epivax ivax toolkit overview_2013
DESCRIPTION
A Brief overview of EpiVax's iVax Toolkit for designing T Cell mediated vaccines. www.epivax.comTRANSCRIPT
iVAX
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iVAX Toolkit – Online Access
iVAX – Quick Facts
• Comprehensive set of epitope mapping algorithms
• Tools to build immunogenic and effective vaccines
• Applications to assay reagent development and
diagnostics
• Interactive and user friendly
• 24/7 access
• On-site training program
• Technical support service
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Vaccine Design Tools and Techniques
• EpiMatrix – maps T cell epitopes
• ClustiMer - Promiscuous / Supertype Epitopes
• BlastiMer - Avoiding “self” - autoimmunity
• Conservatrix – Identifies Conserved Segments
• EpiAssembler - Immunogenic Consensus Sequences
• Aggregatrix – Optimizing the coverage of vaccines
• VaxCAD - Processing and Assembly
iVAX Fully integrated
From genome to vaccine
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Seamless Vaccine Design Integrated toolkit is unique to iVax
Strain 1
Strain 3
Strain 2
core genome dispensable genes
strain-specific genes pangenome
Comparative Genomics Impacts
Vaccine Immunogen Selection
Human
Pathogen
Human Microbiome
Protective
epitopes
Potentially
detrimental cross-
reactive epitopes
Potentially
detrimental cross-
reactive epitopes
Epitope Cross-Reactivity Impacts
Vaccine Immunogen Selection
EpiMatrix
• EpiVax uses EpiMatrix to predict epitopes – matrix based prediction algorithm
• Can predict either class I or class II MHC binding – MHC binding is a prerequisite for immunogenicity
MHC II Pocket
Peptide Epitope
Mature APC
MH
C II
T cell epitopes are linear and directly derived from antigen sequence Binding is determined by amino acid side chains (R groups) and ‘encoded’ in single letter code
8 6/26/2013 Confidential
EpiVax HLA “Supertype” Coverage
• EpiVax tests for binding
potential to the most common
HLA molecules within each of the
“supertypes” shown to the left.
• This allows us to provide results
that are representative of >90% of
human populations worldwide*
without the necessity of testing
each haplotype individually.
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* Southwood et. al., Several Common HLA-DR Types Share Largely
Overlapping Peptide Binding Repertoires. 1998. Journal of Immunology.
EpiMatrix
Confidential 10
•The EpiMatrix algorithm scores all the 9-mers in a given
sequence for binding affinity across a range of common
HLA and reports both detailed and aggregated results.
•Unlike other tools, there are ancillary algorithms that
enhance the usefulness of the tool for immunogenicity
prediction of protein therapeutics and vaccine design.
•Does it work?
Epitope Identification EpiMatrix is the best available epitope discovery tool
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De Groot and Martin. Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics.
Clinical Immunology 2009. 131, 189-201.
Confidential
Easy easy to deliver as peptides ClustiMer
DRB1*0101
DRB1*0301
DRB1*0401
DRB1*0701
DRB1*0801
DRB1*1101
DRB1*1301
DRB1*1501
• T cell epitopes are not randomly distributed but instead tend to cluster in specific regions. – These clusters can be very powerful, enabling significant immune responses to low scoring proteins.
• ClustiMer recognizes T-cell epitope clusters as polypeptides predicted to bind to an unusually large number of HLA alleles.
