Download Molecular docking of identified epitopes and human cTAP1

AN IMMUNOINFORMATICS ANALYSIS AND
STRUCTURE BASED MODELING OF POTENTIAL HLA
CLASS II ALLELE BINDING T CELL EPITOPES FOR
VACCINE DESIGN OF JE
Pawan Sharma
Assistant Professor
Mangalayatan University,
India
Japanese encephalitis virus (JEV) is a flavivirus,
family Flaviviridea
 Causes disease to human beings:
Japanese
Encephalitis (JE)
 Flavivirus genus comprises of 72 other viruses,
viz. Dengue virus, Yellow fever virus and West Nile
virus.

Mode of transmission: Culex tritaeniorhynchus
and C. visnui mosquitoes to human.
 JE virus causes membrane inflammation of brain
and leads to deleterious effects on Central
Nervous System (CNS).

EPIDEMIOLOGY

As reported 67,900 clinical cases of JE occur
annually, with approximately 13,600 to 20,400
deaths, in spite of widespread availability of vaccine
(WHO 2015).



JE virus- ss RNA genome
11,000 nucleotides encoding a single polypeptide of
3432 amino acids.
The virus has seven nonstructural proteins and three
structural proteins
Adopted from Swiss Institute of Bioinformatics, 2010
Geographic Distribution of Japanese Encephalitis Virus
Adopted from Centers for Disease Control and Prevention, August 2015
SEEN IN PICTURE IS A MAN RUSHING HIS CHILD
TO A HOSPITAL IN GHORAKPUR, U.P. , INDIA)
CURRENT STATUS OF VACCINE FOR JE
VIRUS
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3.
Now-a-days, a number of vaccines have been developed for JE in several
countries:
Inactivated mouse brain derived Nakayama strain vaccine is the most
commercially used vaccine
Vero cell derived JE vaccine (IXIARO) which can effectively boost the
immunity
Drawbacks associated with these vaccines:
High cost,
Vaccine production shortage
Neurological adverse effects
All this leads to the serious requirement to develop more compatible and
economically effective vaccines.
Vaccine development methodologies.
Adopted from Drug Discovery Today, Therapeutic Strategies, June 15, 2002
MHC I AND MHC II ANTIGEN
PRESENTATION
Sebastian D. Schuck, HU Berlin, Dessertation, March 13, 2009
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2.
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Advantage of Epitope Vaccine:
More specific immunity
Devoid of side effects in contrast of entire viral proteins
vaccines
Ability to deliver high doses of potential immunogen at
lower cost
Criteria for best epitope for vaccine development:
World wide conservancy of
Epitopes
Stable binding with HLA class I and class II alleles
Smooth passage through TAP for epitopes binding with HLA
class I alleles
Work flow
Identification of T cell epitopes and their conservancy study
Tools: . Propred I, Propred, IEDB and MHC pred 2.0
Screening of epitopes forming stable complex with HLA I & HLA II allele.
Molecular modeling of the identified epitopes and HLA I/II allele.
Tools: Pepstr, Swiss Model and Validation by: Errat, ProSA, Pro Q and RAMPAGE
Molecular docking of identified epitopes and HLA I/II allele.
Tools: by Autodock 4.2 and Hex 8.0
Molecular dynamics simulation of identified epitopes and HLA I/II allele.
Tools: NAnoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD)
Molecular docking of identified epitopes and human cTAP1.
Tools: by Autodock 4.2 and Hex 8.0
• Screening for conserved nanomer peptide.
•Molecular modeling
•Molecular docking
•Molecular dynamic simulation
IDENTIFICATION OF HLA ALLELES AND TAP BINDING EPITOPES
AND THEIR CONSERVANCY STUDY
Identified HLA alleles and TAP binding epitopes of JEV by Propred
I, Propred and MHC pred 2.0 respectively.
S.N0.
Epitope
position
Flavi M
1.
62-70
2.
61-69
Flavi glycoprot
3.
264-272
4.
45-53
Flavi glycoprot c
5.
38-46
6.
55-63
7.
52-60
8.
38-46
9.
55-63
10.
19-27
Flavi E Stem
11.
46-54
12.
8-16
13.
31-39
14.
6-14
15.
9-17
Flavi NS2B
16.
30-38
17. 117-125
18.
10-18
Flavi NS4A
19. 132-140
20. 109-117
21.
76-84
22. 130-138
Flavi NS4B
23.
97-105
24. 201-209
25.
50-58
Flavi NS5
26.
62-70
Predicted T cell
Epitopes
pI
Value
HLA
Alleles,
Class
TAP
Binding
IC50 (nM)
JEV Genotypes
LLLLVAPAY
ILLLLVAPA
5.52
5.52
38, II
45, II
6.68
95.72
QALAGAIVV
MINIEASQL
5.52
4.00
27, I
11, II
2322.74
#
QALAGAIVV*
MINIEAS(VG3,TG5)QL
IPIVSVASL
LVTVNPFVA
VGRLVTVNP
IPIVSVASL
LVTVNPFVA
GHGTVVIEL
5.52
5.52
9.72
5.52
5.52
5.24
43, II
48, II
21, II
43, I
48, I
25, I
2824.88
605.34
3019.95
#
605.34
#
IPIV(SG5)SVASL
LVTVNPFVA*
VGRLVTVNP*
IPIV(SG5)SVASL
LVTVNPFVA*
GHGTVVIEL*
FRTLFGGMS
LKGAQRLAA
FNSIGKAVH
TTLKGAQRL
KGAQRLAAL
9.75
11.00
8.76
11.00
11.00
29, II
34, II
26, II
33, I
29, I
#
#
#
1520.55
3741.11
FRTLFGGMS*
LKGAQRLAA*
FNSIGKAVH*
TTLKGAQRL*
KGAQRLAAL*
FMLAGLMAV
FGYWLTLKT
LMFAIVGGL
5.52
8.59
5.52
32, II
24, II
25, I
937.56
2027.68
25.00
FMLAGLMAV*
FGYWLTLKT*
LMFAIVGGL*
VFLICVLTV
LLLMVVLIP
KMGLGALVL
LAVFLICVL
5.49
5.52
8.75
5.52
46, II
43, II
21, I
27, I
33.42
180.30
2588.21
4.57
VFLICVLTV*
LLLMVVLIP*
KMGLGALVL*
LAVFLICVL*
LVFLGCWGQ
LVTAATLTL
VVLTPLLKH
5.52
5.52
8.73
37, II
39, II
31, II
18.71
95.28
91.62
LVFLGCWGQ*
LVTAATLTL*
VVLTPLLKH*
KATGSASSL
8.75
23, I
1606.94
LLLLVAPAY*
ILLLLVAPA*
KATGSASSL*
LVTVNPFVA epitope showed best binding with
HLA class I and Class II molecules viz. B5102
and DRB1 0405 HLA alleles.
 FRTLFGGMS epitope showed binding with
DRB1 0405 HLA II allele.
 These two epitopes are also showed HLA
binding population coverage

