Source: GRANITE POINT VENTURES LLC submitted to NRP
AI APPROACH TO CURING DEFORMED WING VIRUS IN HONEY BEES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1027604
Grant No.
2021-39410-35936
Cumulative Award Amt.
$650,000.00
Proposal No.
2021-07247
Multistate No.
(N/A)
Project Start Date
Sep 1, 2021
Project End Date
Aug 31, 2024
Grant Year
2021
Program Code
[8.13]- Plant Production and Protection-Engineering
Recipient Organization
GRANITE POINT VENTURES LLC
10 LAKEVIEW CIR
GREENBELT,MD 207701906
Performing Department
(N/A)
Non Technical Summary
Honey bee colonies are struggling to survive. During the 2019-2020 winter, infection by mites, virus, bacteria, and fungi, and reduced forage and pesticides, caused 44% colony mortality (www.beeinformed.org). This level is a dramatic increase over the 15%mortality seen during the last decades of the 20th century. The consequences of sustained 40% colony loss and replacement are serious. According to Bret Adee, the nation's, and world's largest beekeeper with 92,000 hives (NYT, Feb. 16, 2017), the direct impact of colony loss on the $691M apiculture industry and 11,774 commercial beekeepers (IBISWorld Market Report, December 2020) is $240M per year.Deformed wing virus is a major cause of honey bee colony loss. Together with the Varroa mite, nearly every domestic colony is infected (beeinformed.org). The virus disrupts normal brood development, weakens emerging bees, and kills adult bees. Deformed wing virus is concentrated and transmitted by the Varroa mite, making infection and infestation a feedback loop that can overwhelm even the strongest of colonies.There is no FDA approved treatment for Deformed wing virus, nor any other honey bee virus. The goal of this project is to develop an evidence-based cure.The challenge today in small molecule drug development is identifying a drug candidate that is both safe and effective. Typically, a chemistry team tests hundreds of thousands of compounds. The team must strike a balance between potency, side effects, absorption, distribution, metabolism, excretion, and toxicity. Most frequently, optimization fails not because of potential but because of time and money.To address this bottleneck, Atomwise (San Francisco, CA) has developed its AtomNet™ platform (www.atomwise.com). The technology uses a statistical approach that extracts the insights from millions of experimental affinity measurements and thousands of protein structures to predict the binding of small molecules to proteins. Use of this approach has resulted in the identification and synthesis of 90 chemicals that are predicted to bind to, and disrupt, the function of the Deformed wing virus 3C protease enzyme. Proper functioning of this enzyme is essential for virus replication.The goal of this project is to achieve the most critical milestone of a treatment development program, which is to identify a lead chemical that can be developed into a cure for Deformed wing virus disease. The team has in hand 90 chemicals of diverse structure ready for physical screen and that are predicted to bind to the active site of the essential Deformed wing virus 3C protease enzyme.The technical objectives are to physically screen 90 chemicals in live honey bees and biochemical assay to identify a lead compound; to iterateAtomNet™ and physical screen, if necessary to identify a lead compound; to develop the chemical lead into and investigational new animal drug; and to determine the next development steps and seek funding to accomplish these steps.
Animal Health Component
60%
Research Effort Categories
Basic
20%
Applied
60%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2164030110150%
2163010108050%
Goals / Objectives
The goal of this project is to develop a cure or treatment for Deformed wing disease in honey bees. This disease, caused by the Deformed wing virus, is a leading cause of 40% annual honey bee colony loss. This loss puts at risk $34B worth of economic activity and high-value crops such as honey, almonds, blueberries, and apples.Our approach is to use artificial intelligence algorithms to predict the binding of 10M small chemicals to active sites of Deformed wing virus proteins. We expect this approach to increase by 10,000X the likelihood that physical screen of 90 chemicals will identify a chemical that can be further developed through medicinal chemistry into a potent and safe inhibitor of Deformed wing virus.The team has in hand 90 chemicals of diverse structure, that artificial intelligence algorithms predict will bind to the active site of the essential 3C protease enzyme of the Deformed wing virus, that areready for physical screen.The technical and scientific goalof this project is for scientists at partner USDA-ARS Bee Research Lab (Beltsville, MD) to identify a lead compoundby way of physical screen of the 90 chemicals in live honey bees and biochemical assay. Next, through artificial intelligence and medicinal chemistry, for partner Atomwise, Inc. (San Francisco, CA) to further develop the potency and safety of the lead chemical; and for Granite Point Ventures LLC, the SBIR applicant and drug sponsor, to achieve project goals using its scientific, project management, and commercialization expertise.The technical challenges of the project are to scale laboratory processes to enable the physical screen of the90 chemicals, to screen with quality control, to have confidence in assay results, to detectweak signal from noisy background, and to develop objective acceptance criteria for the identifying one or more of the chemicals as a physical lead compound.
Project Methods
The physical screen of 90 chemicals in live honey bees involvesthepreparation and mixing of the chemicals; tender extraction of live honey bee pupae from colony hive frames; injection of the chemicals and flourescent-tagged Deformed wing virus into the pupae by way of fine syringe needle; and assessing chemical effect on virus load by quantification of flourescent signal or quantification of virus copies by genetic analysis using quantitative polymerase chain reaction.The biochemial assay of chemical effect on Deformed wing virus 3C protease activity involves cloning the 3C protease gene into a bacteria proteinexpression vector; inducing expression of 3C protease enzyme; purifying and concentrating the enzyme; and measuring enzyme activity both with and without exposure to each of the 90 chemicals.Assuming the idnetification of a lead compund, medicinal chemistry methods include physical verification of the binding site of the chemical to the 3C protease enzyme by way of protein crystallography, or similar; the computational simulaton of the binding of the chemical to its predicted binding site, and adjustment of the chemical's bonds and structure to achieve increased potency; iterative testing of modified chemicals to quantify and verify increased potency; and testing of the chemical in live honey bees to measure and improve absorption, distribution, metabolism, excretion, and toxicity.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience:The target audience is stakeholders of the beekeeping industry: commercial beekeepers, sideline beekeepers, hobbyist beekeepers, honey producers, pollination service providers, farmers who produce crops that require pollination, and consumers of pollinated crops. The effort to reach this target audience is the preparation of one or more scientific journal articles and white papers that explain the ubiquity and harmful effect of honey bee viruses and the healthful effect of the anti-virus therapy under development. Changes/Problems:The custom ingredients initially purchased for the Deformed Wing virus 3C Protease inhibition assay provided excellent results. But new batches provedproblematic. The team was never able to overcome this, even by hiringBert Gold, PhD, a certified CLIA laboratory director with expertise in developing and verifying for clinical use complicated molecular biology assays, and the advice of Dominic Esposito, PhD, Director of The Protein Expression Laboratory at the Frederick National Laboratory for Cancer Research and an expert in 3C Protease assays. Next, the team identified a set of a dozen chemicals that the project laboratory results, the literature, and the computational screen indicated were likely to inhibit theDeformed Wing virus. These chemicals were applied to live young adult honey bees. None had a statistically significant inhibition of the Deformed Wing virus. What opportunities for training and professional development has the project provided?The project has provided opportunities in project management, team development, clinical assay development, drug product development, and live honey bee studies. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?This is the final reporting period for this project. In the future, the plan is to seek additional research funds to execute the described plans, hire a biochemist to perfect the 3C Protease inhibition assay, andestablish a cell line assay to better develop a drug before applying the developed drug to live honey bees.

