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Lack of a dedicated integrated pipeline for neoantigen discovery in mice hinders cancer immunotherapy research. Novel sequential approaches through recurrent neural networks can improve the accuracy of T-cell epitope binding affinity predictions in mice, and a simplified variant selection process can reduce operational requirements. We have developed a web server tool (NAPCNB) for a full and automatic pipeline based on recurrent neural networks, to predict putative neoantigens from tumoral RNA sequencing reads. The developed software can estimate H-2 peptide ligands, with an AUC comparable or superior to state-of-the-art methods, directly from tumor samples. As a proof-of-concept, we used the B16 melanoma model to test the system’s predictive capabilities, and we report its putative neoantigens. NAP-CNB web server is freely available at http:// bioco mp. cnb. csic. es/ Neoan tigen sApp/ with scripts and datasets accessible through the download section. This work was funded by the Spanish Ministry of Economy, Industry and Competitiveness (TEC2016-28052-R, RTC2017-6600-1, SAF2017-84091-R, BFERO2020.04), the Spanish Ministry of Science and Innovation (FPU18/03199, PID2019-109820RB-I00), the “la Caixa” Foundation (LCF/BQ/EU19/11710071), FERO foundation and Centro Superior de Investigaciones Científicas (JAEINT18/EX/0636).

Lack of a dedicated integrated pipeline for neoantigen discovery in mice hinders cancer immunotherapy research. Novel sequential approaches through recurrent neural networks can improve the accuracy of T-cell epitope immunogenicity predictions in mice, and a simplified variant selection process can reduce operational requirements. We have developed a web server tool (NAP-CNB) for a full and automatic pipeline based on recurrent neural networks, to predict putative neoantigens from tumoral RNA sequencing reads. The developed software can estimate H-2 peptide ligands, with an AUC of 0.95, directly from tumor samples. As a proof-of-concept, we used the B16 melanoma model to test the system’s predictive capabilities, and we report its putative neoantigens. NAP-CNB web server is freely available at http://biocomp.cnb.csic.es/NeoantigensApp/ with scripts and datasets accessible through the download section.

Carbon-nitrogen bond forming reactions oriented to the synthesis of 2-amino-imidazolidines and imidazoles have been investigated. The C-2 amination of imidazolidinones, via the corresponding 2-chlorodihydroimidazoles, led to 2-benzylaminodihydroimidazole or bis(dihydroimidazole)amino derivatives by choosing the adequate experimental conditions. On the other hand, the use of N-acyl-2-methylsulfanyldihydroimidazoles allowed carrying out the reactions with aromatic amines, such as p-anisidine. Finally, palladium catalyzed BuchwaldHartwig amination was the method of choice for C-N coupling between 2-haloimidazoles and aromatic amines in the synthesis of the corresponding imidazoles.