Techniques assisting peptide vaccine and peptidomimetic design. Sidechain exposure in the SARS-CoV-2 spike glycoprotein.
Comput Biol Med
; 128: 104124, 2021 01.
Article
in English
| MEDLINE | ID: covidwho-938855
ABSTRACT
The aim of the present study is to discuss the design of peptide vaccines and peptidomimetics against SARS-COV-2, to develop and apply a method of protein structure analysis that is particularly appropriate to applying and discussing such design, and also to use that method to summarize some important features of the SARS-COV-2 spike protein sequence. A tool for assessing sidechain exposure in the SARS-CoV-2 spike glycoprotein is described. It extends to assessing accessibility of sidechains by considering several different three-dimensional structure determinations of SARS-CoV-2 and SARS-CoV-1 spike protein. The method is designed to be insensitive to a distance limit for counting neighboring atoms and the results are in good agreement with the physical chemical properties and exposure trends of the 20 naturally occurring sidechains. The spike protein sequence is analyzed with comment regarding exposable character. It includes studies of complexes with antibody elements and ACE2. These indicate changes in exposure at sites remote to those at which the antibody binds. They are of interest concerning design of synthetic peptide vaccines, and for peptidomimetics as a basis of drug discovery. The method was also developed in order to provide linear (one-dimensional) information that can be used along with other bioinformatics data of this kind in data mining and machine learning, potentially as genomic data regarding protein polymorphisms to be combined with more traditional clinical data.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Models, Molecular
/
Peptidomimetics
/
Spike Glycoprotein, Coronavirus
/
COVID-19 Vaccines
Type of study:
Prognostic study
/
Reviews
Topics:
Vaccines
Limits:
Humans
Language:
English
Journal:
Comput Biol Med
Year:
2021
Document Type:
Article
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