Impacts
What was accomplished under these goals? As explained in the work products section, the project team continued to develop a key Deformed wing virus 3C Protease inhibition assay,investigated twelve chemicals in live honey bee pupae and adults, and created a plan to build laboratory assays further to develop the reported chemicals as safe and potent in cells, before continued investigation in live honey bee pupae and young adults.

Publications


    Progress 09/01/21 to 08/31/24

    Outputs
    Target Audience:The target audience is stakeholders of the beekeeping industry: commercial beekeepers, sideline beekeepers, hobbyist beekeepers, honey producers, pollination service providers, farmers who produce crops that require pollination, and consumers of pollinated crops. The effort to reach this target audience is the preparation of one or more scientific journal articles and white papers that explain the ubiquity and harmful effect of honey bee viruses and the healthful effect of the antivirus therapy under development. Changes/Problems:The custom ingredients initially purchased for the Deformed Wing virus 3C Protease inhibition assay provided excellent results. But new batches proved problematic. The team could never overcome this, even by hiring Bert Gold, PhD results. But new batches proved problematic. The team was never able to overcome this, even by hiring Bert Gold, PhD, a certified CLIA laboratory director with expertise in developing and verifying for clinical use complicated molecular biology assays, and the advice of Dominic Esposito, PhD, Director of The Protein Expression Laboratory at the Frederick National Laboratory for Cancer Research and an expert in 3C Protease assays. Next, the team identified a dozen chemicals that the project laboratory results, the literature, and the computational screen indicated were likely to inhibit the Deformed Wing virus. These chemicals were applied to live young adult honey bees. None had a statistically significant inhibition of the Deformed Wing virus. What opportunities for training and professional development has the project provided?The project has provided opportunities in project management, team development, clinical assay development, drug product development, and live honey bee studies. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?This is the final reporting period for this project. In the future, the team desires research funds to execute theplanto hirea biochemist to perfect the 3C Protease inhibition assay and to establisha cell line assay to develop a betterdrug before applying the developed drug to live honey bees.

