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From monolayer to microtissue: Measuring what matters in 3D drug discovery

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Darren Heywood, Senior Product Manager at Promega UK, examines assay formats built specifically for 3D measurements.

A 3D microtissue, such as a spheroid or organoid, is not a monolayer with more cells. These are three-dimensional cultures that self-organise into structures resembling real tissue. In a spheroid, as it grows, oxygen and nutrients become limited towards the centre, creating a gradient from actively proliferating cells at the outer edge to quiescent, hard-to-reach cells at the core. Those core cells are, in many respects, the ones that matter most. An assay that reads only the outer rim isn’t measuring the wrong model, it’s measuring the wrong cells. 

That biology is different from monolayer cultures, and in drug discovery it matters. Potency data from the outer layers reflects the cells most directly exposed to drug, not the resistant, quiescent population at the core that drives relapse and clinical failure. It’s a key reason why compounds that look promising in the lab often disappoint in the clinic.  

 

Endpoint assays: Adapted for the biology 

Endpoint assays are the backbone of early compound screening, generating IC50 values and dose-response curves that determine which compounds progress. Running them in 3D is not always straightforward. The most common issue is lysis: standard buffers were designed for flat monolayers, not for cells embedded in matrix, and incomplete lysis means IC50 values are underestimated, reflecting only the most accessible cells rather than the full population. Stronger lysis conditions fix this. CellTiter-Glo 3D was reformulated for this purpose, giving reliable IC50 values from the full depth of the spheroid. The IC50 values are typically higher than in monolayer cultures, not because the assay is less sensitive, but because the spheroid contains quiescent, drug-resistant cells in the hypoxic core that monolayer cultures do not. Caspase-Glo 3/7 3D applies the same enhanced lysis principle to mechanism of action studies, measuring caspase-3/7 activity across the full spheroid depth. In 3D, this readout is more stringent than in 2D. Cells in the hypoxic core actively resist apoptosis through upregulation of anti-apoptotic proteins such as BCL-2 and survivin, a defence mechanism driven by those same oxygen and nutrient gradients. A compound that activates caspase-3/7 in a spheroid is overcoming the hypoxia-driven apoptosis resistance that monolayer cultures do not replicate. 

Understanding whether a compound is killing cells or just stopping them from dividing matters for dosing, combination therapy and the likelihood of resistance. The standard marker for this is Ki-67, a nuclear protein expressed only in cells that are actively cycling and absent in quiescent ones. Conventional Ki-67 measurement requires cell fixation, dissociation or sectioning, followed by microscopy or flow cytometry, none of which works at the throughput a compound screen demands. The Lumit Ki-67 assay sidesteps this by detecting Ki-67 from cell lysates in a standard plate reader format with no fixation, no washing and no specialist equipment, making Ki-67 practical for compound screening. 

 

Real-time kinetic assays: Beyond what endpoints can show 

Endpoint assays give a snapshot of compound activity at a single point in time. What they cannot show is when those effects start, how fast they develop or whether they reverse. This shapes dosing, scheduling and combination decisions. Real-time kinetic assays add reagents to the culture medium without lysing the cells. The 3D structure stays intact and the same well can be read repeatedly, capturing the full-time course of compound activity.  

Kinetic data from 2D cultures does not always translate to 3D. Without the diffusion barriers, quiescent subpopulations and hypoxic gradients that develop in a spheroid, monolayer cells do not present the same resistance mechanisms. Compounds that appear highly active in 2D can show less effect in spheroids of the same cell line. Using the RealTime-Glo Annexin V Apoptosis and Necrosis Assay, Kota et al. showed that Proscillaridin A induced apoptosis at earlier timepoints and at higher rates in oncogenic KRAS spheroids compared with wild-type. This selectivity was completely absent in 2D, where both cell lines were equally inhibited and the compound would have been discarded (Oncogene, 2018). It shows how 3D kinetic measurement can change which compounds advance. What real-time kinetic assays cannot access is what cells release into the medium, and for that a different approach is needed.

