Small Molecule Microarrays Research Articles

Surface modification for small-molecule microarrays and its application to the discovery of a tyrosinase inhibitor

Small-molecule microarrays are powerful, high-throughput tools for gathering information about direct binding events between proteins of interest and small molecules. However, nonspecific binding on modified glass slides is the major factor reducing the quality of information obtained in proteomic screening with small-molecule microarrays. To improve the signal-to-noise ratio by suppressing the background signal, we tested several surface modification methods for glass slides. Jeffamine-coated slides showed a high fluorescence signal and a significantly enhanced signal-to-noise ratio. We applied this surface modification to proteomic screening of potential tyrosinase inhibitors with a small-molecule microarray and identified 2,4,4'-trihydroxychalcone as a new small-molecule binder to tyrosinase. Its actual binding and inhibitory effects on tyrosinase were validated using an SPR binding assay and an enzyme-based inhibition assay, respectively. Thus, we successfully demonstrate the application of Jeffamine-based modification to proteomics screening with small-molecule microarrays.

Binding screens

Small-molecule microarrays facilitate the search for Alzheimer's disease therapeutics by screening compounds that bind to the amyloid-β peptide.

Small Molecule Microarrays Enable the Discovery of Compounds That Bind the Alzheimer’s Aβ Peptide and Reduce its Cytotoxicity

The amyloid-β (Aβ) aggregation pathway is a key target in efforts to discover therapeutics that prevent or delay the onset of Alzheimer's disease. Efforts at rational drug design, however, are hampered by uncertainties about the precise nature of the toxic aggregate. In contrast, high-throughput screening of compound libraries does not require a detailed understanding of the structure of the toxic species, and can provide an unbiased method for the discovery of small molecules that may lead to effective therapeutics. Here, we show that small molecule microarrays (SMMs) represent a particularly promising tool for identifying compounds that bind the Aβ peptide. Microarray slides with thousands of compounds immobilized on their surface were screened for binding to fluorescently labeled Aβ. Seventy-nine compounds were identified by the SMM screen, and then assayed for their ability to inhibit the Aβ-induced killing of PC12 cells. Further experiments focused on exploring the mechanism of rescue for one of these compounds: Electron microscopy and Congo red binding showed that the compound enhances fibril formation, and suggest that it may rescue cells by accelerating Aβ aggregation past an early toxic oligomer. These findings demonstrate that the SMM screen for binding to Aβ is effective at identifying compounds that reduce Aβ toxicity, and can reveal potential therapeutic leads without the biases inherent in methods that focus on inhibitors of aggregation.

Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles

Using a diverse collection of small molecules generated from a variety of sources, we measured protein-binding activities of each individual compound against each of 100 diverse (sequence-unrelated) proteins using small-molecule microarrays. We also analyzed structural features, including complexity, of the small molecules. We found that compounds from different sources (commercial, academic, natural) have different protein-binding behaviors and that these behaviors correlate with general trends in stereochemical and shape descriptors for these compound collections. Increasing the content of sp(3)-hybridized and stereogenic atoms relative to compounds from commercial sources, which comprise the majority of current screening collections, improved binding selectivity and frequency. The results suggest structural features that synthetic chemists can target when synthesizing screening collections for biological discovery. Because binding proteins selectively can be a key feature of high-value probes and drugs, synthesizing compounds having features identified in this study may result in improved performance of screening collections.

Abstract 3693: Small molecule microarray screens for inhibitors of oncogenic ETS factors

Abstract Members of the ETS transcription factors family are involved in many cancers and are often targeted by translocation events that result in oncogenic gene fusions or dysregulated ETS factor expression. For example, the vast majority of prostate cancers harbor translocations involving the ETS factors ERG, ETV1 and ETV4 (most commonly, these are fused to the TMPRSS2 androgen-regulated gene or other house keeping genes). Overexpression of ETS factor gene fusions can induce or sustain malignant characteristics of cancer cells such as survival or invasiveness. However transcription factors have often been deemed “undruggable” by conventional approaches. The focus of this project is to employ novel screening approaches to identify and characterize small molecules that are able to bind and modulate the biological function of oncogenic ETS factors. Toward this end, we have performed Small Molecule Microarray (SMM) screens that involve a total of 80,000 distinct small molecules spanning several categories, including diversity-oriented synthesis (DOS) products, natural products, and other biologically active chemotypes. The SMM screens identified six compound that selectively bind the ETS factor ETV1 with a stringent Zscore. Two of these compounds have shown inhibitory activity in an ETV1-specific promoter-induced luciferase system. Surface Plasmon Resonance analysis has confirmed that each of the two lead compounds binds ETV1 directly, with one compound showing submicromolar binding kinetics. This compound in particular was able to reduce the expression of several ETV1 downstream targets such as MMP1 and MMP7. These efforts suggest that we have identified novel small molecule “perturbagens” of ETV1, an oncogenic ETS transcription factor. More generally, our results suggest that SMM-based screens may offer a robust approach to identify novel compounds that bind and perturb the function of cancer-associated proteins deemed poorly “druggable” by conventional methods. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3693.

