De novo design of epitope-focused antigens for better in vitro diagnostics

Il 14/04/2025 ore 14.30 - 17.00

Via Pietro Castellino n. 111 Napoli c/o Area di Ricerca Napoli 1

Seminar at the Cnr Institute of biochemistry and cell biology, held by Prof. Marco Chino  (Università degli studi di Napoli Federico II - Dip.to di Scienze Chimiche)

Abstract:

De-novo protein design allows a more accurate exploration of the folding space than directed evolution and has provided remarkable benefits to several fields of medicine and biochemistry, such as in-vitro diagnostics (IVD)¹. Specifically, the IVD industry still relies on antibodies due to their cheap price and established production methods. The design of de-novo antigens with high specificity can reduce the time of production of novel antibodies, while increasing their effectiveness. Thanks to the recent advances in the AI field^2,3,4, the chance of success-rate of in-silico de-novo design significantly increased, particularly due to the different models available in the Rosetta suite. We present a workflow focused on the generation of small-protein scaffolds (~50AA) around a known antigen epitope to design de-novo antigens which can elicit higher immune response in host organisms. The workflow begins with a generation phase, using RFdiffusion² to generate the backbone structure and ProteinMPNN³ to sample several sequences from these backbones. A subsequent validation phase leveraging AI folding models, as OmegaFold⁴ and AlphaFold⁵, aims to filter the sequences which are most likely folded to their original backbones. These two phases are cyclically iterated until a high rate of folding accuracy is predicted. The obtained proteins are subsequently screened in-silico to evaluate their immunogenicity⁶, to retain a small set of (3 to 6) designed antigens with the highest predicted values. The workflow is fully generalizable to any given epitope and, as a proof of concept, we applied this workflow to scaffold around two epitopes of HPV-16 and one epitope of SARS-CoV-2 obtaining small de-novo antigens for each epitope. For one epitope of HPV-16, the resulting set of 6 de-novo antigens is currently being screened in-vitro. 

Organizzato da:
Istituto di Biochimica e Biologia cellulare

Referente organizzativo:
Ferdinando Febbraio
CNR - Istituto di Biochimica e Biologia Cellulare
Via Pietro Castellino n. 111 Napoli
ferdinando.febbraio@cnr.it

Modalità di accesso: ingresso libero