75N99224R00001 APECx Amd No. 1.docx

75N99224R00001, APECx

Antigens Predicted for Broad Viral Efficacy through Computational Experimentation (APECx) Health Science Futures (HSF) Office Research & Development Solicitation 75N99224R00001 Amendment No. 1 November 21, 2023

Table of Contents

PART I: OVERVIEW INFORMATION

· Federal Agency Name – Advanced Research Projects Agency for Health (ARPA-H), Health Science Futures Office (HSF)

· Funding Opportunity Title – Antigens Predicted for Broad Viral Efficacy through Computational Experimentation (APECx)

· Announcement Type – Initial Announcement

· Funding Opportunity Number – 75N99224R00001

· Assistance Listing Number – 93.384

· Dates

· Posting Date: November 21, 2023

· Proposers’ Day: November 17, 2023

· Abstract Due Date and time: December 15, 2023, 9:00 AM ET

· Proposal Due Date and Time: February 16, 2024, 5:00 PM ET

Concise description of the funding opportunity – The APECx program aims to transform vaccine antigen (Ag) discovery by leveraging recent advances in protein structure resolution, high-throughput (HT) functional characterization, predictive modeling, and platform vaccine technologies to deliver genus-level evolution-resistant vaccine candidates against various viral infections, including cancer-causing viruses and viruses that cause acute and chronic illnesses. APECx seeks to develop novel Ag design workflows to achieve this goal by coupling advanced experimental techniques for viral protein structure determination, high-throughput functional analysis, and high-throughput immunological assays with structural and functional prediction and modeling algorithms. Current protein structure prediction algorithms have limitations in accurately modeling viral protein structures due to the limited viral structure representation in the protein database (PDB) and the unique characteristics of viral proteins. These algorithms also face challenges in predicting the impact of mutations, post-translational modifications, multi-domain structures, and protein-protein interactions. These structure prediction and modeling capabilities play a crucial role in designing effective vaccine Ag. When these capabilities are improved and combined with high-throughput epitope mapping, Ag discovery and functional analysis, they have the potential to support genus– and family-level chimeric Ag design with predictive immunology markers. APECx seeks to mature and adapt these emerging technologies towards vaccine development for viral diseases and will incorporate equity outcomes for vaccine delivery in the U.S., resulting in a substantial decrease in the disease burden experienced by patients, healthcare systems, and the overall economy.

· Anticipated individual awards – Multiple awards are anticipated.

· Potential award instruments – Cooperative Agreements or Other Transaction Agreements (OT).

· Agency Contact – All inquiries shall be sent to APECx@ARPA-H.gov

PART II: FULL TEXT OF ANNOUNCEMENT

1. Funding Opportunity Description

This publication constitutes a merit-based process in accordance with 2 Code of Federal Regulations (CFR) § 200.205 and is in accordance with section 499A of the Public Health Service Act (PHSA). Any resultant award negotiations will follow all pertinent laws and regulations.

The mission of ARPA-H is to accelerate better health outcomes for everyone by advancing innovative research that addresses society’s most challenging health problems. Awardees will develop groundbreaking new ways to tackle health-related challenges through high-potential, high-impact biomedical and health research. ARPA-H is soliciting proposals to develop toolkits to identify and design chimeric and highly effective vaccine Ag. The focus will be on leveraging high-throughput functional analysis, protein structure prediction and protein engineering to achieve this goal. It is important to note that proposals will not be considered 1) if they merely offer incremental improvements in the existing state of the art, such as Ag discovery leading to vaccines with limited coverage across a viral genus. Additionally, proposals concentrating on virus families that are well-funded and heavily studied (e.g. viral families that include influenza, SARS-CoV-2, and HIV) will be excluded, 2) proposals that do not address the objectives of the program, 3) proposals directed towards policy changes, traditional education and training, or center coordination and construction of physical infrastructure are outside the scope of the ARPA-H mission.

1.1. PROGRAM OVERVIEW

The APECx program aims to create a toolkit to enable accurate chimeric and broadly efficacious vaccine Ag discovery through predictive modeling, high-throughput functional experimentation, and protein engineering. To fundamentally transform the vaccine research and development (R&D) sector, APECx will develop an innovative viral Ag prediction pipeline for broad efficacy by combining expedited experimental protein structure and function determination with high-throughput Ag screening. This will be enhanced with structural and functional prediction and protein modeling algorithms. Product developers will contribute to modeling tool evaluation from the start of the program to ensure discoveries satisfy the translational requirements. The combined effort of all the teams will create a toolkit that will enable the U.S. to achieve genus-level vaccine goals and prevent multiple viral diseases, including those responsible for cancer, acute disease, and chronic illness across the country and the world.

