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Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study
- Source :
- Molecular Diversity
- Publication Year :
- 2021
- Publisher :
- Springer Science and Business Media LLC, 2021.
-
Abstract
- Short synthetic peptide molecules which bind to a specific target protein with a high affinity to exert its function are known as peptide aptamers. The high specificity of aptamers with small-molecule targets (metal ions, dyes and theophylline; ATP) is within 1 pM and 1 μM range, whereas with the proteins (thrombin, CD4 and antibodies) it is in the nanomolar range (which is equivalent to monoclonal antibodies). The recently identified coronavirus (SARS-CoV-2) genome encodes for various proteins, such as envelope, membrane, nucleocapsid, and spike protein. Among these, the protein necessary for the virus to enter inside the host cell is spike protein. The work focuses on designing peptide aptamer targeting the spike receptor-binding domain of SARS-CoV-2. The peptide aptamer has been designed by using bacterial Thioredoxin A as the scaffold protein and an 18-residue-long peptide. The tertiary structure of the peptide aptamer is modeled and docked to spike receptor-binding domain of SARS CoV2. Molecular dynamic simulation has been done to check the stability of the aptamer and receptor-binding domain complex. It was observed that the aptamer binds to spike receptor-binding domain of SARS-CoV-2 in a similar pattern as that of ACE2. The aptamer–receptor-binding domain complex was found to be stable in a 100 ns molecular dynamic simulation. The aptamer is also predicted to be non-antigenic, non-allergenic, non-hemolytic, non-inflammatory, water-soluble with high affinity toward ACE2 than serum albumin. Thus, peptide aptamer can be a novel approach for the therapeutic treatment for SARS-CoV-2. Graphical abstract
- Subjects :
- Scaffold protein
Peptide aptamer
medicine.drug_class
Aptamer
In silico
Peptide
Spike protein
010402 general chemistry
Monoclonal antibody
Antiviral Agents
01 natural sciences
Catalysis
Inorganic Chemistry
Drug Discovery
medicine
Humans
Physical and Theoretical Chemistry
Molecular Biology
chemistry.chemical_classification
Molecular dynamic simulation
SARS-CoV-2
010405 organic chemistry
Organic Chemistry
General Medicine
Protein tertiary structure
COVID-19 Drug Treatment
0104 chemical sciences
chemistry
Spike Glycoprotein, Coronavirus
Molecular docking
Biophysics
Original Article
Target protein
Thioredoxin
Peptides
Aptamers, Peptide
Protein Binding
Information Systems
Subjects
Details
- ISSN :
- 1573501X and 13811991
- Volume :
- 26
- Database :
- OpenAIRE
- Journal :
- Molecular Diversity
- Accession number :
- edsair.doi.dedup.....c867659c5b5e4dbe5e8306c5f8e807e7