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Screening coronavirus and human proteins for sialic acid binding sites using a docking approach
AIMS Biophysics ; 8(3):248-263, 2021.
Article in English | Scopus | ID: covidwho-1367953
ABSTRACT
The initial step of interaction of some pathogens with the host is driven by the interaction of glycoproteins of either side via endcaps of their glycans. These end caps consist of sialic acids or sugar molecules. Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are found to use this route of interaction. The strength and spatial interactions on the single molecule level of sialic acids with either the spike (S) protein of SARS coronaviruses, or human angiotensin-converting enzyme 2 (ACE2) and furin are probed and compared to the binding modes of those sugar molecules which are present in glycans of glycoproteins. The protocol of using single molecules is seen as a simplified but effective mimic of the complex mode of interaction of the glycans. Averaged estimated binding energies from a docking approach result in preferential binding of the sialic acids to a specific binding site of the S protein of human coronavirus OC43 (HCoV-OC43). Furin is proposed to provide better binding sites for sialic acids than ACE2, albeit outweighed by sites for other sugar molecules. Absolute minimal estimated binding energies indicate weak binding affinities and are indifferent to the type of sugar molecules and the proteins. Neither the proposed best binding sites of the sialic acids nor those of the sugar molecules overlap with any of the cleavage sites at the S protein and the active sites of the human proteins. © 2021, AIMS Biophysics. All rights reserved.

Full text: Available Collection: Databases of international organizations Database: Scopus Type of study: Diagnostic study / Screening study Language: English Journal: AIMS Biophysics Year: 2021 Document Type: Article

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Full text: Available Collection: Databases of international organizations Database: Scopus Type of study: Diagnostic study / Screening study Language: English Journal: AIMS Biophysics Year: 2021 Document Type: Article