For label-free and real-time affinity measurements, Creative Biolabs provides advanced Surface Plasmon Resonance (SPR) and Bio-Layer Interferometry (BLI) services based on Biacore, ProteOn and Octet systems. Our strong expertise and extensive experience can provide high-quality services of affinity and kinetics measurement for small molecules (molecular weight lower than 1000 D), which can satisfy your different demands.

Background

High-throughput small molecules screening has been proved to be important in clinical development (such as diagnostics and therapeutics). The main challenge of small molecules screening is the low response level due to their small molecular sizes, which needs solvents to maintain the analyte solubility, and the rapid interactions between small molecules and candidates. To solve the low response level problem, sensor surface is prepared with high levels of ligand (usually 8,000 to 10,000 Response Units for an average-sized protein). For small molecules screening, samples are normally prepared with a fixed concentration in the same buffer because usually there is no opportunity to optimize buffer conditions or concentration.

The main experimental conditions for small molecules affinity measurement and screening include:

• Phosphate is generally used as the composition of running buffer, therefore sample buffer must be matched as closely as possible.
• Additives are needed, such as DMSO and certain kinds of detergents.
• Flow rate is typically 10 μl/min.
• Contact time is set between 15 to 30 sec.
• Report point-before end of sample injection-reduce the indiscriminate binding and give an accurate indication of specific binding ability.
• Regeneration is usually not needed.

There are two paths to evaluate the small molecules affinity: First, the binding responses are compared for analyte molecular weight, and a cut-off level is set. The cut-off can be determined by comparison with the response obtained from known non-binders (negative controls) or set to some level chosen in relation to the distribution of response values. Second, kinetic properties are compared to plot the association rate constant (Ka) against the dissociation rate constant (Kd) on logarithmic axis. Diagonal lines in this plot represent constant affinity, so the compounds that underlying on the same diagonal but separated from each other have the same affinity but different kinetics.

Figure 1. The affinity analysis is represented by diagonal lines. Compounds on the same diagonal have the same affinity but differ in kinetics. (Biacore Assay Handbook)

Affinity Measurement for Small Molecules

Our custom affinity measurement services for small molecules can achieve:

• Calculating chemical diversity-The diversity of a library is reflected as a quantitative description of the differences between these compounds.
• Full kinetics analysis-Obtaining detailed binding kinetics (K_a, K_d and K_D).
• High-throughput screening of novel ligands-Creating/designing a chemicals library and screening the chemicals library to identify compounds that bind to the protein with reasonable affinities.
• Protein binding assay- Measuring the binding ability of small molecules with specific proteins.

Other optional Antibody Affinity Measurement Services:

• Cell Line Affinity Measurement
• Affinity Measurement Services for Specific Antibodies
• Membrane Protein Affinity Measurement
• Affinity Measurement Services for Bivalent Antigens
• Affinity Measurement Services for Dimers/Polymers
• Affinity Measurement Services for Cell Lysates
• Affinity Measurement Services for Various Ligands and Analytes
• Biacore System
• ProteOn System
• Octet system

Published Data

• Evaluating the Affinity and Kinetics of Small Molecule Glycomimetics Using SPR

Fig. 2 SPR sensorgrams showing kinetics of GB0139 binding to human (A) and mouse (C) galectin-3. (Henry Kim, 2023)

Galectin 3, a β-galactoside-binding mammalian lectin, can bind to a variety of cell surface glycoproteins through its carbohydrate recognition domain (CRD), thus affecting cell activation, adhesion, and apoptosis. At the same time, it is associated with a variety of diseases, including fibrosis and cancer. Here, the affinity of human and mouse hemolectin 3 was measured by fluorescence polarization (FP) assays and surface plasmon resonance (SPR) technology, and the compound kinetics was studied. Studies have shown that SPR is a feasible alternative to FP and can be used for early drug discovery screening and the determination of KD values. In addition, it can provide early kinetic characterization of small molecules and generate robust kon and koff values in a high-throughput manner.

