R & D Collaborations> Biomarker Discovery

> Immune Monitoring

> Vaccine Development

> Antibody Signature Profiling

> Functional & Targeted Proteomics

> Drug Discovery & Optimization

Innovative Peptide Solutions

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Why JPT• Use our proprietary synthesis and screening

technologies

• Take advantage of JPT's integrated R&D team for organic & medicinal chemistry, bioinformatics, structural biology, data management and assay development

• Rely on our solid track record and ISO 9001 certification

• Benefit from flexible business arrangements for collaborative projects

Technologies & ApplicationsOver the past decade, JPT has developed a portfolio of proprietary technologies and a series of unique products and services which support research efforts in proteomics and in all developmental phases of novel vaccines against infectious and autoimmune diseases as well as against allergies and cancer.

In addition, JPT’s technologies find application in all areas where peptide screening is needed. Typical examples are: screening for proteoptypic peptides, enzymatic activities (proteases, kinases, phosphatases, methyltransferases), or systematic optimization of peptide lead structures.

Quality AssuranceJPT is DIN EN ISO 9001:2008 certified and GCLP audited.

JPT’s proprietary key technologies are: SPOT

High throughput peptide synthesis and screening technology for peptides & peptidomimetics for T-cell epitope and peptide lead discovery and characterization on proteome-wide levels.

PepStar™

Proprietary technology platform for humoral immune responses for biomarker discovery, seroscreening and immune monitoring.

PepMix™

Defined antigen spanning peptide pools to stimulate CD4+ and CD8+ T-cell responses.

PepTrack™

Peptide libraries of individual peptides optimized for T-cell assays.

SpikeTides™

Light and stable isotope labeled peptides for proteomics.

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02 / About JPT 03 / Projects & Partners

04 / Immune Monitoring & Biomarker Discovery

05 / Humoral Immune Response 06 / Cellular Immune Response 07 / Case Studies

09 / Proteomics 10 / Discovery & Targeted Proteomics 11 / Functional Proteomics 12 / Case Studies

13 / Drug Discovery & Optimization 14 / Peptide Discovery 14 / Hit to Lead / Qualification 14 / Peptide Optimization 15 / Case Studies

17 / Technologies & Know How 17 / Bio-, Cheminformatics & Modeling 18 / Assays & Screening 20 / Chemistry and Technologies

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About JPT

JPT Peptide Technologies is an experienced partner for peptide based R&D colla­borations. Located in Berlin, Germany, JPT has achieved world wide credibility for its commitment to rigorous quality standards and a reputation for developing and implementing innovative peptide based services and research tools for various applications. JPT serves a broad clientele in the pharmaceutical and biotechnology industries as well as researchers in universities and other non­profit organizations.

JPT offers its services in flexible business arrangements

• Fee-for-service projects • FTE based and milestone driven collaboration

projects• Shared risk, partnered development projects• SME qualification for participation on publicly

granted R&D projects

Company History

JPT Peptide Technologies GmbH was established in 2004 as a subsidiary of Jerini AG, a spin-off of Charité in Berlin, focused on the discovery and development of novel peptide-based drugs. In 2008, JPT was ac quired to become a part of BioNTech AG, Mainz (Germany), a company that develops novel immune therapy and diagnostic approaches for various cancers.

JPT is your preferred partner for peptide related projects because of its> Proprietary ultra high-throughput synthesis

and screening basis> Integrated in-house R &D team for organic and

medicinal chemistry, bioinformatics, structural biology, data management and assay develop-ment

> Solid track record of successful R &D projects> ISO 9001:2008 and GCLP regulated quality

assu rance system> Professional project management

and communication> Flexible business arrangements for

collaborative projects

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Recent Projects & Partners

Here we present our extensive but not complete list of recent projects and project partners.

