Spotlight on Innovation: How ICE Bioscience’s Biology Building Block Platform Transforms Early Drug Discovery

This blog post was written by ICE Bioscience, a global contract research organization (CRO) providing preclinical bioscience platforms, focusing on new target, new assay and new technology to support in vitro biology, DMPK and in vivo pharmacology screening and profiling. In this post, they propose a new concept of biology building blocks and demonstrate how to use this platform for hit identification. They also answer some frequently asked questions about innovative drug screening using in vitro biology technology and panel screening. Their services are available on the Scientist.com marketplace.

Q: What is the Biology Building Block (BBB) platform, and what are the key elements that make up the platform for drug discovery?

A: Biology building blocks are the fundamental components used in drug screening, consisting of three key elements: target, assay format and technology. You can think of these elements as uniform-shaped modules, like pieces in a Tetris game. Although the content of each module may vary (for example, different targets, formats or technologies), the overall shape and structure of the modules remain consistent. This uniformity ensures that no matter how the modules are combined, they can always fit together perfectly to form a complete assay.

For instance, when screening for KRAS inhibitors, you start with a “target” module, such as KRAS-G12C. You then select an “assay format” module, like a nucleotide exchange assay. Finally, you choose a “technology” module, such as HTRF (Homogeneous Time-Resolved Fluorescence). Although the content of each module is specific (the target, assay format and technology), they are designed to fit together seamlessly, resulting in a complete assay: “KRAS-G12C nucleotide exchange assay using HTRF.”

The beauty of our BBB platform is that it allows for easy swapping of modules. For example, if you want to screen for a different KRAS variant, you can simply replace the target module with KRAS-G12D while keeping the other two modules the same. The modules’ consistent shape ensures that this new combination will fit perfectly to form a different but equally functional assay.

Q: Is the Biology Building Block platform only suitable for target-based assays, or can it also be used in phenotypic assays?

A: While the BBB platform is exceptionally powerful in target-based assays, it is not limited to this application alone. In fact, it is highly versatile and can also be effectively employed in phenotypic assays.

1. Target-Based Assays:

• The BBB platform excels in target-based assays by allowing precise customization of assays through the combination of target, assay format and technology modules. For example, screening KRAS inhibitors would involve selecting a KRAS target, a nucleotide exchange assay format and HTRF technology, creating a focused assay for that specific target.

2. Phenotypic Assays:

• The BBB platform is equally effective in phenotypic assays, where the focus is on observable biological effects without a predefined target. In these cases, you can flexibly combine assay formats and technologies to monitor phenotypic changes like cell viability or morphology. For instance, a phenotypic screen could involve a cell viability assay paired with high-content imaging to identify compounds with significant biological activity, even without knowing the exact molecular target.

Q: How does ICE Bioscience ensure the Biology Building Block platform stays up-to-date and comprehensive?

A: The key to expanding the BBB platform is continually finding new targets, assay formats and technologies to create novel drug discovery assays. We employ various strategies to collect information for assay development:

• Patents: We follow new patent releases weekly, analyzing about 60 patents each week. After reviewing over 6,000 patents, we rank and collect new targets.
• Conferences: We gather target and assay information from conference posters and open access sources.
• Literature: We summarize targets and assays from scientific literature.
• Databases: We also collect information from commercial databases.

To make this content easily searchable, we have incorporated all these items into the ICE Patent-Target-Assay Database (PTAD), which is currently open to a limited number of users or available upon request, with plans to open it to all users later this year. Users can search for targets and view detailed information on patents, inventors, companies, key materials and our off-the-shelf products and services such as recombinant protein products, biochemical & biophysical assays, cell-based assays and in vivo CDX models.

Q: How many targets are included in the Biology Building Block platform?

A: The ICE Bioscience team has collected over 1,500 targets in the past 14 years, including but not limited to:

• Surface Protein Targets: Ion channels, GPCRs (G-Protein Coupled Receptors), Receptor Tyrosine Kinases (RTKs), Amino Acid Transporters/Exchangers, Cytokine Receptors, Solute Carriers (SLCs), Transporters, Tumor-Associated Antigens (TAAs), etc.
• Cytoplasmic Targets: Kinases, Phosphatases, TPD (Targeted Protein Degradation)-Related Enzymes and Targets, Signal Transduction Proteins, Nuclear Receptors, Protein-Protein Interaction Targets, Cell Death-Related Proteins (e.g., Apoptotic proteins), Cytokines, Metabolic Enzymes, Adaptor Proteins, Mitochondria-Related Enzymes, etc.
• Nuclear or Trans-Nuclear Targets: Transcription Factors, Reporter Elements, Nuclear Translocation Proteins, DNA-Interacting Proteins, DNA Damage Response (DDR) Proteins, Epigenetic Targets (DNA or RNA readers, writers and erasers), etc.