Current approaches to vaccine development are costly, time-consuming, and have not yielded broadly-efficacious vaccines for viral disease. Due to the technical complexities, most developers target a single virus species as the indication for a given vaccine, as the cost and time associated with evaluating the clinical efficacy of a vaccine leads to a risk-averse “one-virus, one-vaccine” development strategy. Novel protein structure prediction algorithms, such as AlphaFold2 (AF2) and RoseTTAFold (RF), have revolutionized protein structure prediction for various applications and have the potential – when combined with high-throughput functional experimentation discoveries – to unlock new possibilities within vaccine development approaches. However, the effectiveness of these algorithms correlates with the amount of experimentally-resolved structure data found in the open-source Protein Data Bank (PDB). The PDB’s structural repertoire is significantly biased toward soluble eukaryotic and bacterial proteins, with viral proteins constituting less than 6% of the total. Additionally, the existing prediction algorithms face challenges in accurately predicting the impact of mutations, post-translational modifications, multi-domain structures, and protein-protein interactions. These core capabilities are essential for in silico approaches to design vaccine Ag that create immune responses that are protective at the relevant mucosal surfaces and provide durable protection beyond a single virus species. These tools have not been paired with orthogonal data generation from functional assessments that would generate data beneficial to vaccine Ag design.

APECx will address these limitations by:

1. Discovering and optimizing new methodologies to generate the necessary structural and functional data needed for modeling viral Ag and incorporating these data into vaccine design tool development – and sharing these data openly

2. Building Artificial intelligence (AI)/Machine learning (ML)-enabled vaccine design tools for translational vaccine and therapeutic development – and sharing these tools openly

3. Demonstrating the predictive and learning abilities of these tools through proof-of-concept studies that evaluate their applicability to broad-spectrum vaccine development

4. Challenging the developers to demonstrate genus/family-level efficacy of these vaccine candidates with independent and validated assays and models

5. Down-selecting the most promising candidates for evaluation in Phase I human clinical studies to demonstrate the capabilities built into the antigen development pipeline

The utilization of these advanced technologies will revolutionize the approach to viral disease prevention, resulting in a substantial decrease in the disease burden experienced by patients, healthcare providers, and the overall economy. Discoveries and toolkits made through APECx will also impact all disease research and development as the principles required for vaccine Ag design apply to understanding protein function/dysfunction related to human disease mechanisms.

1.2. TECHNICAL APPROACH AND STRUCTURE

1.2.1. Technical Areas (TAs)

The APECx program will catalyze the discovery of Investigational New Drug (IND)-ready, broad-spectrum medical countermeasure (MCM) candidates against unknown and existing threats at the viral genus-level. The discovery process includes three technical areas (TA): high throughput biochemical analysis and protein engineering (TA1), protein modeling toolkit for antigen design and discovery pipeline development (TA2), and translational candidate development and clinical evaluation (TA3).

· Technical Area 1 (TA1)- High-throughput (HT) Biochemical Analysis and Protein Engineering: Accelerated throughput of viral Ag discovery with high accuracy, utilizing techniques including but not limited to HT experimental structure determination, HT functional analysis, and model system development for screening of lead Ag candidates.

· Technical Area 2 (TA2)- Protein Modeling Toolkit for Antigen Design: Leverage 3-dimensional (3D) structural and HT functional data information from TA1 and existing viral protein structure data to confidently model challenging targets and predict and design consensus chimeric Ag suitable for genus-level vaccines against existing and emerging viral diseases. (TA2)- Discovery Pipeline Development: APECx will also prioritize integrated model development by soliciting TA2 Only performers to develop, train, and test team-developed toolkits across the performers (inclusive of training data and models developed).

· Technical Area 3 (TA3)- Translational Candidate Development and Clinical Evaluation: Utilize the dataset generated by TA1 and TA2 to discover novel MCMs, optimize them for relevant delivery platforms that are efficacious at a viral genus-level and easily accessible to the public, and iteratively validate approaches generated by TA1 and TA2.

Performers will have the option of submitting proposals that address all TAs (TA1 – 3) or TA2 only. Teams that apply for TA2 independently will have a unique set of milestones and deliverables to perform as an integrative function across the TA1/2/3 teams. The role of TA2 Only teams will be focused on model development and data integration across the program and should focus on the challenges involved with model integration. Ag design iteration and validation will occur mostly within TA1 and TA2, although many of the design features of a translatable vaccine (immunogenicity, manufacturability, and platform delivery technologies) need to align with the goals of TA3 from the onset and be incorporated early on. As teams advance product candidates through proof of concept studies, challenges, and clinical studies, there are opportunities within TA1 and TA2 to iterate and improve on the protein functional design, resolution, and modeling approaches. The iterations will be validated and guided by animal and human data for safety, immunogenicity, and efficacy.

To ensure the applicability of tools developed to the broader community and for the success of APECx candidates, proposers must have demonstrated team capabilities in TA2 alone or across all TAs. Proposals that fail to address the required technical areas will be deemed non-conforming and may be rejected without further review. Proposing teams that address all TAs (TA1–3) must also include data access plans and commercialization plans including Food and Drug Administration (FDA) meeting milestones, technology transfer milestones to contract manufacturing organization (CMO) partners, preclinical proof of concept objectives, and market analysis and partnership models for commercialization. The proposed candidates and MCMs for TA1–3 should meet the specifications listed in the “Metrics and Objectives” sections below.

