Screening chemical microarrays: methods and applications

Identification of novel peptoid agonists of fibroblast growth factor receptor using microarray-based screening

Drug development targeting fibroblast growth factor receptors (FGFRs) represents an emerging theme in the field of medicinal chemistry. Considering the fact that most of the currently identified FGFR agonists are long chain peptides with limited stability, the discovery of novel non-peptide FGFR ligands is still highly demanded. A linear one-bead-one-compound peptoid (oligomers of N-substituted glycine units) library with a theoretical diversity of 10⁶ was designed and synthesized. Microarray-based screening led to the identification of four hit sequences 1-4 as FGFR1α ligands, which were further confirmed using both solution-phase and solid-phase binding assays. Western blot results indicated that peptoids 2-4 activated FGFR signaling pathways, resulting in increased levels of p-Akt and p-ERK in different cell lines. Our work discovered novel peptoid ligands as FGFR agonists, shedding new light on FGFR-based drug discovery.

High-throughput screening of small molecule ligands targeted to live bacteria surface

The discovery of small molecule ligands targeted to the surface of live pathogenic bacteria would enable an entirely new class of antibiotics. We report the development and validation of a microarray-based high-throughput screening platform for bacteria that exploits 300 μm diameter chemical spots in a 1 in. × 3 in. nanolayered glass slide format. Using 24 model compounds and 4 different bacterial strains, we optimized the screening technology, including fluorophore-based optical deconvolution for automated scoring of affinity and cyan-magenta-yellow-key (CMYK) color-coding for scoring of both affinity and specificity. The latter provides a lossless, one-dimensional view of multidimensional data. By linking in silico analysis with cell binding affinity and specificity, we could also begin to identify the physicochemical factors that affect ligand performance. The technology we describe could form the foundation for developing new classes of antibiotics.

Synthesis and characterization of a novel inhibitor of C-reactive protein-mediated proinflammatory effects

BACKGROUND

Numerous studies have shown that high C-reactive protein (CRP) levels predict cardiovascular disease and augur a poor prognosis in patients with acute coronary syndromes. Much in vitro and in vivo data support of a role for CRP in atherogenesis. There is an urgent need to develop inhibitors that specifically block the biological effects of CRP in vivo. The one-bead-one-compound (OBOC) combinatorial library method has been used to discover ligands against several biological targets. In this study, we use a novel fluorescence-based screening method to screen an OBOC combinatorial library for the discovery of peptides against human CRP.

METHODS

Human CRP was labeled with fluorescein isothiocyanate (FITC) and human serum albumin (HuSA) was labeled with phycoerythrin (PE) and used for screening. The OBOC library LWH-01 was synthesized on TentaGel resin beads using a standard solid-phase "split/mix" approach.

RESULTS

By subtraction screening, eight peptides that bind specifically to CRP and not to HuSA were identified. In human aortic endothelial cells (HAECs) incubated with CRP, inhibitors CRPi-2, CRPi-3, and CRPi-6 significantly inhibited CRP-induced superoxide, cytokine release, and nuclear factor-κB (NFκB) activity. Molecular docking studies demonstrate that CRPi-2 interacts with the two Ca(2+) ions in the single subunit of CRP. The binding of CRPi-2 is reminiscent of choline binding.

CONCLUSIONS

Future studies will examine the utility of this inhibitor in animal models and clinical trials.

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.

Particle-based synthesis of peptide arrays

Lithographic methods allow for the combinatorial synthesis of >50,000 oligonucleotides per cm(2), and this has revolutionized the field of genomics. High-density peptide arrays promise to advance the field of proteomics in a similar way, but currently lag behind. This is mainly due to the monomer-by-monomer repeated consecutive coupling of 20 different amino acids associated with lithography, which adds up to an excessive number of coupling cycles. Combinatorial synthesis based on electrically charged solid amino acid particles resolves this problem. A color laser printer or a chip addresses the different charged particles consecutively to a solid support, where, when completed, the whole layer of solid amino acid particles is melted at once. This frees hitherto immobilized amino acids to couple all 20 different amino acids to the support in one single coupling reaction. The method should allow for the translation of entire genomes into sets of overlapping peptides to be used in proteome research.

On-demand cleavable linkers for radioimmunotherapy

Radioimmunotherapy (RIT) using radiolabeled antibodies or its fragments holds great promise for cancer therapy. However, its clinical potential is often limited by the undesirable radiation exposure to normal organs such as liver, kidney, and bone marrow. It is important to develop new strategies in RIT that enable protection of vital organs from radiation exposure while maintaining therapeutic radiation dose to the cancer. One way to achieve this is to clear radiometal rapidly from the circulation after accumulation of radioimmunoconjugates (RIC) in the tumor. Our strategy is to place a highly efficient and specific cleavable linker between radiometal chelate and the tumor targeting agent. Such linker must be resistant to cleavage by enzymes present in the plasma and tumor. After radiotargeting agents have accumulated in the tumor, a cleaving agent (protease) can be administered to the patient "on demand" to cleave the specific linker, resulting in the release of radiometal from the circulating RIC, in a form that can be cleared rapidly by the kidneys. TNKase, a serine protease tissue plasminogen activator and thrombolytic agent, which has been approved for clinical use in patient with acute myocardial infarction, was selected as an on-demand cleaving agent in our model. TNKase specific on-demand cleavable (ODC) linkers were identified through screening random internally quenched fluorescent resonance energy transfer (FRET) "one-bead-one-compound" (OBOC) combinatorial peptide libraries. FRET-OBOC peptide libraries containing L-amino acid(s) in the center of the random linear peptide and D-amino acids flanking both sides of the L-amino acid(s) were used for screening. Peptide beads susceptible to TNKase but resistant to plasma and tumor-associated protease cleavage were isolated for sequence analysis. The focus of this chapter is on the methods that have been used to identify and characterize ODC linkers and protease-specific substrates.

Flow cytometry for drug discovery, receptor pharmacology and high-throughput screening

Although flow cytometry is viewed as a mature technology, there have been dramatic advances in analysis capabilities, sorting, sample handling and sensitivity in the past decade. These advances contribute to its application in biological and chemical diversity, sample throughput, high content, and complex systems biology. This article will evaluate the new opportunities for flow cytometry relating to receptor assembly and pharmacology, as well as a range of screening applications.