At GenScript, we have the technical means & experience to synthesize large numbers of challenging neoantigen peptides and provide tailored optimization tools for your downstream applications.
GenScript’s Neoantigen Peptide Synthesis Service can be used for everything from functional screening of neoantigen candidates for TCR therapy to clinical stage vaccine immunogenicity testing.
| Characteristic | Description | Difficulty |
|---|---|---|
| Length | The isoelectric point (pI) of a peptide chain | Neoantigen peptides range from 8 - 50 amino acids. Peptides over 20 AA are difficult to be synthesized |
| Charge | The isoelectric point (pI) of a peptide chain | Many purification steps only work with specific charges, the further from neutral a peptide is, the synthesis will be more difficult |
| Hydrophobicity | Amino acids which naturally repel water due to their charge | The more hydrophobic a peptide is, the more difficult synthesis and purification will be due to its insolubility in water |
| Yield | The amount of one peptide in weight (mg) | It is very difficult to find a provider who can generate a range of yields for difficult peptides |
| Purity | The percentage of an individual peptide in a solution of peptides | The charge and hydrophobicity (solubility & aggregation) make standard purification difficult |
Neoantigen peptides are usually expressed on the cell surface, and arise due to single amino acid deletions, insertions, or substitutions. Because of this, they vary in length, charge, and hydrophobicity, leading to difficulty in synthesis and purification.
GenScript has developed NeoPre™, a predictive algorithm which is able to determine peptide synthesis difficulty based on sequence alone. NeoPre™ analyzes six intrinsic characteristics of each peptide in order to predict synthetic difficulty, including length, yield, charge (pI), aggregation, hydrophobicity, and purity. NeoPre can then recommend the most efficient approach to successfully synthesizing peptides using one of GenScript’s many synthesis platforms.
Read the full case study here!
| Length | Yield | Purity | pI | Aggregation | Hydrophobicity | Prediction | Recommended Protocol |
|---|---|---|---|---|---|---|---|
| 27 | 20-24 mg | >98% | 7.4 | 24.46296 | -0.25 | Difficult | Automatic synthesis |
| 25 | 4 mg | >98% | 10.2 | 52.2536 | 0.65 | Difficult | Mankind handling with improved coupling reagent, monitored under all process, involving Mid-control process to detect MS results |
| 25 | 24 mg | >98% | 8.6 | 48.3768 | 0.15 | Difficult | Semi-automatic synthesis, monitored under all process to ensure coupling efficiency. "O-Acyl isopeptide method" for peptide synthesis |
| 25 | 4 mg | >98% | 6.4 | 39.3832 | 0.05 | Difficult | R&D |
Example Read Out of NeoPre™. NeoPre™ will analyze individual peptide sequence and assign numerical difficulty values for aggregation, isoelectric point (PI), and hydrophobicity before determining synthetic difficulty and methodology.
| Total | Delivered | Successful Rate | Avg TAT (Days) | |
|---|---|---|---|---|
| Total | 2267 | 2158 | 95.15% | |
| Difficult | 1098 | 1030 | 93.81% | 36% ≤ 6 days |
| Easy | 1169 | 1128 | 96.49% | 39% ≤ 6 days |
Success Rate of Peptide Synthesis Using NeoPre™. GenScript has a 95% success rate for neoantigen peptide synthesis utilizing our NeoPre™ bioinformatics tool. Overall, we were able to synthesize 94% of predicted difficult peptides.
GenScript offers two synthetic technologies specific for hydrophobic peptide production on top of our standard five synthetic methodologies. One of them is our Hi-Syn technology which utilizes an optimized reaction temperature and condensation reagents to increase coupling efficiency.
| Project-YTD | Attempted | Synthesized | Synthesis success rate |
|---|---|---|---|
| Total | 232 | 200 | 86.21% |
Increasing The Success Rate of Difficult Neoantigen Peptides Using HiSyn. GenScript has an overall success rate for difficult neoantigen peptide synthesis of 95% using our technical advances, including our HiSyn technology. Utilizing advanced coupling methods, Hi Syn is a manual technology which has allowed GenScript to synthesize 86.21% of previously un-producible peptides!
| HiSyn | Attempted | Synthesized | Synthesis success rate |
|---|---|---|---|
| Hydrophobic peptide | 88 | 80 | 91% |
Increasing The Success Rate of Solely Hydrophobic Peptides Using HiSyn. Neoantigen peptides tend to be highly hydrophobic, which negatively affects their silubiloty and therefor their ability to be synthesized. In order to increase the overall success rate of difficult hydrophobic peptides, GenScript’s HiSyn technology is able to synthesize 91% of previously un-producible hydrophobic peptides.