Q: How many types of assays and technologies are included in the Biology Building Block platform?

A: We have 700+ recombinant target protein products and have developed over 10,000 assays by combining various targets, assay formats and technologies. These assays can be broadly classified into several categories:

• Protein Expression and Purification are carried out using systems such as E. coli, insect cells and mammalian cells. It includes techniques like liquid chromatography for protein purification and mass spectrometry (LC-MS) for protein analysis.
• Genomic Analysis utilizes automated genomic editing and high-throughput gene function analysis, particularly in CRISPR screening.
• Biophysical Assays include techniques like Surface Plasmon Resonance (SPR), Microscale Thermophoresis (MST), Spectral Shift, Temperature-Related Intensity Change (TRIC) and Thermo-Shift Assays (TSA).
• Biochemical Assays such as absorbance assays, fluorescence-based assays include Fluorescence Intensity (FI), Fluorescence Polarization (FP) and various forms of FRET (Fluorescence Resonance Energy Transfer), like Time-Resolved FRET (TR-FRET). Other techniques include ultra-luminescence/luminescence assays, AlphaLISA/Alpha Screen assays and LC-MS assays.
• Cell-based Assays and Phenotypic Assays encompass a wide range of techniques, including cell line engineering (for knock-out, knock-in and overexpression studies), cell proliferation assays and various immunoassays such as ELISA/AlphaLISA/HTRF, electrochemiluminescence (ECL) technology (e.g., MSD platforms). Electroporation for cell transfection, automated patch clamping for ion channel studies, capillary-based Western blotting (e.g., Jess) and live-cell imaging techniques for continuous monitoring of cellular dynamics (e.g., IncuCyte). We also utilize high content imaging/screening (HCI/HCS), flow cytometry/fluorescence-activated cell sorting (FACS), qPCR, FLIPR assays and more specialized approaches like target engagement, protein-protein interaction assays, NanoBiT/NanoBRET assays and reporter gene assays.

Q: How does ICE Bioscience integrate biology building blocks with screening cascades?

A: ICE Bioscience integrates the BBB platform with screening cascades to optimize the drug discovery process:

1. Target Research and Assay Development: We stay ahead by proactively researching and incorporating new targets, assay formats and technologies from patents, literature and scientific advancements. This strategic early planning ensures our BBB platform is well-prepared and often ahead of the curve, providing timely and effective solutions.
2. Initial Screening: Utilizing our pre-developed BBB modules, we conduct single-dose screening to quickly identify potential hits from compound libraries.
3. Hit Expansion and Dose-Response: We explore hit expansion through structure-activity relationships (SAR) and generate dose-response curves to determine efficacy.
4. Functional and Orthogonal Validation: Hits are validated through cellular target engagement (TE) assays and orthogonal assays, including biophysics confirmation using SPR or MST.
5. Mechanism of Action and Early ADME: We investigate the mechanism of action and conduct early ADME studies to assess the pharmacokinetic properties of the compounds.

Q: How does the Biology Building Block platform support safety, selectivity and off-target profiling?

A: The BBB platform at ICE Bioscience is instrumental in ensuring the safety, selectivity and off-target profiling of drug candidates. Our approach is based on the use of functional safety panels that rigorously assess the pharmacological safety and specificity of compounds.

1. Safety Pharmacology and Functional Safety Panels:

• We offer comprehensive safety panels that assess the impact of drug candidates on critical physiological systems, such as the cardiovascular, central nervous and respiratory systems. These panels utilize functional assays designed through the BBB platform, allowing for early detection of potential adverse effects.

2. Selectivity and Off-Target Profiling:

• The BBB platform enables us to conduct selectivity and off-target profiling through integrated panels that evaluate drug candidates against both intended targets and a broad range of off-targets. By using these functional assays, we can identify any unintended interactions or cross-reactivity that might lead to side effects, ensuring that drug candidates are highly specific to their targets and minimizing off-target risks.

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