Bridging the Gap: The LNP Alliance on Translating Nucleic Acid Therapeutics from Lab to Clinic

Lipid nanoparticle-based therapeutics have moved a long way in a short time, but translating an LNP program from the lab to the clinic is still anything but straightforward. The science is advancing quickly, especially as developers push beyond vaccines and liver-targeted applications, but many of the same questions remain: How do you predict in vivo performance? When should biodistribution and structural characterization come into the process? And how do you bring the right expertise together before a program runs into trouble? 

To explore those issues, Contract Pharma gathered a panel of experts from the newly formed LNP Alliance, including:

• Syed Reza (MD-PhD), Licensing and External Innovation Alliance Management, NOF America Corporation

• Nicholas Boylan (PhD), Senior Director, Scientific Services, Phosphorex

• Jerry Williamson (MBA), CEO, Phosphorex

• Mandy Janssen (PhD), Scientific Director, Characterization, Nano Imaging Services (NIS)

• Sara Little (BS), Associate Director of Oncology, NeoSome Life Sciences

• Jake McDonald (PhD), CEO, Envol Biomedical

Together, the group discussed where LNP programs often stall, how the COVID-19 vaccine era changed the field, and why successful translation increasingly depends on tighter coordination across lipid supply, formulation development, characterization, and preclinical evaluation.

The Conversation

Contract Pharma: Where do LNP-based therapeutic programs most commonly falter on their way to the clinic?

Syed Reza: The fundamental problem with nucleic acid therapeutics compared to other modalities like antibodies and small molecules is that in vitro and in vivo behavior correlation is very challenging. With proteins or small molecules, you can do a lot of meaningful optimization in silico or in vitro, and that tends to translate well in vivo. With LNPs, the complexity of their interactions with human biology makes it very difficult to glean meaningful insights from in vitro work alone. The cost of conducting in vivo evaluation is quite high, so I have observed many innovators trying to delay extensive non-human primate (NHP) or advanced in vivo characterization, only to hit roadblocks as they try to transition to the clinic.

Jake McDonald: LNP characterization and performance testing are expensive, so you generally want to deploy a tiered approach. First, utilizing non-animal methods, then moving up the hierarchy. Over the years, we’ve developed imaging tools and other real-time methods to assess efficacy and safety more efficiently, but the tools available to answer these questions have historically been limited. The engineers can often create new LNP formulations more quickly than the biologists can screen them, so reducing that dimensionality is where we’ve seen the most progress in the last five to ten years.

Nicholas Boylan: From my vantage point in the LNP value chain, scalability is often the most significant challenge. It’s very easy to make small-scale LNP batches on a benchtop system. But when you try to scale up, numerous issues can present themselves. For instance, ionizable lipids with poor solubility can lead to aggregation, complicating downstream purification

Sara Little: The biggest concerns I consistently hear relate to off-target responses and safety. Many developers are creating LNPs without necessarily having deep expertise in targeting different tissues or understanding how delivery will affect the rest of the system. This knowledge gap is where programs tend to stumble.

Jerry Williamson: I’ll add a perspective that’s a bit broader. If you compare the level of extensive knowledge we’ve built over the decades for therapeutics such as small-molecule drugs and monoclonal antibodies, we simply don’t yet have the same depth of experience with LNP-based drug delivery. The success rate shouldn’t be expected to match that of other modalities because, to some degree, we’re still figuring this out.

CP: The COVID-19 vaccines were a watershed moment for LNP technology. Has that momentum resulted in a more robust LNP therapeutic pipeline?

Reza: The COVID experience absolutely demonstrated that ionizable lipids and mRNA can be delivered at scale and are reasonably well-tolerated in a vaccine context. But the industry quickly ran into a critical distinction: genetic therapeutics are administered to sick and frail patients, sometimes at doses 200 times higher than those used in vaccines, and frequently require repeated dosing. The immunogenicity required for a vaccine typically becomes a serious liability for a therapeutic. Although the LNP community is working on it, we don’t yet have a rational, systematic way to engineer immunogenicity out of an LNP system. There is still a lot of trial and error.

