Protease-triggered photosensitizing beacon based on singlet oxygen quenching and activation

We report a new concept for type-II photosensitization, based on incorporating the photosensitizer (PS) and a singlet-oxygen (1O2) quenching/scavenging molecule onto a disease-targeting linker, such that the PS becomes activatable by light only when targeting has occurred. In this first proof-of-concept report, a model photosensitizing beacon was synthesized containing a pyropheophorbide as the PS and a carotenoid as the 1O2 quencher. These were kept in close proximity by the self-folding of a caspase-3-specific peptide sequence. Upon caspase-3-induced cleavage, the 1O2 production increased markedly, as measured directly by 1O2 near-infrared luminescence and lifetime measurements.     

Exploring the Condensation Reaction between Aromatic Nitriles and Amino Thiols To Optimize In Situ Nanoparticle Formation for the Imaging of Proteases and Glycosidases in Cells

The condensation reaction between 6-hydroxy-2-cyanobenzothiazole (CBT) and cysteine has been shown for various applications such as site-specific protein labelling and in vivo cancer imaging. This report further expands the substrate scope of this reaction by varying the substituents on aromatic nitriles and amino thiols and testing their reactivity and ability to form nanoparticles for cell imaging. The structure–activity relationship study leads to the identification of the minimum structural requirement for the macrocyclization and assembly process in forming nanoparticles. One of the scaffolds made of 2-pyrimidinecarbonitrile and cysteine joined by a benzyl linker was applied to design fluorescent probes for imaging caspase-3/7 and β-galactosidase activity in live cells. These results demonstrate the generality of this system for imaging hydrolytic enzymes.     

Quantitative kinetics of proteolytic enzymes determined by a surface concentration-based assay using peptide arrays

Peptide arrays have emerged as a key technology for drug discovery, diagnosis, and cell biology. Despite the promise of these arrays, applications of peptide arrays to quantitative analysis of enzyme kinetics have been limited due to the difficulty in obtaining quantitative information of enzymatic reaction products. In this study, we developed a new approach for the quantitative kinetics analysis of proteases using fluorescence-conjugated peptide arrays, a surface concentration-based assay with solid-phase peptide standards using dry-off measurements, and compared it with an applied concentration-based assay. For fabrication of the peptide arrays, substrate peptides of cMMP-3, caspase-3, caspase-9, and calpain-1 were functionalized with TAMRA and cysteine, and were immobilized onto amine-functionalized arrays using a heterobifunctional linker, N-[γ-maleimidobutyloxy]succinimide ester. The proteolytic activities of the four enzymes were quantitatively analyzed by calculating changes induced by enzymatic reactions in the concentrations of peptides bound to array surfaces. In addition, this assay was successfully applied for calculating the Michaelis constant (K(m,surf)) for the four enzymes. Thus, this new assay has a strong potential for use in the quantitative evaluation of proteases, and for drug discovery through kinetics studies including the determination of K(m) and V(max).     

Design and Synthesis of a Novel Peptidomimetic Inhibitor of Caspase-3

Introduction Thecaspase(cysteinyl aspartateprotease)family representsaclassofintracellularproteases,playinga criticalroleinapoptoticcelldeathpathwaysandactiva tionofpro inflammatorycytokines[1].Theirenzymatic propertiesaregovernedbyanearlyabsolutespecific…     

A novel linker for solid-phase synthesis cleavable under neutral conditions

A novel linker cleavable under neutral conditions has been developed for the solid-phase synthesis of base-labile compounds. The linker is comprised of a 3-azidomethyl-4-hydroxybenzyl alcohol moiety, and the azidomethyl group in the linker is readily converted to an aminomethyl group by treatment with a phosphine reagent in the presence of water to result in an intramolecular cyclization to release the compounds. Using the linker, a base-labile dinucleoside methyl phosphate was synthesized on a highly cross-linked polystyrene (HCP) support and cleaved successfully from the resin without decomposition of the product.     

Cu2+ -mediated assembly of the minor groove binders on the DNA template with sequence selectivity

The ligands (Bpy-H, 5) have been designed to connect the Hoechst33258 skeleton for DNA binding and 2,2'-bipyridine for Cu(2+) complexation. It has been revealed that the new Hoechst ligand long Bpy-H (5L) having a long linker exhibits Cu(2+)-mediated assembly on the DNA template having two A(3)T(3) sites in a selective manner depending on the length of the linker of the ligand as well as on the distance between the two A(3)T(3) sites of DNA. [reaction: see text]     

Detection of mitochondrial caspase activity in real time in situ in live cells.