TA1: High-throughput Biochemical Analysis and Protein Engineering

The current protein structure prediction algorithms, such as AF2 and RF, have been a significant breakthrough in the field of structural biology. These algorithms have demonstrated impressive capabilities in accurately predicting protein structures, which has wide-ranging implications for drug discovery and vaccine development applications. The capabilities of the prediction tools were attainable due to the large quantity of experimental structures available in the PDB. Likewise, high-quality, unbiased, and verifiable data generation is essential for developing AI/ML-based applications, ensuring training accuracy while mitigating the likelihood of errors in the pipeline.

The PDB is biased towards soluble eukaryotic and bacterial proteins, with a limited representation of viral proteins. This lack of diversity in viral protein structures hinders accurate predictions using the modeling tools. Furthermore, these prediction algorithms often struggle to predict the impact of mutations, post-translational modifications, multi-domain structures, and protein-protein interactions, which are all critical modeling capabilities needed for MCM development.

TA1 aims to produce an unabridged structural database of viral proteins and their interactions with host targets from a chosen genus and enhance the capabilities of existing algorithms for modeling and expediting the discovery of MCM against viral targets. Accurate structures of viral proteins and viral protein-host receptor complexes are instrumental to discovering immunogenic epitopes. Combining these structural data with HT functional analysis, biochemical data, and immunological assay data will enhance the discovery of effective viral Ag.

To accomplish this, TA1 performers will carefully select a viral genus and identify viral proteins or protein complexes that play a significant role in pathogenic events. The performers will resolve protein structures that are missing in the PDB and perform functional immunological characterization of the proteins for MCM discovery, utilizing various techniques in structural biology and immunological characterization.

This program announcement outlines the broad scope of the TA1 objectives. A successful proposal should consider each of the following, and include strategies and information to achieve each goal:

· A detailed plan for HT Ag characterization of native viral proteins and consensus chimeric Ag.

· The proposal should provide a detailed description of the HT experimental and technological plans for rapid data generation for Ag selection and evaluation, which includes the initial choices, down-selection and refinement of HT technologies.

· The proposal should provide a detailed description of the HT experimental and technological plans for functional serological analyses and immune cell responses for Ag.

· The readout should reflect the reactivity profile and antigenic diversity.

· The discoverable Ag should include conformational and linear Ag for B and T cells and structure-guided epitope mapping should be considered.

· The proposal should provide clearly defined tractable metrics for each high-throughput screening (HTS) technology.

· A list of relevant antigenic targets from a single genus or multiple, related genera, and a determination of their 3D structures either by themselves or in complex with host proteins in physiologically relevant forms.

· High-value targets refer to viral proteins or protein complexes that play a significant role in pathogenic events, and their structural information can be used to develop MCMs, including vaccines and neutralizing antibodies (nAbs).

· The proposal should outline detailed protein production and structure determination strategies, including novel strategies to address the required throughput.

· The proposal should outline a detailed plan for the utilization of United States Government (USG) infrastructures, such as national synchrotron sources, national nuclear magnetic resonance (NMR) facilities, Cryo-electron microscopy (Cryo-EM) centers, and Cryo-electron tomography (Cryo-ET) centers.

· Rationale for the chosen macromolecules or macromolecular complexes that could lead to novel MCMs.

· One of the program goals is to develop genus-level (or beyond) broad-spectrum vaccines.

· One of the program goals is to contribute to viral structural protein databases for a chosen genus and to provide novel and chimeric structures of proteins relevant to human viral pathogens.

· A plan to produce and supply designed consensus chimeric Ag for immunogenic screenings.

· A plan to elucidate experimental 3D structures of designed consensus chimeric Ag to confirm the accuracy of the structural models created in TA2.

· A plan to elucidate experimental 3D structures of chimeric Ag-nAb complexes to characterize epitopes and correlates of immune response (TA3).

· A consideration of potential obstacles that could require a revision in the work plan or milestones with a discussion of alternative approaches.

· A detailed schedule or timeline for each milestone and the overall goal.

To achieve the goals of the program, performers may propose a variety of technical approaches to elucidate high-value target structures. These approaches can be separate or combined. These may include but are not limited to:

· X-ray crystallography

· Cryo-electron microscopy single particle analysis (Cryo-EM)

· Cryo-electron tomography (Cryo-ET)

· Micro-electron diffraction (Micro-ED)

· Nuclear magnetic resonance (NMR) spectroscopy

· Mass-spectrometry techniques

· Hydrogen-deuterium exchange mass-spectrometry (HDX-MS)

· Cross-linking mass-spectrometry (XL-MS)

· Atomic force microscopy (AFM)

· Other biophysical techniques suitable to study macromolecular structures

To achieve the goals of the program, performers may propose a variety of functional biochemical and immunological characterization techniques in HTS format. These approaches can be separate or combined. These may include but are not limited to:

