Probing the Activity of Matrix Metalloproteinase II with a Sequentially Click-Labeled Silica Nanoparticle FRET Probe

A Genetically Encoded Isonitrile Lysine for Orthogonal Bioorthogonal Labeling Schemes

Bioorthogonal click-reactions represent ideal means for labeling biomolecules selectively and specifically with suitable small synthetic dyes. Genetic code expansion (GCE) technology enables efficient site-selective installation of bioorthogonal handles onto proteins of interest (POIs). Incorporation of bioorthogonalized non-canonical amino acids is a minimally perturbing means of enabling the study of proteins in their native environment. The growing demand for the multiple modification of POIs has triggered the quest for developing orthogonal bioorthogonal reactions that allow simultaneous modification of biomolecules. The recently reported bioorthogonal [4 + 1] cycloaddition reaction of bulky tetrazines and sterically demanding isonitriles has prompted us to develop a non-canonical amino acid (ncAA) bearing a suitable isonitrile function. Herein we disclose the synthesis and genetic incorporation of this ncAA together with studies aiming at assessing the mutual orthogonality between its reaction with bulky tetrazines and the inverse electron demand Diels-Alder (IEDDA) reaction of bicyclononyne (BCN) and tetrazine. Results showed that the new ncAA, bulky-isonitrile-carbamate-lysine (BICK) is efficiently and specifically incorporated into proteins by genetic code expansion, and despite the slow [4 + 1] cycloaddition, enables the labeling of outer membrane receptors such as insulin receptor (IR) with a membrane-impermeable dye. Furthermore, double labeling of protein structures in live and fixed mammalian cells was achieved using the mutually orthogonal bioorthogonal IEDDA and [4 + 1] cycloaddition reaction pair, by introducing BICK through GCE and BCN through a HaloTag technique.

Synergistic transport of a fluorescent coumarin probe marks coumarins as pharmacological modulators of Organic anion-transporting polypeptide, OATP3A1

Organic anion-transporting polypeptide 3A1 (OATP3A1) is a membrane transporter mediating the cellular uptake of various hormones such as estrone-3-sulfate, prostaglandins E1 and E2 and thyroxine. OATP3A1 is widely expressed in the human body and its presence in tissue-blood barriers, neurons and muscle cells marks it as a potential pharmacological target. Herein we demonstrate that an otherwise membrane impermeant, zwitterionic fluorescent coumarin probe, bearing a sulfonate function is a potent substrate of human OATP3A1, thus readily transported into HEK-293-OATP3A1 cells allowing functional investigation and the screen of drug interactions of the OATP3A1 transporter. At the same time, dyes lacking either the sulfonate motif or the coumarin scaffold showed a dramatic decrease in affinity or even a complete loss of transport. Furthermore, we observed a distinct inhibition/activation pattern in the OATP3A1-mediated uptake of closely related fluorescent coumarin derivatives differing only in the presence of the sulfonate moiety. Additionally, we detected a synergistic effect between one of the probes tested and the endogenous OATP substrate estrone-3-sulfate. These data, together with docking results indicate the presence of at least two cooperative substrate binding sites in OATP3A1. Besides providing the first sensitive probe for testing OATP3A1 substrate/inhibitor interactions, our results also help to understand substrate recognition and transport mechanism of the poorly characterized OATP3A1. Moreover, coumarins are good candidates for OATP3A1-targeted drug delivery and as pharmacological modulators of OATP3A1.

