JACOB JOHN- (1RV10CH042)
DRUG DISCOVERY METHODS
High throughput screening
Rational design- hand built drugs
Hit Success rate:<1%
success rate: 20%
Dengue virus (DENV) belongs to the Flavivirus genus of the
Transmitted by Aedes Aegypti.
Dengue hemorrhagic fever (DHF)
Dengue shock syndrome
50 million infections per year
500,000 develop DHF
22000 deaths per year
Limited efficiency of antiviral drugs
Treatment for DHF is blood transfusion
4 serotypes of the virus: DENV 1
to DENV 4
Its genome comprises of a 10.7
kb single positive stranded RNA.
Each serotype provides specific
lifetime immunity, and short-term
All serotypes can cause severe and fatal disease
Genetic variation within serotypes
most prevalent of the four dengue serotypes is Dengue virus type 2
Single stranded RNA
Carries a single stranded RNA as its genome.
The genome encodes only 10 proteins.
Out of which 3 are structural proteins and 7 are non structural
The 3 structural proteins (C. prM and E) form the coat of the
virus and deliver the RNA to target cells.
The seven non structural proteins ( NS1, NS2A, NS2B, NS3,
NS4A, NS4B, NS5) known as NS proteins.
They orchestrate the production of new viruses once the virus
gets inside the cell.
180 identical copies of envelope (E) protein are attached to the
membrane by Transmembrane Segment.
The Protein Data Bank (PDB) is the single worldwide repository
for processing and distribution of 3D structure data of large
molecules of proteins and nucleic acids.
The outermost structural protein termed as the envelope
protein – from the PDB entry 1k4r.
Cryoelectron microscopy is used to
study the life cycle of dengue virus.
Low resolution image of the DENV
obtained using electron microscopy.
Atomic structures of individual pieces
are fit into the image to form the final
The image shown above is from PDB
The envelope protein on the surface of the protein is shown(in white)
The antibodies bound to the viral protein is shown (in blue)
Antibodies distort the structure of the envelope proteins hence
blocking their normal action in infection.
The DENV (+) RNA genome and its co-linear polyprotein
NS3 protein from PDB entry 2vbc NS5 protein from PDB entry 1l97 and 2j7w
In the infectious form of the virus, the envelope protein lays flat on the
surface forming a smooth icosahedral symmetry.
The virus is carried into the cell and into the lysosome.
Organelles: 1.Nucleolus 2.Nucleus 3. ribosomes( little dots) 4. vescicle 5. Rough endoplasmic reticulum 6. Golgi appartus
7. Cytoskeleton 8. Smooth endoplasmic reticulum 9. Mitochondria 10. Vacuol 11. Cytosol 12. Lysosome 13. Centrriol 14. cell
Inside the Lysosome , the acidic environment causes the protein to
snap to a trimeric shape.
Several hydrophobic amino acids at the tip of the
spike pierce into the lyzosomal membrane .
They fuse the virus membrane with the lysosomal
Thus releasing the viral RNA into the cytoplasm
of the cell and infection starts.
Now the proteins in the virus help in replication
NS3 and NS5 are two multifunctional proteins
containing 2 enzymes each.
NS3 from PDB entry 2vbc, contains a Helicase
and Protease enzymes.
NS5 from PDB entry 1l9k and 2j7w contains
Methyl Transferase and Polymerase enzymes.
NS3 protein from PDB entry 2vbc
NS5 protein from PDB entry 1l97 and 2j7w
Each of these enzymes perform a different
part of the life cycle
The Polymerase builds new RNA strands
based on viral RNA.
Helicase Helps to separate these strands.
Methyl Transferase adds a methyl group to
the end of them to protect the RNA and
coaxing the Ribosome to create new proteins
based on them.
Viral proteins are created in one long
polyprotein chain and are finally clipped
together by the enzyme protease.
Blue colour seen is the part of another
protein NS2B which assists the protease
The virus encoded proteins enzymes constitute the potential targets.
Envelope , capsid, helicase, polymerase, proteases, etc
The M and E proteins are considered as targets so far.
The E protein is the most obvious target for therapeutic monoclonal
Out of the 7 NS proteins , NS3 and NS5 are considered as drug targets
because they exhibit enzymic activity.
NS3 becomes active only if the NS2B protein is also bound to it.
In drug design programs NS3/NS2B protein is one of the first targets.
NS5 is another potential target .
Validated target: It is any protein or cellular or viral component whose
inhibition leads to the inhibition of the growth of the virus itself.
2/3rd of the organic compounds are aromatic heterocycles
Majority of drugs used in pharmaceutical and biological industries
Natural drugs : Quinine- was used to prevent and
treat maleria in the 16th century.
Synthetic drugs :Antipyrine- first synthetic drug for fever(1887)
Heterocycles play an important role in biochemical processes
because the side groups of the most typical and essential constituents
of living cells are heterocycles.
A Uracil Based multifunctional compound(fig1)was found to be a
potent inhibitor of dengue virus
But its De-aza derivative (fig 2)is inactive against the virus
Mechanism of action-inhibition of the enzyme, inosine
monophosphate dehydrogenase (IMPDH).
Among the derivatives of 2,4-Diaminoquinazoline the one
shown in fig (2) has the most efficient antiviral activity
It is an inhibitor of the replication of Dengue 2 virus
It has a half maximal effective concentration (EC-50) value
It has a low cytotoxicity (50% cytotoxicity concentration)-
CC-50 value greater than 100μM
we focussed on the method of scaffold hopping in drug
2 methyl 4- hydroxy quinoline was the compound selected
synthesis of 1-Phenyl-1,2,3,4-tetrahydro-β-carboline-3-
carboxylic Acid following general procedures.
Synthesis of hydroxy quinoline using Conrad limpach reaction
Substitution reactions of the two compounds
Reaction of L-Tryptophan with Aromatic Aldehydes to
Give Tetrahydro-β-carboline(1a-cis and 1b-trans).:
L-Tryptophan(MW=204) was taken (2.94 m.mol) in a round
It was dissolved in 10 ml of 0.2 N Sulphuric acid
To this solution 0.5 ml of benzaldehyde(4.4) m.mol was
added and continuously stirred for 9 days.
A precipitate was obtained –(245 mg, and 56%) as a white
It is a mixture of the cis and trans isomers.
Synthesis of 2-methyl-4-hydroxy quinoline:
Conrad Limpach reaction.
In a 100 ml beaker, 0.01 mol, 4.35 mg Aniline, 0.01 mol,
6.35 mg ethyl acetoacetate and 120 mg of p-toluene
sulphonic acid were taken and mixed well.
This was then stirred in a round bottomed flask which
was kept in an oil bath at 100 C.
The progress of the reaction was monitored using TLC
every 30 seconds.
After heating, 10ml Petroleum Ether (60 C-80 C) was
added to the mixture.
The product was collected by suction and purified by re-
crystallisation from DMF-water.
The structure of the DENV virus and its mechanism of action
was studied and reported
Various Heterocyclic compounds were reviewed and their
activity against Dengue Virus were listed out.
Thus we have made an attempt to synthesize 2 simple
• Tetrahydro-β- carboline – 3- carboxylic acid
• 2-methyl 4-hydroxyquinoline