· Single cell sequencing

· Phage display technology

· Peptide library array technology

· Protein microarray technology

· Next-generation sequencing (NGS)

· Mass spectrometry

· Flow cytometry

· Surface Plasmon Resonance (SPR)

· Enzyme-linked immunosorbent assay (ELISA)

· Enzyme-linked immunosorbent spot (ELISpot)

· Biosensor technology

· Epitope binning technology

· Other immunological functional assays

TA1 metrics and timelines that are outlined in Table 2 of section 1.3 will increase in difficulty and complexity over the course of the APECx program. Monthly technical and financial status reports will be required and discussed with the ARPA-H Program Manager Team at monthly meetings. ARPA-H may request performer data as deemed necessary throughout the program to validate progress toward achieving the program goals. The resolved structural datasets and assays developed by performers will be shared with Independent Verification & Validation (IV&V) partners, which consist of extramural and intramural USG labs for analysis and comparison.

TA2: Protein Modeling Toolkit for Antigen Design and Discovery Pipeline Development

MCMs are often designed to target a specific strain of viral species, limiting our capacity to respond to rapidly evolving viruses or multiple viral pathogens that cause similar diseases. A broad-spectrum MCM can protect or treat infections against multiple strains, variants, or species within a viral genus.

Such MCMs can be designed by targeting conserved viral surface proteins that do not vary significantly among different strains, variants, or species. Alternatively, T cell mediated immunity can be targeted by focusing on protein core sequences, which are often the most conserved region of protein orthologs. Vaccines designed using these approaches could provide broader protection and may even have the potential to protect against newly emerging variants.

Obtaining accurate structures of viral surface proteins and understanding how they interact with host cell receptors can provide important information for developing MCMs. Additionally, non-structural viral proteins may provide additional opportunities to identify T cell Ag and future MCM discovery targets. As highlighted in the TA1 overview, TA1 aims to bridge the knowledge gap in viral protein structures and accurately map immunogenic epitopes through various HT biochemical and functional assays. The knowledge of comprehensive Ag structures, along with precise mapping of highly immunogenic epitopes, will facilitate future advancements in the development of broad-spectrum MCMs.

TA2 aims to enhance the understanding of viral structures at the genus level through accurate structure prediction of viral Ag and their interaction with host receptors. Performers will achieve the goal by generating precise protein models using the structural information obtained from TA1 and pre-existing structural information in the PDB. These protein models will provide a comprehensive account of all the protein structures within the genus. Utilizing the structural information and the functional readouts obtained in TA1, TA2 performers will identify targetable Ag and generate consensus chimeric Ag that represent protein orthologs at the genus-level. By doing so, TA2 outcomes will facilitate the development of broad-spectrum MCMs that can effectively target multiple viral species within the genus.

With the anticipation of large datasets produced from the program through HT functional analysis and biochemical and immunological assay results associated with the Ag structures, TA2 Only performers will facilitate and implement data standardization and automated data curation in data generation workflow. Additionally, TA2 performers will make efforts to gather relevant functional and immunological data from public sources. The AI/ML-centric data curation effort will enable the design of an automated Ag prediction pipeline.

This program announcement outlines the broad scope of the TA2 objectives. A successful proposal will consider each of the following, and include strategies and information to achieve each goal:

· A plan to coordinate data across TA1 and TA3 and provide accurate de novo models of physiologically relevant protein structures for a chosen genus or genera.

· One of the program goals is to establish a viral structural genome database of a chosen genus to provide an unbiased structural database of human viral pathogens. TA2 performers will identify missing model templates and inform TA1 approaches to generate experimental structures that can be used as a template for structure prediction of orthogonal proteins within or near the viral genus.

· A plan to coordinate with TA2 Only teams in order to provide data generated throughout the program for the development of data repository and toolkits.

· Performers will utilize existing or novel algorithms to predict accurate viral macromolecular structures utilizing the structure data generated by TA1 tasks.

· Detailed plans and the development of tools to accurately predict the impact of point mutations, order/disorder boundaries, multi-domain structures, and protein-protein interactions.

· Toolkits to generate synthetic chimeric targets from the high-value targets identified in TA1/3 to be used for MCM discovery in a manner beneficial to TA3 for performing broad-spectrum MCM discovery.

· Strategies and laboratory tools to predict the safety, thermostability, and bioprocessing scalability of the biologics candidates using existing or new protein design algorithms.

· Performers should recognize the importance of developing thermostable vaccines and biologics, as these may have to be transported and stored in various environmental conditions. Protein modeling and design teams should help analyze protein structures, predict their stability, and guide the engineering of proteins to enhance thermostability.

· Performers should recognize that efficient and cost-effective bioprocessing is vital for large-scale manufacturing of vaccines and biologics.

· A discussion of potential obstacles that could require a revision in the work plan or milestones with a discussion of alternative approaches.

· A detailed schedule or timeline for each milestone and the overall goal.

