Navigating FDA’s Evolving Nonclinical Landscape: Strategies for Translational Success of Drug Products

Executive Summary

The U.S. Food and Drug Administration (FDA) has formalized a transformative shift in nonclinical safety assessments as part of the drug development process, emphasizing human relevance and mechanistic insight through the expanded adoption of New Approach Methodologies (NAMs). Codified under the Food and Drug Omnibus Reform Act of 2022 (FDORA), this performance-based framework moves beyond conventional animal testing and aligns with the ethical principles of the 3Rs (Replace, Reduce, Refine).

This white paper reflects the FDA's emerging expectations – particularly as articulated by Center for Drug Evaluation and Research/ Office of New Drugs (CDER/OND) reviewers in the recently published paper by Yao et al. (2025)[1] – and outlines what this paradigm means for Sponsors of drug candidates. We highlight how early, strategic planning reduces uncertainty, enhances regulatory confidence, and accelerates translational success.

The FDA’s message is clear: NAMs gain regulatory traction only when supported by strong biological and technical rigor and anchored by a reviewer-ready Context of Use (COU). For Sponsors, mastering these elements is essential to strengthen early decision-making, reduce unnecessary nonclinical studies, and future-proof their drug development programs.

The FDA's Evolving Roadmap on NAMs: A Framework for Regulatory Confidence

FDORA Codification of NAMs

In 2022, FDORA (FDA Modernization Act 2.0) amended the Federal Food, Drug, and Cosmetic Act (FDCA) to remove the statutory requirement for animal testing and formally authorize scientifically valid nonclinical alternatives, including NAMs. In April 2025, FDA published a roadmap that outlines a phased approach to reduce reliance on animal studies and encourages drug candidate Sponsors to incorporate human-relevant methods where appropriate, provided they meet regulatory standards and do not compromise public health.[1]

Defining the NAMs Landscape

NAMs include in vitro, ex vivo, in silico (computational), and in chemico methods designed to improve the prediction of human safety. Among these, Complex In Vitro Models (CIVM) and Microphysiological Systems (MPS), including organ-on-chip technologies represent increasingly sophisticated tools that aim to recapitulate organ-level human biology. Although some NAMs are well established, the critical challenge lies in identifying the most effective points of integration within the nonclinical drug development pathway and demonstrating their validity and correlation with established in vivo endpoints.

Where NAMs Integrate Across the Drug Development Lifecycle

NAMs can be incorporated across the entire nonclinical drug development continuum. When applied thoughtfully, NAMs complement traditional approaches, reduce animal use, and improve development efficiency.

Strategic applications include:

• Discovery/Early Development: High-throughput compound screening; early hazard identification; designing in vitro and in vivo studies through endpoint, dose, and species selection.
• Translational Planning: Identifying potential human risks before first-in-human (FIH) exposure; informing clinical monitoring plans.
• Mechanistic/Troubleshooting: Characterizing unexpected toxicities; guiding inclusion/exclusion criteria for clinical studies, defining stopping rules, and biomarker development.
• Clinical and Post-Discovery Insight: Supporting mechanistic interpretation of safety signals; refining human relevance and informing dose/pharmacokinetic (PK) decisions.

Context of Use (COU): The Cornerstone of Regulatory Acceptance

FDA reviewers consistently identify COU clarity as the strongest predictor of NAM success. Submissions fail when COUs are vague (e.g., “screening cytotoxicity”) rather than tied to a specific regulatory decision (e.g., “assessing relative Drug-Induced Liver Injury (DILI) risk vs comparator”). The case studies discussed in the Yao et al. (2025) manuscript affirm that the FDA evaluates NAM data not as preliminary screens, but as targeted, mechanistic evidence designed to support specific regulatory decisions.