Drug Discovery

• Substrate identification and optimization for se veral orphan enzymes for screening assays

• Design and production of screening libraries of peptides and peptidomimetics

• Identification and optimization of agonistic and antagonistic ligands

• Identification and optimization of affinity ligands• Identification and optimization of stabilizing

peptides as excipients• Development of surrogate bioassays for antigen-

free detection of therapeutic proteins

Immunology

• Identification of serological predictive, prognostic and surrogate biomarkers

• Seromarker identification as immune correlates for protection

• Proteome wide identification of T-cell epitopes for pathogens

• Companion diagnostics for vaccination studies in cancer and infectious diseases

• Design of comprehensive peptide libraries for companion diagnostics and treatment

Proteomics

• Development of next generation standards for targeted proteomics

• Characterization of specificity profiles for pro teins and protein families

• Design and synthesis of peptide libraries for proteome wide detection and quantification of proteins

• Development of molecular probes for the multi-plexed detection and quantification of proteins from biological samples

• Discovery of proteotypic peptide markers for functional proteomics

• Identification of epigenetic states of proteins and characterization of enzymatic alterations of epige netic states

Left: JPT's team of skilled staff and knowledgeable scientists

Partners include

> Bayer Pharma AG

> BioNTech AG

> Cancer Immunotherapy Trials Network (CITN)

> Charité Universitätsmedizin Berlin

> Duke University

> ETH Zürich

> Harvard Medical School

> Hoffmann La-Roche

> Immudex

> Institute for Systems Biology, Seattle

> International AIDS Vaccine Initiative (IAVI)

> National Institute for Biological Standards and Control (NIBSC)

> Oregon Health and Science University

> Zellnet

and various undisclosed partners

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Benefits

• Multiplexed identification of epitopes from antigens or entire proteomes

• State of the art infrastructure (cleanroom, BSL2, organic chemistry labs) & bioinformatic capabilities

• Solid track record • Chemical synthesis methods address sequence

diversity and post-translational modifications

Selected References > “Nonreplicating vaccines can protect african green

monkeys from the memphis 37 strain of respiratory syncytial virus”

Eyles et al., JID (2013)

> “Serum autoantibodies to myelin peptides distin-guish acute disseminated encephalomyelitis from relapsing – remitting multiple sclerosis”

Van Haren et al., Multiple Sclerosis Journal (2013)

> “Neutralization of porcine endogenous retrovirus by antibodies against the characterization of humoral and cellular immune responses elicited by a recom-binant adenovirus serotype 26 HIV-1 Env vaccine in healthy adults (IPCAVD 001)”

Barouch et al., JID (2013)

Immune Monitoring & Biomarker Discovery

Over the last decade, JPT has developed several unique peptide technologies to enable efficient and proteome spanning B­ and T­cell epitope­based biomarker discovery. Several successful projects have lead to new diagnostic and stratification markers in indications such as cancer, infections and autoimmune diseases and allergies. Furthermore, we developed tailored profiling workflows for humoral and cellular immune responses that can be correlated to clinical data. JPT’s com prehensive serological assay platform has been applied in collaborations devel oping epitope resolved immune monitoring tools and molecular correlates for protection in various indications. Correspondingly, JPT’s proprietary overlapping peptide pool platform finds widespread application in the development of clinical immune monitoring tools and novel diagnostic applications focusing on cellular immune responses.

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JPT offers a comprehensive workflow to detect circulating antibodies in patient sam-ples for the development of diagnostic and stratification biomarkers in indications such as infectious and autoimmune diseases as well as cancer. Full length proteins as capture reagents allow the identification and quantification of antibodies directed against entire antigens. In contrast, peptides as capture reagents yield an additional dimension of information. An overlapping peptide scan through an antigen, antigen family or entire proteome allows the detailed mapping of linear epitopes for antibodies along the antigen sequence. Thus, different epitope patterns, epitope spreading, as well as changes of B-cell immune responses against linear epitopes within any antigen can be monitored in detail and correlated to disease progression, therapeutic interven-tion or any other clinical evidence.

The investigation of samples at different time points and with secondary detection anti - bodies of different isotype specificity allows the characterization of time dependency and involvement of different phases of the humoral immune response. In addition, immobilised synthetic peptide libraries allow representation of sequence diversity and defined posttranslational modifications.

JPT’s seroprofiling platform consists of three synergistic but independent modules as follows:

1) PepStar™ High Content Peptide Microarrays for multiplexed biomarker discovery2) PepStar™ Multiwell Peptide Microarray for biomarker verification3) Peptide ELISA for validation of detected biomarkers

The three modules can be applied sequentially in milestone-driven biomarker discovery programs or individually in projects targeting the development of robust humoral immune monitoring tools in indications such as cancer, infectious and autoimmune diseases as well as allergies.