Normal Manual Process
HiSyn Process
Increasing Purity of Peptides Using HiSyn. The same peptide was unable to be synthesized at 50 mg at 95% purity using our standard manual and automatic technologies, however, utilizing HiSyn, we were able to not only produce the peptide at the required yield, but also at the requested purity as shown through the comparing HPLC chromatograms.
GenScripts double coupling technology uses coupling reagents from our hisyn technology in optimized reaction conditions for our microwave synthesis method. GenScript is the first CRO in the field who can apply such optimized reaction technology utilizing microwave technology.
| Project | Total | IPC pass | Synthesis Success rate |
|---|---|---|---|
| Double coupling | 385 | 342 | 88.83% |
Increasing The Success Rate of Difficult Peptides Using Double Coupling. GenScript has an overall success rate for difficult neoantigen peptide synthesis of 95% using our technical advances, including our HiSyn technology. Utilizing advanced coupling methods, Double Coupling is an automatic technology which has allowed GenScript to synthesize 88.83% of previously un-producible peptides!
Normal Automated Process
Double Coupling Automated Process
Increasing Purity of Peptides Using Double Coupling. The same peptide was unable to be synthesized at 19 mg at 90% purity using our standard manual and automatic technologies, however, utilizing HiSyn, we were able to not only produce the peptide at the required yield, but also at the requested purity as shown through the comparing HPLC chromatograms.
Rather then relying on traditional peptide purification protocols, GenScript has optimized standard methods to enhance peptide purity. Through relying on our expertise in purifying both peptides and proteins of different intrinsic properties, we have designed an enhanced purification protocol utilizing numerous different reagents and purification columns. This allows us to reach peptide purities of even the most difficult neoantigen peptides of up to 98%.
| Project | Total | IPC pass | Synthesis Success rate |
|---|---|---|---|
| Purification | 67 | 58 | 86.6% |
Increasing The Purification of Difficult Peptides Using GenScript’s Optimized Purification technology. Utilizing advanced purification methods, GenScript’s optimized purification methodology has allowed GenScript to purify 86.6% of previously produced peptides which were not able to be synthesized at desired purity.
Normal Process
Optimized Purification Process
Increasing Purity of Peptides Using Optimized technology. The same peptide was unable to be purified at 19 mg at 98% purity using our standard manual and automatic technologies, however, utilizing HiSyn, we were able to not only produce the peptide at the required yield, but also at the requested purity as shown through the comparing HPLC chromatograms.
"Screening hundreds of neoantigens in mice to validate the generalizability of SNP-7/8a was a tremendous undertaking that could not have been possible without the diligent efforts of GenScript's peptide chemists who were able to rapidly synthesize even the most challenging sequences at the high purity required."
―Geoffrey Lynn, Ph.D.
Avidea Technologies'
CEO
Proven Reliability
Strong Application Expertise
Produced 1000’s of peptides for TCR therapy screening for 3T Biosciences
Synthesized Difficult peptides at varying amounts for Avidea’s novel SNAP PCV delivery system
Generated highly immunogenic peptides for DNA-based PCV efficacy screening
Track Record of Success
15 years of peptide synthesis production with a 98% success rate
Successful production of neoantigen peptides for the Top 50 immunotherapy companies and academic institutes
Continuous Communication
Global presence allowing for 24/7 communication and technical support
Project-specific managers and milestones
In 2019 GenScript manufactured 2500 neaontigen peptides with a 95% success rate using our tailored neoantigen peptide synthesis platform.
