Medical University of Sofia
Faculty of Pharmacy
Structural Immunoinformatics –
two case studies
M. Atanasova, I. Dimitrov, A. Patronov, I. Doytchinova
Regional Conference in Supercomputing Applications in Science and Industry,
20-21 Sept. 2011, Sunny Beach, Bulgaria
Medical University of Sofia
Faculty of Pharmacy
Immunoinformatics (Computational Immunology, Theoretical Immunology)
Immunoinformastic Approaches:
Sequence - based
peptide
pIC50exp
ILDPFPVTV
ALDPFPPTV
VLDPFPITV
................
8.654
8.170
8.139
.......
FLDPFPATV
8.270
Affinity = f (Chemical Structure)
Motif-based, QMs, ANN, SVM
Structure - based
Affinity = f (Interaction energy)
Molecular docking
Molecular dynamics
Medical University of Sofia
Faculty of Pharmacy
Case study 1: T-cell epitope prediction
of proteins from Boophilus microplus
Ticks are hematophagous parasites that feed on
variety of domestic animals.
B. microplus tick:
Boophilus
microplus tick.
• a hard tick;
• transmits lethal pathogens;
•causes disease and death.
Aim:
to predict peptides originating from B. microplus and binding
with high affinity to murine MHC class II proteins IAd and IEd.
Collaborator:
University of Pretoria, SA
Medical University of Sofia
Faculty of Pharmacy
Case study 1: T-cell epitope prediction
of proteins from Boophilus microplus
Sequence - based
MHCPred and RANKPEP
servers for MHC class II
binding prediction
Approaches
used
Structure - based
Molecular docking calculations
Medical University of Sofia
Faculty of Pharmacy
Case study 1: T-cell epitope prediction
of proteins from Boophilus microplus
Workflow:
Selection of high
1. immunogenic B. microplus
proteins by VaxiJen server.
2.
Presentation of the
selected proteins as sets
of overlapping peptides.
Selection of input X-ray structures of complexes
of murine MHC II protein with a peptide.
Ova/IAd (pdb code: 2iad)
HB/IEk (pdb code:1iea)
3.
Optimization of complexes of each
peptide with each MHC II protein.
Docking
calculations
biding site - 6Å; Chemscore – scoring function; fixed protein
and peptide backbone; ranking – by score; GOLD v.5.0.2.
B. Microplus
Protein
number
peptides
Contig2828
Contig7420
CK181624
Homology modeling
of IEk to IEd structure
59
93
61
Medical University of Sofia
Faculty of Pharmacy
Case study 1: T-cell epitope prediction
of proteins from Boophilus microplus
Binding affinity prediction to IAd by MHCPred and RANKPEP
MHCPred: Predicted binders with IC50 < 50 nM
are highlighted in green.
RANKPEP: Predicted binders with binding threshold:
7.10 are highlighted in purple.
Medical University of Sofia
Faculty of Pharmacy
Case study 1: T-cell epitope prediction
of proteins from Boophilus microplus
Binding affinity prediction to IAd and IEd by Molecular docking
IAd
IEd
The top 2 best clusters of binders are highlighted in magenta.
Medical University of Sofia
Faculty of Pharmacy
Case study 1: T-cell epitope prediction
of proteins from Boophilus microplus
Peptides selected for further experimental studies
Medical University of Sofia
Faculty of Pharmacy
Case study 2: Prediction of peptide binding
to Swine Leukocyte Antigen (SLA-1)
Intestinal
Diarrhea
Respiratory
Coughing
Sore Throat
Physchological
Lethargy
Lack of appetite
Swine Influenza in pigs:
- An acute respiratory disease;
Nasopharynx
Sneezing
Mucous: nose/eyes
Systemic
Fever
Weight loss
Poor growth
- High morbidity depending on the
immune status;
- Can results in important economic
losses.
Swine influenza symptoms
Aim:
to generate quatitative matrices (QMs) for prediction of
peptides binding to SLA-1
CReSA
Centre de Recerca en Sanitat Animal
Medical University of Sofia
Faculty of Pharmacy
Case study 2: Prediction of peptide binding
to Swine Leukocyte Antigen (SLA-1)
Workflow:
1. Homology modeling of SLA-1
from HLA*0201 (pdb:3pwj).
2. Construction of combinatorial
library of peptides.
3. Molecular docking of peptides
to SLA proteins.
4. Forming of docking score-based
QMs (DS-QMs).
