iVAX – Quick Facts• Comprehensive set of epitope mapping algorithms• Tools to build immunogenic and effective vaccines• Applications to assay reagent development anddiagnostics• Interactive and user friendly• 24/7 access• On-site training program• Technical support service
4Vaccine 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 AssemblyiVAX Fully integratedFrom genome to vaccine5Seamless Vaccine DesignIntegrated toolkit is unique to iVax
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 immunogenicityMHC II PocketPeptideEpitopeMatureAPCMHCIIT cell epitopes are linear and directlyderived from antigen sequenceBinding is determined by amino acidside chains (R groups) and ‘encoded’in single letter code86/26/2013 Confidential
EpiVax HLA “Supertype” Coverage• EpiVax tests for bindingpotential to the most commonHLA molecules within each of the“supertypes” shown to the left.• This allows us to provide resultsthat are representative of >90% ofhuman populations worldwide*without the necessity of testingeach haplotype individually.9* Southwood et. al., Several Common HLA-DR Types Share LargelyOverlapping Peptide Binding Repertoires. 1998. Journal of Immunology.
EpiMatrixConfidential10•The EpiMatrix algorithm scores all the 9-mers in a givensequence for binding affinity across a range of commonHLA and reports both detailed and aggregated results.•Unlike other tools, there are ancillary algorithms thatenhance the usefulness of the tool for immunogenicityprediction of protein therapeutics and vaccine design.•Does it work?
Epitope IdentificationEpiMatrix is the best available epitope discovery tool11De Groot and Martin. Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics.Clinical Immunology 2009. 131, 189-201.Confidential
Easy easy to deliver as peptidesClustiMerDRB1*0101DRB1*0301DRB1*0401DRB1*0701DRB1*0801DRB1*1101DRB1*1301DRB1*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 anunusually large number of HLA alleles.• T-cell epitope clusters make excellent vaccine candidates:– compact; relatively easy to deliver as peptides; highly reactive in-vivo126/26/2013 Confidential
13Identifying the most conserved 9-mers allows for protectionagainst more strains with fewer epitopesConservatrix Finds Conserved 9-mersConservedepitopeCTRPNNTRKCTRPNNTRKCTRPNNTRKCTRPNNTRKCTRPNNTRKCTRPNNTRKCTRPNNTRK
14BlastiMer: Epitope ExclusionConfidentialIn all of our vaccines we eliminate cross-reactive epitopesSelfForeign
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 LxF W A K H M W N FW P K V E Q F W AQ A S W P K V E Q N F I S G I Q Y LM W N F I S G I QQ A S W P K V E Q F W A K H M W N F I S G I Q Y LEpiAssembler ProducesImmunogenic Consensus Sequences
VaccineCADVaxCAD will identify junctional epitopes and rearrange chosen epitopes to reducejunctional epitope formation
17-1001020304050HP4117HP4179HP4007HP4111HP4018HP4070HP4034HP4193HP4065HP4181HP4157HP4060HP4068HP4164HP4160HP4175HP4127HP4120HP4126HP4154HP4168HP4119HP4100HP4001HP4061EpiMatrixClusterScorePeptides in Default order in construct HP_IIBEpitope Cluster ScoreJunctional Cluster Score-1001020304050HP4117HP4061HP4181HP4111HP4018HP4070HP4060HP4157HP4065HP4001HP4193HP4034HP4068HP4168HP4160HP4175HP4127HP4126HP4007HP4154HP4164HP4119HP4100HP4120HP4179EpiMatrixClusterScore Peptides in Optimized order in construct HP_IIBEpitope Cluster ScoreJunctional Cluster ScoreVaccineCADVaccineCAD Eliminates Introduced Junctional Epitopes
18DNAVectorDNA insertIntended Protein Product: Many epitopes strung together in a “String-of-Beads”Proteinproduct(folded)Multi-Epitope Gene Design
DNA – chain of epitopes, orpeptide in liposomesICS-optimized proteins in VLPICS-optimized whole proteinsMultiple Delivery Platforms Possible
ImmunogenicityDay 561. epitope DNA vaccine prime (IM)2. epitope peptide boost (IN)ImmunizationsDays 0, 14, 28, 42ChallengeDay 65Case Study: VennVax Immunizationin HLA DR3 Transgenic MiceMoise 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: Survival0%20%40%60%80%100%0 2 4 6 8 10 12 14 16 18SurvivalDays Post-InfectionVennVaxPlaceboMoise et al. Vaccine. 2011; 29:501-11100% protection VS Placebo
MHCTCRiVAX Feature Under Development:JanusMatrixJanusMatrix is designed to predict thepotential for cross reactivity between epitopeclusters and the human genome, based onconservation of TCR-facing residues in theirputative HLA ligands.
Accessing the ToolsContact Jason Del Pozzo: firstname.lastname@example.orgConfidential24PreDeFT: Fee for service in silico immunogenicity analysis. Performed on a proteinby protein basis. Pricing based on length of sequence(s).Limited ISPRI Website: Limited access to EpiVax’ Interactive Protein Screening andReengineering Interface. Available for set numbers of proteins.Unlimited ISPRI Website: Unlimited access to EpiVax’ Interactive Protein Screeningand Reengineering Interface. Available in three year lease periods.Fee for Service: HLA Binding Assays, HLA Transgenic Mice, ELISpot Assays.24