| Literature DB >> 35174519 |
Stefano Pascarella1, Martina Bianchi1, Marta Giovanetti2,3,4, Daniele Narzi5, Roberto Cauda6, Antonio Cassone7, Massimo Ciccozzi8.
Abstract
The COVID-19 pandemic continues to have a threatening impact on a global scale, largely due to the emergence of newly SARS-CoV-2 variants. The Mu (PANGO lineage B.1.621), was first identified in Colombia in January 2021 and was classified as a variant of interest (VOI) in August 2021, due to a constellation of mutations that likely-mediate an unexpectedly enhanced immune resistance to inactivated vaccine-elicited antibodies. Despite recent studies suggesting that the Mu variant appears to have less infectivity than the Delta variant, here we examined the structural effect of the Mu spike protein mutations and predicted the potential impact on infectivity of the Mu variant compared with the Delta and Delta plus spike protein.Entities:
Keywords: SARS coronavirus; antigenic variation; biostatistics & bioinformatics; genetics; virus classification
Mesh:
Substances:
Year: 2022 PMID: 35174519 PMCID: PMC9088528 DOI: 10.1002/jmv.27663
Source DB: PubMed Journal: J Med Virol ISSN: 0146-6615 Impact factor: 20.693
Figure 1(A) Complex between RBD and ACE2 from the Protein Data Bank (PDB) structure 6M0J. Green and grey cartoons indicate ACE2 and RBD, respectively. (B) Top: comparison of the interfaces between the reference and the model Mu RBDs and ACE2 at position 501. Middle: possible salt bridge between E75 and K484 in the Mu variant and comparison with the reference domain. Bottom: comparison of the interfaces between the reference and the model Delta plus RBDs and ACE2 at the position 417. Residue side chains and NAG substituent are reported as stick models
Predicted molecular interaction differences between the reference and variant RBDs and ACE2
| Reference residue | Mu | Delta | Delta plus | |||
|---|---|---|---|---|---|---|
| R346 | K | Exposed; not at interface | ‐ | ‐ | ‐ | ‐ |
| K417 (0.29) | ‐ | ‐ | ‐ | ‐ | N | Removal of the salt bridge between K417 and ACE2 D30 (0.16) |
| L452 | ‐ | ‐ | R | Exposed: near the interface | R | As in Delta |
| T478 | ‐ | ‐ | K | Exposed: near the interface; possible salt bridge with ACE2 E87 | K | As in Delta |
| E484 | K | Near the interface; possible salt bridge with ACE2 E75 | ‐ | ‐ | ‐ | ‐ |
| N501 (0.57) | Y | Van der Waals interaction with ACE2 Y51 and K353 (2.46) | ‐ | ‐ | ‐ | ‐ |
Note: Mutant residues characteristic of each variant are compared.
DrugscorePPI ΔΔGs of interface residues are reported in parenthesis as kcal/mol.
Predicted molecular interaction differences (∆∆E) between the reference and variant RBDs and ACE2 as obtained from MD simulations
| SR Coulomb | SR Lennard‐Jones | Total | |
|---|---|---|---|
| Reference | ‐ | ‐ | ‐ |
| Mu | +8.42 | −6.38 | +2.04 |
| Delta | −2.58 | +6.22 | +3.64 |
| Delta Plus | +20.24 | +2.16 | +22.40 |
Note: SR Coulomb and Lennard‐Jones contributions are explicitly reported. Values reported as kcal/mol, are averaged over the last 100 ns of the simulated equilibrium trajectories.
Abbreviation: SR, short‐ranged.
Predicted differences between variants and reference Spike domain in interaction with antibodies
| Variant | Complexed antibody | Mutation | DrugScorePPIΔΔG | |
|---|---|---|---|---|
| Mu | COVA2‐04 (7JMO) | N501Y | H‐bond to S29 of L1 CDR | 2.46 (0.57) |
| Delta plus | COVA2‐04 (7JMO) | K417N | Loss of K417‐E97 salt bridge (CDR H3) | 0.52 (1.13) |
| Loss of K417‐Y52 H‐bond (CDR H2) | ‐ | |||
| Mu | COVA2‐39 (7JMP) | E484K | Loss of H‐bond E484‐NH‐G54 (CDR H2) | ‐ |
| Mu | 4A8 (7C2L) | Y145N | Loss of VdW interaction to A101, V102, and Y111 (CDR H3) | 0.01 (1.98) |
ΔΔG of the reference residue is reported in parentheses.
Figure 2(A) Complex RBD‐COVA2‐04 reported in the Protein Data Bank (PDB) structure 7JMO. Red and blue cartoons indicate the Ab heavy and light chain, respectively, while the RBD is colored grey. (B) Top: comparison of the interfaces between the reference and the model Mu RBD and the mAb COVA2‐04 at position 501. Bottom: comparison of the interfaces between the reference and the Delta plus RBD and the mAb COVA2‐04 at position 417. Residue side chains and NAG substituent are reported as stick models
Figure 3(A) Complex NTD‐4A8 reported in the Protein Data Bank (PDB) structure 7C2L. Red and blue cartoons indicate the Ab heavy (H) and light chain (L), respectively, while the NTD is colored grey. (B) Comparison of the interfaces between the reference (top) and the model Mu (bottom) NTD and the mAb 4A8