High Content Peptide Microarray> 5000 peptides

~ 100 samples

Multiwell Peptide Microarray~200 peptides~1000 samples

Peptide ELISA�exible design

Multiplexed Epitope Discovery is carried out for candidate proteins. Thousands of peptides can be screened in parallel using high content peptide microarrays.

Hits are con�rmed by Selective Antigen Pro�ling with multiple serum samples. Applying multiwell peptide microarrays, thousands of samples can be tested.

Validation of identi�ed biomarkers by �exible and robust peptide ELISA. Results are transferred towards diagnostic assays.

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JPT offers its expertise in discovery projects for the definition of immunodominant epi topes from various antigens or proteomes and for the development of tailored immune monitoring tools. Our peptide pool technique takes advantage of synthetic overlapping peptides that span entire antigen sequences and has been reported as an excellent tool for the antigen specific stimulation of CD4+ and CD8+ T-cell res-ponses in vitro. As a consequence, JPT's PepMix™ peptide pools have been used as independent readout systems to monitor clinical vaccination and immunotherapy trials and to reactivate polyclonal CD4+ and CD8+ T-cells specific for a spectrum of viral antigens for stem cell recipients in an FDA approved trial.

For discovery projects, JPT developed a unique and economic workflow for pro-teome spanning T-cell epitope discovery using well established and commonly used T-cell assays such as ELISpot. For development of robust immune monitoring tools, our peptide library platform provides access to high quality peptides designed for performance in cellular assays accompanying clinical trials.

Virus, cancer cell or other

Overlapping peptide scan through antigen sequences

Pooling 317 peptides / 4 pools

Pooling 86 peptides / 1 pool

Pooling 119 peptides / 2 pools

Pooling (approx. 100 peptides / pool)

Aliquoting

T-cell assays lead to identi fication of immunodominant peptides

Optional deconvolution and therapeutic options

Antigen sequences

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Antibody response to HIV gp120 is critical for protective activity in HIV­vaccination RV144­study

Identification of immunodominant T­cell antigens in Mycobacterium bovis for vaccine design

• RV144 Thai trial is the first successful HIV vaccination study• Correlate analysis looking for multiple parameters uses JPT's peptide

microarrays for the mapping of humoral immune response• Microarray analysis shows that specific antibody reactivities in V2 loop

correlate with a lower risk of HIV infection

• 119 antigens of M. bovis were produced as peptide pools representing each antigen in overlapping peptides and screened for IFN-γ response in blood from 23 M. bovis-positive cattle

• 59% of the tested antigens induced positive responses

• Proteins of the ESAT-6 family are immunodominant

• Epitope mapping allows for the identification of the most frequently recognized peptides

> “Screening of predicted secreted antigens from mycobacterium bovis reveals the immunodominance of the ESAT-6 protein family”

Jones et al., Infect Immun (2010)

> “The thai phase III HIV type 1 vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120”

Karasavvas et al., AIDS Res Hum Retroviruses (2012)

> “A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling”

Imholte et al., J Immunol Methods (2013)

> “Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial”

Zolla-Pazner et al., PLoS One (2013)

> “Peptide array mapping of env-specific IgG responses in HIV-1 vaccine efficacy trials and chronically infected individuals”

Gottardo et al., PLoS One (2013)

Identification of target antigens and immunodominant T-cell epitopes for vaccine development or biomarker discovery and validation.

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Case Studies

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Dose finding for an experimental HIV vaccine in a phase I clinical trial• Patient samples from IPCAVD 001, the first-in-

human evaluation of a prototype Ad26 vector-based vaccine expressing clade A HIV-1 Env (Ad26.ENVA.01) were evaluated on peptide microarrays for antibody reactivities

• Dose dependent expansion of the magnitude, breadth and epitopic diversity was measured

• A critical dose for the stimulation of a Env-V2 specific B-cell immune response could be defined

> “Characterization of humoral and cellular immune responses elicited by a recombinant adenovirus serotype 26 HIV-1 Env vaccine in healthy adults (IPCAVD 001)”

