Macromolecular scaffolds for immobilizing small molecule microarrays in label-free detection of protein-ligand interactions on solid support

Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.

Evaluation of Kinetics Using Label-Free Optical Biosensors

Optical biosensors provide a platform for qualitatively and quantitatively analyzing various biomolecular interactions. In addition to advantages such as label-free and high-throughput detection, these devices are also capable of measuring real-time binding curves in response to changes in optical properties of biomolecules. These kinetic data may be fitted to models to extract binding affinities such as association rates, dissociation rates, and equilibrium dissociation constants. In these biosensors, one of the binding pair is usually immobilized on a solid substrate for capturing the other. Due to the nature of these surface-based methods, mass transport effects and immobilization heterogenetity may cause problems when fitting the kinetic curves with the simple one-to-one Langmuir model. Here real-time binding curves of various antibody-antigen reactions were obtained by using an ellipsometry-based biosensor, and the results were fitted to the simple one-to-one model as well as a more sophisticated approach. The results show that the one-to-two model fitted much better to the curves than the one-to-one model. The two-site model may be explained by assuming two immobilization configurations on the surface. In summary, in fitting real-time curves obtained from optical biosensors, more sophisticated models are usually required to take surface-related issues, such as immobilization heterogenetity and mass transport effects within targets, into account.

Label-Free Sensing on Microarrays

Microarrays of biological molecules such as DNAs, proteins, carbohydrates, and small molecules provide a high-throughput platform for screening tens of thousands of biomolecular interactions simultaneously, facilitating the functional characterization of these biomolecules in areas of genomics, proteomics, glycomics, and cytomics. Routinely, analysis of binding reactions between solution-phased probes and surface-immobilized targets involves some kinds of fluorescence-based detection methods. Even though these methods have advantages of high sensitivity and wide dynamic range, labeling probes and/or targets inevitably changes their innate properties and in turn affects probe-target interactions in often uncharacterized ways. Therefore, in recent years, various label-free sensing technologies have been developed for characterizing biomolecular interactions in microarray format. These biosensors, to a certain extent, take the place of fluorescent methods by providing a comparable sensitivity as well as retaining the conformational and functional integrality of biomolecules to be investigated. More importantly, some of these biosensors are capable of real-time monitoring probe-target interactions, providing the binding affinities of these reactions. Using label-free biosensors in microarrays has become a current trend in developing high-throughput screening platforms for drug discoveries and applications in all areas of "-omics." This article is aimed to provide principles and recent developments in label-free sensing technologies applicable to microarrays, with special attentions being paid to surface plasmon resonance microscopy and oblique-incidence reflectivity difference microscopy.

Real-time, label-free characterization of oligosaccharide-binding proteins using carbohydrate microarrays and an ellipsometry-based biosensor

Carbohydrates present on cell surfaces mediate cell behavior through interactions with other biomolecules. Due to their structural complexity, diversity, and heterogeneity, it is difficult to fully characterize a variety of carbohydrates and their binding partners. As a result, novel technologies for glycomics applications have been developed, including carbohydrate microarrays and label-free detection methods. In this paper, we report using the combination of oligosaccharide microarrays and the label-free oblique-incidence reflectivity difference (OI-RD) microscopy for real-time characterization of oligosaccharide binding proteins. Aminated human milk oligosaccharides were immobilized on epoxy-coated glass substrates as microarrays for reactions with Family 1 of solute binding proteins from Bifidobacterium longum subsp. infantis (B. infantis). Binding affinities of these protein-oligosaccharide interactions showed preferences of Family 1 of solute binding proteins to host glycans, which helps in characterizing the complex process of human milk oligosaccharides foraging by B. infantis.

Optical Microscopy for Detecting Binding on Small Molecule Microarrays

Small molecule microarrays (SMMs) have revolutionized parallel screening of multiple biological interactions. SMMs are a high-throughput technique for simultaneous detection of up to thousands of biological interactions. Conventional detection technique employed in SMMs is fluorescence spectroscopy. However, the possibility of fluorescent labels affecting the binding properties of small molecules drives the development of label-free screening techniques. Here, we describe two label-free detection techniques using optical microscopy for the detection of binding on SMMs. The first optical detection technique-ellipsometry, and more specifically, oblique incidence reflectivity difference to study the kinetics of the association between small molecule targets and protein probes is discussed. Then, we describe another optical detection technique-surface plasmon resonance microscopy. The sample preparation steps and protocols of the two techniques to study the interactions between SMMs and their protein targets are elaborated in great detail.

