Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor

Abstract

The severe acute respiratory syndrome virus-2 (SARS CoV-2) infection has resulted in the current global pandemic. The binding of SARS CoV-2 spike protein receptor-binding domain (RBD) to the human angiotensin converting enzyme-2 (ACE-2) receptor causes the host infection. The spike protein has undergone several mutations with reference to the initial strain isolated during December 2019 from Wuhan, China. A number of these mutant strains have been reported as variants of concern and as variants being monitored. Some of these mutants are known to be responsible for increased transmissibility of the virus. The reason for the increased transmissibility caused by the point mutations can be understood by studying the structural implications and inter-molecular interactions in the binding of viral spike protein RBD and human ACE-2. Here, we use the crystal structure of the RBD in complex with ACE-2 available in the public domain and analyse the 250 ns molecular dynamics (MD) simulations of wild-type and mutants; K417N, K417T, N440K, N501Y, L452R, T478K, E484K and S494P. The ionic, hydrophobic and hydrogen bond interactions, amino acid residue flexibility, binding energies and structural variations are characterized. The MD simulations provide clues to the molecular mechanisms of ACE-2 receptor binding in wild-type and mutant complexes. The mutant spike proteins RBD were associated with greater binding affinity with ACE-2 receptor.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS CoV-2
• spike protein receptor-binding domain
• Angiotensin converting enzyme-2
• K417N
• K417T
• N440K
• L452R
• T478K
• E484K
• S494P
• N501Y mutants
• Molecular dynamics simulations

Acknowledgements

The authors thank DST-PURSE and UGC UPE2 for funding and CMSD for computational facilities. GKRSN thanks, University of Hyderabad, UGC for the non-NET fellowship.

Disclosure statement

No potential conflict of interest was reported by the author(s).