One of the longstanding challenges in drug discovery has been the inability to directly observe whether a compound engages its target in a cellular environment under physiologically relevant conditions. Traditional biochemical assays often use purified proteins outside their native cellular environment. While these approaches are powerful, they frequently fail to capture the complexity of cellular biology, where protein conformation, localization, binding partners, post-translational modifications, and dynamic signaling states all influence drug behavior. This is even more challenging for difficult target classes such as membrane proteins, transcription factors, protein complexes, and other intrinsically disordered proteins. Many of these targets are highly context-dependent and can behave differently outside the cellular environment. Modern therapeutic modalities have further amplified this problem.
Elmar Nurmemmedov, PhD, MBA
Chief Executive Officer and Co-Founder
CellarisBio
Ivan Babic, PhD
Chief Scientific Officer and Co-Founder
CellarisBio
In this Innovation Spotlight, Elmar Nurmemmedov, the chief executive officer of CellarisBio, highlights the need to address how drug discovery programs can spend years optimizing compounds without fully understanding their cellular mechanism of action and discusses the role of real-time and dynamically state-resolved cell target engagement technologies for advancing modern drug discovery.
Why have membrane proteins and transcription factors been so hard to study?
Membrane proteins and transcription factors are among the most biologically important yet experimentally difficult targets in drug discovery. Membrane proteins exist within highly specialized lipid environments that are extremely difficult to replicate outside living cells. Once extracted or purified, they often lose native structure, conformational flexibility, or functional interactions. This makes it challenging to accurately study how drugs engage these targets under physiologically relevant conditions. Transcription factors are structurally dynamic, transiently assembled, or intrinsically disordered, with functions driven by protein-protein interactions rather than classical binding pockets. As a result, they have historically been considered “undruggable” or difficult to interrogate using conventional biochemical methods. These complexities become even more relevant with modern therapeutic modalities such as molecular glues and degraders, which often rely on transient complex formation, induced proximity, conformational remodeling, or stabilization of protein interactions inside cells.
In many ways, these newer modalities are exposing the limitations of traditional assay systems. Studying these targets increasingly requires technologies capable of real-time monitoring of target behavior directly within native cellular environments rather than relying solely on simplified, and in often cases, endpoint biochemical models. This is one of the core motivations behind MICRO-TAG®, which enables real-time cellular target engagement measurements for the very target classes and mechanisms that have historically been the hardest to study.
What biological insights become possible when researchers can observe target engagement in real time rather than relying on endpoint assays?
Endpoint measurements provide a single snapshot after a biological process has already occurred. In contrast, real-time measurements allow researchers to observe how targets dynamically respond to compounds across changing cellular and thermal conditions. This becomes especially important for modern therapeutic modalities such as molecular glues, degraders, and target stabilizers, where compound activity is often driven by dynamic conformational changes or transient protein interactions rather than simple occupancy of a binding pocket.
With real-time cellular target engagement, researchers can begin to observe stabilization events, destabilization signatures, conformational shifts, kinetic behaviors, partial engagement states, and temperature-dependent interaction patterns that are often invisible in conventional assays. Importantly, compounds that appear similar in traditional endpoint assays can behave very differently when viewed dynamically in a cellular context. That additional mechanistic resolution can help researchers distinguish effective compounds from misleading ones much earlier in discovery.
We believe the field is moving towards a more dynamic understanding of drug action that reflects how drug targets and therapeutic modalities behave within dynamic cellular systems.
CellarisBio’s MICRO-TAG® is a next-generation cellular target engagement platform designed as a fundamentally new framework for studying drug–target interactions in cellular systems.
©iStock, ismagilov
How does MICRO-TAG® differ from traditional target engagement approaches and enable measurements within living cells?
MICRO-TAG® is a next-generation cellular target engagement platform designed as a fundamentally new framework for studying drug–target interactions in cellular systems. The technology combines fluorescence-based Split-RNase enzyme complementation with programmable real-time thermal profiling to enable dynamic measurement of target engagement directly within intact cells or cellular lysates, using standard real-time qPCR instruments. Unlike traditional endpoint approaches that rely on single-temperature, mostly based on temperature of aggregation 50% (Tagg50) measurements or indirect downstream readouts, MICRO-TAG® generates continuous, information-rich engagement profiles across programmable temperature series.
The platform seamlessly integrates into existing real-time instrument infrastructure that is widely available across research and pharmaceutical laboratories. This lowers the barrier for adoption while enabling high-resolution cellular target engagement workflows without specialized hardware requirements. MICRO-TAG® was built to address some of the most difficult areas of modern drug discovery, including membrane proteins, transcription factors, protein complexes, and intrinsically disordered proteins. MICRO-TAG® is also well suited for emerging therapeutic modalities such as molecular glues, targeted degraders, and target stabilizers.
Beyond conventional target engagement studies, real-time MICRO-TAG® enables entirely new applications. For example, MICRO-TAG® can support de novo hit identification and mechanistic classification directly under cellular conditions for cellular DNA-Encoded Libraries (DEL) discovery. This is ground-breaking, as the current DEL discovery methods rely heavily on expressed and purified target proteins, which exclude challenging drug targets. MICRO-TAG® also enables functional cellular target engagement by linking target engagement behavior with biologically relevant cellular states and dynamic protein responses rather than relying solely on static occupancy measurements.