Syntheses of aminoalcohol-derived macrocycles leading to a small-molecule binder to and inhibitor of Sonic Hedgehog

We report the synthesis and biological activity of a library of aminoalcohol-derived macrocycles from which robotnikinin ( 17), a binder to and inhibitor of Sonic Hedgehog, was derived. Using an asymmetric alkylation to set a key stereocenter and an RCM reaction to close the macrocycle, we were able to synthesize compounds for testing. High-throughput screening via small-molecule microarray (SMM) technology led to the discovery of a compound capable of binding ShhN. Follow-up chemistry led to a library of macrocycles with enhanced biological activity relative to the original hit compounds. Differences in ring size and stereochemistry, leading to alterations in the mode of binding, may account for differences in the degree of biological activity. These compounds are the first ones reported that inhibit Shh signaling at the ShhN level.

Fluorous-Based Small-Molecule Microarrays for Protein, Antibody and Enzyme Screening

Microarray techniques based on covalent and noncovalent compound immobilization have been developed for screening proteins, antibodies and enzymes to probe the possible biological roles of these interactions as well as their therapeutic and diagnostic potential. Small-molecule microarrays are particularly valuable for creating and probing multivalent displays of molecules, such as saccharides that mimic the multivalent displays of cell surface-bound compounds. After development of the method for the screening of carbohydrates in a multivalent display format, microarrays based on noncovalent fluorous interactions have seen use in probing protein-binding partners with a range of arrayed compounds. In this article, existing strategies and future perspectives for fluorous-based small-molecule microarrays for protein, antibody and enzyme screening will be presented. To date, qualitative and quantitative fluorous-based microarrays have offered important information regarding biomolecular interactions. Larger compound arrays created with automated fluorous-based synthesis and diagnostic tools based on fluorous-based microarrays are likely ahead.

The End Game of Chemical Genetics: Target Identification

The use of classical genetic and molecular biology methods along with the sequencing of many genomes has proven crucial for elucidating complex biological processes. Despite being invaluable tools, their limitations have led to a search for more versatile alternatives and, thus, to the use of small molecules. Chemical genetics is a rapidly emerging field that uses small-molecule techniques to probe biological systems and is composed of three parts: natural product or small-molecule libraries, phenotypic screening and target identification. Currently, the biggest hurdle in the overall process of chemical genetics is target identification. Efforts to overcome this obstacle have led to advances in the areas of affinity chromatography, yeast haploinsufficiency, complementary DNA (cDNA) overexpression, DNA microarray, small-molecule microarray and RNA interference (RNAi) technologies. While these technologies continue to undergo further optimization, they have been integral in the identification and/or confirmation of many cellular targets and have seen an increase in applications to the drug-development process.

Macromolecular Scaffolds for Immobilizing Small Molecule Microarrays in Label-Free Detection of Protein−Ligand Interactions on Solid Support

We explored two macromolecular scaffolds, bovine serum albumin (BSA) and polyvinyl alcohol (PVA), as chemically complementary platforms for immobilizing small molecule compounds on functionalized glass slides. We conjugated biotin molecules to BSA and amine-derivatized PVA and subsequently immobilized the conjugates on epoxy-functionalized glass slides through reaction of free amine residues on BSA and PVA with surface-bound epoxy groups. We studied binding reactions of such immobilized small molecule targets with solution-phase protein probes using an oblique-incidence reflectivity difference scanning optical microscope. The results showed that both BSA and amine-derivatized PVA were effective and efficient as carriers of small molecules with NHS residues and fluoric residues and for immobilization on epoxy-coated solid surfaces. A significant fraction of the conjugated small molecules retain their innate chemical activity.

