EpiVax_ISPRI_Overview_2013

2,629 views

Published on

EpiVax Non-Confidential Overview of our ISPRI system.

ISPRI is used my R&D scientists to screen protein sequences for their potential immunogenicity. Our OptMatrix add-on can Deimmunize sequences in real-time.

www.epivax.com

Published in: Health & Medicine, Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
2,629
On SlideShare
0
From Embeds
0
Number of Embeds
2,082
Actions
Shares
0
Downloads
9
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

EpiVax_ISPRI_Overview_2013

  1. 1. EpiVax ISPRI Overview20131Confidential
  2. 2. EpiMatrixEpitope Discovery Technology2Confidential
  3. 3. ACDEFGHIKLMNPQRSTVWY1 2 3 4 5 6 7 8 9 10-3.00-2.75-2.50-2.25-2.00-1.75-1.50-1.25-1.00-0.75-0.50-0.250.000.250.500.751.001.251.501.752.00aphical representation of A*0201 motif (based on list of actual peptidesfrom Chicz)1.75-2.001.50-1.751.25-1.501.00-1.250.75-1.000.50-0.750.25-0.500.00-0.25-0. 25-0. 00-0. 50--0.25-0. 75--0.50-1. 00--0.75-1. 25--1.00-1. 50--1.25-1. 75--1.50-2. 00--1.75-2. 25--2.00-2. 50--2.25-2. 75--2.50-3. 00--2.75PositionAminoAcidEpitope MappingEpiMatrix3+ + + + + + + +Graphical Representation of A*0201 Coefficient matrix= indication of binding likelihoodBinding motifsRejected residuesConfidential
  4. 4. 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.4* Southwood et. al., Several Common HLA-DR Types Share LargelyOverlapping Peptide Binding Repertoires. 1998. Journal of Immunology.
  5. 5. Epitope MappingEpiMatrix5De Groot and Martin. Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics.Clinical Immunology 2009. 131, 189-201.Confidential
  6. 6. Tregitope TechnologyA Brief Overview6Confidential
  7. 7. What is a Tregitope?Tregitope 289Tregitope 134Tregitope 09Tregitope 29Tregitope 54Tregitope167Tregitopes - highly conserved T reg epitopesIn Fc and Fab (framework)Are promiscuous (multiple HLA binders)Are present in IgG, not IgA, IgE, IgMMay be present in other self proteins.Confidential7De Groot A.S., et al., Activation of Natural Regulatory T cells by IgG Fc-derived Peptide“Tregitopes”. Blood, 2008,112: 3303. http://tinyurl. com/ASDeGroot-Blood-2008
  8. 8. Tregitope Collaborators8ConfidentialBrigham andWomen’s HospitalChildren’s Hospital ofPhiladelphiaU. Maryland/Uniformed ServicesU. Health SciencesMcGill University/Montreal Children’sHospitalTransplant CD8-Mediated Anti-Gene TherapyResponsesT1D, FVIII, Allergy AllergyNader Najafian Federico MingozziDaniel HuiKatherine HighDavid ScottYan SuXin LiAchsah KeeganPreeta DesguptaBruce Mazer
  9. 9. What is the proof? Step by step . . .(4) Bystander Suppression(2) nTreg induction(3) IL-10 secretion(5) Modulate APC (4) Induction of iTregsWhat is the Evidence?Confidential9(1) Binding
  10. 10. ISPRIProtein Immunogenicity Scale [Tregitope-Adjusted]10EpiMatrix Predicted Excess/Shortfall inAggregate Immunogenicity Relative to aRandom Peptide StandardAll scores are adjusted for the presenceof Tregitopes.*Average of Antibodies Known to InduceAnti-Therapeutic Responses in MoreThan 5% of Patients†Average of Antibodies Known to InduceAnti-Therapeutic Responses in LessThan 5% of Patients- 80 -- 70 -- 60 -- 50 -- 40 -- 30 -- 20 -- 10 -- 00 -- -10 -- -20 -- -30 -- -40 -- -50 -- -60 -- -70 -- -80 -ThrombopoietinHuman EPOImmunogenic Antibodies*Tetanus ToxinInfluenza-HAAlbuminIgG FC RegionEBV-BKRF3Non-immunogenic Antibodies†Follitropin-BetaYour ProteinConfidential
  11. 11. ISPRIInteractive Protein Screening andReengineering Interface11Confidential