Characterization of protein expression levels with label-free detected reverse phase protein arrays

In reverse-phase protein arrays (RPPA), one immobilizes complex samples (e.g., cellular lysate, tissue lysate or serum etc.) on solid supports and performs parallel reactions of antibodies with immobilized protein targets from the complex samples. In this work, we describe a label-free detection of RPPA that enables quantification of RPPA data and thus facilitates comparison of studies performed on different samples and on different solid supports. We applied this detection platform to characterization of phosphoserine aminotransferase (PSAT) expression levels in Acanthamoeba lysates treated with artemether and the results were confirmed by Western blot studies.

Developing an Efficient and General Strategy for Immobilization of Small Molecules onto Microarrays Using Isocyanate Chemistry

Small-molecule microarray (SMM) is an effective platform for identifying lead compounds from large collections of small molecules in drug discovery, and efficient immobilization of molecular compounds is a pre-requisite for the success of such a platform. On an isocyanate functionalized surface, we studied the dependence of immobilization efficiency on chemical residues on molecular compounds, terminal residues on isocyanate functionalized surface, lengths of spacer molecules, and post-printing treatment conditions, and we identified a set of optimized conditions that enable us to immobilize small molecules with significantly improved efficiencies, particularly for those molecules with carboxylic acid residues that are known to have low isocyanate reactivity. We fabricated microarrays of 3375 bioactive compounds on isocyanate functionalized glass slides under these optimized conditions and confirmed that immobilization percentage is over 73%.

Real-time, label-free detection of biomolecular interactions in sandwich assays by the oblique-incidence reflectivity difference technique

One of the most important goals in proteomics is to detect the real-time kinetics of diverse biomolecular interactions. Fluorescence, which requires extrinsic tags, is a commonly and widely used method because of its high convenience and sensitivity. However, in order to maintain the conformational and functional integrality of biomolecules, label-free detection methods are highly under demand. We have developed the oblique-incidence reflectivity difference (OI-RD) technique for label-free, kinetic measurements of protein-biomolecule interactions. Incorporating the total internal refection geometry into the OI-RD technique, we are able to detect as low as 0.1% of a protein monolayer, and this sensitivity is comparable with other label-free techniques such as surface plasmon resonance (SPR). The unique advantage of OI-RD over SPR is no need for dielectric layers. Moreover, using a photodiode array as the detector enables multi-channel detection and also eliminates the over-time signal drift. In this paper, we demonstrate the applicability and feasibility of the OI-RD technique by measuring the kinetics of protein-protein and protein-small molecule interactions in sandwich assays.

"Flow valve" microfluidic devices for simple, detectorless, and label-free analyte quantitation

Simplified analysis systems that offer the performance of benchtop instruments but the convenience of portability are highly desirable. We have developed novel, miniature devices that feature visual inspection readout of a target's concentration from a ~1 μL volume of solution introduced into a microfluidic channel. Microchannels are constructed within an elastomeric material, and channel surfaces are coated with receptors to the target. When a solution is flowed into the channel, the target cross-links multiple receptors on the surface, resulting in constriction of the first few millimeters of the channel and stopping of flow. Quantitation is performed by measuring the distance traveled by the target solution in the channel before flow stops. A key advantage of our approach is that quantitation is accomplished by simple visual inspection of the channel, without the need for complex detection instrumentation. We have tested these devices using the model system of biotin as a receptor and streptavidin as the target. We have also characterized three factors that influence flow distance: solution viscosity, device thickness, and channel height. We found that solution capillary flow distance scales with the negative logarithm of target concentration and have detected streptavidin concentrations as low as 1 ng/mL. Finally, we have identified and evaluated a plausible mechanism wherein time-dependent channel constriction in the first few millimeters leads to concentration-dependent flow distances. Their simplicity coupled with performance makes these "flow valve" systems especially attractive for a host of analysis applications.

