AMINO ACID HYDROPHOBICITY AFFECTS RBD-hACE2 BINDING AFFINITY
In the spike glycoprotein RBD positions at 452 and 486, the amino acids in the wild-type Wuhan-Hu-01 are leucine and phenylalanine, which are substituted by less hydrophobic amino acids methionine and proline in XBC.1, respectively. These mutations in XBC.1, indicate, that a selection pressure might be working towards acquiring the amino acids that are relatively less hydrophobic in spike glycoprotein. Kyte and Doolittle hydrophobicity index is considered for understanding the relative hydrophobicity.8
Hydrophobic interactions have a major role in stabilising the SARS-CoV-2 spike protein.9 When a neutral and hydrophobic amino acid such as phenylalanine is substituted by a neutral and lesser hydrophobic amino acid such as proline at the position 486, this particular substitution might increase the RBD-hACE2 binding affinity. In addition, another substitution at the 452 position where a neutral and hydrophobic amino acid such as leucine is replaced by a neutral and lesser hydrophobic amino acid such as methionine may alter the RBD-hACE2 binding affinity.10 Methionine substitution in XBC.1 spike glycoprotein at position 452 is predicted to increase the RBD-hACE2 binding affinity.11 A general trend of increasing RBD-hACE2 binding affinity is observed when a neutral and less hydrophobic amino acid is incorporated. In contrast, there is a reduction in the binding affinity of RBD-hACE2 when a negatively charged and less hydrophobic amino acid is incorporated.
ZOONOTIC ORIGIN OF L452M IN XBC.1
The mutation L452M has been noticed in SARS-CoV-2 sequences collected from minks; and has been linked to zoonotic transmissions between humans and minks. However, the zoonotic transmissions were observed only when the L452M mutation co-occurred with F486L.12 The binding affinity studies show that the co-occurring mutations L452M and F486L reduced the binding affinity between human ACE2 and RBD but resulted in increased binding between the mink ACE2 receptor and RBD of the spike glycoprotein.13 In the case of XBC.1, the mutation L452M co-occurs with F486P, which might affect the RBD-hACE2 binding affinity. The cumulative effect of L452M and F486P on RBD-hACE2 binding affinity warrants further studies.