## 2 Results and Discussion
Moreover, more non-bonded contacts between the RBD of BA.5 variant and the K9 Nb (207 non-bonded contacts) are predicted than between the RBD of BA.5 variant and the 1.29 Nb (149 non-bonded contacts). This phenomenon aligns with a previous study that suggested that aromatic and non-polar amino acids on Nbs at the interaction sites could be essential for establishing complementary binding to the RBD of BA.5 variant, driven by the hydrophobic characteristics of these residues, enabling favorable interactions with the hydrophobic regions present on the RBM that also contain many non-polar and aromatic amino acids (Figure S7) [23]. Interestingly, the optimal interaction posture of the K9 Nb on the RBD of BA.5 variant illustrated that the residues Asp52, Val31, Val32, Glu44, and Tyr114 strongly interacted with the key amino acids of the RBD of BA.5 variant via hydrogen bonds and hydrophobic interactions. Particularly, Glu44 exhibited a strong interaction through a salt bridge with Arg498, a key amino acid of the RBD of BA.5 variant. These findings support the experimental results that the K9 Nb binds to the RBD of BA.5 variant with high binding affinity. **Prediction of the binding affinity of Nbs when interacting with the RBD of JN.1 variant. ** In late 2023, JN.1 (BA.2.86.1.1), a descendant of the O  
Figure 6: **A comparison of amino acid interactions between the RBD of BA.5 variant and Nbs. ** (**A**) The RBD of BA.5 variant with the 1.29 Nb, (**B**) the RBD of BA.5 variant with the C11 Nb, and (**C**) the RBD of BA.5 variant with the K9 Nb. emerged and rapidly became predominant in France. This variant exhibits alterations in the spike protein at a specific location, thereby enhancing its ability to evade immunity compared with BA.2.86 [28]. As of February 23, 2024, the GISAID database shows that JN.1 variant has become the predominant strain, with 86.0-96.0% GRA in the top 10 countries in the past 4 weeks [14]. We were interested in exploring the potency of the 1.29, C11, and K9 Nbs and their potential interaction strengths with the RBD of JN.1 variant by prediction using molecular docking. Both the 1.29 and C11 Nbs could interact with the RBM of the RBD of JN.1 variant in a manner similar to that of BA.5 variant, by adopting the same interaction posture. Figure 7 illustrates the posture of the 1.29 and C11 Nbs, which allowed for interactions between CDR1 and CDR3 with the RBM of JN.1 variant (as shown in Figure S8). Moreover, both Nbs could bind to the RBD of JN.1 variant with higher interface residues and interface area than for BA.5 variant (Figure S6), resulting in more interactions and a higher binding affinity. Figure 7 confirms that both the 1.29 and C11 Nbs demonstrated a higher binding affinity to JN.1 variant (\(-\)13.32 and \(-\)10.75 kcal/mol, respectively) than to BA.5 variant. This can be attributed to the presence of E484K, a key mutation amino acid in JN.1 variant, which introduced a positive charge. This positive charge facilitated a strong salt bridge interaction (Figures S7 and S9) with Asp45, thereby affecting their structural fit. The E484K mutation has been reported to reduce neutralization [29]. It should be noted that this mutation is present in the Beta and Gamma variants and that the 1.29 Nb was reported to be able to bind to these variants [9]. Additionally, both the 1.29 and C11 Nbs had a lower number of hydrogen bond interactions while exhibiting a higher number of non-contact interactions with JN.1 variant compared to BA.5 variant (Figure S6). Interestingly, Figure 7 illustrates that K9 could interact with the RBD of JN.1 variant with a maximum binding affinity of \(-\)16.57 kcal/mol. Similar to  
Figure 7: **A comparison of amino acid interactions between the RBD of JN.1 variant and Nbs. ** (**A**) The RBD of JN.1 variant with the 1.29 Nb, (**B**) the RBD of JN.1 variant with the C11 Nb, and (**C**) the RBD of JN.1 variant with the K9 Nb. the K9 Nb did not facilitate the direct CDR-RBM interaction.