Barouch et al., JID (2013)

Antigen-specific binding antibody profiles. Sera were tested on peptide arrays to monitor linear antibody responses to peptides spanning Env from clades M, A, B, C, D, CRF02, and CRF01. Mean signal intensity (in week 28 with baselines subtracted) from all subjects in each group is depicted. Black asterisks denote pep-tides with significantly elevated mean signal intensity as com-pared to placebos (p<0.05, Wilcoxon Mann-Whitney tests), and red asterisks denote trends (p<0.10). Peptide Number

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JPT is providing the Proteomics community with a multitude of innovative research tools. Besides high­throughput chemical and analytical approaches to accelerate the discovery of novel biomarkers from biological samples, JPT has developed a new peptide standard technique for absolute quantification of target proteins in clinical and targeted proteomics. Furthermore, JPT has a decade­long track record providing services and project expertise in the area of functional proteomics ranging from elucidation of protein­protein interactions and enzymatic activities to epigenetic events.

Benefits

• Parallel identification and quantification of hundreds of proteins

• Simultaneous determination of post-trans-lational modifications

• Cost efficient multiplexed assay• Reliable high-throughput technique• High sensitivity

Selected References > “Seminal plasma as a source of prostate

cancer peptide biomarker candidates for detection of indolent and advanced disease”

Neuhaus et al., PLOS ONE (2013)

> “Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates”

Kim et al., Journal of the Proteome Research (2013)

> “Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key Msn2 control mechanism”

Sunnåker et al., Sci Signal (2013)

> “N-glycoprotein SRMAtlas: a resource of mass-spectrometric assays for n-glycosites enabling consistent and multiplexed protein quantifica-tion for clinical applications”

Hüttenhain et al., Mol Cell Proteomics (2013)

> “Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments”

Courcelles et al., Journal of Proteome Research (2012)

> “Using iRT, a normalized retention time for more targeted measurement of peptides”

Reiter et al., Proteomics (2012)

> “Automated workflow for large-scale selected reaction monitoring experiments”

Malmström et al., Journal of Proteome Research (2012)

> “Peptides quantification by liquid chromatogra-phy with matrix-assisted laser desorption/Ionization and selected reaction monitoring detection”

Lesur et al., Journal of Proteome Research (2012)

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Discovery & Targeted Proteomics

Two main approaches for mass spectrometry based proteomics exist, discovery or shotgun proteomics and targeted proteomics. Discovery or shotgun proteomics usu-ally aims at the identification of large sets of proteins in complex samples. In targeted proteomics high-selectivity quantitative assays for lower numbers of proteins are developed.

The ultimate goal of targeted proteomics is to specifically address defined biological questions. The significance of targeted proteomics is exemplified by the fact that it was selected as Nature Method of the Year 2012. Multiple reaction monitoring (MRM), which is one of the most frequently used targeted proteomics approaches, utilizes a triple quadrupole mass spectrometer to detect precursor and production pairs, fur-nishing assays for the detection and quantitation of multiple proteins in biological samples.

JPT has been providing the proteomics community with tools for targeted proteomics for years. The needs of researchers for inexpensive, heavily labeled or unla-beled and absolutely quantified peptides triggered the development of the SpikeTides™ product family, which finds widespread application in many laboratories.

In addition, JPT offers complete proteomic studies in collaboration with its partners. Please feel free to dis-cuss all aspects of your project with our experts.

Our Bioinformatics expertise allows for intelligent pep-tide library design that, in combination with out tech-nologies, helps to solve complex problems in target discovery and validation as well as biomedical research.

Impact of JPT's technologies on the proteomics workflow.

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TrypsinTrypsin

Discovery Proteomics

Proteotypic peptides

Shotgun experiment

Identi�cation of characteristic proteotypic peptides with sequence information from databases

High-throughput identi�cation of proteins

Identi�cation and relative/absolute quanti�cation of

protein(s) of interest

(MS spectra of as many proteins as possible)

Targeted Proteomics

MS conditions for identi�cation of characteristic proteotypic peptides

SRM/MRM assay setup

Protein(s) of interestin complex sample

SRM/MRM Experiment(Selected fragmentation reactions monitored)

Proteotypic peptides

SpikeTides™ or SpikeTides™ L

for SRM/MRM assay setup

SpikeTides™ Lfor relative quanti�cation

SpikeTides™ TQLfor absolute quanti�cation

SpikeTides™Fragmentation information

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Functional proteomics studies the biological function of proteins or protein groups and classes on a proteome-wide level. The data are the basis for the elucidation of signaling networks and therefore to understand cell function.

