Isolation of Artificial Binding Proteins (Affimer Reagents) for Use in Molecular and Cellular Biology

Artificial binding proteins have been validated as alternatives to antibodies in their use as research reagents in molecular and cellular biology. For example, they have been used as inhibitors of protein-protein interactions to modulate activity, to facilitate crystallization, and as probes for cellular imaging.Phage display is a widely used approach for isolating target-specific binding reagents, and it has even been used to isolate isoform-specific binding proteins and binders that can distinguish between highly homologous protein domains.Here, we describe methods that have been employed in isolating highly specific artificial binding proteins against a wide range of target proteins.

Affimers as an alternative to antibodies for protein biomarker enrichment

INTRODUCTION

Assessing the specificity of protein binders is an essential first step in protein biomarker assay development. Affimers are novel protein binders and can potentially replace antibodies in multiple protein capture-based assays. Affimers are selected for their high specificity against the target protein and have benefits over antibodies like batch-to-batch reproducibility and are stable across a wide range of chemical conditions. Here we mimicked a typical initial screening of affimers and commercially available monoclonal antibodies against two non-related proteins, IL-37b and proinsulin, to assess the potential of affimers as alternative to antibodies.

METHODS

Binding specificity of anti-IL-37b and anti-proinsulin affimers and antibodies was investigated via magnetic bead-based capture of their recombinant protein targets in human plasma. Captured proteins were analyzed using SDS-PAGE, Coomassie blue staining, Western blotting and LC-MS/MS-based proteomics.

RESULTS

All affimers and antibodies were able to bind their target protein in human plasma. Gel and LC-MS/MS analysis showed that both affimer and antibody-based captures resulted in co-purified background proteins. However, affimer-based captures showed the highest relative enrichment of IL-37b and proinsulin.

CONCLUSIONS

For both proteins tested, affimers show higher specificity in purifying their target proteins from human plasma compared to monoclonal antibodies. These results indicate that affimers are promising antibody-replacement tools for protein biomarker assay development.

Chemiluminescent detection integrated with microdialysis sampling for label-free measuring the affinity of ractopamine monoclonal antibody

A novel label-free protocol was developed for measuring the affinity between ractopamine and its monoclonal antibody (McAb) based on microdialysis (MD) on-line sampling integrated with flow injection chemiluminescent detection. In this study, unbound ractopamine was sampled by MD probe from homogeneous immunoreaction equilibrious systems, and then real-time quantified using flow injection chemiluminescent detection. The quantified concentrations of unbound ractopamine in the immunoreaction equilibrious systems were treated with Scatchard analysis and Klotz analysis to obtain the affinity constant. The mean recovery of MD probe for sampling ractopamine was found to be 24.2%. The affinity constants calculated by Scatchard analysis and Klotz analysis both were 1.0 × 10⁶ M^-1, indicating that the investigated ractopamine mouse McAb was a medium-affinity antibody. The result showed good agreement with that obtained from thiocyanate elution test. This protocol for measuring antibody affinity is free of protein conjugation of hapten and enzyme labeling of McAb. Therefore it avoids affinity decrease resulting from steric hindrance, occupancy of the antigenic determinants, and deactivation of antibody, which has been frequently encountered in the reported conventional approaches. It opens up a new pathway for direct measurement of antibody affinity with a facile, rapid, accurate and low-cost approach.

Engineering fast dissolving sodium acetate mediated crystalline solid dispersion of docetaxel

It is hypothesized that a novel crystalline solid dispersion (CSD) of docetaxel (C-DXT) can be engineered by dispersing native docetaxel (DXT, a BCS class II drug) in sodium acetate crystal (SA). DXT is dissolved in glacial acetic/SA solution and freeze-dried. The resulting C-DXT is characterized by differential scanning calorimetry (DSC), powder X-ray analysis (PXRD), LC-MS/MS, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Quartz crystal microbalance with dissipation monitoring (QCM-D) and dynamic light scattering (DLS). Its cytotoxicity on model cancerous (MCF-7, MDA-MB-468) and normal breast cells (MCF-10A) is assessed by MTS assay. SEM/TEM data and the absence of the characteristics peaks of DXT on the DSC curve (at 193.4 °C) and the XRD scan (at 2θ = 15.31 °C and 23.04 °C) confirm the presence of C-DXT in SA. The LC-MS/MS data indicates the chemical stability of DXT. The yield and C-DXT loading are 95.2% and 6.52% w/w, respectively. The C-DXT rapidly forms an aqueous non-rigid nanosuspension with a faster drug dissolution rate compared to native DXT. Unlike, control Tween 80/ethanol, SA is noncytotoxic to normal cells. However, C-DXT's cytotoxicity is time and dose dependent for all diseased cells. This unique CSD process might be applicable to other hydrophobic bioactive agents to enhance their safety and efficacy.

Quantitative control of CaCO3 growth on quartz crystal microbalance sensors as a signal amplification method

Quantitative control of mass growth on QCM sensor surfaces was realized, providing a potential signal amplification method.