This National Science Foundation (NSF) Biological Sciences program grant to Yale University, totaling $940,000 over 3 years beginning March 1, 2024, aims to systematically identify features of human and viral messenger RNAs (mRNAs) that regulate protein production. The project will employ a massively parallel reporter assay to quantify the impact of RNA modifications, structured RNA elements, and cell-specific factors on mRNA translation. Insights gained will provide a comprehensive...
This $1.8 million project grant from the National Science Foundation's Biological Sciences program (CFDA 47.074) will fund research at Cornell University to develop single molecule tools and techniques for studying coronavirus membrane fusion. The goal is to understand the relationship between coronavirus fusion peptide sequence and target host cell membranes at the nanoscale. Specifically, the awardee will identify and measure the physicochemical interactions between the coronavirus spike...
This Project Grant award of $582,618.00 was provided by the National Institute of Allergy and Infectious Diseases (NIAID) under the Allergy and Infectious Diseases Research Federal Grant Program (CFDA 93.855). The grant supports research to determine the mechanisms by which RNA N6-methyladenosine (m6A) and pseudouridine (Ψ) modifications modulate SARS-CoV-2 replication, gene expression, immunity, and pathogenesis. Key activities include using CRISPR-Cas9 to knock out host RNA...
This Project Grant award, provided by the National Institute of General Medical Sciences (NIGMS) under the Biomedical Research and Research Training program (CFDA 93.859), aims to measure and understand the molecular mechanisms of viral nucleocapsid self-assembly and disassembly. The $370,190 award, effective May 10, 2025 through March 31, 2030, will use a combination of quantitative experimental methods, including interferometric scattering microscopy and cryo-electron microscopy, to study...
This federal Project Grant award from the National Institute of General Medical Sciences (NIGMS) under CFDA 93.859 Biomedical Research and Research Training program provides $447,548 to Brigham Young University to investigate the molecular mechanism by which the SARS-CoV-2 virus hijacks the host cell chaperone system to replicate itself. The research aims to thoroughly test the hypothesis that the SARS-CoV-2 non-structural protein 12 (NSP12), the catalytic subunit of the RNA polymerase, is...
This $131,988 Project Grant from the National Heart, Lung and Blood Institute, part of the Department of Health and Human Services, supports research targeting determinants of SARS-CoV-2 host interaction in airways. Funded through the Cardiovascular Diseases Research program, the grant aims to identify master regulator proteins that mechanistically regulate SARS-CoV-2 interactions in the airways. Using organotypic airway epithelial culture and systems biology tools at Columbia University, the...
This $1,000,000 Cooperative Agreement awarded by the National Science Foundation (NSF) under the Technology, Innovation, and Partnerships (TIP) program (CFDA 47.084) supports research and development efforts by Akanocure Pharmaceuticals Inc. to optimize a novel, broad-spectrum antiviral and immunomodulatory agent for oral administration against coronaviruses. The project focuses on lead optimization, including the design, synthesis, and testing of analogs with improved drug-like properties for...
This Project Grant award from the National Institute of Allergy and Infectious Diseases (NIAID), under the Allergy and Infectious Diseases Research federal grant program (CFDA 93.855), provides $489,500 to support structural studies of the full-length nucleocapsid (N) protein of SARS-CoV-2. The goal is to determine the high-resolution structure of the full-length N protein in complex with the viral RNA using cryogenic electron microscopy. This research aims to advance the understanding of the...
This National Science Foundation (NSF) Mathematical and Physical Sciences (CFDA 47.049) project grant award of $1,500,000 supports research by Dr. Tamar Schlick of New York University and Dr. Alain Laederach of the University of North Carolina at Chapel Hill. The project aims to develop advanced computational tools to predict and control how viral protein synthesis is affected by programmed ribosomal frameshifting (PRF) - the mechanism by which viruses and human cells modify gene expression. Key...
This Project Grant award of $892,050.00 from the National Institute of Allergy and Infectious Diseases (NIAID) under the Allergy and Infectious Diseases Research program (CFDA 93.855) will fund research at the University of Missouri at Kansas City (UMKC) to investigate how plant viruses modulate host chromatin dynamics and gene expression. The key objectives are to: Determine how the PEMV2 virus P26 protein induces chromatin compaction and alters host gene expression, potentially repressing...