MoS2 Field-Effect Transistor-Amyloid-β1-42 Hybrid Device for Signal Amplified Detection of MMP-9

The detection of circulating protein (CP) is very important for the diagnosis and therapeutics of cancer. Conventional techniques based on a specific antibody-antigen interaction are still lacking because of a shortage of cost effectiveness, complicated sandwich structure and tagging process, and inconsistent detection of CP due to the inherent instability of antibodies. Herein, we demonstrate a hybrid device consisting of two-dimensional (2D) nanoscale molybdenum disulfide (MoS₂) field-effect transistor (FET) with an amyloid-β_1-42 (Aβ_1-42) functionalized surface, which amplifies electric signals of the FET in order to detect matrix metalloproteinase-9 (MMP-9), which is a certain type of CP that degrades Aβ_1-42. With the hybrid device, we detected the concentrations of MMP-9 in the range from 1 pM to 10 nM. Moreover, using tapping-mode atomic force microscopy and Kelvin probe force microscopy, we verified that the signal amplification corresponding to the MMP-9 concentrations was caused by the reduced length and the decreased surface potential of degraded Aβ_1-42 due to MMP-9. The hybrid device studied in this paper can be very useful for monitoring MMP-9 activity, as well as serving as a sensing platform for the electrical signal amplification of 2D MoS₂ FET-biosensors.

Fluorescent and Bioluminescent Nanoprobes for In Vitro and In Vivo Detection of Matrix Metalloproteinase Activity

Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that degrade the extracellular matrix (ECM) and regulate the extracellular microenvironment. Despite the significant role that MMP activity plays in cell-cell and cell-ECM interactions, migration, and differentiation, analyses of MMPs in vitro and in vivo have relied upon their abundance using conventional immunoassays, rather than their enzymatic activities. To resolve this issue, diverse nanoprobes have emerged and proven useful as effective activity-based detection tools. Here, we review the recent advances in luminescent nanoprobes and their applications in in vitro diagnosis and in vivo imaging of MMP activity. Nanoprobes with the purpose of sensing MMP activity consist of recognition and detection units, which include MMP-specific substrates and luminescent (fluorescent or bioluminescent) nanoparticles, respectively. With further research into improvement of the optical performance, it is anticipated that luminescent nanoprobes will have great potential for the study of the functional roles of proteases in cancer biology and nanomedicine. [BMB Reports 2015; 48(6): 313-318]

Mini-review: fluorescence imaging in cancer cells using dye-doped nanoparticles

Fluorescence imaging has gained increased attention over the past two decades as a viable means to detect a variety of cancers.

Enzymatically activated near infrared nanoprobes based on amphiphilic block copolymers for optical detection of cancer

BACKGROUND AND OBJECTIVE

Nanotechnology offers the possibility of creating multi-functional structures that can provide solutions for biomedical problems. The nanoprobes herein described are an example of such structures, where nano-scaled particles have been designed to provide high specificity and contrast potential for optical detection of cancer. Specifically, enzymatically activated fluorescent nanoprobes (EANPs) were synthesized as cancer-specific contrast agents for optical imaging.

STUDY DESIGN/MATERIALS AND METHODS

EANPs were prepared by nanoprecipitation of blends of poly(lactic acid)-b-poly(ethylene glycol) and poly(lactic-co-glycolic acid)-b-poly(l-lysine). The lysine moieties were then covalently decorated with the near infrared (NIR) fluorescent molecule AlexaFluor-750 (AF750). Close proximity of the fluorescent molecules to each other resulted in fluorescence quenching, which was reversed by enzymatically mediated cleavage of poly(l-lysine) chains. EANPs were characterized by dynamic light scattering and electron microscopy. Enzymatic development of fluorescence was studied in vitro by fluorescence spectroscopy. Biocompatibility and contrast potential of EANPs were studied in cancerous and noncancerous cells. The potential of the nanoprobes as contrast agents for NIR fluorescence imaging was studied in tissue phantoms.

RESULTS

Spherical EANPs of ∼100 nm were synthesized via nanoprecipitation of polymer blends. Fluorescence activation of EANPs by treatment with a model protease was demonstrated with up to 15-fold optical signal enhancement within 120 minutes. Studies with MDA-MB-231 breast cancer cells demonstrated the cytocompatibility of EANPs, as well as enhanced fluorescence associated with enzymatic activation. Imaging studies in tissue phantoms confirmed the ability of a simple imaging system based on a laser source and CCD camera to image dilute suspensions of the nanoprobe at depths of up to 4 mm, as well as up to a 13-fold signal-to-background ratio for enzymatically activated EANPs compared to un-activated EANPs at the same concentration.