• T-cell epitope clusters make excellent vaccine candidates:
– compact; relatively easy to deliver as peptides; highly reactive in-vivo
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Identifying the most conserved 9-mers allows for protection
against more strains with fewer epitopes
Conservatrix Finds Conserved 9-mers
Conserved
epitope
CTRPNNTRK
CTRPNNTRK CTRPNNTRK
CTRPNNTRK CTRPNNTRK
CTRPNNTRK
CTRPNNTRK
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BlastiMer: Epitope Exclusion
Confidential
In all of our vaccines we eliminate cross-reactive epitopes
Self Foreign
STRAIN 01 Q X S W P K V E Q F W A K H X W N X I S X I Q Y L
STRAIN 02 Q A S W P K V E X F W A K H M W N F I S G I Q Y L
STRAIN 03 Q X S W P K X E Q F W A K H M W N F I S G I Q Y X
STRAIN 04 Q A S W X K V E Q F W A K H M W N F X S X I Q Y L
STRAIN 05 Q X S W P K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 06 Q A S W P K X E Q F W A X H M W N F I S G I Q Y X
STRAIN 07 Q X S W P K V E Q F W A K H M X N F I S G I Q Y L
STRAIN 08 Q A S W X K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 09 Q X S W P K X E Q F W A K H M W N F X S X I X Y X
STRAIN 10 Q A S W P R V E Q F W A K H M W N F I X G I Q Y L
STRAIN 11 Q A S W P K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 12 Q A S W X K V E Q F W A X H M W N F I S G I Q Y X
STRAIN 13 Q A S W P K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 14 Q A S W X K X E Q F W A K H M W N F I S X I Q Y L
STRAIN 15 Q A S W P K V E X F W X K H M W N F I S G I Q Y L
STRAIN 16 Q X S W P K V E Q F W A K H M W N F I X G I Q Y L
STRAIN 17 X A S W X K V E Q F W A K H M W N F I S G I Q Y X
STRAIN 18 Q X S W P K X E Q F W A K H M W N X I S G I Q Y L
STRAIN 19 Q A S W X K V E Q F W A K H M W N F I S X I Q Y L
STRAIN 20 Q A S W P K V E Q F W A X H M W N F I S G I Q Y L
x
F W A K H M W N FW P K V E Q F W A
Q A S W P K V E Q N F I S G I Q Y L
M W N F I S G I Q
Q A S W P K V E Q F W A K H M W N F I S G I Q Y L
EpiAssembler Produces
Immunogenic Consensus Sequences
VaccineCAD
VaxCAD will identify junctional epitopes and rearrange chosen epitopes to reduce
junctional epitope formation
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-10
0
10
20
30
40
50
HP
4117
HP
4179
HP
4007
HP
4111
HP
4018
HP
4070
HP
4034
HP
4193
HP
4065
HP
4181
HP
4157
HP
4060
HP
4068
HP
4164
HP
4160
HP
4175
HP
4127
HP
4120
HP
4126
HP
4154
HP
4168
HP
4119
HP
4100
HP
4001
HP
4061
Ep
iMatr
ix C
lus
ter
Sco
re
Peptides in Default order in construct HP_IIB
Epitope Cluster Score
Junctional Cluster Score
-10
0
10
20
30
40
50
HP
4117
HP
4061
HP
4181
HP
4111
HP
4018
HP
4070
HP
4060
HP
4157
HP
4065
HP
4001
HP
4193
HP
4034
HP
4068
HP
4168
HP
4160
HP
4175
HP
4127
HP
4126
HP
4007
HP
4154
HP
4164
HP
4119
HP
4100
HP
4120
HP
4179
Ep
iMatr
ix C
lus
ter
Sco
re
Peptides in Optimized order in construct HP_IIB
Epitope Cluster Score
Junctional Cluster Score
VaccineCAD
VaccineCAD Eliminates Introduced Junctional Epitopes
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DNA
Vector
DNA insert
Intended Protein Product: Many epitopes strung together in a “String-of-Beads”
Protein
product
(folded)
Multi-Epitope Gene Design
DNA – chain of epitopes, or peptide in liposomes
ICS-optimized proteins in VLP ICS-optimized whole proteins
Multiple Delivery Platforms Possible
Vaccine
Immunogenic
Epitopes
Shared
Immunogenic
Epitopes
smallpox
vaccinia
Case Study: Smallpox Vaccine
VennVax
Immunogenicity
Day 56
1. epitope DNA vaccine prime (IM)
2. epitope peptide boost (IN)
Immunizations
Days 0, 14, 28, 42 Challenge
Day 65
Case Study: VennVax Immunization
in HLA DR3 Transgenic Mice
Moise L et al. Vaccine. 2011;29:501-11
• Challenge done at 10X LD50 for Smallpox
• Related publication: http://www.ncbi.nlm.nih.gov/pubmed/21055490
Case Study:
VennVax Protection: Survival
0%
20%
40%
60%
80%
100%
0 2 4 6 8 10 12 14 16 18
Su
rviv
al
Days Post-Infection
VennVax
Placebo
Moise et al. Vaccine. 2011; 29:501-11
100% protection VS Placebo
MHC
TCR
iVAX Feature Under Development:
JanusMatrix
JanusMatrix is designed to predict the
potential for cross reactivity between epitope
clusters and the human genome, based on
conservation of TCR-facing residues in their
putative HLA ligands.
Accessing the Tools Contact Jason Del Pozzo: [email protected]
Confidential 24
PreDeFT: Fee for service in silico immunogenicity analysis. Performed on a protein by protein basis. Pricing based on length of sequence(s).
Limited ISPRI Website: Limited access to EpiVax’ Interactive Protein Screening and Reengineering Interface. Available for set numbers of proteins.
Unlimited ISPRI Website: Unlimited access to EpiVax’ Interactive Protein Screening and Reengineering Interface. Available in three year lease periods.
Fee for Service: HLA Binding Assays, HLA Transgenic Mice, ELISpot Assays.
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