 

Media-sampling assays: A window into biology that other formats miss 

Media-sampling assays address this by measuring analytes from the culture medium without disturbing the cells, from the same well, throughout the treatment period. 

For metabolic profiling studies, 2D data can overestimate compound activity because the biology that drives metabolic resistance in tumours does not exist in monolayer cultures. Oxygen and nutrient gradients in spheroids drive a Warburg-like glycolytic shift, with elevated glucose consumption and increased lactate secretion, that closely mirrors the tumour microenvironment. In monolayer cultures, cells are uniformly oxygenated and proliferating, so the metabolic readout has little relevance to what a compound encounters in vivo. Glucose-Glo and Lactate-Glo measure these outputs from as little as 2–5µL of conditioned media, leaving the spheroid intact. Glutamine adds a further dimension: quiescent cells in the hypoxic core are less glutamine-dependent than actively cycling cells, so glutaminase inhibitors appear more potent in 2D than in 3D. Glutamine/Glutamate-Glo picks this up early, before it becomes a clinical problem. 

CYP450 activity illustrates what 3D adds for safety assessment. Primary hepatocytes in monolayer lose CYP activity within 24 to 48 hours, often before the experiment is finished. The same cells in 3D microtissues retain it for days to weeks, making drug-drug interaction and metabolic liability studies reliable in a way that 2D cannot. P450-Glo Assays measure CYP activity directly from the culture medium, so the same microtissue can be followed across the full study. 

 

Multiplexing: The complete picture from one well 

In 2D, running separate assays on separate wells is straightforward as cells are plentiful and easily replicated. In 3D, each microtissue takes days to form and cannot be reproduced on demand. Spheroids vary in size, necrotic core depth and matrix density, so data from different wells can carry biological noise unrelated to the compound. When a progression decision rests on whether a compound is cytotoxic or cytostatic, or whether a metabolic effect is a liability or a mechanism, that noise matters. 

The solution is to take all measurements from the same well. Because none of the non-lytic assay formats destroy the culture, they can be measured before the final lytic endpoint read: kinetic viability and cytotoxicity tracked continuously, metabolic readouts sampled from the same medium, and either Caspase-Glo 3/7 3D or Lumit Ki-67 to close. This gives the complete picture from a single well, without the cross-well noise. 

 

Conclusion 

Measuring in 3D is not just about having a better model. It is about accessing biology that monolayers do not contain. Endpoint assays reformulated for enhanced lysis give IC50 values that reflect drug-resistant quiescent cells, not just the proliferating outer rim. Real-time kinetics reveal compound selectivity that 2D screening obscures – Proscillaridin A being the clearest example. Media-sampling assays capture the metabolic state and functional outputs that 2D models cannot maintain. Run together, they show what compounds do in a way that 2D screening cannot match.  

 

About the author  

 

Darren Heywood holds a PhD in Neuroscience from the University of Bristol, specialising in neuronal cell death signalling. Now a Senior Product Manager at Promega UK with 12 years’ experience, he manages the cell health and metabolism portfolio, raising awareness of tools that enable more accurate monitoring of 3D cell health.

 

From DDW Volume 27 – Issue 3, Summer 2026 – Read the digital issue here

The post From monolayer to microtissue: Measuring what matters in 3D drug discovery appeared first on Drug Discovery World (DDW).

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Biotech leaders call for streamlining of INDs as FDA’s Trialblazer rolls out

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The FDA’s new investigational new drug pilot program—one part of HHS’s broader clinical trial modernization initiatives—has lofty goals to expedite first-in-human trials of novel drugs, but experts say it won’t tip the scales much on its own.

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5 companies advancing ATTR assets in the wake of Wainua’s fail

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The Phase 3 failure of AstraZeneca and Ionis Pharmaceuticals’ antisense therapy in transthyretin amyloid cardiomyopathy last month left the space reeling—and readjusting. BioSpace looks at five contenders and where they currently stand.

