Presentation of pathogen-derived
epitopes by major histocompatibility
complex I (MHC-I) can lead to the activation and expansion of specific
CD8
+
T cell clones, eventually resulting in the destruction
of infected target cells. Altered peptide ligands (APLs), designed
to elicit immunogenicity toward a wild-type peptide, may affect the
overall stability of MHC-I/peptide (pMHC) complexes and modulate the
recognition by T cell receptors (TCR). Previous works have demonstrated
that proline substitution at position 3 (p3P) of different MHC-restricted
epitopes, including the immunodominant LCMV-derived epitope gp33 and
escape variants, may be an effective design strategy to increase epitope
immunogenicity. These studies hypothesized that the p3P substitution
increases peptide rigidity, facilitating TCR binding. Here, molecular
dynamics simulations indicate that the p3P modification rigidifies
the APLs in solution predisposing them for the MHC-I loading as well
as once bound to H-2D
b
, predisposing them for TCR binding.
Our results also indicate that peptide position 6, key for interaction
of H-2D
b
/gp33 with the TCR P14, takes a suboptimal conformation
before as well as after binding to the TCR. Analyses of H-2D
b
in complex with APLs, in which position 6 was subjected to an
l
- to
d
-amino acid modification, revealed small conformational
changes and comparable pMHC thermal stability. However, the
l
- to
d
-modification reduced significantly the binding to
P14 even in the presence of the p3P modification. Our combined data
highlight the sensitivity of the TCR for the conformational dynamics
of pMHC and provide further tools to dissect and modulate TCR binding
and immunogenicity via APLs.
Uneven worldwide vaccination coverage against SARS-CoV-2 and emergence of variants escaping immunity call for broadly-effective and easily-deployable therapeutics. We previously described the human single-chain scFv76 antibody, which recognizes SARS-CoV-2 Alfa, Beta, Gamma and Delta variants. We now show that scFv76 also neutralizes infectivity and fusogenic activity of Omicron BA.1 and BA.2 variants. Cryo-EM analysis reveals that scFv76 binds to a well-conserved SARS-CoV-2 spike epitope, providing the structural basis for its broad-spectrum activity. Moreover, we demonstrate that nebulized scFv76 exhibits therapeutic efficacy in a severe hACE2 transgenic mouse model of COVID-19 pneumonia, as shown by body weight and pulmonary viral load data. Counteraction of infection correlates with the inhibition of lung inflammation observed by histopathology and expression of inflammatory cytokines and chemokines. Biomarkers of pulmonary endothelial damage were also significantly reduced in scFv76-treated mice. Altogether the results support the use of nebulized scFv76 for COVID-19 induced by any SARS-CoV-2 variants emerged so far.
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