BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning

0555982 - ÚMG 2023 RIV US eng J - Článek v odborném periodiku
Příhoda, D. - Maamary, J. - Waight, A. - Juan, V. - Fayadat-Dilman, L. - Svozil, Daniel - Bitton, D.
BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning.
MAbs. Roč. 14, č. 1 (2022), č. článku e2020203. ISSN 1942-0862. E-ISSN 1942-0870
Grant CEP: GA MŠMT(CZ) LM2018130
Institucionální podpora: RVO:68378050
Klíčová slova: Antibody humanization * humanness * human-likeness * immunogenicity * deimmunization * immune repertoires * machine learning * deep learning
Obor OECD: Biochemical research methods
Impakt faktor: 5.3, rok: 2022
Způsob publikování: Open access
https://www.tandfonline.com/doi/full/10.1080/19420862.2021.2020203

Despite recent advances in transgenic animal models and display technologies, humanization of mouse sequences remains one of the main routes for therapeutic antibody development. Traditionally, humanization is manual, laborious, and requires expert knowledge. Although automation efforts are advancing, existing methods are either demonstrated on a small scale or are entirely proprietary. To predict the immunogenicity risk, the human-likeness of sequences can be evaluated using existing humanness scores, but these lack diversity, granularity or interpretability. Meanwhile, immune repertoire sequencing has generated rich antibody libraries such as the Observed Antibody Space (OAS) that offer augmented diversity not yet exploited for antibody engineering. Here we present BioPhi, an open-source platform featuring novel methods for humanization (Sapiens) and humanness evaluation (OASis). Sapiens is a deep learning humanization method trained on the OAS using language modeling. Based on an in silico humanization benchmark of 177 antibodies, Sapiens produced sequences at scale while achieving results comparable to that of human experts. OASis is a granular, interpretable and diverse humanness score based on 9-mer peptide search in the OAS. OASis separated human and non-human sequences with high accuracy, and correlated with clinical immunogenicity. BioPhi thus offers an antibody design interface with automated methods that capture the richness of natural antibody repertoires to produce therapeutics with desired properties and accelerate antibody discovery campaigns. The BioPhi platform is accessible at https://biophi.dichlab.org and https://github.com/Merck/BioPhi.
Trvalý link: http://hdl.handle.net/11104/0330851