The Drug Development Lifecycle: Why NDA/BLA Thinking Starts Earlier Than You Think

For many small and startup pharma and biotech companies, the NDA or BLA can feel like a distant milestone—something to worry about after Phase 3 is locked, the data are in, and the program feels "real." Until then, it’s easy to think: We’ll deal with the NDA/BLA when we get there.

But here’s the reality we see time and time again: the NDA or BLA is not a single event at the end of development. It’s the culmination of hundreds of decisions made across clinical, CMC, regulatory, quality, and operations—often years before a submission date is even on the calendar.

That’s not meant to be intimidating. In fact, it’s the opposite. Thinking about your NDA or BLA earlier doesn’t mean overbuilding systems, hiring a massive team, or writing documents years ahead of need. It means starting to think like a Sponsor—and Phase 3 is the right moment to make that mindset shift.

Plus, when you’re already thinking about your NDA/BLA, you can build your IND in such a way that saves tons of time down the road by ensuring you can clone as much of your IND as possible into your NDA/BLA.

This post kicks off our year-long NDA/BLA series, designed specifically for first-time sponsors. We’ll walk through why early NDA/BLA thinking matters, what it really looks like in practice, and how it can reduce risk without slowing you down.

The NDA/BLA Is a Culmination, Not a Cliff

An NDA or BLA doesn’t magically come together because a Phase 3 trial ends successfully. Reviewers aren’t just evaluating your final datasets—they’re assessing the story of your program:

• How your product was developed

• How decisions were made and documented

• How data are traced, verified, and explained

• How quality and compliance were maintained as the program scaled

From the FDA’s perspective, the submission reflects the entire lifecycle of the product, not just the last chapter.

This is why sponsors sometimes feel blindsided late in development. Issues that show up during NDA/BLA preparation—data traceability gaps, inconsistent narratives, missing rationales—often didn’t start in Phase 3. They started much earlier, when teams were appropriately focused on speed and survival, but without an eye toward how decisions would eventually need to be defended.

Early NDA/BLA thinking isn’t about doing everything early. It’s about making today’s decisions with tomorrow’s reviewers in mind.

Why Phase 3 Is the Inflection Point

Phase 3 represents a natural transition for small and startup companies:

• Programs are more expensive and visible

• Timelines are tighter

• External scrutiny increases

• The company’s future may hinge on a single outcome

It’s also the point where the question subtly shifts from "Can this work?" to "Can we defend this to regulators?"

At the start of Phase 3, at minimum, is the moment to start asking:

• Are our clinical, CMC, and regulatory strategies aligned?

• Are we generating data in a way that will support an NDA or BLA—not just a top-line result?

• Do we understand how today’s choices will show up in Module 2 summaries, Module 3 justifications, or Module 5 narratives later?

Thinking like an NDA/BLA sponsor at this stage helps teams avoid costly rework, rushed documentation, and last-minute fire drills as submission approaches.

Early Thinking ≠ Overbuilding

One of the biggest concerns we hear from startup teams is:

“We don’t want to build big pharma infrastructure too early.”

That concern is valid—and necessary. Early NDA/BLA thinking is not about creating heavyweight systems or checking boxes for their own sake. Instead, it’s about being intentional:

• Designing processes that can scale later

• Capturing rationale alongside decisions, not years afterward

• Setting up document and data management practices that won’t collapse under NDA/BLA volume

• Understanding where regulatory operations and quality will eventually need to mature

Done well, this approach actually preserves agility. Teams spend less time untangling the past and more time moving the program forward.

Common Pain Points That Start Too Early to Ignore

Across many first-time NDA and BLA sponsors, we see the same themes emerge during late-stage preparation:

• Data traceability gaps between clinical outputs, analysis datasets, and final narratives

• Inconsistent terminology or positioning across documents authored years apart

• Limited documentation of decision-making, forcing teams to reconstruct rationales under pressure

• Regulatory operations processes that worked for INDs but don’t scale to marketing applications

These issues aren’t caused by lack of expertise or effort. They’re the natural result of teams doing exactly what they needed to do early on—move fast. The solution isn’t slowing down. It’s pairing speed with foresight.

What “Thinking Like a Sponsor” Actually Looks Like

At this stage, NDA/BLA readiness is more about mindset than mechanics. It can look like:

• Asking how Phase 3 trial design choices will support future labeling claims

• Considering how CMC changes will be explained and justified later

• Ensuring quality oversight evolves alongside program complexity

• Beginning to think about how your story will be told coherently across modules

It’s also about recognizing when it’s time to bring in support—whether that’s building submission-ready regulatory operations, strengthening inspection readiness, or adding program management structure to keep cross-functional teams aligned.

Setting the Tone for the Year Ahead

This blog is the first in a year-long series focused on helping small and startup sponsors navigate the NDA/BLA journey with clarity and confidence—from early mindset through submission, review, and beyond. In upcoming posts, we’ll dig into topics like:

• How NDA and BLA strategies differ

• What really changes as you move from IND to NDA/BLA

• How to build infrastructure without overbuilding

• When and how to engage FDA

• What reviewers are looking for—and why

If you’re approaching Phase 3 or starting to think seriously about your NDA or BLA submission, you’re in the right place.

At The Sugar Water Operations Team, we specialize in supporting first-time NDA/BLA sponsors—helping teams think ahead, reduce risk, and build only what they truly need, when they need it. Follow along as the series continues—and start thinking like a sponsor today.