The TA2 Only performers have a unique set of objectives. A successful proposal considers each of the following, and include strategies and information to achieve each goal:

· Plan for building a program data repository, data curation and harmonization pipeline

· The proposal should provide a detailed plan for curating the data generated during the program in a user-friendly manner for the scientific community. The data will include high-confidence models, experimental structures, biochemical assays, and functional data.

· The proposal should provide a detailed plan for curating publicly available structures, biochemical assays, and functional data relevant to the program and integrating them into the repository to develop an Ag prediction pipeline.

· A plan for building an Ag prediction pipeline utilizing the program-specific protein prediction and modeling toolkits, and publicly available toolkits.

· Single Ag and consensus chimeric Ag.

· Conformational and linear Ag for B cells and T cells.

· Combined with immunological functional data for prediction.

· Adaptability of the Ag for vaccine platform for optimal efficacy.

· A discussion of potential obstacles that could require a revision in the work plan or milestones with a discussion of alternative approaches.

· A detailed schedule or timeline for each milestone and the overall goal.

To achieve the goals of the program, performers may propose a variety of technical approaches to produce high-accuracy protein models and consensus chimeric Ag. These approaches can be separate or combined. These may include but are not limited to:

· Existing prediction algorithms or de novo prediction algorithms

· Template-based homology modeling

· Physics-based modeling

· Deep learning-based modeling

· Template-independent ab initio modeling

TA2 metrics and timelines are outlined in Tables 3 and 4 of section 1.3 will increase in difficulty and complexity over the course of the APECx program. Monthly technical and financial status reports will be required and discussed with the ARPA-H Program Manager Team at monthly meetings. ARPA-H may request performer data as deemed necessary throughout the program to validate the project progress. The modeling datasets, toolkits, and the pipeline developed by performers will be shared with Independent Verification & Validation (IV&V), which consists of extramural and intramural USG labs, for analysis and comparison. Additionally, they may also serve as IV&V during certain aspects of the program to validate findings.

TA3: Translational Candidate Development and Clinical Evaluation

Vaccines are universally acknowledged as one of the most cost-effective and equitable MCMs for preventing infectious diseases, particularly viral infections. They play a vital role in reducing the strain on healthcare systems, resulting in substantial savings in medical costs. Vaccines contribute significantly to achieving herd immunity, where a sufficient portion of the population acquire immunity, protecting even those who cannot be vaccinated. Beyond their local impact, vaccines have a profound global health effect. The high efficacy and safety of vaccines make them a cornerstone of public health initiatives, effectively safeguarding individuals and communities against infectious pathogens.

Vaccination induces protective immunity through two arms of the adaptive immune system: humoral immunity (Abs and memory B cells) and cellular immunity (involving helper CD4+ T cells and cytotoxic CD8+ T cells). Abs block infection by binding to viruses and preventing their entry into host cells (among other functions) and serves as correlates of protection for many vaccines. Memory T cells offer an important additional layer of immunity, responding rapidly to limit virus replication and spread once an infection has occurred. The immune response generated at the mucosal surfaces is equally crucial for many viral infections, as it is often the first contact point between infectious virus and the host. For viruses that are associated with mucosal routes of entry and mucosa-based pathogenesis, immunological endpoints including mucosal IgA, mucosal resident memory B and T cells, and mucosal availability of IgG should be pursued.

Unfortunately, there are vaccines for less than 7% of viruses known to infect humans, and many of them provide protection against a single viral species (or even strain/isolate) in ways that are susceptible to evolution. TA3 aims to generate broad-spectrum vaccines based on recursively designed consensus chimeric Ag as described in TA1 and TA2 to provide protection against multiple viral pathogens at a genus-level.

While broad-spectrum vaccines with strong protective immunity are the key characteristics that APECx seek, the program will also emphasize other critical factors. These include ease of administration, safety, low reactogenicity, low production cost, stability, and equitable access to all. Therefore, a vaccine design should carefully consider these factors during the early stages of development, including selecting an appropriate vaccine platform. The choice can significantly impact the vaccine’s characteristics, including its immune response, administration, and manufacturing.

As highlighted in the TA2 overview, TA2 will identify targetable Ag and design consensus chimeric Ag. TA1 will then produce these Ag with high purity. TA3 will perform lead optimization screening and validation to confirm the broad-spectrum efficacy. The identification of nAbs and effector T cells during this process can be used to characterize the target epitopes using structural biology techniques. This will enhance the understanding of the designed consensus Ag and inform the next round of design efforts. The process will recursively iterate until the most effective chimeric Ag is identified. The final candidates will undergo functional assays in animal models or equivalent systems to determine immunogenicity, safety, and efficacy, as well as developability and manufacturability. Suitable candidates will be supported by IND submission to the FDA and for progression to Phase I clinical trials. Therefore, the proposers should document compliance with guidelines that govern Good Laboratory Practice (GLP), as defined by 21 CFR (58), and current Good Manufacturing Practice (cGMP), as defined by 21 CFR (211), manufacturing and IND enabling studies that will be performed under the program as they should be critical for the application.

