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TitleRAIN: a Machine Learning-based identification for HIV-1 bNAbs.
Journal, issue, pagesRes Sq, Year 2024
Publish dateMar 8, 2024
AuthorsLaurent Perez / Mathilde Foglierini /
PubMed AbstractBroadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune ...Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoire is still lacking. Here, we developed a straightforward computational method for apid utomatic dentification of bAbs ) based on Machine Learning methods. In contrast to other approaches using one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of novel HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
External linksRes Sq / PubMed:38903123 / PubMed Central
MethodsEM (single particle)
Resolution3.8 Å
Structure data

19665

8s2e

EMDB-19665, PDB-8s2e:
Fab4251-DS-SOSIP complex
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • hiv whole-genome vector aa1305#18 (others)
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / HIV

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