Peptide-Based Capture of Chikungunya Virus E2 Protein Using Porous Silicon Biosensor.

The detection of pathogens presents specific challenges in ensuring that biosensors remain operable despite exposure to elevated temperatures or other extreme conditions. The most vulnerable component of a biosensor is typically the bioreceptor. Accordingly, the robustness of peptides as bioreceptors offers improved stability and reliability toward harsh environments compared to monoclonal antibodies that may lose their ability to bind target molecules after such exposures. Here, we demonstrate peptide-based capture of the Chikungunya virus E2 protein in a porous silicon microcavity biosensor at room temperature and after exposure of the peptide-functionalized biosensor to high temperature. Contact angle measurements, attenuated total reflectance-Fourier transform infrared spectra, and optical reflectance measurements confirm peptide functionalization and selective E2 protein capture. This work opens the door for other pathogenic biomarker detection using peptide-based capture agents on porous silicon and other surface-based sensor platforms.

Protein-Catalyzed Capture Agents.

Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.

A universal method for the functionalization of dyed magnetic microspheres with peptides.

The need for the functionalization of magnetic, water-soluble dyed microspheres with peptides is apparent with the ever-growing biointeraction capabilities and the increased use of dyed microspheres in multiplex, microsphere-based detection assays. This method describes the attachment of any peptide to dyed magnetic microspheres regardless of peptide length, size, or sequence. The method exploits 'click' chemistry with short reaction times in a mixed organic/water system for simultaneous selective surface functionalization and reduction of microsphere dye leaching. All optimization studies were performed using a Luminex 200 assay platform, but the functionalized microspheres are capable of use in any similar multiplex format.

Protein catalyzed capture agents with tailored performance for in vitro and in vivo applications.

We report on peptide-based ligands matured through the protein catalyzed capture (PCC) agent method to tailor molecular binders for in vitro sensing/diagnostics and in vivo pharmacokinetics parameters. A vascular endothelial growth factor (VEGF) binding peptide and a peptide against the protective antigen (PA) protein of Bacillus anthracis discovered through phage and bacterial display panning technologies, respectively, were modified with click handles and subjected to iterative in situ click chemistry screens using synthetic peptide libraries. Each azide-alkyne cycloaddition iteration, promoted by the respective target proteins, yielded improvements in metrics for the application of interest. The anti-VEGF PCC was explored as a stable in vivo imaging probe. It exhibited excellent stability against proteases and a mean elimination in vivo half-life (T1/2 ) of 36 min. Intraperitoneal injection of the reagent results in slow clearance from the peritoneal cavity and kidney retention at extended times, while intravenous injection translates to rapid renal clearance. The ligand competed with the commercial antibody for binding to VEGF in vivo. The anti-PA ligand was developed for detection assays that perform in demanding physical environments. The matured anti-PA PCC exhibited no solution aggregation, no fragmentation when heated to 100°C, and > 81% binding activity for PA after heating at 90°C for 1 h. We discuss the potential of the PCC agent screening process for the discovery and enrichment of next generation antibody alternatives.

A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands.

We describe a general synthetic strategy for developing high-affinity peptide binders against specific epitopes of challenging protein biomarkers. The epitope of interest is synthesized as a polypeptide, with a detection biotin tag and a strategically placed azide (or alkyne) presenting amino acid. This synthetic epitope (SynEp) is incubated with a library of complementary alkyne or azide presenting peptides. Library elements that bind the SynEp in the correct orientation undergo the Huisgen cycloaddition, and are covalently linked to the SynEp. Hit peptides are tested against the full-length protein to identify the best binder. We describe development of epitope-targeted linear or macrocycle peptide ligands against 12 different diagnostic or therapeutic analytes. The general epitope targeting capability for these low molecular weight synthetic ligands enables a range of therapeutic and diagnostic applications, similar to those of monoclonal antibodies.

A chemically synthesized capture agent enables the selective, sensitive, and robust electrochemical detection of anthrax protective antigen.

We report on a robust and sensitive approach for detecting protective antigen (PA) exotoxin from Bacillus anthracis in complex media. A peptide-based capture agent against PA was developed by improving a bacteria display-developed peptide into a highly selective biligand through in situ click screening against a large, chemically synthesized peptide library. This biligand was coupled with an electrochemical enzyme-linked immunosorbent assay utilizing nanostructured gold electrodes. The resultant assay yielded a limit of detection of PA of 170 pg/mL (2.1 pM) in buffer, with minimal sensitivity reduction in 1% serum. The powdered capture agent could be stably stored for several days at 65 °C, and the full electrochemical biosensor showed no loss of performance after extended storage at 40 °C. The engineered stability and specificity of this assay should be extendable to other cases in which biomolecular detection in demanding environments is required.

Cooperative assembly of Zn cross-linked artificial tripeptides with pendant hydroxyquinoline ligands.

