Transcript Materials and Methods

Potential Phytochemicals for
HIV Reverse Transcriptase
Inhibition : A Docking Study
Abhik Seal1 & Riju Aykkal2
1DOEACC
Centre Kolkata (Jadavpur University
Campus), Kolkata, West Bengal.
[email protected].
2Computer Programmer, Cantonment Board,
Kannur, Kerala.
INTRODUCTION
AIDS (acquired immunodeficiency syndrome), caused by the
HIV (Human Immunodeficiency Virus), is one of the world’s
leading causes of death with a major medical and economic
impact on society.
The enzyme reverse transcriptase (RT) is used by
retroviruses to transcribe their single-stranded RNA
genome into single-stranded DNA and to subsequently
construct a complementary strand of DNA, providing a
DNA double helix capable of integration into host cell
chromosomes.
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It is well know that replication can arrest by inhibiting the
Reverse transcriptase enzyme.
HIV-1 RT is a heterodimer,
consisting of a p66 subunit with
560 amino acids and a p51
subunit with 440 amino acids.
The two subunits form a stable
dimer which is essential for the
enzymatic activity.
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Most of the combinatorial chemistry product have shown adverse
effect in human body and happened to withdrawn from the
market due to its undesirable property, there for people are highly
looking for natural resources ie phytochemicals for potential
desired activity.
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Phytochemicals, as the word implies, are the individual
chemicals from which plants are made.
Baicalin, calanolides, betulinic acid, polycitone A,
lithospermic acid, sulphated polysaccharides,
cyanovirin-N, pokeweed antiviral protein, Geranin,
Curcumin, Gallotannin, Tiliroside, Kaempferol-3-oglucoside, Trachelogenin and alpha-trichobitacin are
some of the examples for anti-HIV agents.
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Materials and Methods
Targert : HIV Reverse transcriptase
(PDBID: 1REV) was retrieved from protein data bank
at 2.6 Ǻ RMSD resolution.
Ligands :
Baicalin, Chicoric-acid, Chlorogenic-acid, Ellagic-acid,
and Hinokiflavone were obtained from PubChem and
Chemspider database.
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Materials and Methods
Databases such as ZINC, PubChem, ChemDB,
ChemSpider, KEGG ligand database and DrugBank are
some of them.
PubChem contains more than 26 million unique
compounds, among which over 870 000 have biological
assay data for more than 3000 molecular targets,
including proteins and genes.
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Materials and Methods
The structures of Efavirenz (CID 64139) approved by FDA in 2006 and
Etravirine (CID 193962) approved by FDA in 2008 were obtained from
PubChem.
efavirenz
Etravirine
3D structures were generated with the help of open babel
(http://openbabel.org/wiki/Main_Page). The 3D structures which are obtained
are minimized using Hyperchem’s MM+ force field.
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Materials and Methods
Target and ligands were prepared using MVD Molegro Virtual Docker (MVD)
was used to detect the active sites and docking was performed by moldock
function, which is an implementation of evolutionary algorithms (EAs),
focused on molecular docking simulations.
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Materials and Methods
Docking was performed with all the potential active sites
detected on HIV reverse transcriptase enzyme.
Important steps before docking
•At first the molecules were prepared and bonds, bond orders, explicit
hydrogens, charges, flexible torsions, were assigned if they were missing by
the MVD program to both the protein and ligands.
•The Ignore distant atoms option is used to ignore atoms far away from the
binding site. (It reduces overall computing time).
•The enforce hydrogen bond directionality option is used to check if
bonding between potential hydrogen bond donors and acceptors can
occur.
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Materials and Methods
If hydrogen bonding is possible, the hydrogen bond energy
contribution to the docking score is assigned a penalty
based on the deviations from the ideal bonding angle.
This can significantly reduce the number of unlikely
hydrogen bonds reported also internal electrostatic
interaction, internal hydrogen bond sp2-sp2 torsions are
calculated from the pose by enabling the ligand evaluation
terms.
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Materials and Methods
The search algorithm is taken as Moldock SE and
numbers of runs are taken 10 and max iterations were
2000 with population size 50 and with an energy
threshold of 100 also at each step least ‘min’
torsions/translations/rotations are tested and the one
giving lowest energy is chosen.
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Materials and Methods
Pose clustering was done by tabu based clustering method, using this
clustering technique each found solution is added to a ‘tabu list’: during the
docking simulation the poses are compared to the ligands in this ‘tabu list’.
If the pose being docked is closer to one of the ligands in the list than
specified by the RMSD threshold, an extra penalty term (the Energy penalty)
is added to the scoring function.
