Research
The COVID-19 pandemic demonstrated the tremendous impact an infectious disease can have on warfighter operational availability, but that pales in comparison with the potential impact of a biowarfare attack. The Generative Unconstrained Intelligent Drug Engineering (GUIDE) program enables a significant shift from past approaches to threat preparedness and offers the opportunity to chart new waters and redefine biological defense.
Protein Engineering
Design, production, and testing of soluble surrogates of complex viral proteins to be used in high throughput screening assays for the detection of antibody binding and to support structural studies. Sandia subject matter experts have experience with a range of viral families and difficulties commonly encountered in viral protein engineering. Our production pipeline allows us to screen candidate antigenic proteins to see which perform best in downstream GUIDE assays.
Molecular Design and Construct Generation
Design, production, and generation of DNA libraries and arrayed plasmid constructs. Constructs are generated using automated liquid handlers and a robust pipeline and are ultimately used for a diverse set of experimental conditions, including high-throughput production of protein arrays.
High Throughput Protein Expression, Purification, and Characterization
Automated liquid handlers are employed to increase the throughput of protein production, both for target agent antigens and antibodies. These proteins can be characterized in downstream binding kinetics assays.
High Throughput Antibody Affinity Assays
We use surface plasmon resonance (SPR) and biolayer interferometry (BLI) to analyze hundreds of thousand antibody-antigen interactions and measure tens of thousand sets of kinetic constants (KD, kd, and ka) in a single experiment.
Pseudovirus and Live Virus Neutralization Assays
We have experience designing replication competent chimeric virus and replication deficient pseudoviruses that enable virology assays such as neutralization and medical countermeasure resistance profiling. Using a strategy of basing the designs on backbones from non-pathogenic or attenuated vaccine strain viruses allows for assay optimization while prioritizing safety. The incorporation of reporter molecules supports high throughput screening pipelines to allow for micro-neutralization assays requiring a minimal amount of test antibodies.
Structural Biology
A new Tundra cryo TEM is available onsite, capable of generating high resolution molecular structures that inform or validate computational therapeutic design. GUIDE employs senior structural biologists and supports structural biologists in training. Significant additional crystallography, CryoEM, and NRM capabilities are also available through our extended research network.
Yeast, Phage, and CHO Library Generation and Screening Capabilities
The GUIDE team has decades of experience in generation and high-throughput analysis of antibody (scFv, nanobody, and Fab) libraries, displayed on phage and/or yeast. We are also developing single-landing pad CHO cells for generation of IgG libraries. These different libraries are sorted en masse based on phenotype, by mags beads (phage and yeast), and flow cytometry (yeast and CHO). We also use flow cytometry for high-throughput kinetic characterization of monoclonal antibodies displayed on yeast and expressed in CHO.
Sequencing
We have long and short read next generation sequencing (NGS) capabilities (PacBio, Nanopore, Illumina) and custom-tailored platforms for NGS sequencing analysis and phenotype assignment.
Preempting threats with prototype preparedness
GUIDE’s interagency approach allows for computational ‘retargeting’ of existing MCMs. Prototypes represent larger threat families, or groups of toxins, bacteria, or viruses. If the biothreat space is a vast ocean and each threat is an island, threat families can be thought of as archipelagos of related threats.
Deep knowledge about one or more prototype islands in the archipelago and availability of MCMs to address those threats allow GUIDE to preemptively retarget MCMs across the archipelago. This method can be used to rapidly respond to an unanticipated threat such as an engineered virus related to an existing viral prototype.
Prototype preparedness requires a comprehensive view of the threat landscape, an expert-informed approach to prototype selection, and the continued refinement of retargeting tools and models to create and validate MCM solutions. The combination of strategically positioned prototype islands with advanced high-performance computing for biologics and small molecule development allows GUIDE to match the dynamic nature of the evolving threat landscape and offers the potential for fully preemptive preparedness across a range of threats.