The recursively designed broad-spectrum vaccines must meet the following specifications:

· Performers must seek rationally designed vaccines that can offer significant protection in in vivo preclinical models, exceeding 60%, against all known viral species within the selected genus.

· Onset of protection must occur within 2 weeks of vaccination and durable > 1 year.

· Vaccine formulation must ensure stability (> 5 years at -80 ºC) with enhanced storage capabilities (-20 ºC viability for 6 months and 4 ºC viability for 2 weeks).

· Ensure safety and reactogenicity are sufficient to provide a highly favorable benefit/risk profile with minimal adverse events.

· Progress candidates to an IND-ready stage.

· If applicable, IND submission and approval.

· Candidate vaccines that progress to Phase I clinical trial must target all populations, including healthy adults, pediatric and marginalized populations.

The desired attributes of the vaccine candidates encompass a robust T cell and B cell response, a high level of nAbs, and the presence of long-lasting memory B and T cells. Achieving strong mucosal immunity, which involves protective IgA and tissue-resident memory T cells (TRM), may necessitate a combination of formatting and adjuvant formulation. To meet the program’s objectives, performers must utilize platforms with a proven track record of success and have received support from the USG. Additionally, the selected platform should be scalable and allow for low-cost manufacturing that ensures accessibility to all. Various platforms can be considered, including but not limited to:

· mRNA

· Virus-like particles (VLP)

· Recombinant subunit

· Nanoparticles

· Viral vectors

To achieve the goals of the program, performers may propose various technical approaches to assess vaccine efficacy in vitro and in vivo. These approaches can be separate or combined. These may include but are not limited to:

· Hybridoma technology

· Phage display technology

· Natural library

· Synthetic library

· Semi-synthetic library

· Single B cell technology

· FACS-based analysis

· Nanowell-based technologies

· Flow cytometry

· ELISA

· Microscopy (confocal and intravital)

· Next-generation sequencing (NGS)

Efforts within TA3 should include co-Investigators with expertise in vaccine translational development and expertise in virology related to the selected viral families and genera of interest.

This program announcement outlines the broad scope of the TA3 objectives. Performers must also provide the following information in the proposal:

· Intended in vitro assays and in vivo models to examine potential human efficacy.

· Justification for the number of animals to be used and other models employed in vitro and in vivo.

· The approval process of the IACUC protocol and OLAW submission will likely take a minimum of 3 months. Performers should have the protocol ready for approval in anticipation of the APECx program award and should include a milestone for IACUC and OLAW approval in synchronization with the program timeline.

· Any prior in vitro and in vivo data for viral genus of interest.

· Viral genus of interest and ability to work with those pathogens, for example, access to high containment facilities (BSL3/4) if applicable and access to the viruses within the genus.

· Anticipated risks/pitfalls and alternative solutions to working with high containment pathogens.

· Strategic plan for collaborations with other TA experts to facilitate the development of IND-ready products.

· Potential obstacles that could require revising the work plan or milestones with a discussion of alternative approaches.

· A detailed schedule or timeline for each milestone and the overall goal.

The progress made by TA3 will be evaluated by program-wide goals before the 36-month APECx Phase 1 period ends. The main goal aims to demonstrate that the candidate vaccines provide correlate or surrogate of protection against the entire genus of their target. The USG labs and resources will oversee and evaluate the candidates, and the results will play a significant role in making Go/No-Go decisions for APECx Phase 2 and determining the advancement of candidate vaccines into clinical trial evaluations.

TA3 metrics and timelines outlined in Tables 5 and 6 of section 1.3 will increase in difficulty and complexity over the course of the APECx program. Monthly technical and financial status reports will be required and discussed with the ARPA-H Program Manager Team at monthly meetings. ARPA-H may request performer data as deemed necessary throughout the program to validate technical progress.

1.2.2. Program Structure

The APECx program is structured as a 5-year effort consisting of 2 phases: (36-month phase 1 and 24-month phase 2) as shown in Figure 1. APECx Phase 1 includes realistic and measurable goals for performers to ensure the success of the program. This also includes checkpoints at the transition between APECx phases. In order to progress towards APECx Phase 2, performers must utilize the resources provided by USG stakeholders, Project Accelerator Transition Innovation Office (PATIO), and the Expert/Entrepreneur in Residence (XIR/EIR) network to develop marketable products capable of eradicating virus-related diseases as significant threats to public health.

