Tales From The Trenches: Developing Potency Assays Outside Big Pharma
By Jeanette Ampudia, biopharma analytical expert
A validated potency assay is a cornerstone of any biologics development program. It's not just a regulatory requirement; it’s a scientific and quality control tool that ensures consistency, efficacy, and product integrity throughout development, manufacturing, and clinical supply.
I once worked with a small team developing a complex immune-modulating biologic where mechanism of action (MoA) wasn’t easily captured by a simple binding assay. We needed to show biological relevance in a reproducible quantitative format.
I don’t expect this story to resonate with those in large pharmaceutical companies that have the infrastructure and processes already in place. But if you’re at a smaller company or in an emerging biotech setting, I hope this experience sheds light on what it takes to build a potency assay from scratch and what pitfalls to avoid.
For cell- and receptor-mediated products, especially those modulating immune signaling or cellular activity, potency assays must not only detect activity but demonstrate sensitivity to clinically relevant variation. It becomes a true gatekeeper — not just for batch release but also for stability tracking, process changes, and regulatory confidence. If you’re working with a first-in-class or mechanism-driven molecule, the pressure to get it right is significant.
Planning Early And Broadly
The first and most critical piece of advice I can offer is this: start with a detailed plan. Not just a plan for the science, but one that includes regulatory checkpoints, CMC alignment, and realistic development timelines. This plan should be reviewed early and often — not just within your R&D group but with external consultants, your internal regulatory team, and your manufacturing partners. The biggest oversight I see is when potency assay development is treated like a siloed lab activity. It isn’t.
The value of cross-functional feedback cannot be overstated.
- CMC may spot scaling or robustness issues.
- Regulatory may flag concerns about assay sensitivity or bridging requirements.
- Consultants can warn of potential pitfalls based on recent agency trends.
These are voices that may not be in your day-to-day workstream, but they will be critical to your success.
Navigating Internal Challenges
Potency assay development often exposes gaps in organizational communication and alignment. In our case, we found that different teams had different expectations for what the assay needed to achieve. Research focused on biological plausibility. Regulatory emphasized robustness and validation. CMC wanted to ensure it was reproducible at manufacturing scale. These are all valid priorities, but unless aligned early, they can pull the assay development in conflicting directions.
At times, our project felt like a moving target. With each new data package, internal opinions shifted. What started as a functional T-cell assay evolved as new MoA data emerged. We had to learn to manage expectations and build consensus in real time — sometimes reminding ourselves and stakeholders that a new direction is evolution, not failure. After all, science is iterative.
CRO Transfers: Cost Vs. Continuity
One of our biggest lessons came when we tech-transferred the assay to a CRO overseas to reduce costs. On paper, the move made financial sense. We learned that geography plays an undeniable role in efficiency. Communication delays, differences in interpretation of protocols, and time zone gaps introduced inefficiencies that ultimately cost us more than we saved. We underestimated the amount of hands-on training and contextual knowledge needed to run it correctly.
Thankfully, we had a parallel effort running with a U.S.-based CRO using a revised version of the assay based on our updated MoA. That group had closer scientific engagement and faster feedback loops, and it ultimately delivered the data package we needed. But that transition took time and came too late to save our original timeline.
Mechanism Of Action Shift And Regulatory Engagement
Perhaps the most humbling part of the process was realizing that we had built an entire assay program on an incomplete understanding of the drug’s mechanism of action. We had spent nearly 18 months developing a T-cell stimulation assay based on early data, only to later uncover a secondary mechanism that appeared to be the primary driver of therapeutic effect.
This discovery forced a major pivot just as we were approaching a key corporate milestone. The good news was that the new mechanism opened up clearer, more measurable biological endpoints. The challenge was convincing both internal leadership and regulatory authorities that this shift was justified — and not a liability.
We proactively engaged the FDA through Type B and C meetings to align on our proposed path forward. While the original mechanism had been published, the new one had not. As such, the agency requested a bridging strategy between our original binding assay (used for release) and the new functional potency assay. This meant demonstrating that the cell-based assay could detect charge variants, stability changes, and lot-to-lot variability with at least the same sensitivity and reliability.
That bridging work became a program in itself. We were fortunate to carry out much of it in-house, giving us tight control over design, timing, and quality. Ultimately, we were able to demonstrate that the new assay not only met FDA expectations — it surpassed the sensitivity and biological relevance of our binding assay.
Reflections And What We’d Do Differently
We often joked during this time that we were “flying the plane as we were building it.” That analogy wasn’t far off. Potency assay development rarely follows a straight line. You are building tools while uncovering new science, managing timelines, and navigating stakeholder expectations.
Looking back, I would emphasize three key takeaways:
- Start cross-functional alignment early. Don’t wait for a submission to pull in CMC or regulatory — engage them at assay concept stage.
- Validate your mechanism rigorously before anchoring your assay around it. Early assumptions are hard to unwind once embedded in your validation plan.
- Don’t underestimate the complexity of outsourcing. A tech transfer is not just a document — it’s a knowledge transfer.
Final Thoughts
Potency assay development requires collaboration, humility, and scientific flexibility. For those of you just getting started, surround yourself with the right voices early, invest in understanding your biology deeply, and design assays that not only reflect MoA but also meet the real-world challenges of validation, reproducibility, and regulatory scrutiny.
It won’t be easy, but it’s doable. And when you finally arrive at a validated FDA-aligned potency assay, every painful lesson will have been worth it.
About The Author:
Jeanette Ampudia is the director of immunology and research operations at Equillium Inc. With a foundation in T-cell biology, immunoassay development, and biomarker discovery, her work bridges discovery and translational research. She supports preclinical- and clinical-stage programs through primary immune cell profiling, functional screening, and mechanistic assay design. She works with conventional and spectral flow cytometry and has contributed to IND- and BLA-enabling efforts across immunology pipelines.