In silico methods for immunogenicity risk assessment and human homology screening for therapeutic antibodies

ABSTRACT

In silico immunogenicity risk assessment has been an important step in the development path for many biologic therapeutics, including monoclonal antibodies. Even if the source of a given biologic is ‘fully human’, T cell epitopes that are contained in the sequences of the biologic may activate the immune system, enabling the development of anti-drug antibodies that can reduce drug efficacy and may contribute to adverse events. Computational tools that identify T cell epitopes from primary amino acid sequences have been used to assess the immunogenic potential of therapeutic candidates for several decades. To facilitate larger scale analyses and accelerate preclinical immunogenicity risk assessment, our group developed an integrated web-based platform called ISPRI, (Immunogenicity Screening and Protein Re-engineering Interface) that provides hands-on access through a secure web-based interface for scientists working in large and mid-sized biotech companies in the US, Europe, and Japan. This toolkit has evolved and now contains an array of algorithms that can be used individually and/or consecutively for immunogenicity assessment and protein engineering. Most analyses start with the advanced epitope mapping tool (EpiMatrix), then proceed to identify epitope clusters using ClustiMer, and then use a tool called JanusMatrix to define whether any of the T cell epitope clusters may generate a regulatory T cell response which may diminish or eliminate anti-drug antibody formation. Candidates can be compared to similar products on a normalized immunogenicity scale. Should modifications to the biologic sequence be an option, a tool for moderating putative immunogenicity by editing T cell epitopes out of the sequence is available (OptiMatrix). Although this perspective discusses the in-silico immunogenicity risk assessment for monoclonal antibodies, bi-specifics, multi-specifics, and antibody-drug conjugates, the analysis of additional therapeutic modalities such as enzyme replacement proteins, blood factor proteins, CAR-T, gene therapy products, and peptide drugs is also made available on the ISPRI platform.

GLOSSARY

ISPRI (Interactive Screening and Protein Reengineering Interface): Integrated, cloud-based, comprehensive toolkit for Immunogenicity Risk Assessment.

EpiMatrix Immunogenicity Score: Combined T effector and Treg Epitope Content per unit protein.

Tregitopes: Treg Epitopes found in IgG Framework that have been shown to modulate antigen-specific effector T cell responses.

ClustiMer: Tool for identifying epitope rich polypeptides from within a given protein sequence.

JanusMatrix: Tool for Predicting Tolerance, Putative Treg Epitopes, and Anti-self-immune responses.

OptiMatrix: Tool for modifying T cell epitope sequences to reduce (or enhance) MHC binding.

KEYWORDS:

• Anti-drug antibodies
• EpiMatrix
• immunogenicity
• immunoinformatics
• JanusMatrix
• monoclonal antibody
• T cell epitope
• tregitope

Acknowledgments

We appreciate and applaud the EpiVax informatics team, Matt Ardito, Jacob Tivin, Mark Bushnell, and Brittany Pavao for the development and application of the immunoinformatics tools available on the ISPRI platform. In addition, we appreciate the data curation & analysis efforts and many contributions of Andres Gutierrez and Frances Terry. We are especially grateful to Frances Terry for the many contributions and the initiation of this article.

Disclosure statement

AD and WM are senior officers and shareholders, and AM, AG, SS, JT, MA, and AR are employees of EpiVax, Inc., a privately owned biotechnology company located in Providence, RI. These authors acknowledge that there is a potential conflict of interest related to their relationship with EpiVax and attest that the work contained in this perspectives article is free of any bias that might be associated with the commercial goals of the company.

Abbreviations

ADA	=	Anti-drug Antibodies
API	=	Application Programming Interface
CDR	=	Complementarity Determining Region
HLA	=	Human Leukocyte Antigen
MAPPs	=	MHC-associated peptide proteomics
MHC	=	Major Histocompatibility Complex
PSSM	=	Position-Specific Scoring Matrix
TCR	=	T cell receptors
Teff	=	T Effector Epitope
Treg	=	Regulatory T cell

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19420862.2024.2333729.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.