mechanism of Action
Doxycycline works by inhibiting protein synthesis by reversibly binding to bacterial ribosome (30s subunit) at the
A site, preventing the attachment of amino acyl t-RNA and leading to the termination of translation. It is more
selective for the bacterial 70s ribosome versus mammalian 80s ribosome. Doxycycline also has selective toxicity

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against bacteria because it has high efficiently transport into bacterial cells. They enter Gram negative bacteria
through porins due to its hydrophilicity, and through their lipophilicity in Gram positive bacteria. The bacteria
mistakes doxycycline for food thus passes through the cytoplasmic membrane by an energy requiring active
transport.

Divalent ions may be significant in Doxycycline effectiveness. Magnesium ions attached to the phosphates on
RNA seem to aid in their initial binding to the ribosome, while magnesium in the cytoplasm will limit their ability
to interact with the ribosome.

Result
The ligand Doxycycline plays a significant role in curing the disease anthrax. The description, interaction,
resistance, mechanism of action determines the effect of drug with respect to anthrax.

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INTERACTION STUDIES USING SWISS-PDB VIEWER

Aim
To analyze the interaction between the docked protein-ligand complex.

Swiss-PDB Viewer
Swiss-Pdb Viewer is an application that provides a user friendly interface allowing analyzing several proteins at
the same time. The proteins can be superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are
easy to obtain thanks to the intuitive graphic and menu interface. Swiss-Pdb Viewer has been developed since
1994 by Nicolas Guex. Swiss-Pdb Viewer is tightly linked to SWISS-MODEL, an automated homology modeling
server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the
Biozentrum in Basel. Working with these two programs greatly reduces the amount of work necessary to generate
models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback
of how well the threaded protein will be accepted by the reference structure before submitting a request to build
missing loops and refine side chain packing. Swiss Pdb Viewer can also read electron density maps, and provides
various tools to build into the density. In addition, various modeling tools are integrated and command files for
popular energy minimization packages can be generated.

Procedure
1. Open the Swiss-PDB Viewer.
2. Load the docked complex obtained from HEX in SPDBV.
3. Go to WindowsÆControl panel.
4. Make the whole molecule invisible and make only the ligand molecule visible using control panel window.
5. Select the ligand using select menuÆselect the neighbouring amino acidÆfrom the dialog box appearing a
distance of 3.00A0Æ click ok.
6. The amino acids around 3.00A distance with respect to the ligand appear in the graphics window. Make the
labels visible using the control panel window.
7. ColorÆby secondary structureÆthe amino acid is colored based on the secondary structure.
8. ToolsÆCompute H bondÆthe H bond interaction between the ligand and the molecules within the distance of
3.00A0 is made visible.

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9. ToolsÆshow H bond distancesÆthe distance of the hbonds are made visible.

Output

Fig.: Interaction between Doxycycline with Anthrax Toxin

Result
The interaction study is done on the docked model of the anthrax toxin receptor protein with the inhibitor
doxycycline.

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CHEMSKETCH
Aim
To generate a 2D structure and SMILES notations of polar amino acids using ChemSketch.

Procedure
1. Open the ChemSketch tool.
2. Select the structure mode to draw a structure.
3. To start drawing click on ‘C’, CH4 appears on the screen, the same way select any desired atom from the
structure tool bar to draw, for example Cl, Br, H, N, O, S etc.

4. The atom name can be edited in the structure mode by selecting the corresponding atom and clicking the
‘edit text button’.
5. To add a double or triple bond, select the bond position with the cursor. A box will highlight it as seen to the
right and then click it once for double bond and same for triple bond and again to go back to single bond.
6. To optimize the structure, especially the rings for standardizing all bond lengths and angles, trigonal and

linear for 2D by using the ‘clean structure’.

7. To generate the name for a structure click ‘generate name from structure’ button.
8. To generate SMILES (Simplified Molecular Input Line Entry System) for a specified molecule first select the
molecule and then go to ‘tool’ and choose ‘generate SMILES notation’.
9. To save files got to ‘file’ in the menu and select ‘save as’ option. It automatically saves it in ‘.sk2’ file format.
To save it in ‘.mol’ file format select ‘export’ from the file menu and give the name.

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Output

Table: Chemical Structure of Non-Polar Amino Acids Generated using ChemSketch

Result
The chemical structure and SMILES notation of polar amino acids were generated using ChemSketch 11.

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HEX
Aim
To predict the interactive molecular docking using Hex 4.2.

Description
Docking
Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each
other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength
of association or binding affinity between two molecules using for example scoring functions. Docking is
frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in
order to in turn predict the affinity and activity of the small molecule.
Hex 4.2
Hex 4.2 is an interactive protein docking and molecular superimposition program. Currently, Hex 4.2 understands
protein and DNA structures in PDB format. Hex 4.2 was written by Davie Ritchie at the University of Aberdeen.
This is the main thing which distinguishes Hex 4.2 from other macro molecular (i.e. protein and DNA) docking
programs and molecular calculations. The graphical nature of Hex 4.2 came about largely to visualize the results
of such docking calculations in a natural and seamless way, without having to export unmanageably many and
usually quite big coordinate files to one of the many existing molecular graphics packages. The graphical
capabilities in Hex 4.2 are relatively primitive, although these days user can do quite a lot with a few calls to
OpenGL.

Procedure
Step1: Open HEX .exe file.
Step2: Go to file-> select open and select receptor to load the protein molecule.
Step3: Again go to open and select ligand to load the ligand molecule.
Step4: After loading the protein and ligand select the controls and click ‘Docking’.
Step5: Docking control box will display, set default option and click ‘Activate’.
Step6: Save the HEX messages and the docked structure.
Output

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Fig.: Anthrax Receptor Toxin with Doxycycline

Fig.: Average Energy Values of Anthrax Receptor Toxin Docked with Doxycycline
Result
The Anthrax Toxin receptor was docked with Doxycyline ligand and the RMS values, the energy values and the
BMP values were observed using HEX4.2

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