Step One: Input EVERY one of your peptides through our proprietary NeoPre™ bioinformatics algorithm to determine synthesis difficulty
Do you want to Know More About GenScript’s Neopre Bioinformatics Algorithm? Check out our Webpage for technologies for Difficult Neoantigen peptide Synthesis Here!
| Peptide # | Sequence | Length | Aggregation | Hydrophobicity | pI | Synthetic Difficulty |
|---|---|---|---|---|---|---|
| Example 1 | XXXXXXXX | 25 | 4.18 | -0.032 | 11.83 | Middle |
| Example 1 | XXXXXXXX | 25 | 4.18 | -0.032 | 11.83 | Middle |
| Example 2 | XXXXXXXX | 25 | 31.63 | 0.49 | 10.06 | Hard |
| Example 3 | XXXXXXXX | 25 | -4.77 | -0.58 | 6.78 | Simple |
Step Two: Based on difficulty and project details we help you pick the right synthesis platform to maximize success
Do you want to Know More About GenScript’s Unique Synthetic Methodologies for Difficult Neoantigen Peptide Synthesis and Purification? Check out our Webpage Here!
| Technology | Use Case |
|---|---|
| Microwave | Automated, High Yield, Fast TAT |
| Liquid-Phase | For modified peptides |
| Solid-Phase | Higher purity peptides |
Step Three: Once your peptides have been produced, GenScript offers library design tools to assist you optimize any neoantigen sequence
| Library | Use |
|---|---|
| Alanine Scanning | Determine the most important individual amino acids |
| Overlapping | Discover the perfect peptide length and sequence |
| T-Cell Truncation | Identify the best epitope for a specific activity |
Neoantigens may require different yields, TAT, number, purity, ect, depending on their downstream application. To accommodate the needs of the neoantigen community, ALL of GenScript’s neoantigen peptide services are fully flexible and customizable.
Example Project 1: TCR Affinity and Immunogenicity Screening
GenScript offers a wide range of services to fit the needs of customers working on the beginning stages of T-cell therapy to clinical stage efficacy screening. Learn the various ways GenScript’s neoantigen peptide synthesis service can be customized to fit the peptide requirements of each phase, even including TCR affinity maturation and epitope identification! Read More »
Project Goal: Generate an Allogenic T-cell Therapy for Patient with Squamous Cell Carcinoma
Phase I: Phase I: After tumor biopsy and NGS, 300 different neoantigens were identified as possible candidates. These sequences were sent to GenScript to synthesize as a crude peptide library to be used for in-vitro functionality screening of TCR Binding Affinity and Efficacy.
| # Peptides Analyzed | # Peptides Synthesized | Avg Peptide length | Yield | Purity | TAT (B.D) | Quality Control | Synthesis Methods Used | Delivery |
|---|---|---|---|---|---|---|---|---|
| 300 | 290 | 30 AA | 2 mg/peptide | 70% | 20 | RP-HPLC LC-MS |
Simple: 68% of Peptides Synthesized Using Microwave Technology Difficult: 22% of Peptides Synthesized Using LP/SP Manual technology |
Lyophilized Peptides in Individual Aliquot Tubes |
Phase II: In-vitro functionality screening identified a top candidate, however, in order to increase the binding affinity and efficacy of the TCR, researchers decided to design and generate an overlapping library to map the specific interaction between neoantigen epitope and TCR.
| Library Type | Length | Offset | Overlap | # of Peptides | Purity | Yield | Delivery Format |
|---|---|---|---|---|---|---|---|
| Overlapping | 11 AA | 3 AA | 6 AA | 100 | 80% | 0.5 mg/peptide | Pooling all quantity of partial peptides (20 peptides/pool) |
Phase III: Once the specific epitope was identified, researchers designed and generated an alanine scanning library to determine which amino acids were most important for therapeutic efficacy, prior to affinity maturation of the TCR.