FAQ

1. What are the advantages of using SPR technology for small molecule affinity and kinetics measurements?

   SPR technology offers real-time, label-free detection of biomolecular interactions, making it highly effective for measuring the affinity and kinetics of small molecules. It allows researchers to directly observe the binding process and calculate both association and dissociation rates, providing a detailed understanding of the interaction dynamics. SPR can also handle a wide range of molecular weights, making it versatile for various types of small molecule studies.

2. How does BLI technology differ from SPR in measuring small molecule interactions?

   BLI technology, like SPR, provides label-free, real-time analysis of biomolecular interactions, but it uses an optical fiber tip coated with a biosensor to measure interference patterns of light. BLI is particularly advantageous for its simplicity and the ability to run multiple samples in parallel without the need for a continuous flow system, which is required in SPR. This makes BLI an excellent choice for high-throughput screening of small molecule interactions.

3. What are the key considerations when selecting SPR over BLI for small molecule studies?

   AKey considerations include the sensitivity of the technology to small molecular weight compounds and the required throughput of the assay. SPR is highly sensitive and can detect very low molecular weight compounds, making it ideal for studying small molecule interactions in great detail. However, SPR typically requires a continuous flow of samples and may be more complex to set up and run than BLI. If high throughput and ease of use are priorities, particularly in early screening phases, BLI might be the better choice.

4. How can the data from SPR and BLI technologies be used to improve small molecule drug development?

   Data from SPR and BLI technologies provide crucial insights into the binding affinity and kinetics of small molecule drug candidates with their targets. By understanding these interactions in detail, researchers can optimize the molecular structure of drug candidates to improve efficacy, reduce off-target effects, and enhance drug stability. This information is vital for making informed decisions during the drug design and development process, ultimately leading to more effective and safer drugs.

5. How does the size of a small molecule affect its measurement using SPR technology?

   Smaller molecules generally produce weaker signals due to their low mass, which can make it challenging to accurately measure their binding interactions. To overcome this, researchers may use higher concentrations of the small molecule or employ enhancement techniques such as signal amplification strategies. This ensures more accurate and reliable measurements of binding kinetics and affinity, even for very small molecules.

6. What are the common challenges faced when using BLI technology for small molecule interaction studies?

   One common challenge in using BLI for small molecule studies is the potential for non-specific binding, where the small molecule interacts with the biosensor surface rather than the immobilized target. This can lead to false positives or skewed data. To mitigate this issue, thorough optimization of assay conditions, such as buffer composition and blocking agents, is essential. Additionally, careful design of the biosensor coating and the use of high-specificity capture methods can help ensure more accurate measurements of the actual interactions between small molecules and their intended targets.

7. Can SPR and BLI technologies be used to measure the affinity of very low-affinity small molecules?

   Both SPR and BLI are capable of measuring low-affinity interactions, but the accuracy and sensitivity may vary depending on the specific setup and the nature of the interaction. For very low-affinity small molecules, SPR technology tends to be preferred due to its higher sensitivity and ability to provide detailed kinetic data even at lower binding strengths. Adjusting the flow rate, increasing the interaction time, and using high-sensitivity chips can enhance the detection capabilities for low-affinity interactions in SPR assays.

8. What role do temperature and buffer conditions play in SPR and BLI assays for small molecule studies?

   Temperature and buffer conditions are critical in both SPR and BLI assays as they can significantly affect the binding kinetics and stability of small molecules. Temperature controls the rate of molecular interactions and can influence the dynamics of the binding and dissociation processes. Buffer conditions, including pH and ionic strength, must be optimized to maintain the structural integrity of both the small molecule and the target protein. This optimization ensures that the measured interactions accurately reflect the physiological conditions under which the small molecule would function in a biological system. Adjusting these parameters appropriately can lead to more reliable and reproducible data in both SPR and BLI assays.

Resources

Use the resources in our library to help you understand your options and make critical decisions for your study.

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