More broadly, MICRO-TAG® adds mechanistic depth to cellular target engagement by enabling observation of ligand-induced stabilization, destabilization, conformational shifts, and target conformation-dependent interaction patterns in real time. Rather than simplifying biology into a single Tagg50 endpoint readout, MICRO-TAG® aims to provide a more dynamic and physiologically relevant understanding of how modern therapeutics interact with targets inside cellular systems.
What does a typical MICRO-TAG® experiment look like?
A typical MICRO-TAG® experiment is designed to be streamlined, flexible, and highly adaptable across a broad range of drug discovery applications. The workflow can be applied to both conventional, well-behaved drug targets as well as highly challenging target classes that are difficult to interrogate using traditional approaches.
Cells expressing a MICRO-TAG®-fused target protein are treated with compounds of interest and transferred directly into a real-time instrument-compatible plate together with detection reagents (FRET substrate and tag-binding protein). The assay then proceeds through a programmable real-time temperature series in which sequential heating and fluorescence detection steps are integrated into a single automated run. As ligand-bound targets remain thermodynamically stabilized during the temperature series, the system continuously measures soluble target populations through MICRO-TAG®’s fluorescence enzyme complementation chemistry.
MICRO-TAG® generates multi-layered target engagement datasets by simultaneously capturing target behavior across multiple temperatures and compound doses, creating a richer and more mechanistically informative view of target engagement. Researchers can analyze these datasets using methods such as area-under-the-curve or slope-based analysis to quantify target engagement behavior across the thermal series. Data processing and visualization can be readily performed using widely adopted analysis platforms such as GraphPad Prism.
The workflow eliminates the need for prior determination of an exact target melting temperature (Tagg50), simplifying experimental setup and reducing workflow complexity. The step-gradient format also minimizes sample handling and enables rapid “mix-and-detect” execution directly within standard real-time instruments. The workflow is highly amenable to automation and high-throughput drug discovery environments. The real-time step-gradient approach can be implemented in multi-well plate formats and integrated into scalable screening workflows ranging from rapid single-concentration screening to detailed dose-response and mechanistic characterization studies. Overall, MICRO-TAG® combines operational simplicity with rich biological output, enabling researchers to study drug–target interactions dynamically and at scale within physiologically relevant cellular systems.
Where do you see MICRO-TAG® having the biggest impact in the drug discovery pipeline?
We see MICRO-TAG® as part of a larger transition in drug discovery toward cellular biophysical technologies that measure complex biology dynamically, directly, and within cellular systems rather than through simplified, compressed, and static models.
We believe MICRO-TAG® has the potential to significantly reshape early-stage drug discovery by bringing physiologically relevant cellular and proteomic context into discovery workflows earlier for small molecules, medium-sized molecules, and peptides. The platform can add rigor to compound selection, accelerate hit identification-to-optimization decision-making, and improve confidence in mechanism-of-action assessment before programs advance into costly downstream stages. This can be especially transformative for some of the most challenging and historically under-addressed target classes in drug discovery, which were difficult to study using conventional protein-based biophysical methods or traditional cellular target engagement approaches.
For membrane proteins and receptors, the field has long faced limitations in developing scalable, functionally relevant cellular assays that can capture native target behavior. We see MICRO-TAG® opening new opportunities for discovery against complex cell-surface targets by enabling direct and dynamic cellular target engagement measurements in physiologically relevant systems. Similarly, transcription factors and conformationally dynamic intracellular targets, including proteins such as β-catenin, cMYC, androgen receptor, and IRF5, have historically lacked robust and scalable cellular engagement technologies. MICRO-TAG® was designed to help address these challenges by enabling real-time monitoring of target behavior directly within the cellular environment where these proteins naturally function.
We also believe MICRO-TAG® could have substantial impact on emerging therapeutic modalities such as molecular glues, targeted degraders, and target stabilizers. These modalities often depend on transient interactions, induced proximity, conformational remodeling, or stabilization of protein complexes inside cells, which are mechanisms that are difficult to capture using conventional endpoint assays. Historically, many molecular glue discoveries have relied heavily on serendipity. We believe real-time cellular target engagement technologies can help make discovery of these modalities more systematic, mechanistically informed, and scalable.
Beyond serving as a target engagement tool, MICRO-TAG® also enables entirely new workflows such as Cellular DEL discovery, where de novo hit identification and mechanistic characterization can occur directly under cellular conditions. In practice, this translates into richer therapeutic pipelines to include targets that previously were considered challenging or undruggable. This will apply to many therapeutic areas, such as oncology, metabolic disease, longevity, etc.
Finally, one of the most exciting aspects of MICRO-TAG® is the mechanistic depth enabled by its real-time temperature-series approach. Rather than generating a single endpoint measurement, the platform can reveal stabilization and destabilization behaviors across multiple conformational and thermal states. We believe this deeper view of target engagement biology will help researchers identify compounds with more durable or mutation-resistant interaction profiles earlier in development, potentially improving long-term therapeutic robustness and clinical durability.
