Cryogenic Electron Microscopy (Cryo-EM)

Cryo-electron microscopy (Cryo-EM) has become a powerful tool for structure-based drug discovery (SBDD), providing high-resolution structural information for targets that can be difficult to study using traditional X-ray crystallography approaches.

By enabling structural insights into challenging biological systems, Cryo-EM can help accelerate hit identification, lead optimisation and mechanism-of-action studies.

Cryo-EM can be used on any soluble protein >100kDa and is especially well suited to structurally complex or intractable targets, including:

• Membrane proteins and ion channels
• Large macromolecular assemblies and multi-protein complexes
• Ternary complexes (e.g. PROTACs, molecular glues)
• Conformationally dynamic or heterogeneous systems
• Proteins with significant post-translational modifications (e.g. glycosylation)

Domainex scientists can assess your target and advise whether Cryo-EM is the most appropriate structural biology approach for your programme.

At Domainex, cryo-EM is embedded within a multidisciplinary discovery framework that tightly integrates:

• Protein science: Construct design, expression system optimisation, purification, and stabilisation strategies
• Biophysics: Orthogonal validation of protein quality, conformational integrity, and ligand engagement
• Computational chemistry (CADD): Structural modelling, binding mode elucidation, and compound design
• Medicinal chemistry: Structural biology uncovers the 3D shapes of disease-causing proteins, allowing medicinal chemists to custom-design small molecules or biologics that bind precisely to these targets to neutralise them

This unified approach enables iterative optimisation cycles between experimental and computational disciplines, accelerating decision-making and reducing programme risk. 

High-quality, conformationally homogeneous protein samples are critical determinants of cryo-EM success. Domainex applies advanced protein science strategies including:

• Rational construct engineering to remove disorder and enhance stability
• Optimisation of expression systems (e.g. mammalian, insect, and bacterial)
• Use of ligands, cofactors, antibodies or nanobodies to stabilise specific conformations
• Complex reconstitution for multi-component systems

These approaches maximise particle quality, improve grid behaviour, and increase the likelihood of obtaining high-resolution reconstructions. 

Biophysical characterisation provides essential, quantitative validation of both protein samples and ligand interactions prior to and alongside cryo-EM studies. Techniques may include:

• Differential Scanning Fluorimetry (DSF) and calorimetry for stability assessment
• Grating-Coupled Interferometry and Surface Plasmon Resonance (GCI/SPR) or Spectral Shift for binding kinetics and affinity
• Dynamic Light Scattering (DLS) and mass photometry for oligomeric state and homogeneity

Integration of these datasets ensures that cryo-EM structures are interpreted within a robust physicochemical context, enhancing the reliability of downstream SBDD decisions. 

Domainex use Computational chemistry (CADD) to extract maximum value from cryo-EM datasets through:

• Atomic model refinement and validation against density maps
• Binding pose prediction and optimisation
• Structure-based virtual screening and hit identification
• Free energy and molecular dynamics simulations to explore conformational landscapes

The iterative integration of experimental structures with computational modelling enables rapid progression from structural insight to chemical optimisation. 

Domainex delivers a comprehensive, end-to-end cryo-EM workflow comprising:

1. Sample preparation - protein optimisation, complex formation, and vitrification
2. Grid screening and optimisation - iterative refinement of particle distribution and orientation
3. Data acquisition - high-throughput collection using state-of-the-art instrumentation
4. Image processing - particle picking, 2D classification, and 3D reconstruction
5. Map refinement - high-resolution density map generation and validation
6. Model building - atomic interpretation and structural analysis

Each stage is tightly integrated with upstream and downstream scientific disciplines to maximise efficiency and data quality. 

Cryo-EM projects at Domainex generate:

• High-resolution 3D density maps
• Refined, validated atomic models
• Detailed analyses of protein-ligand or protein-protein interfaces
• Mechanistic insights into target biology and modulation
• Comprehensive reports supporting programme progression

All deliverables are aligned to enable direct application in medicinal chemistry and SBDD workflows. 

Yes. Cryo-EM is increasingly applied to resolve ligand-bound states and higher-order complexes, including:

• Small molecule binding (where resolution permits)
• Ternary complexes relevant to targeted protein degradation
• Allosteric modulation and conformational transitions

When complemented by biophysical validation and CADD analysis, cryo-EM enables detailed mechanistic understanding of target engagement and modulation. 

Domainex’s co-located expertise across structural biology, protein science, biophysics, and computational chemistry enables:

• Rapid experimental iteration across disciplines
• Early identification and mitigation of developability risks
• Data-driven progression through discovery milestones
• Efficient translation of structural insights into chemical matter

This integrated model reduces reliance on fragmented workflows and provides a coherent, high-confidence path from target validation to candidate optimisation.