Modeling of identified nanomer peptides
3D conformation prediction of identified conserved LVTVNPFVA epitope nanomer
peptide for Japanese Encephalitis. PEPstr, Swiss Model
Epitope LVTVNPFVA Model
HLA Class DRB1 0405 Model
MOLECULAR MODELING OF THE IDENTIFIED EPITOPES AND HLA I/II ALLELE
Calculated Errat, ProQ and Pro SA scores for B5102 and DRB1 0405 HLA alleles
Fig.1: ProSA analysis: (a) Z score plot of DRB1 0405 allele (b) Z score plot of
B5102 allele
MOLECULAR DOCKING OF IDENTIFIED EPITOPES AND HLA I/II ALLELE.
Fig.2: Epitope LVTVNPFVA (sticks)
and B*5102 allele (solid spheres)
complex obtained by Autodock 4.2,
showing
two
Hbond
viz.
ASP53:HN1 and SER28:HN1.
Fig.3: Epitope FRTLFGGMS (sticks)
and DRB1*0405 allele (solid
sphere) complex obtained by
Autodock 4.2, showing two H-bond
viz. CSY44: HN1 and PHE46: HN1.
MOLECULAR DYNAMICS SIMULATION OF IDENTIFIED EPITOPES AND HLA I/II
ALLELE.
A: Graph displaying RMSD in relation
to time (picoseconds) for NAMD-VMD
simulation of LVTVNPFVA and B 5102
complex, with highest RMSD value of
11.4 Å at 12,000 picoseconds.
B: Graph displaying RMSD in relation
to time (picoseconds) for NAMD-VMD
simulation of FRTLFGGMS and DRB1
0405 complex, with highest RMSD
value of 7.6 Å at 8,000 picoseconds.
Molecular docking of identified epitopes and human cTAP1.
Fig.4:
The docking study of identified highly conserved epitope LVTVNPFVA (grey solid spheres)
with cTAP1 (white solid spheres) channel cavity facilitating the smooth passage of the epitope from
cytoplasm to ER lumen. (a) This docking study shows that the epitope peptide gets hold at the
upper part of the cavity by two hydrogen bonds. (b) With very optimal binding energy it is gripped by
lower part of the cavity. (c) The Docking study by Autodock 4.2 shows the epitope is forming 2
hydrogen bonds at the upper portion of cTAP1 viz. ARG515: ALA9 and TYR555: THR3, having
binding energy of -1.88. If we put these two states of binding in sequence then we may conclude a
smooth facilitation for epitope peptide transport from cytoplasm to ER lumen.
CONCLUSION
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The peptides LVTVNPFVA and FRTLFGGMS are completely
conserved epitopes with super antigenic property.
Identified epitopes LVTVNPFVA and FRTLFGGMS of
envelope protein form stable complex with B5102 and
DRB1 0405 HLA alleles respectively.
Also, smooth facilitation of epitopes LVTVNPFVA through
cTAP1 shows actual acceptance of the epitope in cytosolic
antigen processing for further presentation by HLA class I.
Hence these identified epitopes are most promising as
vaccine candidates for JE and can also be useful as
diagnostic agents for JE.
Here we look forward to use these results as a platform for
further trails for vaccine development against JE.
REFERENCES

WHO (2015) Weekly epidemiological record. 90: 69–88.

Singh A et al. (2015) A Japanese encephalitis vaccine from India induces durable and crossprotective immunity against temporally and spatially wide-ranging global field strains. Journal of
Infectious Diseases (2015): jiv023.

Sharma P, Saxena K, Mishra S, Kumar A (2014) A comprehensive analysis of predicted HLA
binding peptides of JE viral proteins specific to north Indian Isolates. Bioinformation 10:334-34.

Erra EO, Askling HH, Rombo L, Riutta J, Vene S, Yoksan S, Lindquist L, Pakkanen SH, Huhtamo
E, Vapalahti O, Kantele A (2012) A single dose of vero cell-derived Japanese encephalitis (JE)
vaccine (Ixiaro) effectively boosts immunity in travelers primed with mouse brain-derived JE
vaccines. Clin Infect Dis 55:825-34.

Tang H, Liu XS, Fang YZ, Pan L, Zhang ZW et al (2012) The epitopes of foot and mouth disease.
Asian J Anim Vet Adv 7:1261–1265.

Procko E and Gaudet R (2009) Antigen processing and presentation: TAPping into ABC
Transporters. Current Opinion in Immunology 21:84–91.
Thank you
(Shokran)