Apoptosis plays an important role in many physiological and pathological processes. The initiation and execution of the cell death program requires activation of multiple caspases in a stringently temporal order. Here we describe a method that allows real-time observation of caspase activation in situ in live cells based on fluorescent resonance energy transfer (FRET) measurement using the prism and reflector imaging spectroscopy system (PARISS). When a fusion protein consisting of CFP connected to YFP via an intervening caspase substrate that has been targeted to a specific subcellular location is excited with a light source whose wavelength matches the cyan fluorescent protein (CFP) excitation peak, the energy absorbed by the CFP fluorophore is not emitted as fluorescence. Instead, the excitation energy is absorbed by the nearby yellow fluorescent protein (YFP) fluorophore that is covalently linked to CFP through a short peptide containing the caspase substrate. Cleavage of the linker peptide by caspases results in loss of FRET due to the separation of CFP and YFP fluorophores. Using a mitochondrially targeted CFP-caspase 3 substrate-YFP construct (mC3Y), we demonstrate for the first time that there is caspase-3-like activity in the mitochondrial matrix of some cells at very late stage of apoptosis.     

Evaluation of a new linker system cleaved using samarium(II) iodide. Application in the solid phase synthesis of carbonyl compounds

A new linker design for solid phase synthesis has been developed that is cleaved under mild, neutral conditions using samarium(II) iodide. The feasibility of the linker approach has been illustrated in the solid phase synthesis of ketones and amides using an oxygen linker. Insights into the mechanism of the samarium(II) iodide cleavage reaction are described and the potential of a sequential cleavage carbon-carbon bond forming process is assessed.     

Recent advances in the development of activatable multifunctional probes for in vivo imaging of caspase-3

Caspases are a family of proteases that play critical roles in controlling inflammation and cell death.Apoptosis is a caspase-3 mainly controlled behavior to avoid inflammation and damage to surrounding cells,whereas anomalistic cell apoptosis may be associated with many diseases.The detection and imaging of caspase-3 will be of great significance in evaluating the early therapeutic effect of tumors.Developing smart fluorescent probes may be helpful for the visualization of the rapeutic effect compared with "always on" probes.Thus,more and more works toward activatable fluorescent probes for caspase-3 imaging have been reported.In addition,multifunctional probes have also been designed to further improve the imaging of caspase-3.Herein,this review systematically summarized the representative wo rk of caspase-3 from the perspective of molecular design that it will play a guiding role in the design of probes that respond to caspase-3.Also,challenges and perspectives toward the field for imaging of cell apoptosis(caspase-3) are also discussed.     

A Useful Disulfide Linker for Single‐Bead Analysis of Peptide Libraries

A disulfide‐linker for conventional peptide synthesis, attached to a PEGA‐resin, has been developed. Reductive hydrolysis cleaves the linker within minutes, liberating the synthesized peptide for rapid sequencing by tandem mass spectrometry. The method has been tested for ten peptides in a single‐bead fashion.     

Cluster Linker Approach: Preparation of a Luminescent Porous Framework with NbO Topology by Linking Silver Ions with Gold(I) Clusters

A cluster‐based luminescent porous metal–organic framework has been constructed through a “cluster linker” approach. The luminescent gold(I) cluster, prefunctionalized with pyrazinyl groups, was used as a cluster linker, similar to an organic linker, to connect silver ions in order to form a 3D framework. 1D channels with 1.1 nm diameter were observed in the framework. The cluster with its intrinsic luminescence was incorporated into a porous framework to give a luminescent bifunctional NbO net. This MOF shows solvatochromic behavior, and the interactions between solvent molecules and silver ions inside the channels account for the changes in absorption and emission spectra.     

Chemiluminescent determination of the activity of caspase-3 using a specific peptide substrate and magnetic beads

We report on a new scheme for the determination of the activity of caspase-3 using a specific peptide labeled with N-(4-aminobutyl)-N-ethylisoluminol (ABEI) as a chemiluminescent (CL) probe and on the development of magnetic separation technology. Firstly, the ABEI-labeled and biotinylated peptide was prepared and conjugated to streptavidin-coated magnetic beads (MBs) to form f-MBs (functionalized magnetic beads). The f-MBs contain a site (DEVD, Asp-Glu-Val-Asp) that is cleaved by caspase-3. Upon cleavage, the terminal residue attached to ABEI can dissociate from the f-MBs and can be used for CL detection. CL intensity is linearly related to the concentration of caspase-3 in the range 1.0 to 600 ng mL^?1, with a detection limit of 0.3 ng mL^?1. The relative standard deviation of the assay is 3.6 % at a level of 50 ng mL^?1 of caspase-3 (for n?=?11). The CL assay has been applied to the determination of caspase-3 in Jurkat cell extract with recoveries between 96.6 % and 106.1 % (n?=?5).

A novel heterobifunctional linker for facile access to bioconjugates

A convenient synthesis of a novel heterobifunctional linker molecule is described. The linker contains a thiol-reactive nitropyridyl disulfide group (Npys) and an aldehyde-reactive aminooxy group with a propensity to form disulfide and oxime linkages. The utility of the linker molecule to cross-link different biomolecules has been demonstrated by employing it in the efficient preparation of a peptide-oligonucleotide conjugate. The linker reported herein could be a useful tool for cross-coupling of different but appropriately functionalised biomolecules.     