Functional proteomics includes the characterization of enzyme activities as well as protein-protein interactions and the functional state of proteins. Combining our technologies and expertise, we are able to map changes in signaling pathways as a consequence of cell-treatment or changes in environmental conditions. This can either be done by the large scale measurement of enzymatic activities such as kinase, phosphatase, protease or of other protein modifying enzymes. In addition, valuable information about the epigenetic state of proteins can be collected.

Additionally, we have developed innovative ways to evaluate and present complex data sets that is indispensable to the optimal exploitation of experimental results.

Characterization of signal transduction networks. Proteome wide screening for substrates of Sirtuin class enzymes by peptide micro-arrays and structural characterization of enzyme-substrate com-plexes. For further details see page 12.

SIRT 1

Substrate Specificity Profiles Complex Structure

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• Methylation of arginine and lysine residues is part of the epigenetic code in histones

• PRMT5-MEP50 is known to catalyze the methylation of Arg-residues

• A complex peptide library displayed on peptide microarrays was used to characterize the histone methyltransferase PRMT5-MEP50

• Results show that PRMT5-MEP50 modifies Arg3 in the N-terminal tail of H2A and H4

• This activity is modulated by substrate PTMs: phos-phorylation of neighbouring Ser inhibits activity, acetylation of C-terminal Lys residues enhances activity

> “Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity”

Ho et al., PLoS One (2013)

PRMT5-MEP50 histone methyltransferase activity is modulated by substrate PTMs. High-density histone peptide arrays incubated with PRMT5-MEP50. Data from H4 peptides are shown, each row represents a discrete peptide. The left panel shows individual modifications present on each peptide, the histogram on the right panel shows the relative activity on each peptide. The signal on the unmodified 1-20 peptide is indicated in blue. Inhibition by Ser1 phosphoryla-tion is indicated in red.

• The human class of sirtuins consists of 7 members, only a limited number of substrates is known

• The 7 human sirtuins were tested for enzymatic activity on a library of 6802 human acetylation sites immobilized on peptide microarrays

• Substrates were identified and substrate specifici-ty profiles could be generated (see figure on p. 11)

• These results help to understand the role of single sirtuins in signaling networks

> “An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms”

Rauh et al., Nat Commun (2013)

Deciphering substrate specificity of human sirtuins

Characterization of PRMT5­MEP50 histone methyltransferase in dependence of post­translational substrate modifications

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JPT Peptide Technologies applies its portfolio of proprietary peptide technologies and bioinformatic and medicinal chemistry know­how to manage R &D projects for contract research and R &D collaborations in peptide discovery, hit­to­lead qualification and peptide optimization. Our experience in drug discovery and optimization finds application in peptide based drug discovery and vaccine projects, in the discovery of peptidic additives for the cosmetic and nutritional industry, in the development of affinity ligands for purification of biomolecules, as well as in content determination for novel immune diagnostics.

Example Projects

• Identification and optimization of agonistic and antagonistic ligands

• Enzyme substrate identification and optimization for screening assay development

• Design and production of screening libraries of peptides and peptidomimetics

• Identification and optimization of affinity ligands• Identification and optimization of stabilizing pep-

tides as excipients• Development of surrogate bioassays for antigen-

free detection of therapeutic proteins

Selected References> “High density peptide microarrays for proteome-

wide fingerprinting of kinase activities in cell lysates” Thiele et al., Methods Mol. Biol. (2010)

> “Novel small molecule bradykinin B1 receptor antag-onists. Part 1-3”

Schnatbaum et al., Bioorg. Med. Chem. Lett. (2010)

> “Small molecule bradykinin B2 receptor modulators” Gibson, Schnatbaum et al., WO 2010/031589 (2010)

> “TFPI Inhibitors and methods of use” Reimer et al., WO 2010/071894 (2010)