Immobilization strategies for small molecule, peptide and protein microarrays

Protein, peptide and small molecule microarrays are valuable tools in biological research. In the last decade, substantial progress has been achieved to make these powerful technologies more reliable and available for researchers. This review describes chemical preparation methods for these microarrays with focus on site-selective and bioorthogonal immobilization reactions, particularly the Staudinger ligation and the thiol-ene reaction. In addition, the application of peptide microarrays, which were prepared by Staudinger ligation, to substrate specificity mapping is illustrated.

A small molecule that binds Hedgehog and blocks its signaling in human cells

Small-molecule inhibition of extracellular proteins that activate membrane receptors has proved to be extremely challenging. Diversity-oriented synthesis and small-molecule microarrays enabled the discovery of robotnikinin, a small molecule that binds the extracellular Sonic Hedgehog (Shh) protein and blocks Shh-signaling in cell lines, human primary keratinocytes and a synthetic model of human skin. Shh pathway activity is rescued by small-molecule agonists of Smoothened, which functions immediately downstream of the Shh receptor Patched.

Small molecule microarray-facilitated screening of affinity-based probes (AfBPs) for γ-secretase

A small molecule microarray (SMM) platform is developed herein, which enables high-throughput discovery of affinity-based probes (AfBPs) against gamma-secretase.

Fluorous Tags Catching on Microarrays

Tag team: Not only hydrophilic carbohydrates but also hydrophobic compounds such as histone deacetylase inhibitors and biotin can be incorporated into fluorous-based small-molecule microarrays. A range of fluorous-tagged molecules can be patterned and screened for bioactivity on a fluorous surface with hit rates comparable to those seen by solution-based and surface plasmon resonance-based bioassays.

A novel immobilization strategy using oligonucleotide as linker for small molecule microarrays construction

A novel immobilization method based on oligonucleotide as linker has been developed for small molecule microarrays (SMMs) construction. The oligonucleotide tail was employed as a linker in solid-phase synthesis. Small molecules could be easily conjugated at the 5′ end of the oligonucleotide, previously modified with a functional group. Being a reactive species, the oligonucleotide was activated by UV irradiation, for the attachment of the conjugate to the slide surface. The method was successfully applied to structurally distinct small molecules, including biotin, antibiotic and drug. This immobilization strategy showed high efficiency, 1.1 fmol of small molecules in the spotting solution per spot gave a detectable signal (mean S/N = 10.9). The results suggest that it is very promising for exploring interaction between small molecules and proteins, and high throughput detecting the chemical compounds.

Home-built integrated microarray system (IMAS). A three-laser confocal fluorescence scanner coupled with a microarray printer

Microarray technology covers the urgent need to exploit the accumulated genetic information from large-scale sequencing projects and facilitate investigations on a genome-wide scale. Although most applications focus on DNA microarrays, the technology has expanded to microarrays of proteins, peptides, carbohydrates, and small molecules aiming either at detection/quantification of biomolecules or investigation of biomolecular interactions in a massively parallel manner. Microarray experiments require two specialized instruments: An arrayer (or printer), for construction of microarrays, and a readout instrument (scanner). We have designed, constructed, and characterized the first integrated microarray system (IMAS) that combines the functions of a microarrayer and a three-laser confocal fluorescence scanner into a single instrument and provides excellent flexibility for the researcher. The three-axis robotic system that moves the printing head carrying multiple pins for arraying is also used for moving the microarray slide in front of a stationary optical system during scanning. Since the translation stages are the most expensive and crucial components of microarray printers and scanners, the proposed design reduces considerably the cost of the instrument and enhances remarkably its operative flexibility. Experiments were carried out at resolutions of 2.5, 5, 10, and 20 microm. The scanner detects 0.128 nmol L(-1) carboxyfluorescein (spots with diameters of 70 microm) corresponding to 1.8 molecules microm(-2). The linear range extends over 3.5 orders of magnitude (R(2) = 0.997) and the dynamic range covers almost five orders of magnitude. DNA microarray model experiments were carried out, including staining with SYBR Green I and hybridization with oligonucleotides labeled with the fluorescent dyes Alexa 488, Alexa 594, and Alexa 633.

