iVAX

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iVAX Toolkit – Online Access

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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

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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

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•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:

Final Immunogenic Consensus Sequence

VaccineCAD

VaxCAD will identify junctional epitopes and rearrange chosen epitopes to reduce

junctional epitope formation

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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

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Sco

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Peptides in Default order in construct HP_IIB

Epitope Cluster Score

Junctional Cluster Score

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0

10

20

30

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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

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HP

4175

HP

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HP

4126

HP

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HP

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HP

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HP

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HP

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HP

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HP

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Peptides in Optimized order in construct HP_IIB

Epitope Cluster Score

Junctional Cluster Score

VaccineCAD

VaccineCAD Eliminates Introduced Junctional Epitopes

MHC

TCR

JanusMatrix – T cell facing vs. MHC facing

conservation

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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

Accessing the Tools Contact Jason Del Pozzo: bda@epivax.com

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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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