Simultaneous measurement of 10,000 protein-ligand affinity constants using microarray-based kinetic constant assays

Fluorescence-based endpoint detection of microarrays with 10,000 or more molecular targets is a most useful tool for high-throughput profiling of biomolecular interactions, including screening large molecular libraries for novel protein ligands. However, endpoint fluorescence data such as images of reacted microarrays contain little information on kinetic rate constants, and the reliability of endpoint data as measures of binding affinity depends on reaction conditions and postreaction processing. We here report a simultaneous measurement of binding curves of a protein probe with 10,000 molecular targets in a microarray with an ellipsometry-based (label-free) optical scanner. The reaction rate constants extracted from these curves (k(on), k(off), and k(a)=k(on)/k(off)) are used to characterize the probe-target interactions instead of the endpoints. This work advances the microarray technology to a new milestone, namely, from an endpoint assay to a kinetic constant assay platform. The throughput of this binding curve assay platform is comparable to those at the National Institutes of Health Molecular Library Screening Centers, making it a practical method in screening compound libraries for novel ligands and for system-wide affinity profiling of proteins, viruses, or whole cells against diverse molecular targets.

High Throughput, Label-free Screening Small Molecule Compound Libraries for Protein-Ligands using Combination of Small Molecule Microarrays and a Special Ellipsometry-based Optical Scanner

Small-molecule compounds remain the major source of therapeutic and preventative drugs. Developing new drugs against a protein target often requires screening large collections of compounds with diverse structures for ligands or ligand fragments that exhibit sufficiently affinity and desirable inhibition effect on the target before further optimization and development. Since the number of small molecule compounds is large, high-throughput screening (HTS) methods are needed. Small-molecule microarrays (SMM) on a solid support in combination with a suitable binding assay form a viable HTS platform. We demonstrate that by combining an oblique-incidence reflectivity difference optical scanner with SMM we can screen 10,000 small-molecule compounds on a single glass slide for protein ligands without fluorescence labeling. Furthermore using such a label-free assay platform we can simultaneously acquire binding curves of a solution-phase protein to over 10,000 immobilized compounds, thus enabling full characterization of protein-ligand interactions over a wide range of affinity constants.

Techniques for molecular imaging probe design

Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology--all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.

Techniques for Molecular Imaging Probe Design

Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology—all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.

Fluorescent labeling agents change binding profiles of glycan-binding proteins

Interactions of glycan-binding proteins (GBPs) with glycans are essential in cell adhesion, bacterial/viral infection, and cellular signaling pathways. Experimental characterization of these interactions based on glycan microarrays typically involves (1) labeling GBPs directly with fluorescent reagents before incubation with the microarrays, or (2) labeling GBPs with biotin before the incubation and detecting the captured GBPs after the incubation using fluorescently labeled streptavidin, or (3) detecting the captured GBPs after the incubation using fluorescently labeled antibodies raised against the GBPs. The fluorescent signal is mostly measured ex situ after excess fluorescent materials are washed off. In this study, by using a label-free optical scanner for glycan microarray detection, we measured binding curves of 7 plant lectins to 24 glycans: four β1-4-linked galactosides, three β1-3-linked galactosides, one β-linked galactoside, one α-linked N-acetylgalactosaminide, eight α2-3-linked sialosides, and seven α2-6-linked sialosides. From association and dissociation constants deduced by global-fitting the binding curves, we found that (1) labeling lectins directly with fluorescent agents change binding profiles of lectins, in some cases by orders of magnitude; (2) those lectin-glycan binding reactions characterized with large dissociation rates, though biologically relevant, are easily missed or deemed insignificant in ex situ fluorescence-based assays as most captured lectins are washed off before detection. This study highlights the importance of label-free real-time detection of protein-ligand interactions and the potential pitfall in interpreting fluorescence-based assays for characterization of protein-glycan interactions.

Use of real-time, label-free analysis in revealing low-affinity binding to blood group antigens by Helicobacter pylori

Infectious diseases are often initiated by microbial adherence that is mediated by the binding of attachment molecules, termed adhesins, to cell surface receptors on host cells. We present an experimental system, oblique-incidence reflectivity difference (OI-RD) microscopy, which allows the detection of novel, low-affinity microbial attachment mechanisms that may be essential for infectious processes. OI-RD microscopy was used to analyze direct binding of the oncopathogen, Helicobacter pylori ( H. pylori ) to immobilized glycoconjugates in real time with no need for labeling tags. The results suggest the presence of additional Lewis b blood group antigen (Le(b)) binding adhesins that have not been detected previously. OI-RD microscopy also confirmed the high-affinity binding of H. pylori outer-membrane protein BabA to Le(b). The OI-RD microscopy method is broadly applicable to real-time characterization of intact microbial binding to host receptors and offers new strategies to elucidate the molecular interactions of infectious agents with human host cells.