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Title: Mutating novel interaction sites in NRP1 reduces SARS-CoV-2 spike protein internalization

Journal Article · · iScience

The global pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has become a severe global health problem because of its rapid spread. Both Ace2 and NRP1 provide initial viral binding sites for SARS-CoV-2. Here, we show that cysteine residues located in the vestigial plasminogen-apple-nematode (PAN) domain of NRP1 are necessary for SARS-CoV-2 spike protein internalization. Mutating novel cysteine residues in the PAN altered NRP1 stability and downstream activation of extracellular signal-regulated kinase (ERK) signaling pathway and impaired its interaction with the spike protein. This resulted in a significant reduction in spike protein abundance in Vero-E6 cells for the original, alpha, and delta SARS-CoV-2 variants even in the presence of the Ace2. Moreover, mutating these cysteine residues in NRP1 significantly lowered its association with Plexin-A1. As the spike protein is a critical component for targeted therapy, our biochemical study may represent a distinct mechanism to develop a path for future therapeutic discovery.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC)
Grant/Contract Number:
AC05-00OR22725; 3130F004
OSTI ID:
1958900
Alternate ID(s):
OSTI ID: 1993703
Journal Information:
iScience, Journal Name: iScience Vol. 26 Journal Issue: 4; ISSN 2589-0042
Publisher:
ElsevierCopyright Statement
Country of Publication:
Netherlands
Language:
English

References (76)

