Computational Aspects in Dengue Vaccine Research

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Computational Aspects in Dengue Vaccine Research

• Celia Aurora T. Torres, Ph.D.
• Molecular Medicine and Biotechnology Research Lab
• National Institute of Molecular Biology
• and Biotechnology
• University of the Philippines Diliman

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All about Dengue
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DENGUE DENGUE HEMORRHAGIC FEVER

• Dengue and Dengue Hemorrhagic Fever (DHF) are
  caused by the mosquito-borne dengue virus that
  belongs to the genus Flavivirus, family
  Flaviviridae
• There are four antigenically distinct, but
  related, dengue virus serotypes, DEN-1, DEN-2,
  DEN-3 and DEN-4
• The primary vector of dengue virus are
  mosquitoes belonging to the genus of Aedes,
  specifically Ae. aegypti, Ae.
  albopictus,and Ae. polynesiensis

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Global Resurgence of Dengue and DHF

• Reinfestation by Ae. aegypti of American tropical
  regions
• Lack of effective vector control in endemic areas
• Uncontrolled population growth and uncontrolled
  urbanization
• Increased air travel
• Deterioration of public health infrastructures
  (crisis mentality)

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Local Resurgence of Dengue

• In 1998, there were 35,648 reported cases of
  dengue, with about 1.5 of these cases being
  fatalities, as reported by sentinel hospitals of
  the Dept. of Health (DOH)
• Metro Manila accounted for 17.4 of the above
  cases
• Every year, there are hundreds to thousands of
  dengue cases in the country

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Pathogenesis of Dengue and DHF
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Antibody-Dependent Enhancement
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Implications of the Above in Dengue Vaccine
Development

• A vaccine against dengue should ideally have the
  following features
• can prevent infection against all four serotypes
  to prevent DHF that may arise from sequential
  infection
• can elicit strong cytotoxic T lymphocyte (CTL)
  responses
• should be stable at room temperature, for ease
  and low cost of use in tropical countries

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Why Develop Multi-Epitope DNA Vaccines Against
Dengue?
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What are DNA Vaccines?
From Scientific American, July 1995
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Advantages of DNA Vaccines Over Other Types of
Vaccines

• cheaper and easier to produce
• safer
• can elicit antibody and cellular immune responses
• stable at a broad range of temperature (no
  cold-chain requirement)
• can be designed and produced by genetic
  engineering to have only the desired antigens or
  antigenic sequences (epitopes) in the vaccine

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What are Epitopes?

• Epitopes are the specific sequences in an antigen
  that are recognized by the components of the
  immune response
• There are three types of epitopes
• B epitopes are recognized by antibodies
• T-helper (Th) epitopes are recognized by T-helper
  cells
• CTL epitopes are recognized by the cytotoxic T
  lymphocytes

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What are Epitopes?
www.som.soton.ac.uk/.../cancersciences/
members/the/the.htm
T-cell epitope
www.umass.edu/microbio/ rasmol/epitope.htm
B-cell epitope
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How do we predict epitopes using computational
methods?

• Analyze protein sequence
• For B-cell epitopes, predict secondary structure,
  hydrophobicity, mobility/flexibility
• For T-cell epitopes, look for anchor residues and
  predict proteasomal cleavage

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All about proteins
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The Central Dogma
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Protein Synthesis
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The Genetic Code
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From gene sequence to protein function

• In other words, theoretically, you can surmise
  the function of proteins from their genetic
  sequence!

