Computational characterisation of peptide binding stability to HLA-C allotypes and its association with HIV-1 infection progression and HIV-1 related neurocognitive impairment

Mauro Voi¹Antonella Sangalli¹Erica Ginevra Milano²Carola De Martinis¹Elisa Orlandi¹Stefano Tamburin¹Elisa Mantovani¹Angela Federico¹Massimiliano Lanzafame³Emanuela Lattuada⁴Gustavo Adolfo Arganãraz⁵Bosco Christiano Maciel Da Silva⁶Alberto Jose Da Silva Duarte⁶Jorge Casseb⁷Enrique Roberto Argañaraz⁵Marina Malena⁸Marco Albani²Alessandra Ruggiero¹Maria Grazia Romanelli¹Maria Teresa Valenti¹Giovanni Grazioso²Donato Zipeto^1*

• ¹Neurosciences, Biomedicine and Movement Sciences, Universita degli Studi di Verona, Verona, Italy
• ²Department of Pharmaceutical Sciences, Universita degli Studi di Milano, Milan, Italy
• ³Centre for Medical Sciences (CISMED), Universita degli Studi di Trento, Trento, Italy
• ⁴Unit of Infectious Diseases, Santa Chiara Hospital, Provincia autonoma di Trento Azienda Provinciale per i Servizi Sanitari, Trento, Italy
• ⁵Laboratory of Molecular Neurovirology, Department of Pharmacy, Faculty of Health Science, Universidade de Brasilia, Brasília, Brazil
• ⁶Medical Investigation Laboratory Unit 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, São Paulo, Brazil
• ⁷Faculty of Medicine, Institute of Tropical Medicine, Universidade de Sao Paulo, São Paulo, Brazil
• ⁸U.O.S. Infectious Diseases, AULSS5, Ospedale Santa Maria della Misericordia, Rovigo, Italy

HLA-C molecules play a critical role in the immune response, particularly in antigen presentation and immune modulation. To investigate the effect of the most common HLA-C allotypes on the stability of the HLA-C-beta-2 microglobulin-peptide complex, we used the NetMHCpan-4.2 bioinformatic tool that predicts peptide binding to MHC class I molecules. This allowed us to predict the probability of a broad set of peptides to be naturally processed, presented on each HLA-C allotype, and ultimately recognised by the immune system, measured by EL-score. By plotting the EL-score against the percentile of the peptide's stability rank position, curves were drawn to illustrate the relative stability of the binding interaction of each HLA-C allotype tested, and the area under the curve was calculated to determine a stability score for each HLA-C variant. This approach permits us to greatly improve the classification of HLA-C allotypes according to their stability, overcoming the previous coarse stable and unstable binary classification. Analysis of two well-characterised HIV-1 patient cohorts, one focused on disease progression and the other on neurocognitive impairment, demonstrated a significant association between unstable HLA-C alleles, faster disease progression, and worse HIV-associated neurocognitive outcomes. These findings underscore the role of HLA-C stability in AIDS progression, suggesting that profiling HLA-C stability may serve as a predictive tool for HIV-1 disease management and assessing neurocognitive risk, with potential implications in personalised medicine.