This ensures a greater diversity of the returned solutions since the docking
engine will focus its search on poses different from earlier poses found.
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Materials and Methods
The energy penalty was set to 100, RMSD threshold was
2.00 and RMSD calculation by atom ID (fast) were set.
After the docking simulation is over the poses which
were generated were sorted by rerank score.
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Materials and Methods
Binding affinities were calculated using Molegro data
modeler
MVD used to find :
Ligand Efficiency 1(LE 1) as Moldock score divided by Heavy
Atoms count,
ligand efficiency 2(LE2) as a result of binding Affinity divided
by Heavy Atoms count and
Ligand Efficiency 3 (LE 3) as rerank Score divided by Heavy
Atoms count.
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Materials and Methods
MolDock showed better overall performance in docking
simulations when compared with other software more than 87 %
percent in docking accuracy.
ADMET (Absorption, Distribution, Metabolism,
Excretion and Toxicity) properties were predicted using
PreADMET server (http://preadmet.bmdrc.org/)
to know whether the phytochemicals has the potential
of adverse effect in human.
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Results and Discussion
A total of five cavities were detected in reverse
transcriptase enzyme (PDB ID: 1REV) by using
Molegro Virtual Docker and which were named cav1
(497.664 Ǻ3),
cav2 (425.984 Ǻ3),
cav3 (387.584 Ǻ3),
cav4 (365.568 Ǻ3) &
cav5 (342.016 Ǻ3)
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Results and Discussion
All the phytochemicals and two known potential antiHIV compounds such as Efavirenz and Etravirine were
used as ligand at mentioned 5 cavities of reverse
transcriptase enzyme (PDB ID: 1REV) and the results
were discussed based on rerank score, along with the
hydrogen bond interaction values, the hydrogen bond
number and other electrostatic interaction values
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Results and Discussion
Table 1.
Ligand name
Cavity MolDock
Score
Rerank
Score
No. of H H Bond Binding
Bond
Energy affinity
Baicalin
5
-147.368
-115.633
9
-10.1906
-12.06
Chicoric-acid
4
-150.561
-125.266
15
-14.7271
-7.499
Chlorogenic-acid
4
-103.246
-103.526
9
-11.9998
-7.105
Ellagic-acid
Hinokiflavone
4
5
-170.674
-162.071
-127.682
-123.556
9
7
-14.7271
-7.8715
-7.989
-7.235
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Results and Discussion
According to the rerank score obtained, all phytochemicals reported better
rerank score and also highly bound with reverse transcriptase than Efavirenz
(highest rerank score was -90.998 at cavity four). while comparing the
result with Etravirine (rerank score = -113.622), compounds such as :
Baicalin (-115.633), Chicoric-acid (-125.266), Ellagic-acid (-127.682) and
Hinokiflavone (-123.556) found to be good than the result of etravirine
whereas and Chlorogenic acid(-103.526) showed rerank score comparatively
lesser than Etravirine.
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POSES
Efavirenz at cavity 4
Chlorogenic Acid in cavity 4
Etravirine at Cavity 5
Hinkoflavone in cavity 5
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Results and Discussion
ADMET PROPERTIES:
The molecules were searched for Lipinski rule of 5, lead like
rule, CMC like rule, MDDR like rule, WDI like rule, Reactive
functional group for drug likeness. Caco-2cell permeability,
Madin-Darby Canine Kidney Cell Permeability (MDCK),
Human Intestinal Absortion (HIA), Skin Permeability, BloodBrain Barrier (BBB) penetration. along with the mutagenicity
and carcinogenicity test based on Ames Test using PreADMET
online webserver
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Results and Discussion
The results of ADMET and drug-likeness are given as
table 2.
In silico ames test reported mutagenic effects in
Ellagic-acid and Hinokiflavone. Compounds such as
Chicoric-acid and Ellagic-acid are found to be
carcinogenic as its report from rat model showed
positive to carcinogen(table 2).
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Table 2.
LIGAND NAME
AMES TEST
CARCINOGENITY
(MOUSE)
CARCINOGENITY
(RAT)
Baicalin
NM
Negative
Negative
Chicoric-acid
NM
Negative
Positive
Chlorogenic-acid
NM
Negative
Negative
Ellagic-acid
M
Negative
Positive
Hinokiflavone
M
Negative
Negative
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Results and Discussion
Further studies are required to reduce and confirm the
predicted adverse effects. The study reported six
potential compounds as reverse transcriptase inhibitor
and compared with the exisitng reverse transcriptase
inhibitor and found highly effective thus this
compounds would probably become a lead for further
drug discovery process.
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