ivax : web-based vaccine design platform
DESCRIPTION
iVAX is a web-based vaccine design platform that allows you to build an epitope driven vaccine directly from a pathogen genome in a matter or hours or days. Analyze pathogen gene sequences for conserved antigens to provide better strain coverage, build sequences of the most effective, immunogenic epitopes, optimize protein sequences for efficient, targeted immune protection. In addition to designing vaccines from the ground up you can also use iVAX to predict the efficacy of existing vaccines or vaccines in development. iVAX has been validated in producing 5 prototype vaccines : tularemia, vaccinia / smallpox, H. pylori, pandemic influenza H7N9 (bird flu) and pandemic influenza H1N1 (swine flu).TRANSCRIPT
iVAX Overview
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iVAX Toolkit – Online Access
Whole (live/killed)
vaccinesSubunit vaccines
Genome-Derived, Epitope Driven (GD-ED)
Vaccines
Better understanding of vaccine MOA
Improve vaccine safety and efficacy
Accelerate Vaccine Design
Design next-gen vaccinesbetter/safer/faster
T cells = Immune System Body Armor
T cell response cannot prevent Infection but . . .
T cell response can arm against Disease
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Vaccine Design Tools and Techniques
Analysis
Validation
Engineering
Strain 1
Strain 3
Strain 2
core genomedispensable genes
strain-specific genespangenome
Comparative Genomics ImpactsVaccine Immunogen Selection
Epitope Cross-Reactivity ImpactsVaccine 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
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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Mature APC
Protein MHC II Pocket
Peptide Epitope
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.
9* 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.
• In protein therapeutics and existing vaccines these tools can predict immunogenicity (efficacy). In the design of vaccines these tools allow for educated selection of pathogen genome sequences to make the most effective, efficient and safe vaccine
Easy easy to deliver as peptidesClustiMer
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
Conservedepitope
CTRPNNTRK
CTRPNNTRKCTRPNNTRK
CTRPNNTRKCTRPNNTRK
CTRPNNTRK
CTRPNNTRK
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BlastiMer: Epitope Exclusion
In all of our vaccines we eliminate cross-reactive epitopesIn all of our vaccines we eliminate cross-reactive epitopes
SelfSelfForeignForeign
MHC
TCR
New iVAX feature: JanusMatrix Homology Analysis
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.
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VLQSSGLSYS( T cell epitope)
FLQDSNLYK(T cell epitope with same TCR face)
Another human protein
A different human protein
A human protein
Source protein
Predicted 9-mer epitope from a source protein
Human protein where cross-reactive epitopes are present
9-mer from human prevalent proteome, 100% TCR face identical to source epitope
Source Protein or large peptide
JanusMatrix Cross-reactivity Networks
All induced Teff response
Example: HCV Vaccine22/23 epitopes vs. human proteome
vs. human proteome vs. human microbiome
Induced Treg response
Example: HCV VaccineOne “special” epitope: cross-reactive
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 LSTRAIN 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 LSTRAIN 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 XSTRAIN 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 LSTRAIN 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 LSTRAIN 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 XSTRAIN 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 LSTRAIN 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 LSTRAIN 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 XSTRAIN 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 LSTRAIN 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 LSTRAIN 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 XSTRAIN 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 LSTRAIN 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 LSTRAIN 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 LSTRAIN 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 LSTRAIN 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 XSTRAIN 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 LSTRAIN 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 LSTRAIN 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 LM 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
HP
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HP
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HP
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07
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HP
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HP
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HP
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HP
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-10
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50Epitope Cluster ScoreJunctional Cluster Score
Peptides in Default order in construct HP_IIB
Ep
iMa
trix
Clu
ste
r S
co
re
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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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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HP
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07
HP
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HP
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64
HP
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19
HP
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00
HP
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20
HP
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-10
0
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50Epitope Cluster ScoreJunctional Cluster Score
Peptides in Optimized order in construct HP_IIBE
piM
atr
ix C
lus
ter
Sc
ore
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)
Output: Multi-Epitope Gene Design
DNA – chain of epitopes, or peptide in liposomes ICS-optimized proteins in VLPICS-optimized whole proteins
Multiple Delivery Platforms Possible
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iVAX: Case Studies
Vaccine
Immunogenic
Epitopes
Shared
Immunogenic
Epitopes
smallpoxvaccinia
Case Study: Smallpox VaccineVennVax
Immunoinformatics Summary
(18/110) Epitopes derived from structural proteins
(66/110) Epitopes derived from regulatory factors
(26/110) Epitopes derived from Hypothetical and unknown proteins
AF095689 (Xian tan)
M35027
(Copenhagen)
U94848 (Ankara)
AY243312(WR)
Y16780
(V. Minor)