> “Small molecule antagonists of the bradykinin B1 receptor”

Reimer et al., WO 2009/036996 (2009)

> “Peptide arrays for enzyme profiling” Zerweck et al., Methods Mol. Biol. (2009)

PeptideDiscovery

Random/Knowledge-based

Libraries

Hit to LeadQualification

SAR AnalysisPrioritization

PeptideOptimizationIterative Activity/PhysChem/ADME

Optimization

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Peptide Discovery

Over the past decade, JPT has run several successful projects for the identification of peptide hits. Among them were specific substrates for orphan proteases, kinases, phosphatases and acetyltransferases. The key to most of these screening projects was the application of JPT's proprietary PepSpot™ or PepStar™ technologies. These respective libraries were designed by either knowledge based methods or from ran-domized sequences. In collaboration with Bayer AG, Germany, high content peptide and peptidomimetics libraries were created for screening of undisclosed targets. Overall, several million compounds were selected, synthesized and screened.

Hit­to­lead / Qualification

At JPT, we pay particular attention to the thorough qualification of hits. For this, hits are resynthesized, purified and characterized in multiple assays that are relevant to the target parameters/properties. Along with SAR analyses, profiling results enable a clear prioritization and selection of the most promising leads for optimization. JPT has been engaged in several hit qualification/hit-to-lead projects, where hits for kinases, proteases, transferases, isomerases and phosphatases were transferred into qualified leads. The projects were done in-house or during perennial collaborations with industry partners. The hit qualification process at JPT is supported by an estab-lished network of service providers which addresses basically all properties relevant to drug discovery and other applications.

Peptide Optimization

Peptide optimization projects at JPT are conducted with purified compounds that are synthesized on polymeric resins or in solution. If required, proprietary high con-tent technologies such as SPOT™ and PepStar™ support the optimization work. The process is highly iterative, taking into account all relevant optimization parameters. In this res pect, we emphasize the evaluation and consider late-stage goals (e.g. PK/Tox properties) from very early in the optimization process (to allow early fall-back if necessary). During optimization, the lead peptides are usually converted to smaller and less peptide-like compounds (i.e. by incorporating unnatural amino acids, small molecule building blocks or steric constraints). Lead optimization projects are not limited to the area of drug discovery. Our expertise is employed in many other areas of biomedical research as well as the nutritional and cosmetic industry. Exem plarily, JPT’s scientists have a profound experience in the development of specific peptidic affinity ligands for the purification of therapeutic proteins.

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SAR characterization and optimization of a 13­meric cyclic antigen for anti­myc antibody• The key residues of a cyclic peptide for binding to an anti-myc antibody

were to be identified• A substitutional analysis of the myc tag sequence (EQKLISEEDL, incorporated

into a 13-meric cyclic peptide) was performed using more than 170 cyclic peptides on microarray slides. All peptides were screened for binding to an anti-c-myc antibody. One peptide was also inserted into a proteolytically stable microprotein to enhance pharmacokinetic properties

• Key residues and tolerable substitutions were identified. Cyclization was shown to be beneficial for binding affinity

Substrate specificity analysis of a 13-meric cyclic antigen for anti-myc antibody Left: Cyclic myc peptide with highlighted key residues ESIL. The Cys-Cys bridge is marked in yellow. Right: Results of a substitutional analysis of this cyclic myc peptide. Red colour indicates strong specific binding, light yellow indicates less or no binding. The results for the WT peptideare highlighted by the black boxes.

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Optimization of a 21­mer hit to a 9­mer peptide • Various cycles of substitutional anlyses, truncation and deletion

analyses were used to optimize a peptide in terms of molecular weight, binding characteristics and physicochemical properties

• The 21-mer hit peptide with two internal disulphide bonds was optimized towards a nonapeptide with retained biological activ-ity and superior physicochemical properties

Left: The figures depict the results of substitutional analyses of the initial peptides, which where used as a basis for convertion into a smaller and more stable peptide. Red indicates strong binding light yellow or white indicate less or no binding. Black brackets show positions of disulfide bonds. Below: Table showing various properties measured for intermediate compounds at different stages of peptide optimization.

