Binder design for targeting SARS-CoV-2 spike protein: An in silico perspective

Ali Etemadi; Hamid Reza Moradi; Farideh Mohammadian; Mohammad Hossein Karimi-Jafari; Babak Negahdari; Yazdan Asgari; Mohammadali Mazloomi

doi:10.1016/j.genrep.2021.101452

Binder design for targeting SARS-CoV-2 spike protein: An in silico perspective

Gene Rep. 2022 Mar:26:101452. doi: 10.1016/j.genrep.2021.101452. Epub 2021 Nov 26.

Authors

Ali Etemadi¹, Hamid Reza Moradi¹, Farideh Mohammadian², Mohammad Hossein Karimi-Jafari³, Babak Negahdari¹, Yazdan Asgari¹, Mohammadali Mazloomi¹

Affiliations

¹ Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
² Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
³ Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

Abstract

Introduction: The COVID-19 pandemic is now affecting all people around the world and getting worse. New antiviral medications are desperately needed other than the few approved medications that have shown no promising efficacy so far.

Methods: Here we report three blocking binders for targeting SARS-CoV-2 spike protein to block the interaction between the spike protein on the SARS-CoV-2 and the angiotensin-converting enzyme 2 (ACE2) receptors, responsible for viral homing into the alveolar epithelium type II cells (AECII).

Results: The design process is based on the collected natural scaffolds and using Rosetta interface for designing the binders.

Conclusion: Based on the structural analysis, three binders were selected, and the results showed that they might be promising as new therapeutic targets for blocking COVID-19.

Keywords: ACE2; Antiviral medications; Binder design; COVID-19; Pandemic; SARS.