Document text
Principal Investigator: Thomas Miller Gallagher
Organization: LOYOLA UNIVERSITY CHICAGO
Fiscal Year: 2023
Award: $244,800
Funding agency: National Institute of Allergy and Infectious Diseases
PROJECT SUMMARY
The continuous adaptation of SARS-CoV-2 generates variants of concern (VOC). New VOCs arise
independently and outcompete previous ones, consistent with ever increasing viral fitness. Most VOC
adaptations reside in the spikes (S), the complex multidomain glycoprotein trimers that bind viruses to cells
and mediate virus-cell membrane fusion. Well-characterized adaptations in the S receptor binding domains
(RBDs) alter RBD structural dynamics, receptor affinities, and antibody interactions. However, adaptations in
other S domains remain largely under-evaluated. This includes the S2 domains that execute virus-cell
membrane fusion. This proposal aims to elucidate consequences of VOC adaptive changes in the S2 domains.
The current VOC, omicron (o), has accumulated over six S2 mutations. Our central objective is to evaluate the
ways these and other S2 adaptations alter S protein dynamics to facilitate human cell entry. We will utilize a
collection of viral membrane fusion and cell entry assay systems to determine whether S2 changes reset the
dynamics of transient S protein intermediate states. These transitory states include RBD elevations that control
receptor binding and S2 refoldings from prefusion to fusion intermediate and through to postfusion
configurations. Our assay systems will employ fusion-competent virus-like particles (VLPs) for sensitive
evaluation of entry steps, soluble receptors as probes for RBD exposures, HR2 peptides for detection of
specific S transitional intermediates, replication-competent VSVSARS-CoV-2-S for selecting HR2 peptide-resistant
variants, and SARS-CoV-2 replicons and recombinant SARS-CoV-2 viruses for convincingly assigning specific
S2 amino acid substitutions to consequential redirection of virus-cell entry pathways.
Our preliminary results suggest that omicron S2 adaptations operate allosterically to alter S-receptor
interactions. The first aim will determine how S2 fusion domains control RBDs and their interactions
with receptors. We will identify specific VOC S2 mutations that control receptor reactivity and S stability. We
will determine how these mutations change viral entry requirements. Our initial results also suggest that
omicron S2 mutations change the pace of the conformational transitions facilitating membrane fusion. The
second aim will determine how S2 mutations control dynamics of fusion domains. We will determine
whether the rates of S2 structural transitions vary between VOCs. We will also select and characterize variants
resistant to inhibitors of the S2 structural dynamics and will find out whether these resistant variants have
unique requirements for the receptors and proteases that determine cell susceptibility to infection.
The results of this study will clarify currently obscure selective forces driving the human adaptation of past (α,
β, γ, δ), current (ο), and future VOCs. We expect the results will illuminate properties of the membrane fusion –
inducing S2 domains in ways that reveal new targets for inhibition of CoV entry.
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><Affinity><Amino Acid Substitution><Amino Acids><Animals><Anti-viral Drug Resistance><Anti-viral Drug Resistant><Antibodies><Antiviral Drug Resistance><Antiviral Drug Resistant><Apical><Assay><B.1.1.529><Binding><Bioassay><Biochemical><Biologic Assays><Biological><Biological Assay><COVID-19 S protein><COVID-19 spike glycoprotein><COVID-19 spike protein><COVID-19 variant><COVID-19 variant forms><COVID-19 variant strains><COVID-19 virus><COVID19 S protein><COVID19 spike glycoprotein><COVID19 spike protein><COVID19 virus><Cell Body><Cell membrane><Cells><CoV S protein><CoV glycoprotein S><CoV spike glycoprotein><CoV spike protein><CoV-2><CoV2><Collection><Communication><Communities><Complex><Coronaviridae><Coronavirus><Coronavirus glycoprotein S><Coronavirus spike protein><Cytoplasmic Membrane><Detection><Distant><Endocytosis><Engineering><Equilibrium><Esteroproteases><Evaluation><Evolution><Future><Genetic Alteration><Genetic Change><Genetic defect><Glycoproteins><Goals><Human><Infection><Kinetics><Link><MERS corona virus><MERS coronavirus><MERS virus><MERS-CoV><Measures><Mediating><Membrane Fusion><Middle East Respiratory Syndrome Corona Virus><Middle East Respiratory Syndrome Coronavirus><Middle East Respiratory Syndrome Virus><Middle East Respiratory Syndrome-CoV><Middle East Respiratory coronavirus><Middle Eastern Respiratory Syndrome Corona virus><Middle Eastern Respiratory Syndrome Coronavirus><Middle Eastern Respiratory Syndrome Virus><Middle Eastern Respiratory Syndrome-CoV><Modern Man><Molecular Configuration><Molecular Conformation><Molecular Interaction><Molecular Stereochemistry><Mutation><Omicron variant><Pathway interactions><Peptidases><Peptide Hydrolases><Peptides><Plasma Membrane><Predisposition><Property><Protease Gene><Proteases><Protein Conformation><Protein Dynamics><Proteinases><Proteins><Proteolytic Enzymes><Receptor Cell><Receptor Protein><Recombinants><Replication Unit><Replicon><Resistance><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 B.1.1.529><SARS-CoV-2 S protein><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 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><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 spike glycoprotein><Severe acute respiratory syndrome coronavirus 2 spike protein><Severe acute respiratory syndrome related corona virus 2><Site><Structure><Surface><Susceptibility><System><Transmission><Variant><Variation><Viral><Viral Drug Resistance><Viral Receptor><Viral Shedding><Virulence><Virus><Virus Receptors><Virus Shedding><Virus-like particle><Wuhan coronavirus><aminoacid><balance><balance function><biologic><conformation><conformational><conformational conversion><conformational state><conformational transition><conformationally><conformations><corona virus><coronavirus S protein><coronavirus disease 2019 S protein><coronavirus disease 2019 spike glycoprotein><coronavirus disease 2019 spike protein><coronavirus disease 2019 variant><coronavirus disease 2019 variant forms><coronavirus disease 2019 variant strains><coronavirus disease 2019 virus><coronavirus disease-19 virus><coronavirus spike glycoprotein><driving force><genome mutation><global health><hCoV19><inhibitor><insight><nCoV2><omicron variant of COVID-19><omicron variant of SARS-CoV-2><pathway><plasmalemma><receptor><receptor binding><receptor bound><recombinant virus><resistance mutation><resistance to anti-viral><resistance to antiviral><resistant><resistant mutation><resistant to anti-viral><resistant to antiviral><severe acute respiratory syndrome coronavirus 2 B.1.1.529><severe acute respiratory syndrome coronavirus 2 variant><severe acute respiratory syndrome coronavirus 2 variant forms><severe acute respiratory syndrome coronavirus 2 variant strains><tool><transmission process><variants of concern><viral fitness><virus tropism><virus-like nanoparticles><viruslike particle>