CONCLUSION

Nanoprecipitation of copolymer blends containing poly(l-lysine) was utilized as a method for preparation of highly functional nanoprobes with high potential as contrast agents for fluorescence based imaging of cancer. Lasers Surg. Med. 47:579-594, 2015. © 2015 Wiley Periodicals, Inc.

Signal enhancement of silicon nanowire-based biosensor for detection of matrix metalloproteinase-2 using DNA-Au nanoparticle complexes

Silicon nanowires have been used in the development of ultrasensitive biosensors or chemical sensors, which is originated in its high surface-to-volume ratio and function as field-effect transistor (FET). In this study, we developed an ultrasensitive DNA-gold (Au) nanoparticle complex-modified silicon nanowire field effect transistor (SiNW-FET) biosensor to detect matrix metalloproteinase-2 (MMP-2), which has been of particular interest as protein biomarker because of its relation to several important human diseases, through an enzymatic cleavage reaction of a specific peptide sequence (IPVSLRSG). SiNW patterns with a width of 100 nm and height of 100 nm were fabricated on a p-type silicon-on-insulator (SOI) wafer by electron-beam lithography. Next, negatively charged DNA-Au nanoparticle complexes coupled with the specific peptide (KKGGGGGG-IPVSLRSG-EEEEEE) were applied on the SiNWs to create a more sensitive system, which was then bound to aldehyde-functionalized SiNW. The enhanced negatively charged nanoparticle complexes by attached DNA were used to enhance the conductance change of the p-SiNW by MMP-2 cleavage reaction of the specific peptide. MMP-2 was successfully measured within a range of 100 fM to 10 nM, and the conductance signal of the p-type SiNW by the MMP-2 cleavage reaction was enhanced over 10-fold by using the DNA-Au nanoparticle complexes compared with using SiNW-attached negative single peptide sequences.

Stepwise orthogonal click chemistry toward fabrication of paclitaxel/galactose functionalized fluorescent nanoparticles for HepG2 cell targeting and delivery

In this report, we used stepwise orthogonal click chemistry (SOCC) involving strain-promoted azide-alkyne cycloaddition (SPAAC) and microwave-assisted Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) to assemble an anticancer drug (paclitaxel, PTX) and a targeting ligand (trivalent galactoside, TGal) on a fluorescent silicon oxide nanoparticle (NP) by using dialkyne linker 8 as a bridge. The fluorescent NH2@Cy3SiO2NP was fabricated using a competition method to incorporate Cy3 without loss of the original surface amine density on the NPs. The concept of SOCC was first investigated in a solution-phase model study that showed quantitative reaction yield. In the fabrication of TGal-PTX@Cy3SiO2NP, the expensive compound azido-functionalized PTX 12 used in SPAAC can be easily recovered due to the absence of other reagents in the reaction mixture. High loading of the sugar ligand on the NP surface serves a targeting function and also overcomes the low water solubility of PTX. Confocal fluorescence microscopy and cytotoxicity assay showed that TGal-PTX@Cy3SiO2NP was taken up by HepG2 cells and was affected by the microtubule skeleton in these cells and inhibited the proliferation of these cells in a dose-dependent manner. The presence of a fluorescent probe, a targeting ligand, and an anticancer drug on the multifunctional TGal-PTX@Cy3SiO2NP allows for real-time imaging, specific cancer-cell targeting, and the cell-killing effect which is better than free PTX.