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StockWatch: Capricor Plunges as FDA Panel, Staff Question Effectiveness of Lead Candidate Deramiocel

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After seeing its lead candidate rejected by the FDA last year, Capricor Therapeutics (Nasdaq: CAPR) is hoping for a better outcome for its resubmitted biologics license application (BLA) for its lead pipeline candidate Deramiocel, a cell therapy indicated as a treatment for cardiomyopathy in Duchenne muscular dystrophy (DMD).

That hope appeared less likely than ever as the FDA’s Cellular, Tissue, and Gene Therapies Advisory Committee on Wednesday recommended against agency approval of Deramiocel, concluding in a 9-3 vote with no abstentions that the available evidence from the Phase III HOPE-3 trial (NCT05126758) did not “provide substantial evidence of effectiveness” for Deramiocel as a treatment for cardiomyopathy in Duchenne muscular dystrophy (DMD).

The advisory committee vote is likely to influence how the FDA acts on the resubmitted BLA for Deramiocel, with the agency having set an August 22 target decision date under the Prescription Drug User Fee Act (PDUFA). The FDA typically (but not always) heeds the advice of its advisory committees or “adcomms,” which in turn typically (but not always) heed the evaluations of agency staff.

Deramiocel is an allogeneic cardiosphere-derived cell (CDC) therapy candidate. CDCs are designed to act by secreting exosomes that target macrophages and alter their expression profile to adopt a healing rather than pro-inflammatory phenotype.

According to Capricor, preclinical and clinical studies have shown Deramiocel to preserve cardiac and skeletal muscle function in muscular dystrophies such as DMD by exerting strong immunomodulatory and anti-fibrotic activity.

Negative FDA evaluation

FDA reviewers paved the road to Deramiocel’s poor reception from the adcomm on July 27 with a negative evaluation of the resubmitted BLA. Their assessment concluded that data submitted to the FDA from HOPE-3 and the earlier Phase II HOPE-2 trial (NCT03406780) “does not provide substantial evidence of effectiveness for Deramiocel in DMD”—though Capricor’s indication for Deramiocel is specifically cardiomyopathy in DMD.

The unnamed FDA staffers took issue with:

  • Whether Deramiocel achieved HOPE-3’s primary and secondary endpoints.
  • The hypersensitivity shown by 42% of Deramiocel patients vs. 15% of placebo patients;
  • Capricor’s failing to submit to the agency an updated statistical analysis plan (SAP) for review before it resubmitted its BLA for Deramiocel in February.

Capricor declared HOPE-3 a successful trial in December, citing as a statistically significant benefit the reported 54% slowing of skeletal muscle disease progression on the primary endpoint, Performance of the Upper Limb version 2.0 (PUL 2.0) percentage change from baseline in the 105-patient intent-to-treat (ITT) population with evaluable PUL v2.0 assessments at 12 months. Capricor also reported a 91% slowing of progression measured by left ventricular ejection fraction (LVEF) in the 83-patient ITT population with centrally reviewed and evaluable cardiac MRI LVEF assessments at 12 months.

The FDA, however, says HOPE-3 can only be deemed a success after the company made changes to its SAP that included modifications to the primary and key secondary endpoint definitions, its analytical methods; and the data imputation strategy for intercurrent events.

“Although the applicant provides justifications for these changes, FDA does not agree that the scientific rationale for those changes was supported and considers the changes unwarranted based on the study’s design, powering, and original statistical assumptions,” the FDA staffers contended.

The reviewers also alleged that the distinctive adverse event profiles seen between Deramiocel and placebo patients “raises the possibility that treatment assignment could be inferred even under formal blinding conditions.”

“This risk of functional unblinding,” they added, “was further extended by the open-label period of HOPE-3, during which additional treatment-related data accumulated and may have made treatment assignment more apparent.”