  12. 12. ISPRIInteractive Protein Screening and Reengineering Interface• EpiVax has developed a secure, interactive work environment that isseamlessly linked to EpiVax’s proprietary in silico immunogenicity screeningtoolkit.• This interactive biologics screening and optimizing work environment givesaccess to the same in silico tools used by the EpiVax bioinformatics team.• ISPRI can be used for high throughput unlimited screening of partial andcomplete sequences of biological (protein therapeutic) candidates.• The toolkit can be used to identify within each protein sequence potentiallyimmunogenic regions (known as epitope clusters) and to fine map thoseindividual amino acids which contribute most to the immunogenic potentialof the cluster.• The output is customized to best fit the needs and preferences of theclient.12Confidential
  13. 13. ISPRIAvailable Tools13• EpiMatrix– Screen the protein sequences of product candidates for the presence of putative T cell epitopes.• Immunogenicity Protein Scale– Rate the immunogenic potential of each submitted sequence on a normalized scale and compareeach protein to other immunogenic proteins and antibodies• Tregitope Analysis– Identify within each submitted sequence putative regulatory T-cell epitopes (i.e. sub-regionscontained within the submitted sequences which may relate to natural regulatory T cells and whichmay help to dampen the immune potential of the submitted antibody sequence)• ClustiMer– Identify T-cell epitope clusters contained within product candidates• Immunogenic Cluster Scale– Rate the immunogenic potential of each T-cell epitope cluster on a normalized scale and compareeach T-cell epitope cluster to other well-known immunogenic epitope clusters• BlastiMer– Blast T-cell epitope clusters against the non-redundant protein or patent database at GenBank• OptiMatrix– The protein re-design algorithm that provides a list of critical amino acid residues and potentialamino acid substitutions that are conserved in existing databases (based on published sequences)and that do not introduce new epitopes.Confidential
  14. 14. EpiVax Immunogenicity Hypothesis As Applied:Immune Response = Sum of EpitopesT cell response depends on:T cell epitope content + HLA of subjectProtein Immunogenicity can be RankedepitopeProtein Therapeutic1 + 1 + 1 = Responseepitopeepitope•De Groot A.S. and L. Moise. Prediction of immunogenicity for therapeutic proteins: State of the art. CurrentOpinions in Drug Development and Discovery. May 2007. 10(3):332-40.Approach – Whole Antigens
  15. 15. ISPRIProtein Immunogenicity Scale15EpiMatrix Predicted Excess/Shortfall inAggregate Immunogenicity Relative to aRandom Peptide StandardAll scores are adjusted for the presenceof Tregitopes.*Average of Antibodies Known to InduceAnti-Therapeutic Responses in MoreThan 5% of Patients†Average of Antibodies Known to InduceAnti-Therapeutic Responses in LessThan 5% of Patients- 80 -- 70 -- 60 -- 50 -- 40 -- 30 -- 20 -- 10 -- 00 -- -10 -- -20 -- -30 -- -40 -- -50 -- -60 -- -70 -- -80 -ThrombopoietinHuman EPOImmunogenic Antibodies*Tetanus ToxinInfluenza-HAAlbuminIgG FC RegionEBV-BKRF3Non-immunogenic Antibodies†Follitropin-BetaYour ProteinConfidential
