EpiVax_ISPIR_VS_IEDB_comparison_Immunogenicity_of_protein_drugs_Mar2014

EpiVax vs. IEDB A Comparison

I M M U N E E P I TO P E D ATA B A S E A N D A N A LY S I S R E S O U R C E

EpiVax Management Team www.epivax.com/about/management-team/

2

In Vivo In Vitro In Silico

Modify sequences to reduce

immunogenicity

Screen multiple therapeutic candidates

Human SCID

Mouse Model

HLA Transgenic

Mouse Model

Either

Examine:

• Non-sequence-

driven

immunogenicity

• Natural antigen

processing and

by DCs

• Peptide/MHC

stability

• T cell activation

thresholds

• Post-

translational

modification

• Formulation-

induced changes

Perform HLA Binding and T Cell

Assays with proteins /

target epitopes

Rank for immunogenicity

based on predicted

epitope content

Proceed to Drug

Development

Investigate artificial LN

Vary Ratio of T cells to dendritic

cells

Test PBMC Responses

The EpiVax Approach to Immunogenicity Screening

From: http://bit.ly/The_TCWP - T cell “White Paper”

http://bit.ly/The_TCWP

ISPRI is an integrated, interactive set of tools

specifically designed for immunogenicity

analysis. ISPRI provides the depth of analysis

that is necessary to accurately predict clinical

immunogenicity

ISPRI vs. IEDB in silico services

Epitope Mapping

Cluster Analysis

ARB

NN-align

SMM align

Protein Re-engineering

Epitope Ranking

Epitope Mapping

EpiMatrix

ClustiMer /EpiBar

OptiMatrix

iTEM

Immunogenicity Scale

DeFT (OptiMatrix)

In Vitro / In vivo Assays

JanusMatrix

JMX-Adjusted Score

Target Selection

Tregitope Tolerization

IEDB is a collection of tools that are not integrated in any

coherent fashion. Epitope prediction is possible, but

seamless immunogenicity screening and protein re-

engineering is not.

ISPRI: Developed for Biologics Available Tools

4

• 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 compare

each protein to other immunogenic proteins and antibodies

• Tregitope Analysis – Identify within each submitted sequence putative regulatory T-cell epitopes (i.e. sub-regions

contained within the submitted sequences which may relate to natural regulatory T cells and which

may help to dampen the immune potential of the submitted antibody sequence)

• ClustiMer / EpiBar – 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 compare

each T-cell epitope cluster to other well-known immunogenic epitope clusters

• BlastiMer / JanusMatrix – Blast: Compare epitope clusters against the non-redundant protein or patent database at GenBank

– Homology: Compare epitopes to human genome epitopes that have the same TCR face.

• OptiMatrix – The protein re-design algorithm that provides a list of critical amino acid residues and potential

amino acid substitutions that are conserved in existing databases (based on published seque-

nces) and that do not introduce new epitopes.

EpiVax vs. IEDB

5

Features EpiVax IEDB

Highly Accurate Epitope Prediction 1

Cluster Tool / EpiBar 2

Immunogenicity Scale * X

iTEM Analysis * X

Tregitope Predictions * X

Deimmunization tools X

Human Genome Comparison X

High-Throughput Analysis X

Published Validation 3

Expert Consulting Services X

* These features were developed and validated by, and are only available at, EpiVax.

1 Head to head comparison favors EpiMatrix: see De Groot and Martin, Clinical Immunology, 2009. http://bit.ly/De_Groot_and_Martin

2 IEDB Cluster tool is available, but untested; for EpiVax validation, see “T cell epitope, Friend or Foe” http://bit.ly/T-friend-or-foe

3 Extent of IEDB validation is unknown (positive results may be published, but negative results are not tracked).

http://bit.ly/De_Groot_and_Martin

http://bit.ly/De_Groot_and_Martin

http://bit.ly/T-friend-or-foe







Epitope Predictions


Epitope Predictions EpiVax

7

•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

–Full suite of HLA-based predictions are available; Class II usually used for biologics.