Figure 1. Program Structure and General Overview

Antigen (Ag), Proof of concept (POC), Contract manufacturing organization (CMO)

1.2.3. Equity Requirements

ARPA-H has indicated it is committed to equitable healthcare access irrespective of race, ethnicity, gender/gender identity, sexual orientation, disability, geography, employment, insurance, and socioeconomic status. Access to preventative healthcare tools, like vaccines, and adherence to full vaccine schedules for many viral diseases is inequitable across the U.S. Getting preventative healthcare is extremely challenging across the socioeconomic spectrum and studies have shown that lower socioeconomic status and minority populations have greater challenges in accessing vaccines and adhering to multi-dose vaccines schedules (such as hepatitis A/B, human papilloma virus, and the SARS-CoV-2 vaccine series). Further, resistance to needles and lack of educational marketing tools for vaccines and vaccine-preventable diseases prevents the full benefit of these public health tools from being realized across the U.S. and internationally. It is also the goal of the program to negotiate full coverage through all health insurance via USG entities (Center for Medicare and Medicaid Innovation (CMMI), Centers for Medicare & Medicaid Services (CMS), Indian Health Service (IHS), and more) so that APECx vaccines are accessible to all. To meet equity and accessibility goals, APECx is developing target product profiles (TPP – an example below in Table 7 of section 1.3) that will account for equitable access and acceptance of vaccine candidates and their delivery in formats that increase equity in vaccination for all. The final TPP requirements will be available to performers no later than Q3 Yr1 of APECx Phase 1. The APECx program team is also establishing an ethics steering committee to advise on scientific methods/approaches to advance health equity. Membership will consist of disease advocacy groups, ethicists, and external content experts (virologist, immunologist, vaccinologist, epidemiologist, etc.). Additionally, proposers should include a discussion on the disease burden of selected viral genera, with emphasis on disease distribution in historically marginalized groups if such disparities exist.

1.2.4. Data Sharing Plan

Proposers must agree to openly share deidentified/sanitized data acquired during the period of performance. Any member of the scientific community should have access to the data; registration to a specific repository website is acceptable, but approval needs to be automatic. The specific repository where data will be deposited will be chosen in agreement with the ARPA-H program manager. The proposers will need to present explicit solutions to address the significant data storage and computing challenges presented by the program, with the understanding that the plans and repository may change later in the program.

1.2.5. APECx Go/No-Go Phase 2 Checkpoint

At Q3 Yr3 in APECx Phase 1, there will be a down selection of teams based on performance against APECx Phase 1 metrics as described in the metrics tables. Progression to Phase 2 will be also dependent on funding availability. Additionally, any performer that does not meet the equity requirements may also be given a “No-Go” determination. APECx Phase 2 will not have specific TA1 and TA2 requirements, however, there may be funds available in Phase 2 for TA1 and TA2 to provide additional support to TA3 if necessary.

TA1 Goal – APECx Phase 1 (36 Months): High-throughput Biochemical Analysis and Protein Engineering

During the 36-month APECx Phase 1, performers will establish cloning, expression and purification, resolve structures, and perform functional immunological characterization of the targets. In collaboration with TA2, TA1 will accumulate and curate a viral structure database and determine experimental structures of designed consensus chimeric Ag structures to validate the models and perform additional functional characterization of the Ag. Performers will elucidate experimental 3D structures of chimeric Ag-nAb complexes to map epitopes. See Figure 1 for a full program overview.

· Goals of APECx Phase 1 (metrics defined in 1.3 PROGRAM METRICS)

· By Q2 Yr1: establish a HT experimental workflow for Ag characterization.

· By Q4 Yr1: identify high-value targets, screen for expression, and produce the proteins in preparation for experimental structure determination.

· By Q2 Yr2: complete HT structure characterization of high-value targets.

· The local resolution of the structures should be 3.2Å or better for MCM discovery.

· The local resolution of the structures should be 2.0Å or better for protein complex analysis.

· By Q2 Yr2: complete functional immunological analyses and epitope mapping on single Ag and consensus chimeric Ag.

· The HT data and its quality should be ready for AI/ML training and the development of the MCM discovery pipeline.

· By Q3 Yr2: produce proteins of designed consensus chimeric Ag and determine experimental structures for TA2.

· By Q3 Yr2: complete structural complexes of consensus chimeric Ag and nAb to support TA3’s effort to characterize epitopes and nAbs.

TA2 Goal - APECx Phase 1 (36 Months): Protein Modeling Toolkit for Antigen and Discovery Pipeline Development

During the 36-month APECx Phase 1, performers will coordinate with TA1 and TA3 performers and create accurate de novo models of physiologically relevant protein structures for a chosen genus or genera. TA2 outcomes will establish a viral structural genome database by combining high-accuracy model structures, the structures obtained from TA1, and pre-existing structural information in PDB. TA2 performers will generate consensus chimeric Ag from the high-value targets for MCM discovery. The TA2 Only performers will establish a program data repository, curate both program-generated data and publicly available data for training in AI/ML. The TA2 Only performers will use the data to create an automated Ag prediction pipeline.

· Goals of APECx Phase 1 (metrics defined in 1.3 PROGRAM METRICS)

· By Q4 Yr1: complete prediction of 50% genus coverage with composite accuracy score > 90% in the core domains and accurate prediction of disorder boundaries. The genus coverage should reach 80% by Q2 Yr2.

· By Q2 Yr2: improve structure prediction with composite accuracy score > 60% in physiological conditions relevant to viral proteins (Lysosome, cytosol, extracellular, etc). The prediction accuracy score should reach > 75% by Q1 Yr3.

· By Q1 Yr3: improve structure prediction with additional metrics (order/disorder boundary, mutation, domain interaction, protein complexes).