  16. 16. ISPRIEpiMatrix Protein Report16Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501Start Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score1 DIQMTQSPS 9 0.91 0.17 0.35 0.06 0.09 0.86 -0.08 -0.01 02 IQMTQSPSS 10 2.15 1.35 2.26 1.58 2.17 1.88 2.24 2.52 63 QMTQSPSSL 11 1.11 0.28 0.5 0.96 0.29 0.39 0.9 0.4 04 MTQSPSSLS 12 1.87 2.26 2.02 1.88 1.06 1.66 1.79 2.05 75 TQSPSSLSA 13 0.51 0.28 1.31 0.69 -0.04 0.54 1.09 1.05 0. . . . . . . . . . . .. . . . . . . . . . . .46 LLIYAASTL 54 1.41 1.08 0.99 2.16 1.54 0.85 2.28 2.3 347 LIYFASTLQ 55 1.91 1.85 2.46 2.07 1.79 1.08 1.79 2.1 748 IYFASTLQS 56 1.73 2.01 2.68 1.26 1.58 1.82 2.11 2.07 649 YFASTLQSG 57 0.64 1.6 0.59 0.32 1.42 1.28 0.04 1.09 0. . . . . . . . . . . .. . . . . . . . . . . .98 FGQGKTVEI 106 0.7 1.9 -0.02 0.2 0.93 0.34 1.41 1.12 199 GQGKTVEIK 107 -0.28 -0.84 0.31 0.01 0.03 -0.57 -0.47 -1.24 0DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 Total2.4 2.26 2.8 3.11 2.41 2.29 2.28 2.52 --23.41 12.17 15.96 18.16 10.2 13.2 16.47 16.99 126.5612 6 7 9 5 7 8 8 62Deviation from Expectation: 38.46 Deviation per 1000 AA: 48.56Adjusted for Regulatory Epitopes Deviation from Expectation: -21.24 Deviation per 1000 AA: -26.82Total Assessments Performed: 792EpiMatrix ReportAccession: YOUR_PROTEIN - Sequence: YOUR_PROTEINMaximum Single Z scoreSum of Significant Z scoresCount of Significant Z ScoresAA Sequence HitsSummarized ResultsAssessmentHitEpiBarEpiMatrix Immunogenicity ScoreEpiMatrix Tregitope-adjusted ScoreConfidential
  17. 17. 17Correlation of antibody immunogenicity withoutTregitope adjusted EPX ScoresCorrelation to observed Immunogenicity before accounting for TregitopesR2=0.17
  18. 18. Factoring in Tregitopes. . .T cell response depends on:T cell epitope content – Tregitope content + HLA of subjectProtein Immunogenicity can be RankedepitopeProtein Therapeutic1 + 1 - Regulatory T cell epitope* = ResponseepitopeepitopeImmunogenicity Scale for Monoclonals183/6/2013 Confidential
  19. 19. 19Correlation of antibody immunogenicity withTregitope adjusted EPX ScoresAccounting for Tregitopes results in more accurate predictions.Correlation to observed immunogenicity after accounting for TregitopesR2=0.76
  20. 20. Antibodies: A Special Case- 80 -- 70 -- 60 -- 50 -- 40 -- 30 -- 20 -- 10 -- 00 -- -10 -- -20 -- -30 -- -40 -- -50 -- -60 -- -70 -- -80 -IgG FC RegionNuvion (0%)Avastin (0%)AB01 (EPX Adjusted Score: -46.98)AB02 (EPX Adjusted Score: -44.48)AB03 (EPX Adjusted Score: -44.81)AB04 (EPX Adjusted Score: -45.81)AB05 (EPX Adjusted Score: -45.88)AB06 (EPX Adjusted Score: -47.85)AB07 (EPX Adjusted Score: -46.99)AB08 (EPX Adjusted Score: -46.30)AB09 (EPX Adjusted Score: -47.40)AB10 (EPX Adjusted Score: -45.88)AB11 (EPX Adjusted Score: -47.40)Synagis (1%)Simulect (1.4%)Humira (12%)Bivatuzumab (6.7%)Remicade (26%)Rituxan (27%)Campath (45%)Humicade (7%)Reopro (5.8%)Tysabri (7%)LeukArrest (0%)Herceptin (0.1%)New drug203/6/2013 ConfidentialDue to the presence of Tregitopes, antibodies tend to fall loweron the immunogenicity scale.We have developed a refined method using regressionanalysis to predict the immunogenicity of antibody sequencesbased on observed clinical responses.We have found that a balance in favor of Tregitope (regulatory)content over neo-epitope (effector) content is correlated withreduced clinical immunogenicity.NeoEpitopeContentTregitope ContentHigh LowLowAvastin (0%)Herceptin (0%)Mylotarg (3%)Simulect (1%)Synagis (1%)HighCampath (45%)Remicade (26%)Rituxan (27%)
  21. 21. ISPRIClustiMer identifies local immunogenic potential21DRB1*0101DRB1*0301DRB1*0401DRB1*0701DRB1*0801DRB1*1101DRB1*1301DRB1*1501• T cell epitopes are not randomly distributed throughout protein sequences but instead tendto cluster in specific regions.• ClustiMer is used to identify T-cell epitope clusters. It identifies polypeptides predicted tobind 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• These clusters can be very powerful. One or more dominant T-cell epitope clusters canenable significant immune responses to even otherwise low scoring proteins.Confidential