MRNA NUCLEAR EXPORT MACHINERY AS TARGET OF SARS-COV-2 NSP1 PROTEIN - THE GLOBAL COVID-19 PANDEMIC CAUSED BY THE SARS-COV-2 OUTBREAK UNDERSCORES THE NEED FOR UNDERSTANDING VIRAL-HOST INTERACTIONS THAT IMPACT HOST GENE EXPRESSION AND ANTIVIRAL RESPONSES. A CRITICAL VIRULENCE FACTOR OF CORONAVIRUSES IS THE NONSTRUCTURAL PROTEIN 1 (NSP1). WE UNCOVERED A PREVIOUSLY UNKNOWN MECHANISM OF NSP1- MEDIATED INHIBITION OF HOST ANTIVIRAL RESPONSES: NSP1 TARGETS THE CELLULAR MRNA NUCLEAR EXPORT PATHWAY. NUCLEAR EXPORT OF CELLULAR MRNAS THROUGH THE NUCLEAR PORE COMPLEX (NPC) IS OBLIGATORY FOR EUKARYOTIC GENE EXPRESSION INCLUDING THOSE GENES ENCODING ANTIVIRAL FACTORS. BY CONTRAST, SARS-COV-2 MRNA SYNTHESIS TAKES PLACE AT VIRAL TRANSCRIPTIONAL FACTORIES IN THE CYTOPLASM. WE HAVE DEMONSTRATED THAT SARS-COV-2 NSP1 PROTEIN INHIBITS HOST MRNA NUCLEAR EXPORT BY TARGETING THE CELLULAR NXF1-NXT1 COMPLEX, A RECEPTOR REQUIRED FOR MRNA TRANSLOCATION THROUGH THE NPC TO THE CYTOPLASM. WE IDENTIFIED MUTATIONS IN NSP1 THAT SPECIFICALLY REDUCE ITS BINDING TO NXF1- NXT1. IMPORTANTLY, A SARS-COV-2 RECOMBINANT VIRUS CARRYING A MUTANT NSP1 DEFICIENT IN NXF1-NXT1 BINDING IS UNABLE TO INHIBIT MRNA NUCLEAR EXPORT AND IS ATTENUATED IN CELLS AND IN MICE. TOGETHER, OUR DATA INDICATE THAT NSP1 IS A REGULATOR OF HOST MRNA NUCLEAR EXPORT VIA BLOCKING NXF1 FUNCTION, OVERCOMING CELLULAR ANTIVIRAL RESPONSES. THIS PROPOSAL COMBINES THE SYNERGISTIC EXPERTISE BETWEEN THE PRINCIPAL INVESTIGATORS IN BIOCHEMISTRY, CELL BIOLOGY, STRUCTURAL BIOLOGY, AND VIRAL PATHOGENESIS TO INVESTIGATE IN DEPTH THE MOLECULAR MECHANISMS OF SARS-COV-2 NSP1 PROTEIN FUNCTION AS INHIBITOR OF MRNA NUCLEAR EXPORT AND ITS IMPACT ON THE VIRUS LIFE CYCLE AND ON VIRULENCE. IN AIM 1, WE WILL USE BIOCHEMICAL, GENETIC, AND IMAGING APPROACHES TO DETERMINE THE INTERACTIONS WITHIN THE MRNA EXPORT MACHINERY THAT LEAD TO NSP1 INHIBITION OF MRNA EXPORT. IN ADDITION, WE WILL USE A COMBINATION OF BIOPHYSICAL AND STRUCTURAL BIOLOGY APPROACHES TO DETERMINE THE MOLECULAR BASIS FOR THE RECOGNITION BETWEEN NSP1 AND NXF1-NXT1. THESE FINDINGS WILL UNCOVER NEW MECHANISMS THAT MEDIATE OR REGULATE CELLULAR MRNA NUCLEAR EXPORT AND HOW THEY ARE TARGETED BY SARS-COV-2. IN AIM 2, WE WILL ASSESS THE FUNCTIONS OF THE NSP1-NXF1 INTERACTION DURING VIRUS REPLICATION AND PATHOGENESIS. WE WILL GENERATE LOSS-OF-FUNCTION RECOMBINANT VIRUSES CARRYING NSP1 MUTANTS DEFECTIVE IN NXF1 BINDING AND INVESTIGATE THE IMPACT OF THESE MUTATIONS ON HOST MRNA EXPORT, VIRAL REPLICATION, INDUCTION OF HOST RESPONSES IN INFECTED CELLS, AND ON VIRAL PATHOGENESIS IN TWO ANIMAL MODELS, MICE AND HAMSTERS. ADDITIONALLY, NSP1 POLYMORPHISMS ASSOCIATED WITH NEW VARIANTS OF CONCERN HAVE BEEN FOUND. WE WILL THEREFORE ADDRESS THE FUNCTIONAL SIGNIFICANCE OF THESE POLYMORPHISMS FOR THE NSP1- NXF1 INTERACTION AND FOR VIRAL PATHOGENESIS. MOREOVER, WE WILL IDENTIFY THE HOST MRNAS WHOSE NUCLEAR EXPORT ARE IMPACTED BY NSP1 AND DETERMINE THEIR ROLE IN ANTIVIRAL RESPONSE. THESE EXTENSIVE STUDIES WILL LIKELY NOT ONLY DEFINE NOVEL VIRULENCE FUNCTION(S) OF SARS-COV-2 NSP1, BUT ALSO SHED LIGHT ON NOVEL ANTIVIRAL DEFENSE MECHANISMS. SINCE ANTAGONIZING NSP1 FUNCTION RESULTS IN EXPRESSION OF MRNAS ENCODING ANTIVIRAL FACTORS, OUR PROPOSED STUDIES MAY UNCOVER NEW STRATEGIES FOR DESIGNING ANTIVIRALS AGAINST SARS-COV-2.