Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations

Kundan Solanki; Sajjan Rajpoot; Ashutosh Kumar; Kam Y J Zhang; Tomokazu Ohishi; Nik Hirani; Khandu Wadhonkar; Pramod Patidar; Qiuwei Pan; Mirza S Baig

doi:10.2217/fvl-2022-0003

Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations

Kundan Solanki, Sajjan Rajpoot, Ashutosh Kumar, Kam Y J Zhang, Tomokazu Ohishi, Nik Hirani, Khandu Wadhonkar, Pramod Patidar, Qiuwei Pan^*, Mirza S Baig^*

^*Corresponding author for this work

Gastroenterology & Hepatology

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.

Original language	English
Pages (from-to)	723-732
Number of pages	10
Journal	Future Virology
Volume	17
Issue number	10
Early online date	2 Aug 2022
DOIs	https://doi.org/10.2217/fvl-2022-0003
Publication status	Published - 1 Oct 2022

Bibliographical note

Financial & competing interests disclosure
This work is supported by Cumulative Professional Development Allowance (CPDA) and Research Development Fund (RDF) from
the Indian Institute of Technology Indore (IITI) to MS Baig. The authors have no other relevant affiliations or financial involvement
with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the
manuscript apart from those disclosed.
No writing assistance was utilized in the production of this manuscript.

© 2022 Mirza S Baig.

Funding Information:
This work is supported by Cumulative Professional Development Allowance (CPDA) and Research Development Fund (RDF) from the Indian Institute of Technology Indore (IITI) to MS Baig. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Publisher Copyright:
© 2022 Mirza S Baig.

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fvl-2022-0003Final published version, 8.59 MBLicence: CC BY

Cite this

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title = "Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations",

abstract = "Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials \& methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.",

author = "Kundan Solanki and Sajjan Rajpoot and Ashutosh Kumar and \{J Zhang\}, \{Kam Y\} and Tomokazu Ohishi and Nik Hirani and Khandu Wadhonkar and Pramod Patidar and Qiuwei Pan and Baig, \{Mirza S\}",

note = "Financial \& competing interests disclosure This work is supported by Cumulative Professional Development Allowance (CPDA) and Research Development Fund (RDF) from the Indian Institute of Technology Indore (IITI) to MS Baig. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript. {\textcopyright} 2022 Mirza S Baig. Funding Information: This work is supported by Cumulative Professional Development Allowance (CPDA) and Research Development Fund (RDF) from the Indian Institute of Technology Indore (IITI) to MS Baig. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. Publisher Copyright: {\textcopyright} 2022 Mirza S Baig.",

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AU - Solanki, Kundan

AU - Rajpoot, Sajjan

AU - Kumar, Ashutosh

AU - J Zhang, Kam Y

AU - Ohishi, Tomokazu

AU - Hirani, Nik

AU - Wadhonkar, Khandu

AU - Patidar, Pramod

AU - Pan, Qiuwei

AU - Baig, Mirza S

N1 - Financial & competing interests disclosure This work is supported by Cumulative Professional Development Allowance (CPDA) and Research Development Fund (RDF) from the Indian Institute of Technology Indore (IITI) to MS Baig. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript. © 2022 Mirza S Baig. Funding Information: This work is supported by Cumulative Professional Development Allowance (CPDA) and Research Development Fund (RDF) from the Indian Institute of Technology Indore (IITI) to MS Baig. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. Publisher Copyright: © 2022 Mirza S Baig.

PY - 2022/10/1

Y1 - 2022/10/1

N2 - Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.

AB - Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.

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EP - 732

JO - Future Virology

JF - Future Virology

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ER -

Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations

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