· By Q1 Yr3: improve structure prediction to include translational additions that can be represented/modeled in silico (i.e., sugar moieties) and to model multiple conformations with predictive modeling with composite accuracy score > 75%.

· Goals of APECx Phase 1 for TA2 Only performers (metrics defined in 1.3 PROGRAM METRICS)

· By Q1 Yr2: complete program data repository and establish data harmonization pipeline.

· The pipeline will be capable of unsupervised data curation, and the deposited data will be ready for AI/ML training.

· The pipeline will include data curation and standardization of publicly available data relevant to the viral targets.

· By Q3 Yr3: create a pipeline for consensus chimeric Ag prediction, specifically targeting viral vaccines.

· The pipeline will have the capacity to predict chimeric conformational Ag, linear B cell Ag, and T cell Ag with the potential for genus-level efficacy.

· The pipeline will have the capacity to predict the most suitable vaccine platform supported by USG for optimal efficacy.

· By Q4 Yr3: compile all structural datasets and functional-immunological readouts generated by the APECx program to a data repository that is secure, accountable, and accessible to a broad scientific community.

TA3 Goal - APECx Phase 1 (36 Months): Translational Candidate Development and Clinical Evaluation

During the 36-month APECx Phase 1, performers will assess the efficacy of the recursively designed MCMs from TA1/2 in preclinical models.

· Goals of APECx Phase 1 (metrics defined in 1.3 PROGRAM METRICS)

· By Q3 Yr2: selection of previously demonstrated and established vaccine platform.

· By Q4 Yr2: selection of vaccine administration route for optimal efficacy.

· By Q2 Yr3: establish in vitro and in vivo models to assess vaccines.

· By Q4 Yr3: demonstrate vaccine efficacy against ≥ 60% of known viral pathogens within a genus.

· By Q4 Yr3: determine vaccine durability, and protective immunity assessed by animal responses to vaccination and following vaccinated animals out 1 year.

· By Q4 Yr3: profile functional immune response following vaccination to determine protective immunity versus immunopathology.

· By Q4 Yr3: submit Pre-IND meeting package following challenge.

· By Q4 Yr3: secure contract with an established partner for producing GLP/cGMP vaccines to advance to APECx Phase 2.

TA2 Only Goal - APECx Phase 2 (24 Months): Completion of Data Repository and Translational Toolkits, and Discovery Pipeline Maturation and Public Release

· Goals of APECx Phase 1 for TA2 Only performers (metrics defined in 1.3 PROGRAM METRICS)

· By Q2 Yr4: complete the data repository and make it accessible to a broad scientific community.

· By Q1 Yr5: refine the toolkits and pipelines to ensure usability and flexibility for a wide user base.

TA3 Goal - APECx Phase 2 (24 Months): Phase I Clinical Trials

During the 24-month APECx phase 2, performers will proceed with MCM candidates to Phase I clinical trials. APECx performers will adhere to the guidelines outlined by FDA in “Toxicity Grading Scale for Healthy Adult and Adolescent Volunteers Enrolled in Preventive Vaccine Clinical Trials” and “Considerations for Developmental Toxicity Studies for Preventive and Therapeutic Vaccines for Infectious Disease Indications” during the clinical trials.

· Goals of APECx Phase 2 (metrics defined in 1.3 PROGRAM METRICS)

· Phase I clinical trial

· Having met all prior criteria in APECx Phase 1, the MCM candidates should meet or exceed all prior criteria in Phase I Clinical Trials.

· Demonstrate safety in human trials.

· Demonstrate established manufacturer of therapeutic with cGMP capacity for Phase II/III/Commercial (≥ 1000 patients).

· Use PATIO assets to commercialize vaccine and exit the Program.

1.3. PROGRAM METRICS

To evaluate the effectiveness of a proposed solution in achieving the stated program objectives, the following program metrics will serve as the basis for determination of satisfactory progress to warrant continued funding. Although the program metrics are specified below, proposers should note that the Government has identified these goals with the intention of bounding the scope of effort while affording maximum flexibility, creativity, and innovation of proposed solutions to the goals. Proposals should cite the quantitative and qualitative success criteria that the effort will achieve at each phase’s program milestone, as well as the measurement of intermediary metrics. If the metrics are not meaningful for a particular case, proposing teams are expected to provide their own metrics and describe the quantitative improvement that those metrics represent over the state-of-the-art. Power analysis calculations may be needed to support the proposed metrics.

1.3.1. TA1 and TA2 Metrics and Objectives

The overall APECx goal based on the timeline is shown in Figure 1. The overall program goals are listed in Table 1. The expected metrics per phase in TA1 are listed in Table 2 and TA2 in Table 3. In addition to frequent performance reviews throughout the phases, performers must provide an end-of-phase final report that summarizes all efforts and data for each completed APECx Phase.

Table 1. TA1, TA2 and TA3 Overall Program Goals for APECx The overall program goals for all TAs are listed in Table 1, which includes the expected outcome for each goal.