Boylan: The exploration of utilizing LNPs beyond vaccines and hepatic diseases is accelerating, but we’re still on the learning curve. When LNPs were first developed for liver targeting, the mechanism was fairly well understood. Specifically, serum proteins like Apolipoprotein E (ApoE) bind to the surface and facilitate hepatocyte uptake. Now that we’re trying to re-engineer these systems for extra-hepatic targets like the lung, immune cells, and CNS, we’re still learning how to facilitate that targeting, whether by re-engineering the particle surface or by conjugating targeting ligands. High-throughput screening approaches, including DNA barcoding methods that allow multiple formulations to be evaluated simultaneously in a single animal, are becoming increasingly important.

McDonald: There has definitely been a momentum shift toward LNP-based delivery. Historically, many developers relied on viral vectors, but we’re seeing far less of that now, and the pandemic almost certainly accelerated the shift. 

Little: In terms of the work we’re doing at NeoSome, a greater percentage of programs now involve gene editing that relies on LNP delivery. We’re definitely seeing a lot of innovation and advancement in the space.

Mandy Janssen: From a characterization standpoint, the mRNA vaccine era did something important: it brought an enormous volume and diversity of LNP formulations into analytical workflows, and what that revealed is how structurally variable LNPs can be, even within a single “platform.” The assumption that formulation success in one context readily transfers to another can obscure the fact that small changes in lipid composition, cargo, or process conditions yield meaningfully different structures.

CP: When should the biodistribution strategy enter the development process, and what can getting it wrong cost a program?

Boylan: Biodistribution strategy work should begin at the outset of a program, ideally before you lock in a lead formulation candidate. These considerations will directly inform your choice of ionizable lipid, the overall LNP composition, and whether an active targeting approach is necessary. For liver-targeted applications, LNPs will naturally accumulate there; it’s relatively low-hanging fruit. But for extra-hepatic targets, there’s always a balance between how much of the formulation reaches the target tissue versus how much ends up in the liver. Confirming biodistribution early in the program ensures that the most promising candidates are advanced and minimizes the risk of getting the wrong biodistribution, which can result in significant delays, added cost, and potential safety concerns due to off-target effects.   

Little: Early biodistribution studies can make or break a program. You can have positive in vitro results but still get unexpected results after administering a formulation to an animal. If the therapeutic doesn’t achieve the desired targeting in a mouse, it is unlikely to work in a human system, and proceeding to more expensive primate models is, at this point, premature.

Reza: We encourage clients to screen a variety of ionizable lipids and LNP compositions early, checking for potency and biodistribution as a fundamental screening step. The goal is to have candidates that are well-validated in both rodent models and in vitro human cell-based immunogenicity assays before moving into NHP studies, where you will generate a much higher level of confidence in the therapeutic’s performance, but testing costs are much higher.

McDonald: The tools available to answer biodistribution questions have advanced considerably. Over the last five to ten years, we’ve seen meaningful progress in the use of imaging, both ex vivo and in vivo, to evaluate whether a formulation is hitting its intended target or producing off-target effects. We’ve also seen innovations on the analytical side, including DNA barcoding approaches that allow you to tag multiple test articles and evaluate them simultaneously in a single animal. The reality is that engineers are often faster at generating new LNP permutations than biologists are at screening them, so the name of the game is reducing the dimensionality of the screening problem. Smarter integration of test articles and more disciplined down-selection are where the field has made its biggest strides.

CP: Cryo-EM characterization can reveal structural details about LNPs that conventional analytics simply cannot. At what stage of development should structural characterization be integrated, and how often does it change the direction of a program?

Janssen: Structural characterization should be integrated from early formulation development, not held until late preclinical stages when the window to act on findings has largely closed. In practice, cryo-TEM changes program direction more often than teams expect. Bleb formation, lamellar disorganization, elevated empty particle fractions, and overall heterogeneity are not detectable with standard tools such as dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), and bulk encapsulation assays. Yet, each has direct implications for potency and stability. Finding these issues early, during excipient screening or process optimization, is what makes structural data formative rather than merely confirmatory.

Cryo-TEM plays important roles beyond early-phase development. For IND-enabling work, it provides the morphological identity data that regulatory submissions increasingly expect. For troubleshooting, it serves as a source of truth when bulk assays disagree or when a batch fails to meet specifications. For targeted LNPs specifically, cryo-electron tomography (cryo-ET) is particularly valuable, as it enables direct visualization of surface-bound antibodies or ligands in three dimensions, making it uniquely suited to confirming conjugation and assessing ligand distribution, which no bulk assay can provide.