–Separate website available for vaccine design: iVAX

–http://www.epivax.com/vaccine-design-redesign/ivax-web-based-vaccine-design/

Mature

APC

MHC II Pocket

Epitope

Protein

http://www.epivax.com/vaccine-design-redesign/ivax-web-based-vaccine-design/













Epitope Predictions EpiMatrix [Class II] vs. IEDB

De Groot AS, Martin W. Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics. Clin Immunol. 2009 May;131(2):189-201

Comparison Data Taken From:

Wang P, Sidney J, Dow C, Mothé B, Sette A, et al. (2008) A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a

Consensus Approach. PLoS Comput Biol 4(4): e1000048. Doi:10.1371/journal.pcbi.1000048

8

Perfect =100% Random = 50%

On average, EpiMatrix predicts T cell epitopes more accurately than IEDB.

IMMUNE EPITOPE DATABASE

AND ANALYSIS RESOURCE

Cluster Tools


10

Cluster Tools EpiVax - ClustiMer

DRB1*0101

DRB1*0301

DRB1*0401

DRB1*0701

DRB1*0801

DRB1*1101

DRB1*1301

DRB1*1501

• T cell epitopes are not randomly distributed throughout protein sequences but instead tend to cluster in specific regions.

– These clusters can be very powerful. One or more dominant T-cell epitope clusters can enable significant immune responses to even otherwise low scoring proteins.

• ClustiMer is used to identify T-cell epitope clusters. It identifies 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

Cluster Analysis IEDB

11

This tool groups epitopes into clusters based on sequence identity. A cluster is defined as a

group of sequences which have a sequence similarity greater than the minimum

sequence identity threshold specified by the user. This is a different definition than the one

used by ClustiMer, and so it will yield different results.

Example Results:

IEDB Epitope Cluster Analysis is untested and also does not yield a

detailed report like ClustiMer, only a simple identification of clusters.



Immunogenicity Scales


Immunogenicity Scales EpiVax

13

- 80 -

- 70 -

- 60 -

- 50 -

- 40 -

- 30 -

- 20 -

- 10 -

- 00 -

- -10 -

- -20 -

- -30 -

- -40 -

- -50 -

- -60 -

- -70 -

- -80 -

Thrombopoietin

Erythropoietin

IgA

Fibrinogen-Gamma

Albumin

IgG FC Region

GMCSF

Follitropin-Beta

Fibrinogen-Alpha

Beta-2-Microglobulin

Interferon-Beta

GHRH

Tetanus Toxin

Influenza-HA

Tetanus Toxin (825-850)

HCV NPC NS3 (1248-1267)

Influenza HA (306-319)

Tetanus Toxin (947-967)

Human CLIP

EBV BHRF1(171-189)

20-mer Theoretical Minimum

- +40 -

- -

- +30 -

- -

- +20 -

- -

- +10 -

- -

- 0.0 -

- -

- -10 -

Your Protein Here

Your Peptide or

Cluster Here

EpiVax has developed an immunogenicity scale to compare predicted immunogenicity across

whole proteins, clusters and antibodies. This allows for easy comparison between different

sequences of different lengths and to known compounds.

Immunogenicity Scales IEDB

14

No Immunogenicity Scales are available on IEDB.



iTEM Analysis


• iTEM uses HLA-specific EpiMatrix scores to

measure potential for response to peptide antigen

Can be used to predict which patients (with which

HLA) will develop an antibody response in a

clinical trial…

. . . Immunopharmacogenomics

iTEM Analysis EpiVax

Individualized T cell Epitope Measure

16

A Method for Individualizing the Prediction

of Immunogenicity of Protein Vaccines and

Biologic Therapeutics: Individualized T Cell

Epitope Measure (iTEM), Apr 2010

http://www.hindawi.com/journals/bmri/2010/961752/abs/






iTEM Analysis IEDB

17

No such analysis is available on IEDB.