| Library Type | Length | Purity | Yield | Delivery Format |
|---|---|---|---|---|
| Alanine Scanning | 11 AA | 98% | 4 mg/peptide | Lyophilized Peptides in Individual Aliquot Tubes (1 mg/tube) |
Example Project 2: PCV Development
When generating a PCV, researchers require an array of peptide services due the specific needs of in vitro functionality screening, pre-clinical safety basement in laboratory models, and clinical efficacy analysis. Learn how GenScript’s neoantigen peptide synthesis service has flexible services which allow for reliable peptides for any phase of PCV development. Read More »
Project Goal: Generate a Personalized Cancer Vaccine for a patient with Glioblastoma
Phase I: After tumor biopsy and NGS, 150 different neoantigens were identified as possible candidates. These sequences were sent to GenScript to synthesize as a purified peptide library to be used for in-vitro functionality screening.
| # Peptides Analyzed | # Peptides Synthesized | Avg Peptide length | Yield | Purity | TAT (B.D) | Quality Control | Synthesis Methods Used | Delivery |
|---|---|---|---|---|---|---|---|---|
| 150 | 145 | 28 AA | 2 mg/peptide | 75% | 20 | RP-HPLC LC-MS Solubility Testing |
Simple: 60% of Peptides Synthesized Using Microwave Technology Difficult: 40% of Peptides Synthesized Using LP/SP Manual technology |
Lyophilized Peptides in Individual Aliquot Tubes (1 mg/vial) |
Phase II: In-vitro functionality screening identified 20 peptides for pre-clinical PCV development for non-human primate.
| # Peptides Analyzed | # Peptides Synthesized | Avg Peptide length | Yield | Purity | TAT (B.D) | Quality Control | Synthesis Methods Used | Delivery |
|---|---|---|---|---|---|---|---|---|
| 20 | 19 | 35 AA | 500 mg/peptide | 98% | 30 | RP-HPLC LC-MS Solubility Testing |
Simple: 30% of Peptides Synthesized Using Microwave Technology Difficult: 70% of Peptides Synthesized Using LP/SP Manual technology |
Lyophilized Peptides in Individual Aliquot Tube |
Phase III: After the vaccine was deemed “safe” through pre-clinical testing; the vaccine was used in a human patient. After inoculation, researchers required “vaccine” and “non-vaccine control” neoantigen peptides for clinical in-vitro efficacy screening of patient derived PBMC’s.
| # Peptides Analyzed | # Peptides Synthesized | Avg Peptide length | Yield | Purity | TAT (B.D) | Quality Control | Synthesis Methods Used | Delivery |
|---|---|---|---|---|---|---|---|---|
| 25 | 25 | 34 AA | 14 mg/peptide | 70% | 20 | RP-HPLC LC-MS |
Simple: 35% of Peptides Synthesized Using Microwave Technology Difficult: 65% of Peptides Synthesized Using LP/SP Manual technology |
Lyophilized Peptides in Individual Aliquot Tube (2 mg/vial) |
Case Study: Pairing of Neoantigen-Reactive T-Cell Receptors Validated Against Mutated Peptides
Application Note: Identifying COVID-19 Vaccine Epitopes Using Peptide Based T cell Activation Assays New
Application Note: Identifying COVID-19 Vaccine Epitopes Using Peptide Based T cell Activation Assays New
Poster: GenScript’s Novel Technologies for Difficult Neoantigen Peptide Synthesis? New
Poster: GenScript’s Novel Technologies for Difficult Neoantigen Peptide Synthesis? New
Nature Interview with 3T Biosciences: Using Neoantigen Peptides for Personalized T cell therapyNew
Nature Interview with 3T Biosciences: Using Neoantigen Peptides for Personalized T cell therapyNew
Interviews: Neoantigen-based precision therapeuticsNew
Interviews: Neoantigen-based precision therapeuticsNew
Editorials: Neoantigens: presenting new vaccine opportunities in immuno-oncologyNew
Editorials: Neoantigens: presenting new vaccine opportunities in immuno-oncologyNew
Editorials: Neoantigen Peptides in Precision Medicine
Editorials: Neoantigen Peptides in Precision Medicine
Podcast Review: Personalized cancer vaccine prospects improve with self-assembling nanoparticles
Podcast Review: Personalized cancer vaccine prospects improve with self-assembling nanoparticles