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Bio­, Cheminformatics & Molecular Modeling

JPT Peptide Technologies has long standing expertise in biomedical screening and peptide lead optimization programs with its comprehensive bioinformatic and chem-informatic capabilities.

We offer this unique know-how as part of our high content peptide microarray and custom peptide synthesis service or in R &D collaborations focusing on seromarker profiling, peptide hit discovery and optimization.

Service Specifications

• In depth discussions of your project and definition of a suitable strategy based on scientific feasibility and experience

• Detailed project proposal on how our bioinformatic and cheminformatic expertise can support your project

• Obtain detailed and comprehensive service reports

Benefits

• Long term track record on the discovery and deve lopment of peptides in drug discovery and diagnostic development

• State of the art prediction, data interpretation and data mining algorithms and software paired with chemical and biological know-how

• Expertise available as a fee-for-service or in collaborative partnerships

Selected References> “Design and synthesis of a new class of selective

integrin α5β1 antagonists” Stragies et al., J. of Medicinal Chemistry (2007)

> “Translating peptides into small molecules” Hummel et al., Mol. BioSyst. (2006)

Use of homology model for the selection of cytosolic loop peptides for a GPCR (MSH).

X-ray loop structure (left) and model (right) stabilized by scaffold.

Technologies & Know How

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Applications

• Biomarker discovery for cancer, infectious & auto-immune disease and allergy

• Seroprofiling and antibody epitope mapping• Development of immune diagnostic and patient

stratification tools• Clinical monitoring and companion diagnostics• Elucidation of antigen and epitope spreading

during disease progression and therapeutic intervention

• Detection of immunodominant regions in antigens and of novel vaccine targets

• Identification of substrates for orphan enzymes and enzymatic assays

• Characterization of protein-protein interactions• Investigation of posttranslational modifications

and epigenetics

Selected References> “Characterization of humoral and cellular immune

responses elicited by a recombinant adenovirus serotype 26 HIV-1 Env vaccine in healthy adults”

Barouch et al., J Infect Dis (2013)

> “Peptide array mapping of env-specific IgG responses in HIV-1 vaccine efficacy trials and chronically infected individuals”

Gottardo et al., PLoS One (2013) > “Serum autoantibodies to myelin peptides distin-

guish acute disseminated encephalomyelitis from relapsing - remitting multiple sclerosis”

Haren et al., Multiple Sclerosis J (2013)

> “A sequence in subdomain 2 of DBL1a of plasmo-dium falciparum erythrocyte membrane protein 1 induces strain transcending antibodies”

Blonqvist et al., PLoS One (2013)

Assays & Screening

JPT's experienced scientists will develop the optimal peptide screening strategy for your pro ject. Assays are performed in an S2 laboratory environment using automated incubation stations assuring robust and reproducible performance.

Overlapping peptides

Antigen sequence

Blood serum / plasma

Binding region

PepStar™ Microarray Antigen of interest

Labeled secondary antibody

Principle of antibody epitope mapping by overlapping peptides. The antigen sequence is displayed by a set of overlapping peptides. Antibodies from patient sample bind to epitopes presented by the peptides and are subsequently detected by a labeled secondary antibody. Using this information, epitopes recognized by circulating antibodies can be determined.

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Technologies defining JPT's biomarker discovery platform. High Content and Multiwell Microarrays are two manifestations of our unique PepStar™ technology. These formats allow efficient screening of a high number of peptides and samples, respectively. The robust and straightforward Peptide ELISA is applied, as an alter native technology, for the validation and development of diagnostic tests.

Benefits

• Proprietary technologies for multiplexed identi fi-cation and quantification of epitopes for multiple antigens or entire proteomes

• Addressing of natural sequence diversity and posttranslational modifications

• Cost efficient and modular workflow allows efficient and tailored planning of projects (see figure below).

1) Multiplexed epitope discovery enabling screening of thousands of peptides in parallel using high content peptide microarrays.

2) Selective antigen profiling for systematic screen-ing of large numbers of test samples using multi-well peptide microarrays.