Tregitope Predictions


Epitope can be either

effector or regulatory

Presence of Epitope Indicates Immune Potential

Mature

APC

T reg T eff

19

Accounting for Tregitopes results in more accurate predictions.

Correlation to observed immunogenicity after accounting for Tregitopes

R2=0.76

Tregitope Predictions EpiVax

20

EpiVax discovered and patented sequences called Tregitopes, promiscuous T cell epitopes that

have been shown to activate regulatory T cells. In the EpiVax immunogenicity analysis the

presence of a Tregitope decreases the potential for immunogenicity.

The inclusion of Tregitopes in predictions is particularly crucial in comparing antibodies, which often contain Tregitope sequences.

Tregitope Predictions IEDB

21

In IEDB and other tools, the effect of Tregitopes are not taken into account.

Instead they will show up as effector epitopes, erroneously increasing the

predicted immunogenicity.



DeImmunization


DeImmunization EpiVax - OptiMatrix

23

Select a different amino acid and see its effect immediately

EpiVax’s OptiMatrix tool allows the user to:

• Decrease potential immunogenicity of T cell epitopes by weakening “agretope” (interface with

HLA molecule)

• identify and iteratively modify key AA residues

• OptiMatrix provides a logo report which shows the contribution of each amino acid to overall

immunogenicity of the peptide

• Change any amino acid and see its affect on immunogenicity in real time

• “Best Single Change” function auto calculated the AA modification that results in the most

drastic decrease in predicted immunogenicity

http://bit.ly/EpiDeFT



OptiMatrix Interactive Peptide Deimmunization

24

Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501

Start Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score

254 PRGYFKIRT 262 -0.23 0

255 RGYFKIRTG 263 -0.2 0

256 GYFKIRTGK 264 -0.19 0

257 YFKIRTGKT 265 -0.9 2.38 2.41 2.51 1.4 2.2 1.98 5

258 FKIRTGKTT 266 -0.83 2.41 2.13 1.69 1.32 1.53 3

259 KIRTGKTTI 267 -0.14 1.44 0

260 IRTGKTTIM 268 0 1.97 1.42 1.48 1

261 RTGKTTIMR 269 -0.21 1.33 0

DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 Total

2.41 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 19.68

2 1 1 2 1 1 0 1 9

Scores Adjusted for Tregitope: -- EpiMatrix Score: 13.08 EpiMatrix Score (w/o flanks): 16.05

Sum of Significant Z scores

Count of Significant Z Scores

Total Assessments Performed: 64 Hydrophobicity: -0.84 EpiMatrix Score: 13.08 EpiMatrix Score (w/o flanks): 16.05

AA SequenceHydro-

phobicityHits

Summarized Results (25-SEP-2009)

Maximum Single Z score

OptiMatrix:

24 http://bit.ly/EpiDeFT



OptiMatrix See the effects of amino acid substitution in real-time

Confidential 25

OptiMatrix:

Click multiple times to continue deimmunizing

25 http://bit.ly/EpiDeFT



DeImmunization IEDB

26

No such tool is available on IEDB.



High Throughput Analysis


28

High Throughput Analysis EpiVax

The High-Throughput analysis allows users to compare a large number potential

antibody candidates by ranking the immunogenicity of heavy and light chains.

http://www.epivax.com/immunogenicity-screening/ht_report/





High Throughput Analysis IEDB

29




Human Genome Comparison

30


Human Genome Comparison EpiVax - JanusMatrix

Each MHC ligand has two faces,

The MHC-binding face (agretope),

and the TCR-interacting face (epitope)

TCR

MHC

The JanusMatrix algorithm searches for putative MHC

ligands which are identical at the contact residues but

may vary at the MHC-binding residues.