P1
P2
P3
Modeled
P9
P7
P6
proteins:
SLA-1*0101 P5
SLA-1*0401
SLA-1*0501 SLA-1*1101
7 anchor positions X 19 aa =
133 + 1 original ligand = 134 peptides
biding site - 6Å; Chemscore –
scoring function; fixed protein and
ligand apart from the residues from
the tested peptide position; ranking
– by lowest RMS; GOLD v.5.0.2.
normalization of the binding
energies and compilation into QMs.
Medical University of Sofia
Faculty of Pharmacy
Case study 2: Prediction of peptide binding
to Swine Leukocyte Antigen (SLA-1)
Combinatorial library
Workflow:
peptide
1. Homology modeling of SLA-1
from HLA*0201 (pdb:3pwj).
PKYVKQNTLKLAT - 71.47
PKXVKQNTLKLAT - 63.72
PKYXKQNTLKLAT
…
PKYVKXNTLKLAT
…
PKYVKQNXLKLAT
…
PKYVKQNTXKLAT
…
PKYVKQNTLKXAT
…
PKYVKQNTLKLXT
…
2. Construction of combinatorial
library of peptides.
3. Molecular docking of peptides
to SLA proteins.
4. Forming of docking score-based
QMs (DS-QMs).
avr score normalized
+ 0.456
- 0.123
…
…
…
…
…
…
QM
aa\pocket
A
C
D
E
…
1
2
3
5
6
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
…
… …
… …
… …
… …
…
7
9
…
…
…
…
…
Medical University of Sofia
Faculty of Pharmacy
Case study 2: Prediction of peptide binding
to Swine Leukocyte Antigen (SLA-1)
SLA allele
Pocket 2 profile
P2 accepts
0101
Tyr9, Ala24, Val34, Met45, Glu63, Lys66, Gln67
Leu, Met, Asn
0501
Ser9, Ala24, Val34, Met45, Glu63, Lys66, Gln67
Trp, Leu, Phe
0401
Tyr9, Ala24, Val34, Met45, Glu63, Asn66, Val67
Leu, Met, Thr
1101
Ser9, Glu24, Val34, Met45, Glu63, Arg66, Val67
Leu, Met, Ile
0101 - Leu
0101 – Asn
0501 - Trp
Medical University of Sofia
Faculty of Pharmacy
Case study 2: Prediction of peptide binding
to Swine Leukocyte Antigen (SLA-1)
SLA allele
Pocket 2 profile
P2 accepts
0101
Tyr9, Ala24, Val34, Met45, Glu63, Lys66, Gln67
Leu, Met, Asn
0501
Ser9, Ala24, Val34, Met45, Glu63, Lys66, Gln67
Trp, Leu, Phe
0401
Tyr9, Ala24, Val34, Met45, Glu63, Asn66, Val67
Leu, Met, Thr
1101
Ser9, Glu24, Val34, Met45, Glu63, Arg66, Val67
Leu, Met, Ile
0401 - Met
1101 - Met
Medical University of Sofia
Faculty of Pharmacy
Case study 2: Prediction of peptide binding
to Swine Leukocyte Antigen (SLA-1)
SIV proteins screened
to predict SLA binders:
- hemagglutinin (HA)
- nucleocapsid protein (NP)
- matrix protein 1 (M1)
- polymerase PB1 (PB1)
binders to SLA-1*0101
>gi|91177888|gb|ABE27153.1| hemagglutinin [Influenza A virus
(A/swine/Spain/53207/2004(H1N1))]
MEAKLFVLFCAFTALKADTICVGYHANNSTDTVDTILEKNVTVTHSVNLLENSHNGKLCSLNGKAPLQLG
NCNVAGWILGNPECDLLLTANSWSYIIETSNSKNGACYPGEFADYEELREQLSTVSSFERFEIFPKATSW
PNHETTKGTTVACSHSGANSFYRNLLWIVKKGNSYPKLSKSYTNNKGKEVLVIWGVHHPPTDSNQQTLYQ