    Impacts
    What was accomplished under these goals? As explained in the work products section, the project team continued to develop a key Deformed wing virus 3C Protease inhibition assay; investigated twelve chemicals in live honey bee pupae and adults; and created a plan tofurther develop the reported chemicals as safe and potent in cells before continued investigation in live honey beepupae and young adults.

    Publications


      Progress 09/01/22 to 08/31/23

      Outputs
      Target Audience:The target audience is stakeholders of the beekeeping industry: commercial beekeepers, sideline beekeepers, hobbyist beekeepers, honey producers, pollination service providers, farmers who produce crops that require pollination, and consumers of pollinated crops. The effort to reach this target audience is the preparation of one or more scientific journal articles and white papers that explain the ubiquity and harmful effect of honey bee viruses, and the healthful effect of the anti-virus therapy under development. Changes/Problems:While the team achieved rapid progress with the original batches of custom ingredients for the Deformed wing virus 3C Protease inhibition assay, new batches proved to be problematic. Previously the team was able to consistently generate robust enzyme signal. However, this was not the case withthe new batches of ingredients. Loss of robust signal has meant that the team cannot finalize the set of validand true 3C Protease inhibitors. To resolve thisblockage of the 3C Protease enzyme assay, the team has secured the services of Bert Gold, PhD, a certified CLIA laboratory director with expertise in developing and verifying for clinical use complicated molecular biology assays, and the advice of Dominic Esposito, PhD, Director of The Protein Expression Laboratory at the Frederick National Laboratory for Cancer Research and an expert in 3C Protease assays. These steps have resulted in the construction of a detailed technical plan, aMaterial Transfer and Research Agreement between the USDA Bee Research Laboratory and the Frederick National Laboratory, and the possibility for technicans in Dr. Esposito's lab to independently perform the 3C Protease inhibition assay. What opportunities for training and professional development has the project provided?The project has provided opportunities in project management, team development, clinical assay development, and live honey bee studies. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?The plan going forward is to rely on 3C Protease inhibition assay experts to resolve inconsistencies in the 3C Protease inhibition assay, eliminate from further consideration all but the most inhibitory chemicals, obtain consistent results in the live honey bee pupae and live adult honey bee studies, and to advance the most promising chemical to field trials.

      Impacts
      What was accomplished under these goals? As explained in the work products section, the project team continued to develop a key Deformed wing virus 3C Protease inhibition assay, advanced six chemicals from assessment in the 3C Protease inhibition assay to investigation in live honey beepupae and live honey bee adults, and investigated these six chemicals inlive honey bee pupae and live adult honey bees.

      Publications


        Progress 09/01/21 to 08/31/22

        Outputs
        Target Audience:The target audience is stakeholders of the beekeeping industry: commercial beekeepers, sideline beekeepers, hobbyist beekeepers, honey producers, pollination service providers, farmers who produce crops that require pollination, and consumers of pollinated crops. The effort to reach this target audience is the preparation of one or more scientific journal articles and white papers that explain the ubiquity and harmful effect of honey bee viruses, and the healthful effect of the anti-virus therapy under development. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has provided opportunities in project management, team development, and clinical assay development. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?The plan going forward is as described in the abstract. Namely, now that the project team has successfully identified a small discovery hit set of chemicals, the plan is to further develop the potency, safety, and efficacy of the hit set chemicals into one or more treatment leads. The apporach is tophysically characterizethe shape of the protease enzyme active site, to optimizethe shape and fit of the chemicals into the enzyme active site, and to iterate physical assay until the team achieves a safe, potent, and efficacious virus treatment.

        Impacts
        What was accomplished under these goals? As explained in the work products section, during the performance period the project team developed a biochemical assay, and physically screened 96-AI selected chemicals and one chemical from the literature in the biochemical assay and in live honey bee pupae. This has resulted in the best-case scenario of identifying discovery hits and apotential treatement lead compound.

        Publications