Capricor answers back

Capricor answered back the same day. CEO Linda Marbán, PhD, told Reuters she was “completely shocked at how they decided to review and analyze ​this data,” while the company issued a statement faulting the FDA for relying on an “obsolete” analysis: “Our results are governed by the final analysis plan, SAP version 3.0, which was finalized prior to unblinding.”

“It is critical to understand that the post-hoc analyses in the FDA’s briefing materials rely on SAP version 1.1, an unsigned incomplete internal draft which became obsolete with the addition of cohort B and did not include content specifically requested by FDA,” Capricor explained. “We believe Deramiocel offers a meaningful treatment option for boys and young men living with Duchenne, who continue to face a significant unmet medical need.”

The company sought to back up that contention on Wednesday, when it released updated data from HOPE-3 that were published in The Lancet. The updated data showed Deramiocel to have improved cardiac and skeletal muscle function in Phase I–II studies of DMD, and also found that deramiocel could slow muscle weakening in boys and young men with advanced DMD, and may also slow heart damage in those who already have heart muscle disease.

But at 12 months of follow-up, Deramiocel’s performance on the study’s key secondary endpoint of LVEF “did not reach statistical significance, although the difference [favored] Deramiocel,” researchers reported, as the Deramiocel group vs. placebo showed a least-squares mean ranked change in LVEF of 57·47 ranks compared with 45·82 for placebo.

“These findings reinforce deramiocel as a safe, effective, and promising therapy for individuals living with DMD. Longer follow-up is needed to establish durability, long-term safety, and effects on clinically important cardiac outcomes,” the research team from Capricor and its clinical partners wrote in the study.

They added: “A 54% reduction in mean skeletal-muscle disease progression over 12 months, if sustained, would be equivalent to delaying approximately 1 year of untreated progression over 2 years.”

Investors unpersuaded

Capricor’s responses during the week failed to persuade investors. They responded to the negative FDA staff briefing on Deramiocel with a sharp sell-off that sent the company’s shares nosediving 64.5% to $7.00, from $19.70 at the close of trading July 24. The decline reached 85% when Capricor shares hit a 52-week low of $2.97 early Thursday.

After the downgrades and second stock plunge of the week, however, Capricor investors began to “buy the dip” and sent the company’s shares partially rebounding to $4.19 on Thursday (a 36% one-day slide) and $3.85 at Friday’s closing bell, down 8%. Overall for the week, Capricor’s stock suffered an 80% one-week decline.

News of the FDA adcomm vote led to downgrades of Capricor stock and severe 12-month price target downgrades by at least six investment firms:

  • Piper Sandler (Edward Tenthoff)—From “Overweight” to “Neutral,” all but wiping out its price target 97%, from $58 to $2.
  • Cantor Fitzgerald (Kristen Kluska)—From “Overweight” to “Neutral,” eviscerating its price target 94%, from $62 to $3.50.
  • Ladenburg Thalmann (Aydin Huseynov, MD)—From “Buy” to “Neutral,” no price target announced.
  • Maxim Group (Jason McCarthy, PhD)—From “Buy” to “Hold,” no price target announced.
  • C. Wainwright (Joseph Pantginis, PhD)—From “Buy” to “Neutral,” removing its $60 price target reiterated in May.
  • Oppenheimer (Leland Gershell, MD, PhD)—From “Outperform” to “Perform,” removing its $54 price target reiterated in March.

“The briefing documents raise many ​more concerns versus what we originally were anticipating, putting Capricor in a tough situation” for the adcomm meeting, Kluska said Monday in remarks reported by Reuters.

The six firms joined three others that lowered their ratings on Capricor shares earlier in the week:

  • Alliance Global Partners (Matthew Venezia)—From “Buy” to “Neutral,” chopping its price target 86%, from $51 to $7 on Tuesday.
  • Riley Financial (Madison El-Saadi, PhD)—From “Buy” to “Neutral,” slashing its price target 84% from $63 to $10 on Monday.
  • Roth Capital Partners (Boobalan Pachaiyappan, PhD)—From “Buy” to “Neutral,” slicing its price target 82% from $38 to $7 on Monday.

