Screening and affinity optimization of single domain antibody targeting the SARS-CoV-2 nucleocapsid protein

Qian Yang; Mengru Yan; Juan Lin; Yongkang Lu; Shuang Lin; Zhong Li; He Wang; Juhua Yang; Nanwen Zhang; Xiaole Chen

doi:10.7717/peerj.17846

Screening and affinity optimization of single domain antibody targeting the SARS-CoV-2 nucleocapsid protein

PeerJ. 2024 Aug 30:12:e17846. doi: 10.7717/peerj.17846. eCollection 2024.

Authors

Qian Yang^#^{1

2}, Mengru Yan^#¹, Juan Lin¹, Yongkang Lu¹, Shuang Lin¹, Zhong Li¹, He Wang³, Juhua Yang¹, Nanwen Zhang^{2

4}, Xiaole Chen^{1

5}

Affiliations

¹ Department of Bioengineering and Biopharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China.
² Fujian Key Laboratory of Natural Medicine Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China.
³ Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China.
⁴ Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, China.
⁵ Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, Fuzhou, Fujian, China.

^# Contributed equally.

Abstract

The coronavirus disease 2019 (COVID-19) pandemic, which caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), lead to a crisis with devastating disasters to global public economy and health. Several studies suggest that the SARS-CoV-2 nucleocapsid protein (N protein) is one of uppermost structural constituents of SARS-CoV-2 and is relatively conserved which could become a specific diagnostic marker. In this study, eight single domain antibodies recognized the N protein specifically which were named pN01-pN08 were screened using human phage display library. According to multiple sequence alignment and molecular docking analyses, the interaction mechanism between antibody and N protein was predicted. ELISA results indicated pN01-pN08 with high affinity to protein N. To improve their efficacy, two fusion proteins were prepared and their affinity was tested. These finding showed that fusion proteins had higher affinity than single domain antibodies and will be used as diagnosis for the pandemic of SARS-CoV-2.

Keywords: Fusion protein; Phage display; SARS-CoV-2; Single domain antibody.

MeSH terms

Antibodies, Viral* / immunology
Antibody Affinity
COVID-19* / diagnosis
COVID-19* / immunology
Coronavirus Nucleocapsid Proteins* / chemistry
Coronavirus Nucleocapsid Proteins* / immunology
Enzyme-Linked Immunosorbent Assay / methods
Humans
Molecular Docking Simulation*
Peptide Library
Phosphoproteins / chemistry
Phosphoproteins / immunology
Recombinant Fusion Proteins / chemistry
Recombinant Fusion Proteins / genetics
Recombinant Fusion Proteins / immunology
SARS-CoV-2* / immunology
Single-Domain Antibodies* / chemistry
Single-Domain Antibodies* / immunology

Substances

Single-Domain Antibodies
Coronavirus Nucleocapsid Proteins
Antibodies, Viral
nucleocapsid phosphoprotein, SARS-CoV-2
Phosphoproteins
Recombinant Fusion Proteins
Peptide Library

Grants and funding

This work was supported by the National Natural Science Foundation, China (Grant No. 81402842), the Natural Science Foundation of Fujian Province, China (Grant No. 2020J01634), the Emergency Project on New Coronavirus Pneumonia Prevention Research of Fujian Medical University (Grant No. 2020YJ004) and the Startup Fund for Scientific Research, Fujian Medical University (XRCZX2020032) previously identified as the “High-level Personnel Research Start-up Fund of Fujian Medical University (Grant No. 60000121)”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.