• Identical T cell-facing residues

• Same HLA allele and minimally

different MHC-facing residues

Find predicted 9-mer ligands with:

http://www.ncbi.nlm.nih.gov/pubmed/23584251 MHC/HLA

TCR

http://www.ncbi.nlm.nih.gov/pubmed/23584251

Human Genome Comparison IEDB

32




Expert Consulting Services


Expert Consulting Services EpiVax

34

Algorithms only go so far in immunogenicity prediction – immunoinformatics

expertise is the greatest tool contained in the ISPRI system. We have worked with

the ISPRI tools since 1998 and can help interpret the data for your team.

Annie De Groot, MD (CEO) William Martin (CIO)

http://www.epivax.com/about/epivax-team/





In Silico Immunogenicity

Screening Services

35

ISPRI Website: Cloud-based Interactive Protein Screening and Reengineering

Interface, leased to large pharma world-wide. Your scientists use ISPRI to predict

overall and regional immunogenicity. Available for annual lease for a set number of

protein sequences (Limited) or Unlimited Sequences. Includes continued

consultation and training with experts at EpiVax. http://bit.ly/ISPRI

PreDeFT: Highly detailed in silico immunogenicity analysis covering overall and

regional immunogenic potential of a protein therapeutic. Delivered as a “FDA

ready” report. EpiVax “Genius Team” uses ISPRI for you. http://bit.ly/PreDeFT

HT Screening: High-throughput immunogenicity screening of large sets of

antibody heavy-light chain combinations, for overall and comparative immunogenic

potential. http://bit.ly/PreDeFTht

DeFT: (Deimmunization of a Functional Therapeutic) is a tested process of

analysis, reengineering and confirmation. http://bit.ly/EpiDeFT

Sales contacts: [email protected] (US/other) or [email protected] (EUR)

http://bit.ly/ISPRI

http://bit.ly/ISPRI

http://bit.ly/ISPRI

http://bit.ly/ISPRI

http://bit.ly/ISPRI

http://bit.ly/ISPRI

http://bit.ly/PreDeFT






http://bit.ly/PreDeFTht












mailto:[email protected]

mailto:[email protected]

Expert Consulting Services IEDB

36

No expert consulting services are available through IEDB.



Published Validation

37


ISPRI Validation in Print (A Sample)

38

Koren E, De Groot AS, Jawa V, Beck KD, Boone T, Rivera D, Li L, Mytych D,

Koscec M, Weeraratne D, Swanson S, Martin W. Clinical validation of the “in

silico” prediction of immunogenicity of a human recombinant therapeutic protein

Clin Immunol. 2007 Jul. http://bit.ly/epiClinVal

De Groot AS, Martin W. Reducing risk, improving outcomes: bioengineering less

immunogenic protein therapeutics. Clin Immunol. 2009 May;131(2):189-201.

http://bit.ly/epiClinIm

Jawa, V., Cousens, L., & De Groot, A. S. (2013). Immunogenicity of Therapeutic

Fusion proteins: Contributory Factors and Clinical Experience. Fusion Protein

Technologies for Biopharmaceuticals: Applications and Challenges, 75-90.

http://bit.ly/epiFcFuse

Jawa V, Cousens LP, Awwad M, Wakshull E, Kropshofer H, De Groot AS. T-cell

dependent immunogenicity of protein therapeutics: Preclinical assessment and

mitigation http://bit.ly/The_TCWP

http://bit.ly/epiClinVal

http://bit.ly/epiClinVal

http://bit.ly/epiClinIm





http://epivax.us1.list-manage1.com/track/click?u=6a5a073ce56e8c2a19963e003&id=71bf827c8b&e=c72dadeb9a

39

1: De Groot AS, Ardito M, Terry F, Levitz L, Ross T, Moise L, Martin W. Low immunogenicity predicted for emerging avian-origin H7N9: implication for influenza vaccine design. Hum Vaccin Immunother. 2013 May;9(5):950-6. doi: 10.4161/hv.24939. Epub

2013 May 1. PubMed PMID: 23807079; PubMed Central PMCID: PMC3899161.

2: Cousens LP, Tassone R, Mazer BD, Ramachandiran V, Scott DW, De Groot AS. Tregitope update: mechanism of action parallels IVIg. Autoimmun Rev. 2013 Jan;12(3):436-43. doi: 10.1016/j.autrev.2012.08.017. Epub 2012 Aug 28. Review. PubMed

PMID: 22944299.