MapLight data divides investors, analysts

Investors and the Wall Street analysts who cover their favorite companies sometimes don’t see eye to eye. That was apparent this past week when MapLight Therapeutics (Nasdaq: MPLT) shares went on something of a roller-coaster ride, as mixed clinical results for its lead drug in a mid-stage trial in schizophrenia sent the stock nosediving on investor fears—until reassurances from analysts reversed the slide and sent those shares back in the positive direction.

The up-and-down week ended with MapLight shares sliding 64%.

MapLight’s wayward week started on July 27 when the company released data from its 307-patient Phase II ZEPHYR trial (NCT07038876) assessing its lead pipeline candidate ML-007C-MA in adults with an acute exacerbation of schizophrenia. ML-007C-MA is an oral, extended-release, fixed-dose combination of the M1/M4 muscarinic agonist candidate ML-007, co-formulated with a peripherally acting anticholinergic.

MapLight trumpeted what it termed positive results from ZEPHYR, though the data appeared to be more mixed: On the positive side, the 210/3 mg twice-daily (BID) dose of ML-007C-MA showed statistically significant and clinically meaningful reduction in its Positive and Negative Syndrome Scale (PANSS) total score compared to placebo at Week 5 in a In the modified intent-to-treat (mITT) population, with an effect size of 0.37 and a least squares mean 4.5-point improvement vs. placebo (p=0.015).

However, the 330/6 mg once-daily (QD) dose of ML-007C-MA did not achieve statistical significance on the primary endpoint, even as it showed an effect size of 0.23 and a 2.8-point improvement over placebo (p=0.110)—as well as separation on CGI-S (p=0.036), PANSS positive Marder factor (p=0.045), and Readiness for Discharge Questionnaire (p=0.027), and numerical separation on other endpoints.

That result investors scurrying to sell off their MapLight shares, since it raised questions about whether ML-007C-MA could effectively with Cobenfy® (xanomeline and trospium chloride), the schizophrenia drug marketed by Bristol Myers Squibb (BMS; NYSE: BMY). Cobenfy, which won FDA approval in 2024, showed larger PANSS reductions of 8.4 and 9.6 points in a pair of Phase III trials compared with placebo.

Cobenfy generated $119 million in product revenues in the first half of this year, nearly double (up 92%) from January–June 2025), in addition to $155 million during all of last year.

The BID dose also showed robust and clinically meaningful improvement in cognitive performance, based on the pre-specified secondary endpoint assessed via the Cogstate battery in participants with baseline cognitive impairment (effect size=0.51; 0.44 points vs. placebo; p=0.041). But the cognitive benefit did not show correlation with the change in PANSS score, something that MapLight said suggested that “the effect was independent of, and not secondary to, improvement in psychotic symptoms.”

“We are very encouraged by these results, which show that ML-007C-MA delivered clinically meaningful antipsychotic efficacy alongside a favorable tolerability profile designed to translate into real-world use,” Chris Kroeger, MD, MapLight’s co-founder and CEO, said in a statement.

Encouraged enough, Kroeger added, that MapLight plans to discuss a path forward for ML-007C-MA in schizophrenia, including the design of a Phase III trial, at an End-of-Phase II (EOP2) meeting with FDA officials. Data from that trial, combined with results from ZEPHYR, are intended to support an initial New Drug Application (NDA) submission for the drug.

Investors sharply disagreed with MapLight’s optimism, sending the company’s shares plummeting 73% on July 27, from $36.56 to $9.90. But several analysts questioned the wisdom of investors selling off shares on a single PANSS number.

“The PANSS score is but one component of what might drive success from a commercial point of view,” cautioned Sumant Kulkarni, a senior analyst covering biotechnology with Canaccord Genuity, wrote in a research note. “At the same time, we need to see more data from additional trials on safety and efficacy.”