X69198
(V. Major) L2
2579
Bangladesh
2. Identified highly conserved 9-mers
3. Identified promiscuous Class II T cell epitopes and Class I epitopes
4. Eliminated human homologous epitopes
1. Downloaded 7 complete genomes from GenBank.
Moise L et al. Vaccine. 2009;27:6471-9
Immunogenicity Day 56
1. epitope DNA vaccine prime (IM)2. epitope peptide boost (IN)
ImmunizationsDays 0, 14, 28, 42
ChallengeDay 65
Case Study: VennVax Immunizationin 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
100% survival of Vaccinated mice vs. 17% of placebo
0 5 10 15 20 250
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20
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Placebo
Vaccinated
Day Post Immunization
Pe
rce
nt
Su
rviv
al
DNA DNA boost boost Challenge17%
0 20 40 60 80 100
100%
VennVax protects againstlethal vaccinia challenge
Moise L et al. Vaccine. 2011;29:501-11
VennVax Protection: Morbidity
0 5 10 15 2065
70
75
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100
105
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115 VennVax
Placebo
Days Post-Infection
Pe
rce
nt
of
Pre
-Ch
alle
ng
e W
eig
ht
Case Study: VennVax Protection: Antibody Titers
Moise et al. Vaccine. 2011; 29:501-11
VennVax conferred protection without any B cell epitopes
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• 5 prototype vaccines using iVAX with 3 validated in animal models (VennVax, TulyVax, and H.pylori)
• Validation of remaining prototype vaccines (FluVax) currently in progress
Other Vaccine Design Case Studies
gB-2 (EPX Score: -24.56)
- 80 -
- 70 -
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- -20 -
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- -60 -
- -70 -
- -80 -
Thrombopoietin
Human EPO
Tetanus Toxin
Influenza-HA
Albumin
IgG FC Region
EBV-BKRF3
Fibrinogen-Alpha
Follitropin-Beta
HA A/California/07/2009 (H1N1)
HA A/Victoria/361/2011 (H3N2)
HA A/Texas/50/2012 (H3N2)
HA A/Shanghai/1/2013 (H7N9) . . . . . . . .. . . . . . . . -8.11HA A/mallard/Netherlands/09/2005 (H7N7) . . . . . . -8.63
Random Expectation
HA A/mallard/Netherlands/12/2000 (H7N3) .. . . . . .-9.91
HA A/chicken/Italy/13474/1999 (H7N1) . . . . . . . . . -6.23
H7 HAImmunogenic Potential
Immunogenicity of H7N9 HA predicted to be LOWPrevious vaccines poorly immunogenic
H7N9: Prediction of low-immunogenicity
H1N1 (2009)
H7N9 (2013)
T Cell Epitope Content1 HIGH VERY LOW
T Cell Epitope Cross Reactivity2 MEDIUM VERY
LOW
Cross-Reactive Antibody Immunity3 LOW LOW
Predictive protective effect of
vaccination in standard influenza
vaccine
HIGH LOW
IAV T Cell Epitope Responses by CategoryAverage Immune Response N=4 Subjects
In Novartis Phase I trial of H7N9 cell culture vaccine showed only 6% of 400 healthy volunteers achieved a protective response when given two doses of the 15ug un-adjuvanted vaccine
EpiVax predictions
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IVAX makes vaccines:
More Effective: IVAX can be used to design more targeted, immunogenic vaccines or predict the immunogenicity of existing vaccines
Safer: Epitope-driven DNA or Sub-unit vaccines mitigate the risks associated with live, attenuated or VLPs without sacrificing efficacy. Less antigenic load.
Faster: After H7N9 genome was released EpiVax personnel were able to complete a vaccine sequence in less than 48 hours – approx 20 hours total labor.
Accessing the ToolsContact Jason Del Pozzo: [email protected]
Confidential33
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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