Attributes of a Reviewer-Ready COU

A successful COU requires:

• Biological relevance justification aligned with the clinical context
• Transparent and clear study purpose and limitations
• Sufficient methodological detail and justification including:
• cell origin and characterization
• replicates and statistical plan
• dose selection rationale
• controls (positive, negative, vehicle)
• sensitivity, specificity, and performance metrics of assay
• timing and relevance of endpoints
• discussion of deviations and impact
• Supportive literature to contextualize model relevance

Regulatory Acceptance Spectrum for NAMs

FDA recognizes NAMs across various categories, as outlined in the table below.

OECD=Organization for Economic Co-operation and Development; ICCVAM=Interagency Coordinating Committee on the Validation of Alternative Methods; Bovine Corneal Opacity and Permeability; RhCE = Reconstructed Human Cornea-Like Epithelium; MEFL= Malformation and Embryo-Fetal Lethality; DILI= Drug-Induced Liver Injury.

Regulatory Lessons: Common Gaps in NAM Submissions

FDA reviewers repeatedly highlight technical and strategic deficiencies that undermine otherwise promising NAM data, as summarized below.

• Insufficient Biological or Technical Rigor (DILI Models): A study investigating DILI susceptibility, while providing useful supportive information, was not relied upon for regulatory decision-making due to:
  • Inadequate representation of the disease pathology (lacking immune components) and disease progression
  • Underpowered donor selection for primary human hepatocytes for the intended endpoints (only three donors were used without justification)
  • Missing assay sensitivity/specificity data
  • Lack of justification for the types of controls used and selected drug concentrations
  • Limited clinical relevance of exposure durations

• Poor Assay Definition and Characterization (Gastrointestinal Organoids): A study attempting to assess species (rodent vs non-rodent) sensitivity for intestinal toxicity failed regulatory reliance due to fundamental gaps:
  • • Minimal information was provided to the reviewers which made the evaluation of data challenging; additionally, there was no clear COU established
    • Poor characterization of the organoids (donor demographics, morphology); furthermore, only organoids derived from duodenal tissue were used in this assay
    • Lack of effective controls (ineffective positive control; no negative control included)
    • Lack of sufficient assay detail (e.g., no purity was provided for the test compounds) and no justification was provided for the number of replicates
    • Single, simplistic endpoint (cell viability) was measured, which inadequately reflected the complex in vivo toxicity observed in animal studies (inflammation, ulceration)
• Limited Translational Relevance (Local Toxicity - Inhalation Models): A submission using human airway tissue models to assess inhalation safety failed due to unreliable dose extrapolation and insufficient data for repeated-dose administration consistent with clinical use:

• • • Poor recapitulation of critical airway-organ interactions during inhalation exposure, such as metabolic processes
    • The data used non-validated in silico computational modeling for In Vitro to In Vivo Extrapolation (IVIVE), and the in vitro concentrations tested were vastly disproportionate (100 to 15,000 times higher) than the estimated human tissue concentrations, thereby negating clinical relevance
    • Positive control was not supported by justification and an oversimplified endpoint was used (cell death), without accounting for other functional changes that are commonly seen due to toxicity via the inhalation route of exposure

Best Practices: Scientific and Technical Rigor for NAM Acceptance

Across FDA case reviews, one unifying theme is clear: robust experimental design remains essential, and studies must be transparently reported, regardless of whether studies are performed in accordance with Good Laboratory Practice (GLP) (USFDA 21 CFR58) or non-GLP.

Sponsors should ensure:

• Clear definition of biological system and clinical relevance
• Justification of biological and technical replicates
• Rationale for dose selection in clear alignment with clinical exposure or human-relevant concentrations
• Use of appropriate positive, negative, and vehicle controls
• Transparent reporting of endpoint selection, timing of treatment, and how the methods used and results generated relate to the clinical scenario
• Description of assay performance, including sensitivity, specificity, and inclusion of any known limitations
• Documentation and discussion of deviations

In several cases, reviewers accepted non-GLP NAMs where reports were thorough, transparent, and well-justified - highlighting that scientific rigor can outweigh GLP status for NAMs inclusion.