That data could come, he continued, from the Phase II VISTA trial (NCT06887192) assessing ML-007C-MA as a treatment for hallucinations and delusions associated with Alzheimer’s disease psychosis, a potentially larger market for the drug.

However, Kulkarni cut Canaccord Genuity’s peak-year 2037 sales forecast for ML-007C-MA by more than half in schizophrenia, from approximately $1 billion to approximately $400 million. He also shrunk by one-third his firm’s peak sales forecast for ML-007C-MA in ADP, from $3 billion to $2 billion, and lowered ***HOW its forecast of MapLight’s operating expenses.

As a result of these changes, Kulkarni cut Canaccord Genuity’s 12-month price target on MapLight shares 44%, from $43 to $24.

“Although [ML-007C-MA] did not meet the Street’s upside expectations, there are still several positives to consider,” Jefferies equity analyst Andrew Tsai wrote Friday. He said ZEPHYR was still successful enough as a pivotal Phase II trial to count as one of two positive Phase II or III trials needed for FDA approval. And twice daily ML-007C-MA showed competitive adverse event percentages among patients compared to Cobenfy, he added, citing:

  • Constipation—9% for ML-007C-MA vs. 13–21% for Cobenfy.
  • Nausea—29% vs. 19%.
  • Vomiting—13% vs. 9–16% for Cobenfy.

By mid-week, investors appeared to take the analyst commentary to heart. MapLight shares rebounded, climbing 24% to $12.31 on Tuesday, then jumped another 22% to $15.02 Wednesday. The rest of the week didn’t look as good for MapLight, however, as its shares fell about 7% to $14.03 Thursday and dropped another 7% Friday, finishing the week at $13.03.

Leaders & laggards

  • Novo Nordisk (Nasdaq Copenhagen: NOVO-B) shares slumped 8% from DKK 330.90 ($51.03) to DKK 306.50 ($47.27) Friday, while its American Depositary Shares (Nasdaq: NVO) skidded 9% from $51.61 to $47.08, after the cardiometabolic drug giant acknowledged that its once-monthly 15 mg dose of ziltivekimab failed the Phase III ZEUS trial (NCT05021835) assessing the IL-6 inhibitor vs. placebo in reducing the risk of major adverse cardiovascular events (MACE), defined as cardiovascular death, non-fatal heart attack, or non-fatal stroke. Ziltivekimab failed to translate reductions in cardiovascular inflammation into fewer major cardiovascular events, Novo Nordisk said. Overall rates of adverse events (AEs) and serious AEs in ziltivekimab patients were similar to those seen with placebo. A higher proportion of people treated with ziltivekimab had serious infections compared to placebo—a finding consistent with targeting IL-6 inhibition, according to the company—while no difference in all-cause mortality was seen.
  • Replimune Group (Nasdaq: REPL) shares more than doubled, jumping 107% from $5.41 to $11.20 Friday, the day after the FDA’s Cellular, Tissue, and Gene Therapies Advisory Committee sided with the company by voting 10-3 that the results from the Phase I/II IGNYTE trial (NCT03767348) were evaluable and clinically meaningful. Repligen is seeking FDA approval of its third biologics license application (BLA) for RP1 (vusolimogene oderparepvec, a genetically engineered oncolytic viral immunotherapy, in combination with nivolumab, the programmed death-1 (PD-1) immune checkpoint inhibitor marketed by Bristol Myers Squibb (NYSE: BMY) as Opdivo®, as a treatment for advanced melanoma in patients who have progressed on prior anti-PD-1 therapy. “We are encouraged by today’s outcome and would like to thank the committee for its thoughtful discussion of the IGNYTE data,” Repligen CEO Sushil Patel, PhD, said in a statement. Cantor Fitzgerald analyst Li Watsek upgraded Replimune shares from “Neutral” to “Overweight,” with no price target on the stock.

The post StockWatch: Capricor Plunges as FDA Panel, Staff Question Effectiveness of Lead Candidate Deramiocel appeared first on GEN – Genetic Engineering and Biotechnology News.

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