  22. 22. ISPRICluster Immunogenicity Scale22EpiMatrix Predicted Excess/Shortfall inAggregate Immunogenicity Relative to aRandom Peptide StandardTetanus Toxin (825-850)NPC NS3 (1248-1267)Influenza-HA (306-319)P. Falciparum (72-86)Human CLIPP. Falciparum (512-526)Theoretical Minimum- 40 -- -- 30 -- -- 20 -- -- 10 -- -- 00 -- -- -10 -NAME ADDRESS SCOREYOUR_PROTEIN1 318-341 31.14YOUR_PROTEIN1 206-225 17.76YOUR_PROTEIN1 159-176 13.81YOUR_PROTEIN1 055-070 13.62YOUR_PROTEIN1 293-314 10.61Confidential
  23. 23. DRAFT23The Humira heavy chain contains relatively fewneo-epitopes and a significant number of knownTregitopes.The Humira light chain contains few neo-epitopesand a significant number of known Tregitopes.Tregitope adjusted scores of the submittedsequences rate against the same series ofstandard controls.Indicates a drop in significantpotential for immunogenicityHumira – Overall Protein ImmunogenicityTregitope Adjusted Protein ScoresHUMIRA_VHHUMIRA_VL
  24. 24. DRAFT24Humira – T Cell Epitope ClustersRegional Immunogenicity MattersOther clusters, when Tregitope adjusted –may cause proliferation but phenotype ofproliferating cells should be evaluated . . .Could be TregitopesTwo epitopes with high EMX scores areexpected to contribute to immunogenicity . . .HUMIRA_VH 033-048 -01.65Tetanus Toxin (825-850)HCV NS3 (1248-1267)Influenza-HA (306-319)Human CLIPTheoretical Minimum- 40 -- -- 30 -- -- 20 -- -- 10 -- -- 00 -- -- -10 -NAME ADDRESS SCORETetanus Toxin (586-605)HUMIRA_VH 076-094 -00.45HUMIRA_VH 091-113 33.92HUMIRA_VL 043-065 29.62HUMIRA_VH 008-031 01.32HUMIRA_VL 001-015 -02.47HUMIRA_VL 068-086 01.48HUMIRA_VH 065-081 01.69
  25. 25. 25BlastiMerBLAST helps to find viable substitutionsConfidential• BLAST functions:– Submit T cell epitope clusters to NCBI GenBank BLAST• Compare to Non-redundant DatabasePatent DatabaseHuman Sequence Database• View Summary or detailed Alignment Reports
  26. 26. 26BlastiMerBLAST helps to find human-like sequencesConfidential
  27. 27. OptiMatrixInteractive Peptide DeimmunizationConfidential27Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501Start Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score254 PRGYFKIRT 262 -0.23 0255 RGYFKIRTG 263 -0.2 0256 GYFKIRTGK 264 -0.19 0257 YFKIRTGKT 265 -0.9 2.38 2.41 2.51 1.4 2.2 1.98 5258 FKIRTGKTT 266 -0.83 2.41 2.13 1.69 1.32 1.53 3259 KIRTGKTTI 267 -0.14 1.44 0260 IRTGKTTIM 268 0 1.97 1.42 1.48 1261 RTGKTTIMR 269 -0.21 1.33 0DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 Total2.41 1.97 2.41 2.51 1.69 2.2 1.48 1.98 --4.79 1.97 2.41 4.64 1.69 2.2 0 1.98 19.682 1 1 2 1 1 0 1 9Scores Adjusted for Tregitope: -- EpiMatrix Score: 13.08 EpiMatrix Score (w/o flanks): 16.05Sum of Significant Z scoresCount of Significant Z ScoresTotal Assessments Performed: 64 Hydrophobicity: -0.84 EpiMatrix Score: 13.08 EpiMatrix Score (w/o flanks): 16.05AA SequenceHydro-phobicityHitsSummarized Results (25-SEP-2009)Maximum Single Z scoreOptiMatrix:
  28. 28. OptiMatrixSee the effects of amino acid substitution in real-timeConfidential28OptiMatrix:Click multiple times to continue deimmunizing
  29. 29. ISPRI SummaryConfidential29Benefits of in-silico immunogenicity screening using theISPRI website include• Streamlined and efficient pipeline development• Decreased in vitro and in vivo costs• Improved return on R&D• Support for IND and other regulatory filings
  30. 30. 30CIO/DIRECTOR OF BIOINFORMATICS Bill Martinmartinb@epivax.comBIOINFORMATICS PROGRAM MANAGER Frances Terryfterry@epivax.comBIOINFORMATICS PROGRAMMER/ANALYST Jacob Tivinjtivin@epivax.comISPRI ContactsBDA – SALES INQUIRES Anthony Marcelloamarcello@epivax.com

×