3: De Groot AS, Cousens L, Mingozzi F, Martin W. Tregitope peptides: the active pharmaceutical ingredient of IVIG? Clin Dev Immunol. 2013;2013:493138. doi: 10.1155/2013/493138. Epub 2013 Dec 25. PubMed PMID: 24454476; PubMed Central

PMCID: PMC3886585.

4: Cou5sens LP, Najafian N, Mingozzi F, Elyaman W, Mazer B, Moise L, Messitt TJ, Su Y, Sayegh M, High K, Khoury SJ, Scott DW, De Groot AS. In vitro and in vivo studies of IgG-derived Treg epitopes (Tregitopes): a promising new tool for tolerance

induction and treatment of autoimmunity. J Clin Immunol. 2013 Jan;33 Suppl 1:S43-9. doi: 10.1007/s10875-012-9762-4. Epub 2012 Sep 2. Review. PubMed PMID: 22941509; PubMed Central PMCID: PMC3538121.

5: Jawa V, Cousens LP, Awwad M, Wakshull E, Kropshofer H, De Groot AS. T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation. Clin Immunol. 2013 Dec;149(3):534-55. doi:

10.1016/j.clim.2013.09.006. Epub 2013 Sep 25. Review. PubMed PMID: 24263283.

6: De Groot AS, Terry F, Cousens L, Martin W. Beyond humanization and de-immunization: tolerization as a method for reducing the immunogenicity of biologics. Expert Rev Clin Pharmacol. 2013 Nov;6(6):651-62. doi:

10.1586/17512433.2013.835698. PubMed PMID: 24164613.

7: Hui DJ, Basner-Tschakarjan E, Chen Y, Davidson RJ, Buchlis G, Yazicioglu M, Pien GC, Finn JD, Haurigot V, Tai A, Scott DW, Cousens LP, Zhou S, De Groot AS, Mingozzi F. Modulation of CD8+ T cell responses to AAV vectors with IgG-derived MHC class

II epitopes. Mol Ther. 2013 Sep;21(9):1727-37. doi:

8.1038/mt.2013.166. Epub 2013 Jul 16. PubMed PMID: 23857231. 4: Su Y, Rossi R, De Groot AS, Scott DW . Regulatory T cell epitopes (Tregitopes) in IgG induce tolerance in vivo and lack immunogenicity per se. J Leukoc Biol.

2013 Aug;94(2):377-83. doi: 10.1189/jlb.0912441. Epub 2013 May 31. PubMed PMID: 23729499.

9: Moise L, Gutierrez AH, Bailey-Kellogg C, Terry F, Leng Q, Abdel Hady KM, VerBerkmoes NC, Sztein MB, Losikoff PT, Martin WD, Rothman AL, De Groot AS. The two-faced T cell epitope: examining the host-microbe interface with JanusMatrix. Hum

Vaccin Immunother. 2013 Jul;9(7):1577-86. doi: 10.4161/hv.24615. Epub 2013 Apr 12. PubMed PMID.

