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Principal Investigator: Weishan Huang
Organization: LOUISIANA STATE UNIV A&M COL BATON ROUGE
Fiscal Year: 2023
Award: $203,149
Funding agency: National Institute of Allergy and Infectious Diseases
Project Summary/Abstract
SARS-CoV-2, the etiological pathogen of COVID-19, has resulted in a pandemic. There remains an urgent
need for innovative technologies which facilitate the development of affordable antiviral precision medicine.
SARS-CoV-2 is an enveloped virus, and the structure of the trimeric spike protein clusters on the virion has been
solved. To develop innovative, affordable, and biocompatible antiviral candidates against SARS-CoV-2 infection
and transmission, we exploited the structural characteristics of viral surface proteins that can be matched at
nanoscale precision by engineered DNA nanostructure platforms. Based on the structure of the SARS-CoV-2
virion and surface spike trimer layout, we have synthesized a designer DNA nanostructure (DDN) that takes the
form of a macromolecular ‘net’ whose vertices are a precise mechanical match to the spacing and positioning of
the spike protein matrix displayed on the virus outer surface. We hypothesize that the structural properties and
the layout patterns of SARS-CoV-2 spike proteins can be exploited to design DDNs with nanoscale precision
which are capable of matching and capturing intact SARS-CoV-2 virions with ultrahigh binding avidity and
selectivity, thereby blocking SARS-CoV-2 infection. We have screened and found DNA aptamers and
nanobodies that are specific for the spike receptor-binding domain (RBD). These spike binders can be
incorporated into the ‘knots’ of the DDN net to allow the simultaneous binding of multiple DNA aptamers with
multiple spikes on the viral surface in a polyvalent, pattern-matching fashion. The DNA ‘net’-aptamer prototype
construct has afforded dramatic increase in SARS-CoV-2 binding avidity. This construct can work as a decoy to
block viral entry into host cells and is about 1,000-fold more potent than the free aptamer. In this R21 proposal,
we aim to extend this technology to enable the incorporation of multiple types of probes against spike RBD and
to validate the safety and effectiveness of DDNs in antiviral therapy in vitro and in vivo. We propose two specific
aims: to (1) design, synthesize, validate, and further optimize the virus-capturing avidity against various SARS-
CoV-2 variants of concern (VOCs); and (2) to determine the antiviral potency and cytotoxicity of the designed
DDNs during SARS-CoV-2 infections in vitro in human lung epithelial cells and in vivo in human ACE2-knockin
mice. Completion of this work will help us define the antiviral potency and safety of the DNA nanostructures that
are designed to perfectly match epitope layouts on the viral surface to capture and wrap live viruses. The
estimated cost of DDN treatment is approximately $10/dose (a price that likely decreases at large-scale
synthesis), making it an affordable therapy. This DDN platform may further contribute to the rapid development
of antiviral precision medicine against emerging SARS-CoV-2 VOCs, as well as other enveloped viruses such
as influenza and HIV.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><2019-nCoV S protein><2019-nCoV spike glycoprotein><2019-nCoV spike protein><2019-nCoV variant><2019-nCoV variant forms><2019-nCoV variant strains><ACE2><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Agar Gel Electrophoresis><Agarose Gel Electrophoresis><Agarose Gel Fractionation><Animal Model><Animal Models and Related Studies><Antigenic Determinants><Antigens><Antiviral Therapy><Area><Assay><Atomic Force Microscopy><Avidity><B.1.1.529><B.1.617.2><Binding><Binding Determinants><Bioassay><Biologic Assays><Biological Assay><Brazil P.1><Brazil variant><Brazilian variant><COVID-19><COVID-19 S protein><COVID-19 infection><COVID-19 spike glycoprotein><COVID-19 spike protein><COVID-19 variant><COVID-19 variant forms><COVID-19 variant strains><COVID-19 virus><COVID-19 virus infection><COVID19><COVID19 S protein><COVID19 infection><COVID19 spike glycoprotein><COVID19 spike protein><COVID19 virus><CV-19><CV19><Causality><Cell Body><Cell Surface Glycoproteins><Cell model><Cells><Cellular model><Characteristics><CoV-2><CoV2><Collection><DNA><Delta variant><Deoxyribonucleic Acid><Detection><Development><Dose><Effectiveness><Engineering><Epithelial Cells><Epitopes><Etiology><Exhibits><Force Microscopy><Gamma variant><Goals><Grippe><HIV><Human><Human Immunodeficiency Viruses><In Vitro><Infection><Influenza><KI mice><Knock-in Mouse><Knowledge><LAV-HTLV-III><Lung><Lung Respiratory System><Lymphadenopathy-Associated Virus><Lytotoxicity><Mechanics><Medicine><Membrane Glycoproteins><Membrane Protein Gene><Membrane Proteins><Membrane-Associated Proteins><Modern Man><Molecular><Molecular Genetics><Molecular Interaction><NIH><Nanostructures><Nanotechnology><National Institutes of Health><Omicron variant><P.1 strain><P.1 variant><Pattern><Position><Positioning Attribute><Preventive><Price><Property><Proteins><Receptor Protein><Resistance><Route><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 B.1.1.529><SARS-CoV-2 B.1.617.2><SARS-CoV-2 P.1><SARS-CoV-2 S protein><SARS-CoV-2 delta><SARS-CoV-2 infection><SARS-CoV-2 inhibitor><SARS-CoV-2 omicron><SARS-CoV-2 omicron variant><SARS-CoV-2 spike glycoprotein><SARS-CoV-2 spike protein><SARS-CoV-2 variant><SARS-CoV-2 variant forms><SARS-CoV-2 variant strains><SARS-CoV2><SARS-CoV2 S protein><SARS-CoV2 infection><SARS-CoV2 spike glycoprotein><SARS-CoV2 spike protein><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Safety><Scanning Force Microscopy><Sensitivity and Specificity><Series><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 S protein><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome coronavirus 2 inhibitor><Severe acute respiratory syndrome coronavirus 2 spike glycoprotein><Severe acute respiratory syndrome coronavirus 2 spike protein><Severe acute respiratory syndrome related corona virus 2><Shapes><Structure><Surface><Surface Glycoproteins><Surface Proteins><Technology><Testing><Therapeutic><Toxic effect><Toxicities><Transmission><United States National Institutes of Health><Validation><Viral><Viral Diseases><Virion><Virus><Virus Diseases><Virus Particle><Virus-HIV><Work><Wuhan coronavirus><after COVID-19 infection><after SARS-CoV-2 infection><after SARS-CoV2 infection><after infection by SARS-CoV-2><after severe acute respiratory distress 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