An artificial peptide with three pendant hydroxyquinoline (hq) ligands on a palindromic backbone was designed and used to form multimetallic assemblies. Reaction of the tripeptide with zinc acetate led to a highly fluorescent tripeptide duplex with three Zn(II) coordinative cross-links. The binding process was monitored using spectrophotometric absorbance and emission titrations; NMR spectroscopy and mass spectrometry confirmed the identity and stoichiometry of the product structure. Titrations monitoring duplex formation of the zinc-tripeptide structure had a sigmoidal shape, equilibrium constant larger than the monomeric analogue, and a Hill coefficient >1, all of which indicate positive cooperativity. Photophysical characterization of the quantum yield, excited state lifetime, and polarization anisotropy are compared with the monometallic zinc-hq analogue. A higher than expected quantum yield for the trimetallic complex suggests a structure in which the central chromophore is shielded from solvent by π-stacking with neighboring Zn(II) complexes.

Assembly of a trifunctional artificial peptide into an anti-parallel duplex with three Cu(II) cross-links.

Analogous to self-assembly in natural DNA or proteins, we describe the synthesis of a heterofunctional artificial tripeptide that self-assembles into an antiparallel duplex by coordination of three Cu(II) ions. The tripeptide contains three pendant ligands, pyridine (py), methyl bipyridine (bpy), and terpyridine (tpy), in series on an aminoethylglycine (aeg) backbone. These ligands chelate three Cu(II) ions, forming two [Cu(tpy)(py)](2+) and one [Cu(bpy)(2)](2+) complexes, that cross-link two tripeptide strands to give a trimetallic supramolecular structure. The tripeptide and metal-linked tripeptide duplex are characterized with NMR spectroscopy, mass spectrometry, and analytical high performance liquid chromatography (HPLC). Spectrophotometric titrations are used to quantitatively examine the stoichiometry of binding. Together with electron paramagnetic resonance (EPR) spectroscopy, the identities of the Cu(II) complexes and their environments are examined. The EPR spectrum reveals a significant amount of coupling between metal centers compared to a dimetallic dipeptide analogue. EPR and UV-vis absorbance spectroscopy, together with molecular modeling, provide evidence that the tripeptide acts as a scaffold to hold the metal centers in close proximity.

The application of (Z)-3-aryl-3-haloenoic acids to the synthesis of (Z)-5-benzylidene-4-arylpyrrol-2(5H)-ones.

Studies directed at the synthesis of (Z)-5-benzylidene-4-arylpyrrol-2(5H)-ones from (Z)-3-aryl-3-haloenoic acids are described. The successful strategy relies on the preparation of (Z)-3-aryl-3-haloenoic acids from acetophenones through the corresponding (Z)-3-aryl-3-haloenals and the conversion of the (Z)-3-aryl-3-haloenoic acids to (Z)-5-benzylidene-4-aryl-5H-furan-2-ones. The furanones were subsequently treated with primary amines and dehydrated to the corresponding (Z)-5-benzylidene-4-arylpyrrol-2(5H)-ones.

Cu(II) cross-linked antiparallel dipeptide duplexes using heterofunctional ligand-substituted aminoethylglycine.

Two artificial dipeptides containing both a pendant monodentate (pyridine (py)) and tridentate (terpyridine (tpy) or phenyl terpyridine (varphi-tpy)) ligand on an aminoethylglycine (aeg) backbone have been synthesized. These oligopeptides are fully characterized by one and two-dimensional NMR spectroscopy, mass spectrometry, and elemental analysis. The ligands were chosen because they coordinate Cu(2+) to form [Cu(py)(tpy)](2+) complexes; when bound to the dipeptide scaffold, Cu(2+) chelation cross-links the strands to form double-stranded duplex structures with an antiparallel arrangement. Using spectrophotometric titrations, we observe coordination of one Cu(2+) metal per dipeptide strand. Mass spectrometry, NMR spectroscopy, vapor pressure osmometry, and HPLC confirm that the resulting structures are the dipeptide duplex cross-linked by two metal centers.

The Application of Vinylogous Iminium Salt Derivatives and Microwave Accelerated Vilsmeier-Haack Reactions to Efficient Relay Syntheses of the Polycitone and Storniamide Natural Products.

Studies directed at the synthesis of polycitone and storniamide natural products via vinylogous iminium salts and microwave accelerated Vilsmeier-Haack formylations are described. The successful strategy relies on the formation of a 2,4-disubstituted pyrrole or a 2,3,4-trisubstituted pyrrole from a vinamidinium salt or vinamidinium salt derivative followed by formylation at the 5-position of the pyrrole. Subsequent transformations of the selectively formylated pyrroles lead to efficient and regiocontrolled relay syntheses of the respective pyrrole containing natural products.