iVAX
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iVAX Toolkit – Online Access
Vaccine Design Tools and Techniques
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iVAX Fully integrated From genome to vaccine • EpiMatrix – maps T cell epitopes • ClustiMer - Promiscuous / Supertype Epitopes Seamless Vaccine • BlastiMer - Avoiding “self” - autoimmunity
Design
• Conservatrix – Identifies Conserved Segments
Integrated toolkit is • EpiAssembler - Immunogenic Consensus Sequences unique to iVax
• Aggregatrix – Optimizing the coverage of vaccines • VaxCAD - Processing and Assembly
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Comparative Genomics Impacts Vaccine Immunogen Selection Strain 1
dispensable genes
core genome
Strain 3 Strain 2
pangenome
strain-specific genes
Epitope Cross-Reactivity Impacts Vaccine Immunogen Selection
Human Potentially detrimental crossreactive epitopes
Human Microbiome
Potentially detrimental crossreactive epitopes
Pathogen
Protective epitopes
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
MHC II
Mature APC
Peptide Epitope
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
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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.
* Southwood et. al., Several Common HLA-DR Types Share Largely Overlapping Peptide Binding Repertoires. 1998. Journal of Immunology. 8
EpiMatrix •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?
Confidential
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Epitope Identification EpiMatrix is the best available epitope discovery tool
De Groot and Martin. Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics. Clinical Immunology 2009. 131, 189-201. Confidential
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ClustiMer Easy •
easy to deliver as peptides
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.
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ClustiMer recognizes T-cell epitope clusters as polypeptides predicted to bind to an unusually large number of HLA alleles.
DRB1*0101
DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801
DRB1*1101 DRB1*1301 DRB1*1501
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T-cell epitope clusters make excellent vaccine candidates: – compact; relatively easy to deliver as peptides; highly reactive in-vivo 11 3/25/2013
Confidential
Conservatrix Finds Conserved 9-mers
CTRPNNTRK CTRPNNTRK CTRPNNTRK CTRPNNTRK CTRPNNTRK CTRPNNTRK
CTRPNNTRK
Conserved epitope
Identifying the most conserved 9-mers allows for protection against more strains with fewer epitopes 12
BlastiMer: Epitope Exclusion
Foreign
Self
In all of our vaccines we eliminate cross-reactive epitopes
Confidential
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EpiAssembler: Final Immunogenic Consensus Sequence STRAIN 01 STRAIN 02 STRAIN 03 STRAIN 04 STRAIN 05 STRAIN 06 STRAIN 07 STRAIN 08 STRAIN 09 STRAIN 10 STRAIN 11 STRAIN 12 STRAIN 13 STRAIN 14 STRAIN 15 STRAIN 16 STRAIN 17 STRAIN 18 STRAIN 19 STRAIN 20
Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q X Q Q Q
Q
X A X A X A X A X A A A A A A X A X A A
A
S S S S S S S S S S S S S S S S S S S S
S
W W W W W W W W W W W W W W W W W W W W
P P P X P P P X P P P X P X P P X P X P
K K K K K K K K K x R K K K K K K K K K K
V V X V V X V V X V V V V X V V V X V V
E E E E E E E E E E E E E E E E E E E E
Q X Q Q Q Q Q Q Q Q Q Q Q Q X Q Q Q Q Q
F F F F F F F F F F F F F F F F F F F F
W W W W W W W W W W W W W W W W W W W W
A A A A A A A A A A A A A A X A A A A A
K K K K K X K K K K K X K K K K K K K X
H H H H H H H H H H H H H H H H H H H H
X M M M M M M M M M M M M M M M M M M M
W W W W W W X W W W W W W W W W W W W W
N N N N N N N N N N N N N N N N N N N N
X F F F F F F F F F F F F F F F F X F F
I I I X I I I I X I I I I I I I I I I I
S S S S S S S S S X S S S S S X S S S S
X G G X G G G G X G G G G X G G G G X G
I I I I I I I I I I I I I I I I I I I I
Q Q Q Q Q Q Q Q X Q Q Q Q Q Q Q Q Q Q Q
Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
L L X L L X L L X L L X L L L L X L L L
Y
L
F W A K H M W N F M W N F I S G I Q W P K V E Q F W A
W
P
K
V
E
Q
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
VaccineCAD VaxCAD will identify junctional epitopes and rearrange chosen epitopes to reduce junctional epitope formation
Epitope Cluster Score Junctional Cluster Score
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10
0
-10
Peptides in Default order in construct HP_IIB 50
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HP4117 HP4061 HP4181 HP4111 HP4018 HP4070 HP4060 HP4157 HP4065 HP4001 HP4193 HP4034 HP4068 HP4168 HP4160 HP4175 HP4127 HP4126 HP4007 HP4154 HP4164 HP4119 HP4100 HP4120 HP4179
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EpiMatrix Cluster Score
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HP4117 HP4179 HP4007 HP4111 HP4018 HP4070 HP4034 HP4193 HP4065 HP4181 HP4157 HP4060 HP4068 HP4164 HP4160 HP4175 HP4127 HP4120 HP4126 HP4154 HP4168 HP4119 HP4100 HP4001 HP4061
EpiMatrix Cluster Score
VaccineCAD
Epitope Cluster Score Junctional Cluster Score
40
30
20
10 0
-10
Peptides in Optimized order in construct HP_IIB
VaccineCAD Eliminates Introduced Junctional Epitopes 16
JanusMatrix – T cell facing vs. MHC facing conservation
TCR
MHC
Multi-Epitope Gene Design Intended Protein Product: Many epitopes strung together in a “String-of-Beads�
DNA insert
DNA Vector
Protein product (folded)
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Multiple Delivery Platforms Possible DNA – chain of epitopes, or peptide in liposomes
ICS-optimized whole proteins
ICS-optimized proteins in VLP
Accessing the Tools Contact Jason Del Pozzo: bda@epivax.com
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.
Confidential
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