10: Cousens LP, Su Y, McClaine E, Li X, Terry F, Smith R, Lee J, Martin W, Scott DW, De Groot AS. Application of IgG-derived natural Treg epitopes (IgG Tregitopes) to antigen-specific tolerance induction in a murine model of type 1 diabetes. J

Diabetes Res. 2013;2013:621693. doi: 10.1155/2013/621693. Epub 2013 Apr 23. PubMed PMID: 23710469; 11: Elfaki ME, Khalil EA, De Groot AS, Musa AM, Gutierrez A, Younis BM, Salih KA, El-Hassan AM. Immunogenicity and immune

modulatory effects of in silico predicted L. donovani candidate peptide vaccines. Hum Vaccin Immunother. 2012 Dec 1;8(12):1769-74. doi: 10.4161/hv.21881. Epub 2012 Aug 24. PubMed PMID: 22922767; PubMed Central

12: Cousens LP, Mingozzi F, van der Marel S, Su Y, Garman R, Ferreira V, Martin W, Scott DW, De Groot AS. Teaching tolerance: New approaches to enzyme replacement therapy for Pompe disease. Hum Vaccin Immunother. 2012

Oct;8(10):1459-64. doi: 10.4161/hv.21405. Epub 2012 Oct 1. PubMed PMID: 23095864; PubMed

13. Gutiérrez AH, Moise L, De Groot AS. Of [Hamsters] and men: a new perspective on host cell proteins. Hum Vaccin Immunother. 2012 Sep;8(9):1172-4. doi: 10.4161/hv.22378. Epub 2012 Sep 1. PubMed PMID: 23124469; PubMed Central PMCID:

PMC3579895.

14: van der Marel S, Majowicz A, Kwikkers K, van Logtenstein R, te Velde AA, De Groot AS, Meijer SL, van Deventer SJ, Petry H, Hommes DW, Ferreira V. Adeno-associated virus mediated delivery of Tregitope 167 ameliorates experimental colitis. World J

Gastroenterol. 2012 Aug 28;18(32):4288-99. doi: 10.3748/wjg.v18.i32.4288. PubMed PMID: 22969191.

15: Moise L, Song C, Martin WD, Tassone R, De Groot AS, Scott DW. Effect of HLA DR epitope de-immunization of Factor VIII in vitro and in vivo. Clin Immunol. 2012 Mar;142(3):320-31. doi: 10.1016/j.clim.2011.11.010. Epub 2011 Dec 8. PubMed PMID:

22222093; PubMed Central PMCID: PMC3288193.

16: Inaba H, Martin W, Ardito M, De Groot AS, De Groot LJ. The role of glutamic or aspartic acid in position four of the epitope binding motif and thyrotropin receptor-extracellular domain epitope selection in Graves' disease. J Clin Endocrinol Metab. 2010

Jun;95(6):2909-16. doi: 10.1210/jc.2009-2393. Epub 2010 Apr 14. PubMed PMID: 20392871; PubMed Central

17: De Groot AS, Baker M, Cohen T. Species neutral correlates of immunogenicity for vaccines and protein therapeutics: fact or science fiction. Hum Vaccin. 2010 May;6(5):371.

18: Scott DW, De Groot AS. Can we prevent immunogenicity of human protein drugs? Ann Rheum Dis. 2010 Jan;69 Suppl 1:i72-76. doi: 10.1136/ard.2009.117564. Review.

19: Cohen T, Moise L, Ardito M, Martin W, De Groot AS. A method for individualizing the prediction of immunogenicity of protein vaccines and biologic therapeutics: individualized T cell epitope measure (iTEM). J Biomed Biotechnol. 2010;2010. pii: 961752. doi:

10.1155/2010/961752. Epub 2010 Jul 18. PubMed PMID: 20706613; PubMed Central PMCID:

20: De Groot AS. Exploring the immunome: A brave new world for human vaccine development. Hum Vaccin. 2009 Dec;5(12):790-3. Epub 2009 Dec 15. PubMed PMID: 20009527.

21: Weber CA, Mehta PJ, Ardito M, Moise L, Martin B, De Groot AS. T cell epitope: friend or foe? Immunogenicity of biologics in context. Adv Drug Deliv Rev. 2009 Sep 30;61(11):965-76. doi: 10.1016/j.addr.2009.07.001. Epub 2009 Jul 18. Review. PubMed

PMID: 19619593.