A graphene oxide-based FRET sensor for rapid and sensitive detection of matrix metalloproteinase 2 in human serum sample

Graphene oxide (GO) has been widely used to develop fluorescence resonance energy transfer (FRET) biosensors for tumor markers (e.g., matrix metalloproteinases, MMPs) due to its superior fluorescence quenching capacity and unique adsorption characteristics for biomolecules. In this study, fluorescein isothiocyanate-labeled peptide (Pep-FITC) was assembled onto the GO surface through covalent binding to construct a GO-Pep-FITC FRET sensor for sensitive, rapid, and accurate detection of MMP-2 in complex serum samples. Compared to similar GO-based FRET sensors fabricated through physical adsorption, the as prepared ones via covalent binding are significantly more stable under physiological conditions, enabling their detection of MMP-2 with high sensitivity (detection limit: 2.5ng/mL). More importantly, it allows for rapid MMP-2 detection (within 3h) even in complex biological samples with satisfactory accuracy and the relative standard deviation ≤7.03%. Our studies further suggest that such a platform developed here for sensitive, rapid, and accurate detection of biomarkers holds great promise for clinical diagnosis of protease-related diseases.

Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes

Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes.

Chemical biology for understanding matrix metalloproteinase function

The matrix metalloproteinase (MMP) family has long been associated with normal physiological processes such as embryonic implantation, tissue remodeling, organ development, and wound healing, as well as multiple aspects of cancer initiation and progression, osteoarthritis, inflammatory and vascular diseases, and neurodegenerative diseases. The development of chemically designed MMP probes has advanced our understanding of the roles of MMPs in disease in addition to shedding considerable light on the mechanisms of MMP action. The first generation of protease-activated agents has demonstrated proof of principle as well as providing impetus for in vivo applications. One common problem has been a lack of agent stability at nontargeted tissues and organs due to activation by multiple proteases. The present review considers how chemical biology has impacted the progress made in understanding the roles of MMPs in disease and the basic mechanisms of MMP action.

A graphene oxide-peptide fluorescence sensor tailor-made for simple and sensitive detection of matrix metalloproteinase 2

A graphene oxide-peptide based fluorescence sensor has been developed for matrix metalloproteinase 2 (MMP2), and its applicability has been demonstrated by monitoring the concentration of MMP2 secreted by HeLa cells, revealing that HeLa cells with a density of 5.48 × 10(5) cells per mL can produce 22 nM in cell culture media in 24 h.

β-cyclodextrin as the vehicle for forming ratiometric mercury ion sensor usable in aqueous media, biological fluids, and live cells

The selective and sensitive detection methods for toxic transition-metal ions, which are rapid, facile, and applicable to the environmental and biological milieus, are of great importance. In this study, we designed a β-CD-based ratiometric sensor for detecting mercury ions in aqueous media, some biological fluids, and live cells. In this sensing platform, the thiocarbamido-containing probe dye was covalently linked onto the hydrophilic β-CD rim, which is conducive to complexing with metal ion, while the donor dye was anchored inside hydrophobic β-CD cavity via the adamantyl moiety, which is good for avoiding self-aggregation and enhancing the quantum yield of the donor dye. Upon associating with mercury ion, the probe dye undergoes ring-opening process and serves as the energy acceptor and constitutes the FRET system with the donor dye; by this way ratiometric detection of mercury ion in water can be realized with the detection limit of 10 nM. The cyclodextrin plays a crucial role for the sensing system; it not only accommodates both the donor dye and the probe dye which can form FRET system upon addition of Hg(2+) but also makes the sensor water-soluble and cell membrane permeable. This nontoxic sensing platform can be used for mercury ion detection in aqueous medium, biological fluids, and live cells (L929 and Hela). We also found that, upon being taken up by L929 cells, the sensor exhibited no cytotoxicity, and the cell proliferation was not affected.

Upconverting luminescent nanoparticles for use in bioconjugation and bioimaging

Upconverting luminescent nanoparticles (UCNPs) display the unique property of emitting visible light following photoexcitation with near-infrared laser light. This results in features such as virtually zero autofluorescence of (biological) matter and easy separation of the emission peaks from stray light. Other features include rather narrow emission bands, very high chemical stability, the lack of bleaching, and the absence of blinking effects. This article reviews the work performed in the past few years with UCNPs in terms of surface modifications, bioconjugation, and optical (cellular) imaging.