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Protein Structure Prediction

• Requires only sequence information
• Secondary structure prediction
• Protein threading or fold family recognition
• Ab-initio structure prediction
• Homology modeling

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Protein antigenicity prediction algorithms

• Hopp and WoodsHopp, T.P. and Woods, K.R. (1981).
  Prediction of protein antigenic determinants from
  amino acid sequences. Proceedings of the National
  Academy of Sciences USA, 78 3824-3828.ParkerPa
  rker, J.M.R., Guo, D. and Hodges, R.S. (1986).
  New hydrophilicity scale derived from
  high-performance liquid chromatography retention
  data correlation of predicted surface residues
  with antigenicity and X-ray derived accessible
  sites. Biochemistry, 25, 5425.Protrusion Index
  (Thornton)Thornton, J.M, Edwards, M.S., Tayler,
  W.R. and Barlow, D.J. (1986). Location of
  'continuous' antigenic determinants in the
  protruding regions of proteins. EMBO Journal, 5
  409-413.WellingWelling, G.W, Wiejer, W.J, Van
  der Zee, R. and Welling-Webster, S. (1985).
  Prediction of sequential antigenic regions in
  proteins. FEBS Letters, 188 215-218.

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Protein hydrophilicity algorithms

• Goldman, Engelman and Steitz (GES)Engelman,
  D.M., Steitz, T.A. and Goldman, A. (1986).
  Identifying nonpolar transmembrane helices in
  amino acid sequences of membrane proteins. Annual
  Review of Biophysics and Biophysical Chemistry,
  15 321-353.von Heijnevon Heijne, G. (1981).
  On the hydrophobic nature of signal sequences.
  European Journal of Biochemistry, 116 419-422.

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Protein secondary structure prediction algorithms

• GOR II method (Garnier and Robson)Garnier, J.
  and Robson, B. (1989). The GOR method for
  predicting secondary structures in proteins. In
  Prediction of Protein Structure and the
  Principles of Protein Conformation (ed. G.D.
  Fasman), Vol. 11, pp. 417-465. Plenum Press, New
  York.Garnier, J., Osguthorpe, D.J. and Robson,
  B. (1978). Analysis of the accuracy and
  implications of simple methods for predicting the
  secondary structure of globular proteins. Journal
  of Molecular Biology, 120 97-120.Chou and
  FasmanChou, P.Y. and Fasman, G.D. (1974).
  Conformational parameters for amino acids in
  helical, ß-sheet, and random coil regions
  calculated from proteins. Biochemistry, 13
  211-222.Lewis, P.N., Momany, F.A. and Scheraga,
  H. A. (1971). Folding of polypeptide chains in
  proteins a proposed mechanism for folding.
  Proceedings of the National Academy of Sciences
  USA, 68 2293-2297.Chou, P.Y. and Fasman, G.D.
  (1978). Empirical predictions of protein
  conformation. Annual Review of Biochemistry, 47
  251-276.Chou, P.Y. and Fasman, G.D. (1978).
  Prediction of the secondary structure of proteins
  from their amino acid sequence. Advances in
  Enzymology, 47 45-148.

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T cell epitopes and prediction

• Blythe, M.J., Doytchinova, I.A. and Flower, D.R.
  (2002). JenPep a database of quantitative
  functional peptide data for immunology.
  Bioinformatics, 18 434-439.
• Yu, K., Petrovsky, N., Schonbach, C., Koh, J.Y.
  and Brusic, V. (2002). Methods for prediction of
  peptide binding to MHC molecules a comparative
  study. Molecular Medicine, 8 137-48.
• Brusic, V., Petrovsky, N., Zhang, G. and Bajic,
  V. (2002). Prediction of promiscuous peptides
  that bind HLA class I molecules. Immunology and
  Cell Biology, 80 280-285.
• Jung, G., Fleckenstein, B., von der Mülbe, F.,
  Wessels, J., Niethammer, D. and Wiesmüller, K-H.
  (2001). From combinatorial libraries to MHC
  ligand motifs, T-cell superagonists and
  antagonists. Biologicals, 29 179-181.

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The Promise of Computational Methods for Epitope
Prediction

• Intensive computation is needed for
  close-to-accurate epitope prediction
• Such algorithms would have to incorporate all the
  known parameters that affect epitope antigenicity
• Algorithms should be updated as more information
  is acquired regarding important parameters that
  affect antigenicity
• Predicted epitopes must then be confirmed through
  laboratory in vivo and in vitro experiments

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Thank You!