22: De Groot AS, Martin W. Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics. Clin Immunol. 2009 May;131(2):189-201. doi: 10.1016/j.clim.2009.01.009. Epub 2009 Mar 6. Review. PubMed PMID: 19269256. 23:

De Groot AS, Moise L, McMurry JA, Wambre E, Van Overtvelt L, Moingeon P, Scott DW, Martin W. Activation of natural regulatory T cells by IgG Fc-derived peptide "Tregitopes". Blood. 2008 Oct 15;112(8):3303-11. doi: 10.1182/blood-2008-02-138073. Epub

2008 Jul 25. .

24: De Groot AS, McMurry J, Moise L. Prediction of immunogenicity: in silico paradigms, ex vivo and in vivo correlates. Curr Opin Pharmacol. 2008 Oct;8(5):620-6. doi: 10.1016/j.coph.2008.08.002. Epub 2008 Sep 19. Review. PubMed PMID: 18775515.

25: De Groot AS, Scott DW. Immunogenicity of protein therapeutics. Trends Immunol. 2007 Nov;28(11):482-90. Epub 2007 Oct 25. Review. PubMed PMID: 17964218. 26: De Groot AS, Moise L. Prediction of immunogenicity for therapeutic proteins: state of

the art. Curr Opin Drug Discov Devel. 2007 May;10(3):332-40. Review. PubMed PMID: 17554860.

27: De Groot AS, Goldberg M, Moise L, Martin W. Evolutionary deimmunization: an ancillary mechanism for self-tolerance? Cell Immunol. 2006 Dec;244(2):148-53. Epub 2007 Apr 18. 28: De Groot AS. Immunomics: discovering new targets for vaccines and

therapeutics. Drug Discov Today. 2006 Mar;11(5-6):203-9. Review. PubMed PMID: 6580597.

29: De Groot AS, Knopp PM, Martin W. De-immunization of therapeutic proteins by T-cell epitope modification. Dev Biol (Basel). 2005;122:171-94. Review. PubMed PMID: 16375261.

30: De Groot AS, Rayner J, Martin W. Modelling the immunogenicity of therapeutic proteins using T cell epitope mapping. Dev Biol (Basel). 2003;112:71-80. PubMed PMID: 12762506.

Published Validation EpiVax: > 60 Publications in Protein Therapeutics

http://www.epivax.com/publications/



Published Validation

Biologic Therapeutics IEDB

40

Paul S, Kolla RV, Sidney J, Weiskopf D, Fleri W, Kim Y, Peters B, Sette A. Evaluating the immunogenicity of protein drugs

by applying in vitro MHC binding data and the immune epitope database and analysis resource. Clin Dev Immunol.

2013;2013:467852. doi: 10.1155/2013/467852. Epub 2013 Oct 8.



EpiVax Services

41 http://www.epivax.com/

http://www.epivax.com/

http://www.epivax.com/

42

CIO/DIRECTOR OF BIOINFORMATICS Bill Martin [email protected]

BIOINFORMATICS PROGRAM MANAGER Frances Terry [email protected]

BIOINFORMATICS PROGRAMMER/ANALYST Jacob Tivin [email protected]

EpiVax “Genius” Team

BDA – SALES INQUIRES Anthony Marcello [email protected] Phoebe De Groot De [email protected]

Accessing the Tools Contact Jason Del Pozzo: [email protected]

Confidential 43

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.

43 EpiVax Confidential

EpiVax_ISPIR_VS_IEDB_comparison_Immunogenicity_of_protein_drugs_Mar2014

Health & Medicine

epitope predictions

tcell epitope clusters

immunogenicity analysis

pocket epitope protein

accurate epitope prediction

analysis resource

features epivax iedb

iedb cluster tool