NNHTYVSVGSSKYYQRFTPEIVARPKVREQAGRMNYYWTLLDQGDTITFEATGNLIAPWHAFALNKGSSS
GIMMSDAHVHNCTTKCQTPHGALKSNLPFQNVHPITIGECPKYVKSTQLRMATGLRNIPSTQSRGLFGAI
AGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQIAIDGISNKVNSVIEKMNIQFTSVGKEFNNLEKR
IENLNKKVDDGFLDVWTYNAELLILLENERTLDFHDFNVKNLYEKVKSQLRNNAKEIGNGCFEFYHKCDN
ECMESVKNGTYNYPRYSEESKLNREEIDGVKLESVGVHQILAIYSTVASSLVLLVSLGAISFWMCSNGSL
QCRICI
binders to SLA-1*0401
>gi|91177888|gb|ABE27153.1| hemagglutinin [Influenza A virus
(A/swine/Spain/53207/2004(H1N1))]
MEAKLFVLFCAFTALKADTICVGYHANNSTDTVDTILEKNVTVTHSVNLLENSHNGKLCSLNGKAPLQLG
NCNVAGWILGNPECDLLLTANSWSYIIETSNSKNGACYPGEFADYEELREQLSTVSSFERFEIFPKATSW
PNHETTKGTTVACSHSGANSFYRNLLWIVKKGNSYPKLSKSYTNNKGKEVLVIWGVHHPPTDSNQQTLYQ
NNHTYVSVGSSKYYQRFTPEIVARPKVREQAGRMNYYWTLLDQGDTITFEATGNLIAPWHAFALNKGSSS
GIMMSDAHVHNCTTKCQTPHGALKSNLPFQNVHPITIGECPKYVKSTQLRMATGLRNIPSTQSRGLFGAI
AGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQIAIDGISNKVNSVIEKMNIQFTSVGKEFNNLEKR
IENLNKKVDDGFLDVWTYNAELLILLENERTLDFHDFNVKNLYEKVKSQLRNNAKEIGNGCFEFYHKCDN
ECMESVKNGTYNYPRYSEESKLNREEIDGVKLESVGVHQILAIYSTVASSLVLLVSLGAISFWMCSNGSL
QCRICI
binders to SLA-1*0501
>gi|91177888|gb|ABE27153.1| hemagglutinin [Influenza A virus
(A/swine/Spain/53207/2004(H1N1))]
MEAKLFVLFCAFTALKADTICVGYHANNSTDTVDTILEKNVTVTHSVNLLENSHNGKLCSLNGKAPLQLG
NCNVAGWILGNPECDLLLTANSWSYIIETSNSKNGACYPGEFADYEELREQLSTVSSFERFEIFPKATSW
PNHETTKGTTVACSHSGANSFYRNLLWIVKKGNSYPKLSKSYTNNKGKEVLVIWGVHHPPTDSNQQTLYQ
NNHTYVSVGSSKYYQRFTPEIVARPKVREQAGRMNYYWTLLDQGDTITFEATGNLIAPWHAFALNKGSSS
GIMMSDAHVHNCTTKCQTPHGALKSNLPFQNVHPITIGECPKYVKSTQLRMATGLRNIPSTQSRGLFGAI
AGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQIAIDGISNKVNSVIEKMNIQFTSVGKEFNNLEKR
IENLNKKVDDGFLDVWTYNAELLILLENERTLDFHDFNVKNLYEKVKSQLRNNAKEIGNGCFEFYHKCDN
ECMESVKNGTYNYPRYSEESKLNREEIDGVKLESVGVHQILAIYSTVASSLVLLVSLGAISFWMCSNGSL
QCRICI
binders to SLA-1*1101
>gi|91177888|gb|ABE27153.1| hemagglutinin [Influenza A virus
(A/swine/Spain/53207/2004(H1N1))]
MEAKLFVLFCAFTALKADTICVGYHANNSTDTVDTILEKNVTVTHSVNLLENSHNGKLCSLNGKAPLQLG
NCNVAGWILGNPECDLLLTANSWSYIIETSNSKNGACYPGEFADYEELREQLSTVSSFERFEIFPKATSW
PNHETTKGTTVACSHSGANSFYRNLLWIVKKGNSYPKLSKSYTNNKGKEVLVIWGVHHPPTDSNQQTLYQ
NNHTYVSVGSSKYYQRFTPEIVARPKVREQAGRMNYYWTLLDQGDTITFEATGNLIAPWHAFALNKGSSS
GIMMSDAHVHNCTTKCQTPHGALKSNLPFQNVHPITIGECPKYVKSTQLRMATGLRNIPSTQSRGLFGAI
AGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQIAIDGISNKVNSVIEKMNIQFTSVGKEFNNLEKR
IENLNKKVDDGFLDVWTYNAELLILLENERTLDFHDFNVKNLYEKVKSQLRNNAKEIGNGCFEFYHKCDN
ECMESVKNGTYNYPRYSEESKLNREEIDGVKLESVGVHQILAIYSTVASSLVLLVSLGAISFWMCSNGSL
QCRICI
Thank you
for your attention!