3) Marker validation and transfer of results towards diagnostic assays using peptide ELISA

• Minimal consumption of patient material and proteins

• Low background combined with high sensitivity• Robust assay protocols ensuring reproducible

results

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> Multiplexed Epitope Discovery > Marker Validation> Selective Antigen Pro�ling

Peptide Microarray Peptide Microarray Peptide ELISA

High Content:6912 peptides in 3 copies/sample

Multiwell:192 peptides in 3 copies/21 samples

1-96 peptides/samples

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Chemistry and Technologies

Peptide Synthesis

Extraordinarily high capacity and quality in automated synthesis, analysis and purification.

Applications and Specifications

• Applied in all kinds of peptide based projects• Wide range of peptide modifications• From 1 mg to several grams• Analyses: LC-MS MALDI-MS, HPLC,

optionally AAA, NMR, CE, peptide content, solubility, stability testing, bacterial endotoxin and sterility analysis

Applications and Specifications

• Antibody epitope mapping• Seromarker discovery• Development of immune diagnostics• Peptide optimization• Screening for protein-protein interactions• Characterization of enzymes and enzyme

substrate identification/optimization (e.g. kinases, acetyl transferases, proteases)

• Up to 7000 peptides/slide in triplicates• >1000 slides from one synthesis• HT-Purification by chemo-selective

immobilization of target peptides

Benefits

• Screening of tens of thousands of peptides in parallel

• Only smallest sample volumes needed (sera, blood, purified biologics…)

• Economical production of large batches of identical microarrays

• Peptides in triplicates guarantee high reliability• Low background combined with high sensitivity• Incubation manually or automated • Flexible read-out via fluorescence, radioactive

labeling or silver staining

High Content PepStar™ Microarrays

JPT Peptide Technologies applies its unique PepStar™ peptide microarray platform to generate high content peptide microarrays on glass slides.

Applications and Specifications

• Screening projects for bioactive peptides, T-cell epitopes, peptidic ligands, substrates, proteotypic peptides, biomarkers etc.

• Systematic optimization of peptidic lead structures• Assembly of peptide pools for immune monitoring• Scale: 10-100 nmol / compound

Benefits

• Highly parallel synthesis approach (30.000 peptides or mimetics / week)

• Quick turnaround (2 weeks)• Low cost (from 7 €/$ per peptide)

High­troughput SPOT™ Synthesis

JPT Peptide Technologies has the unique ability to produce peptide libraries made of up to 1 million single, individual peptides with rapid turnaround at unmatched pricing.

Benefits

• Substantial, long-standing expertise• Exceptional quality and reliability for even

complex or unusual peptide sequences• Appreciated by customers worldwide for

many years• DIN ISO 9001 certification• Stringent quality control

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Applications

• Optimization and validation of SRM/MRM assays• Relative and absolute quantification of proteins• Selection of best proteotypic peptides showing

high mass spectrometry signal response• Development of kits for the quantification of entire

proteomic pathways

Benefits

• Thousands of economic SpikeTides™ for MRM assays

• Unmatched turnaround times (10.000 peptides per week!)

• Fully compatible with downstream analyses like MS and HPLC

• SpikeTides™ quantification significantly more cost effective than AAA

Applications

• Stepwise transformation of peptides into more druglike molecules

• Example: Identification and optimization of specific substrates for “orphan” proteases, kinases, phosphatases and acetyltransferases

• Example: Development of specific affinity ligands for the purification of therapeutic proteins

Benefits

• Experienced project team (from discovery to preclinical development)

• Long standing record in peptide and small molecule chemistry

• High capacity automated synthesis, analytics and purification

• Solid and solution phase capabilities • Extensive building block library

Proteotypic SpikeTides™ Peptides

SpikeTides™ are small-scale, inexpensive, heavily labeled or unlabeled and/or absolutely quantified peptides for single reaction monitoring (SRM) and multiple reaction monitoring (MRM).

Medicinal Chemistry

Long-standing experience from discovery to preclinical development projects backed by very high synthesis capacities.

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We take pride in our competent service and swift response. Please do not hesitate to contact us for further information. We also very much welcome your feedback and comments.

Volmerstraße 5 12489 Berlin Germany

P. O. Box 2619Acton, MA 01720USA

USA/Canada T 1-888-578-2660 F 1-888-578-2666

European Head Office T +49 -30 - 6392-7878 F +49 -30 - 6392-7888

JPT Peptide Technologieswww.jpt.com | peptide@ jpt.com