Small-molecule microarrays as tools in ligand discovery

Small molecules that bind and modulate specific protein targets are increasingly used as tools to decipher protein function in a cellular context. Identifying specific small-molecule probes for each protein in the proteome will require miniaturized assays that permit screening of large collections of compounds against large numbers of proteins in a highly parallel fashion. Simple and general binding assays involving small-molecule microarrays can be used to identify probes for nearly any protein in the proteome. The assay may be used to identify ligands for proteins in the absence of knowledge about structure or function. In this tutorial review, we introduce small-molecule microarrays (SMMs) as tools for ligand discovery; discuss methods for manufacturing SMMs, including both non-covalent and covalent attachment strategies; and provide examples of ligand discovery involving SMMs.

Fluorous‐Based Small‐Molecule Microarrays for the Discovery of Histone Deacetylase Inhibitors

Noncovalent immobilization is an attractive method for identifying inhibitors of histone deacetylases (HDACs). Fluorous-based small-molecule microarrays were validated as an effective method. Three enzymes and three assays (microarray, biochemical activity, and surface plasmon resonance) were used to identify inhibitors of HDACs and to compare them.

Quantitative Inhibitor Fingerprinting of Metalloproteases Using Small Molecule Microarrays

Current methods to identify interactions on small molecule microarrays (SMMs) introduce false positives that are difficult to dissect from the "real" binding events without tedious downstream re-evaluation. To specifically elucidate only activity-dependent ligand binding interactions, we have developed a technique that can be universally applied to present SMM systems. Our method makes use of a dual-color application strategy and is based on the simultaneous application of differentially treated samples. Overcoming the limitations of slide-to-slide variation, this method directly revealed activity-dependent interactions through a one-step application of protein samples on SMMs. Besides providing lead molecules for further development, the high-throughput screening results confer activity-dependent fingerprints for quantitative characterization and differentiation of proteins. The procedure was tested using a synthetic hydroxamate peptide library with 1400 discrete sequences permuted combinatorially across P1', P2', and P3' positions. Functional profiling across a panel of metalloproteases provided 44,800 datapoints within just eight SMM slides. These data were globally analyzed for activities, specificity, potency, and hierarchical clustering providing unique insights into inhibitor design and preference within this group of enzymes. Quantitative K(D) measurements performed on SMMs using one of the enzymes in the panel, Anthrax Lethal Factor, the toxic component of a notorious bioterror agent, unraveled several lead micromolar binders for further development. Overall, the effectiveness of the SMM platform is shown to be enhanced and extended using the strategy presented in this work.

Detecting Binding Interactions Using Microarrays of Natural Product Extracts

Small-molecule microarrays have been used to discover biologically active small molecules in collections of synthetic compounds. Here we utilize a versatile isocyanate chemistry to immobilize extracts from microorganisms in a microarray format. Specific bioactive small molecules are detected in crude extracts of Streptomyces hygroscopicus, and the amount of specific to nonspecific binding of a protein to an immobilized compound on a microarray can be estimated. These natural product-extract microarrays (NPEMs) provide new tools for characterizing the metabolic products of organisms and for discovering biologically active small molecules from nature.

Simultaneous detection of sulfamethazine, streptomycin, and tylosin in milk by microplate-array based SMM–FIA

This paper presents an approach to simultaneously detect sulfamethazine, streptomycin, and tylosin in milk by indirect competitive multianalyte Fluorescence immunoassay (FIA). Microscope glass slides modified with agarose were used for the preparation of small molecule microarrays (SMMs). Bovine serum albumin (BSA) conjugates of the haptens were immobilized on glass slides. The system consists of four glass slides containing 96 wells formed by an enclosing hydrophobic mask, which precisely matches a standard microplate. All liquid handling and sample processing were fully automated as 96-wells ELISA format. Monoclonal antibodies against sulfamethazine, streptomycin, and tylosin allowed the simultaneous detection of the respective analytes. Antibody binding was detected by a second antibody labeled with Cy5 generating fluorescence, which was scanned with chip scanner. The detection limits for three analytes were 3.26 ng/ml (sulfamethazine), 2.01 ng/ml (streptomycin), and 6.37 ng/ml (tylosin), being far below the respective MRLs. The system proved to be the first SMM–FIA platform having the potential to test for numerous antibiotics in parallel, such being of considerable interest for the control of safety in the food industry.