Structural and Simulation analysis of hot spot residues interactions of SARS-CoV 2 with Human ACE2 receptor.

Structural and Simulation analysis of hot spot residues interactions of SARS-CoV 2 with Human ACE2 receptor.

Publication date: May 25, 2020

The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE 2) receptor initiates the entry of corona virus into the host cells leading to the infection. However, considering the mutations reported in the SARS-CoV 2 (nCoV), the structural changes and the binding interactions of the S-protein RBD of nCoV were not clear. The present study was designed to elucidate the structural changes, hot spot binding residues and their interactions between the nCoV S-protein RBD and ACE2 receptor through computational approaches. Based on the sequence alignment, a total of 58 residues were found mutated in nCoV S-protein RBD. These mutations led to the structural changes in the nCoV S-protein RBD 3d structure with 4 helices, 10 sheets and intermittent loops. The nCoV RBD was found binding to ACE2 receptor with 11 hydrogen bonds and 1 salt bridge. The major hot spot amino acids involved in the binding identified by interaction analysis after simulations includes Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 34 amino acid residues of ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 417 residues in nCoV S-protein RBD. Based on the hydrogen bonding, RMSD and RMSF, total and potential energies, the nCoV was found binding to ACE 2 receptor with higher stability and rigidity. Concluding, the hotspots information will be useful in designing blockers for the nCoV spike protein RBD.

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Concepts Keywords
Amino Acid Androgen receptor
Amino Acids Coronavirus
Asn Coronaviridae
Asp Intracellular receptors
Corona Virus Animal virology
Dyn Transcription factors
Enzyme Viruses
Gln Branches of biology
Glu EGR1
Helices Angiotensin
Hydrogen Bonding Simulation
Hydrogen Bonds
Infection
Lys
Pandemic
Potential Energies
Protein
RBD
Receptor
RMSD
Salt Bridge
SARS
Sequence Alignment
Tyr

Semantics

Type Source Name
disease MESH virus disease
drug DRUGBANK Angiotensin II
disease MESH infection
drug DRUGBANK Amino acids
drug DRUGBANK Glutamic Acid
drug DRUGBANK L-Tyrosine
drug DRUGBANK L-Aspartic Acid
drug DRUGBANK L-Lysine
drug DRUGBANK L-Asparagine

Original Article

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