CP: Ionizable lipid selection is often described as one of the most consequential decisions in LNP development. How should developers approach this selection process?

Reza: Some people think of this as searching for El Dorado; one golden lipid that does everything. But that doesn’t exist. There are currently about half a dozen ionizable lipids that have been used in the clinic. When we speak with partners, the preference is almost always to work with a lipid that already has human exposure data. But beyond science, the decision is also heavily driven by business considerations like intellectual property, licensing access, and whether you’re acquiring just the lipid or an entire validated LNP formulation package. If you’re licensing a lipid with a validated formulation, you can streamline your efforts. If you’re working with a novel ionizable lipid, you’re starting with more freedom but also more unknowns.

CP: How is the LNP Alliance collaboratively working to address patient safety concerns? 

Reza: Immunogenicity is a huge topic, but we are developing a better understanding of which components of an LNP drive inflammatory responses. The choice of ionizable lipid is a primary consideration, as some are more immunogenic than others. Our in vitro macrophage assay is very useful for predicting immunogenicity, and we’re closely monitoring the induction of anti-PEG antibodies. For instance, we recently concluded a study with Envol in NHPs comparing two PEG lipid types, and there are early signals that the choice of PEG lipid meaningfully affects this response. A third factor is impurities, particularly from RNA or lipid degradation products. That’s where Phosphorex’s manufacturing controls and sophisticated analytics are critically important.

Little: While there are patient safety concerns related to repeat dosing, LNP therapeutics tend to fare a bit better than some other strategies on this front. Developers are, in many cases, moving away from viral vectors due to patient safety concerns about redosing because of off-target effects, and their larger particle size can limit biodistribution, with certain viruses being rapidly cleared by the liver and kidneys.

CP: Can you describe how the Alliance has functioned in practice and some of the benefits of the collaborative effort?

Williamson: The fundamental premise of the LNP Alliance is that a biotech or pharma company trying to develop an LNP-based drug has to bring together all of the expertise that we collectively represent. Assembling all of the experience we have within the LNP Alliance would take a lot of time and would incur high costs. We each have our areas of specialization: NOF provides expertise and supply in ionizable lipids; Phosphorex handles formulation development and manufacturing; NeoSome provides in vitro and in vivo evaluation in rodent models; Envol provides non-human primate studies and preclinical toxicology; NIS offers advanced characterization expertise. Combined, we cover the full translational arc. As I said, the collective we have built would take a lot of time and money for a biotech to build, and large CDMOs are often serving multiple modalities, so they tend not to have this level of specialized depth.

Reza: The first major collaborative project we completed was a translation study in rodent and non-human primate models evaluating our ionizable lipids, and was planned jointly by Phosphorex, NOF, Envol, and NeoSome. One very practical issue we encountered was that the animals gained weight between selection and dosing, resulting in unexpectedly higher required material volumes. We had to redesign batch production at Phosphorex to keep up with rising material requirements. The lesson from the effort was to plan for at least a 25 percent material overage and build in close communication between partners throughout the effort. It’s that kind of real-world, cross-organizational problem-solving that is so promising for future work.

McDonald: Companies come to us to evaluate a wide range of LNP permutations, systematically controlling variables to understand their impact on efficacy or toxicity. In many cases, though, they’re using whatever screening tools are most readily available rather than the tools best suited to answer their specific questions. That’s one of the real advantages of the LNP Alliance: we’re not just deploying existing tools, we’re developing new models and new capabilities that give developers a genuinely better chance of identifying what’s going to work.

Boylan: Each time we work together, we become more efficient. The planning, the lead time, the anticipation of challenges, all of that improves with shared experience.

Where Translation Happens

The LNP field stands at an inflection point. The science has matured enough to move well beyond hepatic targets and vaccine applications, yet the gap between what developers need to achieve, available tools, and what empirical knowledge can reliably support remains significant. Closing that gap will not happen through any single organization working in isolation.

Translating LNP-based therapeutics to the clinic is, at its core, a multidisciplinary problem that demands expertise in lipid chemistry, formulation engineering, structural characterization, and preclinical biology working in close, continuous coordination. The LNP Alliance was built on this exact premise and is working to provide specialized expertise to dramatically increase the clinical and commercial success of LNP therapeutics.

To learn more about the LNP Alliance, visit www.lnpalliance.org.

Meet the LNP Alliance Panel