Neuropilin 1 is an entry factor that promotes EBV infection of nasopharyngeal epithelial cells journal February 2015
Antiviral drugs targeting endosomal membrane proteins inhibit distant animal and human pathogenic viruses journal February 2021
Virus-receptor interactions of SARS-CoV-2 spikereceptor-binding domain and human neuropilin-1 b1 domain journal July 2021
Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity journal November 2020
IKKβ phosphorylation regulates RPS3 nuclear translocation and NF-κB function during infection with Escherichia coli strain O157:H7 journal March 2011
Ribosomal Protein S5 Interacts with the Internal Ribosomal Entry Site of Hepatitis C Virus journal June 2001
Structural and Functional Relation of Neuropilins book January 2002
Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2 journal July 2021
Human DNA Virus Exploitation of the MAPK-ERK Cascade journal July 2019
Neuropilin Is a Semaphorin III Receptor journal August 1997
Comparative Proteomic Analysis of Anti-Cancer Mechanism by Periplocin Treatment in Lung Cancer Cells journal January 2014
Neuropilin regulation of angiogenesis journal November 2014
Cell surface detection of vimentin, ACE2 and SARS-CoV-2 Spike proteins reveals selective colocalization at primary cilia journal April 2022
Ribosomal Protein S3: A KH Domain Subunit in NF-κB Complexes that Mediates Selective Gene Regulation journal November 2007
A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect journal April 2014
Neuropilin-1 is a host factor for SARS-CoV-2 infection journal November 2020
The proteasome: Overview of structure and functions journal January 2009
β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway journal December 2020
Immunopathology of Hyperinflammation in COVID-19 journal January 2021
A Neuropilin-1 Antagonist Exerts Antitumor Immunity by Inhibiting the Suppressive Function of Intratumoral Regulatory T Cells journal January 2020
The PAN module: the N-terminal domains of plasminogen and hepatocyte growth factor are homologous with the apple domains of the prekallikrein family and with a novel domain found in numerous nematode proteins journal November 1999
Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding journal November 2007
Neuropilin-2, a Novel Member of the Neuropilin Family, Is a High Affinity Receptor for the Semaphorins Sema E and Sema IV but Not Sema III journal September 1997
NF-κB Pathway as a Potential Target for Treatment of Critical Stage COVID-19 Patients journal December 2020
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor journal April 2020
Plexin/neuropilin complexes mediate repulsion by the axonal guidance signal semaphorin 3A journal May 2000
Protein kinase LKB1 promotes RAB7-mediated neuropilin-1 degradation to inhibit angiogenesis journal September 2014
Early Events in the Endoplasmic Reticulum Unfolded Protein Response journal November 2018
MEK inhibitors reduce cellular expression of ACE2, pERK, pRb while stimulating NK-mediated cytotoxicity and attenuating inflammatory cytokines relevant to SARS-CoV-2 infection journal November 2020
C-end rule peptides mediate neuropilin-1-dependent cell, vascular, and tissue penetration journal September 2009
PSMB7 is associated with anthracycline resistance and is a prognostic biomarker in breast cancer journal December 2009
VEGF165 mediates formation of complexes containing VEGFR-2 and neuropilin-1 that enhance VEGF165-receptor binding journal January 2002
Maternal-larval population genetic traits in Stylophora pistillata, a hermaphroditic brooding coral species journal December 2011
Role of the ERK1/2 Signaling Pathway in the Replication of Junín and Tacaribe Viruses journal April 2018
Functional and Genomic Analyses Reveal an Essential Coordination between the Unfolded Protein Response and ER-Associated Degradation journal April 2000
Vascular endothelial growth factor regulates Stanniocalcin-1 expression via Neuropilin-1-dependent regulation of KDR and synergism with fibroblast growth Factor-2 journal March 2008
Inhibition of PlexA1-mediated brain tumor growth and tumor-associated angiogenesis using a transmembrane domain targeting peptide journal August 2016
Successful methods for transplanting fragments of Acropora formosa and Acropora hyacinthus journal May 2005
Targeting Neuropilin-1 with Nanobodies Reduces Colorectal Carcinoma Development journal November 2020
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability journal January 2013
Molecular basis of the new COVID-19 target neuropilin-1 in complex with SARS-CoV-2 S1 C-end rule peptide and small-molecule antagonists journal August 2021
Sox2 is associated with cancer stem-like properties in colorectal cancer journal December 2018
NF-κB c-Rel Dictates the Inflammatory Threshold by Acting as a Transcriptional Repressor journal March 2020
Neuropilin-1 Binds Vascular Endothelial Growth Factor 165, Placenta Growth Factor-2, and Heparin via Its b1b2 Domain journal July 2002
Receptor complexes for each of the Class 3 Semaphorins journal January 2012
The 20S proteasome processes NF-κB1 p105 into p50 in a translation-independent manner journal April 2006
RNA viruses and the mitogenic Raf/MEK/ERK signal transduction cascade journal August 2008
Characterization of the Interaction between Hantavirus Nucleocapsid Protein (N) and Ribosomal Protein S19 (RPS19) journal April 2011
Coronavirus infection, ER stress, apoptosis and innate immunity journal June 2014
A phase I study of the human monoclonal anti-NRP1 antibody MNRP1685A in patients with advanced solid tumors journal March 2014
Dual Function of NRP1 in Axon Guidance and Subcellular Target Recognition in Cerebellum journal September 2016
The immunoproteasome and viral infection: a complex regulator of inflammation journal January 2015
KIF20A promotes the development of fibrosarcoma via PI3K-Akt signaling pathway journal November 2022
Fast gapped-read alignment with Bowtie 2 journal March 2012
Rig-I regulates NF-κB activity through binding to Nf-κb1 3′-UTR mRNA journal April 2013
Neuropilin-1: A Key Protein to Consider in the Progression of Pediatric Brain Tumors journal July 2021
Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling journal July 2022
SARS-CoV-2 Infection-Induced Promoter Hypomethylation as an Epigenetic Modulator of Heat Shock Protein A1L (HSPA1L) Gene journal February 2021
The role of TACC3 in mitotic spindle organization journal August 2017
The A5 antigen, a candidate for the neuronal recognition molecule, has homologies to complement components and coagulation factors journal August 1991
Plexin-Neuropilin-1 Complexes Form Functional Semaphorin-3A Receptors journal October 1999
HMMER web server: 2015 update journal May 2015
Visna Virus-Induced Activation of MAPK Is Required for Virus Replication and Correlates with Virus-Induced Neuropathology journal January 2002
Origin and the Early Evolution of the Phylum Mollusca journal November 2017
Characterization of peptide binding to the SARS-CoV-2 host factor neuropilin journal October 2021
The many faces of semaphorins: from development to pathology journal October 2008
Signaling through the P38 and ERK pathways: a common link between HIV replication and the immune response journal August 2010
ERO1-β, a pancreas-specific disulfide oxidase, promotes insulin biogenesis and glucose homeostasis journal March 2010
An adhesive domain detected in functionally diverse receptors journal February 1993
Neuropilins: expression and roles in the epithelium journal March 2012
Neuropilins in the Context of Tumor Vasculature journal February 2019
Molluscs journal July 2012
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal December 2014
Effect of C-Terminal Sequence on Competitive Semaphorin Binding to Neuropilin-1 journal November 2013
RPLP1 and RPLP2 Are Essential Flavivirus Host Factors That Promote Early Viral Protein Accumulation journal February 2017
Induction of Herpud1 expression by ER stress is regulated by Nrf1 journal January 2015