R35GM141818

Hybrid Methods for Dynamic Structure Analysis of Proteins from Pathogenic Microorganisms - Project Summary

This research program aims to investigate the general hypothesis that understanding the conformational diversity of proteins will provide new insights into their biology and enable medical research. The program is directed towards two classes of systems: integral membrane proteins (IMPs) and viral-host interactions.

Integral membrane proteins play critical roles as gatekeepers, receptors, transporters, homeostasis regulators, and drug targets. These functions are mediated by the conformational plasticity of the IMP in the membrane environment. However, preparing and reconstituting IMPS in appropriate membrane mimicking environments is challenging. Therefore, cost-effective technologies for isotope-enrichment in condensed volumes, hybrid approaches combining NMR with evolutionary co-variation (ECS), novel methods of contact prediction, and innovative modeling methods from the protein structure prediction community will be applied to structure-function studies of IMPS. The selected IMPS, chosen from important human pathogens including E. coli, K. pneumoniae, and P. aeruginosa, are potential targets for antibiotic discovery. ECS will also be combined with NMR data to determine structures of multiple "native states" of proteins.

The second component of the program is directed towards viral-host biomolecular complexes and antiviral drug discovery. Innovative paramagnetic NMR methods, together with small angle X-ray scattering (SAXS), electron-electron double resonance spectroscopy (DEER), and Förster resonance energy transfer (FRET), will be utilized to rigorously define dynamic interdomain structural distributions conferred by the partially-ordered linkers of the Murine Moloney Leukemia Virus (MLV) integrase (IN). These data will be interpreted in the context of maximum occupancy probabilities (MAXOCC) and used to probe the role(s) of this flexibility in the gene integration mechanisms of G-retroviruses. Interdomain linkers also function to provide flexibility needed for binding partner promiscuity. The program will also determine how the interdomain linker sequences of Influenza non-structural protein 1 (NS1) confer appropriate plasticity to define its specificity and affinity for host proteins and RNAs. This structural and functional promiscuity underlies NS1's mechanisms for suppressing the cellular innate immune response to influenza infection, and rigorous characterization of its dynamic structural basis will provide fundamental information for live-attenuated virus vaccine development.

The program will also apply its platform to investigate drugs that inhibit SARS-CoV2 virus by binding its main protease (MPro). Three drugs, already approved for use in humans and originally designed to inhibit the NSP3/4A protease of Hepatitis C virus, have been identified to also inhibit SARS-CoV2 in viral replication assays at low micromolar concentrations. Computational docking studies have also identified several other FDA-approved drugs that may inhibit MPro. Enzyme kinetic, biophysical chemistry, and X-ray crystallography studies will be used to characterize complexes formed between these protease inhibitor drugs and MPro, and to develop their potential as COVID-19 therapeutics or as lead compounds for new therapeutic development.

Rensselaer Polytechnic Institute

THE NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES (NIGMS) SUPPORTS BASIC RESEARCH THAT INCREASES OUR UNDERSTANDING OF BIOLOGICAL PROCESSES AND LAYS THE FOUNDATION FOR ADVANCES IN DISEASE DIAGNOSIS, TREATMENT, AND PREVENTION. NIGMS ALSO SUPPORTS RESEARCH IN SPECIFIC CLINICAL AREAS THAT AFFECT MULTIPLE ORGAN SYSTEMS: ANESTHESIOLOGY AND PERI-OPERATIVE PAIN, CLINICAL PHARMACOLOGY ?COMMON TO MULTIPLE DRUGS AND TREATMENTS, AND INJURY, CRITICAL ILLNESS, SEPSIS, AND WOUND HEALING.? NIGMS-FUNDED SCIENTISTS INVESTIGATE HOW LIVING SYSTEMS WORK AT A RANGE OF LEVELSFROM MOLECULES AND CELLS TO TISSUES AND ORGANSIN RESEARCH ORGANISMS, HUMANS, AND POPULATIONS. ADDITIONALLY, TO ENSURE THE VITALITY AND CONTINUED PRODUCTIVITY OF THE RESEARCH ENTERPRISE, NIGMS PROVIDES LEADERSHIP IN SUPPORTING THE TRAINING OF THE NEXT GENERATION OF SCIENTISTS, ENHANCING THE DIVERSITY OF THE SCIENTIFIC WORKFORCE, AND DEVELOPING RESEARCH CAPACITY THROUGHOUT THE COUNTRY.

93.859 - Biomedical Research and Research Training

National Institute of General Medical Sciences (NIGMS) [HHS - NIH]

Troy, New York 121804113 United States

Single Zip Code

Maximizing Investigators' Research Award (R35 - Clinical Trial Optional) (PAR-19-367)

Amendment Since initial award the total obligations have increased 400% from $658,000 to $3,290,000.