Impact of the double mutants on spike protein of SARS-CoV-2 B.1.617 lineage to the human ACE2 receptor binding: A structural insight

• The recent emergence of novel SARS-CoV-2 variants has threatened the efforts to contain the COVID-19 pandemic. The emergence of these “variants of concern” has increased viral transmissibility or immune escape and has supplanted the ancestral strains. The novel variants harbored by the B.1.617 lineage (Kappa and Delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. The double mutations carried by these novel variants are primarily responsible for an upsurge number of COVID-19 cases in India. In this study, we thoroughly investigated the impact of these double mutations on the binding capability to the human host receptor. We performed several structural analyses and found that the studied double mutations increase the binding affinity of the spike protein to the human host receptor (ACE2). Furthermore, our study showed that these double mutants might be a dominant contributor enhancing the receptor-binding affinity of SARS-CoV-2 and consequently making it more stable. We also investigated the impact of these mutations on the binding affinity of two monoclonal antibodies (Abs) (2-15 and LY-CoV555) and found that the presence of the double mutations also hinders its binding with the studied Abs. The principal component analysis, free energy landscape, intermolecular interaction, and other investigations provided a deeper structural insight to better understand the molecular mechanism responsible for increased viral transmissibility of these variants. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Ämnesord

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Microbiology in the medical area (hsv//eng)

Nyckelord

COVID-19

Delta variant

Double mutant

Kappa variant

Molecular dynamics

SARS-CoV-2

Variant

angiotensin converting enzyme 2

bamlanivimab

monoclonal antibody

nonstructural protein 3

receptor binding domain

unclassified drug

viral protein

virus spike protein

Article

binding affinity

binding site

computer simulation

controlled study

crystal structure

gene interaction

gene mutation

genetic analysis

human

hydrogen bond

hydrophobicity

mathematical analysis

molecular docking

molecular interaction

nonhuman

pandemic

principal component analysis

receptor binding

SARS-CoV-2 variant VUI-21APR-01

virus transmission

Publikations- och innehållstyp

ref (ämneskategori)

art (ämneskategori)