The Future Trajectory: NAMs as Transformative Translational Tools

Microphysiological Systems (MPS) and Organ-on-a-Chip

FDA’s acceptance of the first human Liver-Chip MPS Letter of Intent into Innovative Science and Technology Approaches for New Drugs (ISTAND, 2024) is a pivotal milestone. The qualified tool aims to assess relative DILI risk, addressing species discordance before Investigational New Drug (IND) submission. As more tools achieve qualification, MPS platforms will increasingly inform IND-enabling dose selection and mechanistic safety predictions.

Computational Toxicology, Artificial Intelligence, and In Silico Modeling

Regulatory reliance on computational tools already exists (e.g., ICH M7(R2) for genotoxicity). The next phase will integrate AI/ML, multi-omics, and population variability to strengthen predictive modeling for endpoints such as DILI. While standalone predictive use of these models remains aspirational currently, these computational tools can significantly strengthen WoE arguments and inform clinical risk management.

Emerging Applications in Gene and Cell Therapy

Innovative therapeutics like gene therapies often present toxicity profiles poorly captured in animals. For example, the risk of sensory neuropathies, often subtle or unmonitored in animal toxicology, drives the need for human-relevant cellular models. Advances in iPSC-derived sensory neuron models (Dorsal Root Ganglia) are demonstrating utility in anticipating human-specific risks such as Chemotherapy-Induced Peripheral Neuropathy before clinical exposure.

Strategic Value: Turning Regulatory Expectations into Translational Success

The FDA's NAMs paradigm offers tremendous opportunity, along with significant complexity. Biologics Consulting can help Sponsors by:

• Mastering the Context of Use (COU): Crafting precise, defensible COUs that clearly articulate regulatory intent and increase FDA reviewer confidence
• Building Robust Weight of Evidence (WoE) Packages: Our nonclinical experts can integrate NAMs, PK modeling, and historical animal toxicity data into cohesive WoE assessments to support IND-enabling decisions
• Collaborating on NAMs Study Design and Data: Working with Contract Research Organizations (CROs) to review study protocols and results, helping to design fit-for-purpose NAMs studies that supplement animal testing or, when justified, replace it
• Future-Proofing Nonclinical Programs: Guiding Sponsors on emerging technologies and preparing for early FDA engagement (e.g., INTERACT, ISTAND, pre-IND), to reduce late-stage risk and improve acceptance of FDA submission packages.

Realistic Expectations: NAMs as Complementary, Not Standalone Tools

FDA reviewers acknowledge that while NAMs have the potential to offer improved human relevance for investigating drug candidate safety and efficacy, in vivo systems remain complex, and no single NAM can currently replace all aspects of animal testing across all key in vivo endpoints. However, their value as complementary translational tools is undeniable. NAMs can provide mechanistic insights, support clinical biomarker selection, refine risk assessments, and contextualize unexpected findings. As technology advances and methods become more widely used and validated, the integration of NAMs with traditional toxicology testing and assessments will increasingly shape more predictive, human-aligned safety strategies.

Conclusion

The FDA’s embrace of NAMs under FDORA marks a definitive shift toward human-relevant nonclinical science in the drug development space. With the right strategy, Sponsors can leverage NAMs to strengthen regulatory confidence, streamline development, and reduce overall program risk.

Biologics Consulting empowers innovation through nonclinical and regulatory strategies aligned with FDA’s evolving paradigm. Contact us to discuss your drug development program and explore how our experts can support your nonclinical testing strategy.

[1] Yao J, Peretz J, Bebenek I, et al. FDA/CDER/OND Experience With New Approach Methodologies (NAMs). Int J Toxicol. Published online November 13, 2025. doi:10.1177/10915818251384270

[2] U.S. Food and Drug Administration. Roadmap to reducing animal testing in preclinical safety studies. April 10, 2025.