Solid-phase approach to tetrahydroquinolones using a sulfur linker cleaved by SmI2

[reaction: see text] A sulfur alpha-heteroatom-substituted carbonyl (HASC) linker has been utilized in a solid-phase approach to tetrahydroquinolones. The route illustrates the compatibility of the linker system with palladium-catalyzed transformations and its utility for library synthesis. The linker is cleaved by electron transfer from samarium(II) iodide.     

A new phenoxyacetate-based linker system for the solid-phase synthesis of oligosaccharides

[structure: see text]. A novel linker system has been designed, and its first application to solid-phase oligosaccharide synthesis is described. The use of the highly reactive o-nitro-phenoxyacetate linker allows a fast and quantitative cleavage using mild basic conditions. This method combined with the trichloroacetimidate glycosylation exhibits highly promising results as demonstrated for the synthesis of tetrasaccharide 1 (n = 3) containing glucose beta(1 --> 4) and beta(1 --> 6) linkages.     

Single‐Crystal to Single‐Crystal Linker Substitution,Linker Place Exchange,and Transmetalation Reactions in Interpenetrated Pillared–Bilayer Zinc(II) Metal–Organic Frameworks

A twofold interpenetrated pillared–bilayer framework, {[Zn₃( L )₂( L₂ )(DMF)] ? (18DMF)(6H₂O)}_n ( 1 ), has been synthesized from the ligands tris(4′‐carboxybiphenyl)amine ( H₃L ) and 1,2‐bis(4‐pyridyl)ethylene ( L₂ ). The structure contains [Zn₃(COO)₆] secondary building units (SBUs), in which three Zn^II ions are almost linear with carboxylate bridging. This framework undergoes reversible pillar linker substitution reactions at the terminal Zn^II centers with three different dipyridyl linkers of different lengths to afford three daughter frameworks, 2 – 4 . Frameworks 2 – 4 are interconvertible through reversible linker substitution reactions. Also, competitive linker‐exchange experiments show preferential incorporation of linker L₃ in the parent framework 1 . The larger linker L₅ does not undergo such substitution reactions and framework 5 , which contains this linker, can be synthesized solvothermally as a twofold interpenetrated structure. Interestingly, when framework 5 is dipped in a solution of L₃ in DMF, linker substitution takes place as before, but linker L₅ now moves and diagonally binds two Zn^II centers to afford 6 as a nonpenetrated single framework. This linker place exchange reaction is unprecedented. All of these reactions take place in a single‐crystal to single‐crystal (SC‐SC) manner, and have been observed directly through X‐ray crystallography. In addition, each 3D framework undergoes complete copper(II) transmetalation.     

Design of new bidentate ligands constructed of two Hoechst 33258 units for discrimination of the length of two A3T3 binding motifs

[structure: see text] The aim of this study is to develop bidentate minor-groove binders that bind the double binding motifs cooperatively. The new bidentate ligands (1) have been designed by connecting two Hoechst 33258 units with a polyether linker for cooperative binding with two remote A3T3 sites of DNA. The linker is introduced to the benzimidazole ring so that it is located at the convex side of the Hoechst unit. DNA binding affinity of the ligands was evaluated by measuring surface plasmon resonance (SPR), circular dichroism, and fluorescence spectra. Interestingly, the bidentate ligands (1) did not show affinity to DNA1 with a single A3T3 motif but showed selective affinity to DNA2 with two A3T3 motifs. The Long Bis-H (1L) having a long polyether linker showed specific binding to DNA2(6) with two A3T3 motifs separated by six nonbinding base pairs. The Long Bis-H (1L) has also shown specific binding to the three-way junction DNA4 with two A3T3 motifs. This study has demonstrated that DNA with double binding motifs can be selectively recognized by the newly designed bidentate ligands.     

An optimized activity-based probe for the study of caspase-6 activation

Although significant efforts have been made to understand the mechanisms of caspase activation during apoptosis, many questions remain regarding how and when executioner caspases get activated. We describe the design and synthesis of an activity-based probe that labels caspase-3/-6/-7, allowing direct monitoring of all executioner caspases simultaneously. This probe has enhanced in vivo properties and reduced cross-reactivity compared to our previously reported probe, AB50. Using this probe, we find that caspase-6 undergoes a conformational change and can bind substrates even in the absence of cleavage of the proenzyme. We also demonstrate that caspase-6 activation does not require active caspase-3/-7, suggesting that it may autoactivate or be cleaved by other proteases. Together, our results suggest that caspase-6 activation proceeds through a unique mechanism that may be important for its diverse biological functions.     

An improved aldehyde linker for the solid phase synthesis of hindered amides

A novel aldehyde dual-linker system has been developed for the solid phase synthesis of sterically hindered amides. The linker [5-(4-formyl-3-hydroxyphenoxy)pentanoic acid] exploits an intramolecular oxygen-nitrogen acyl transfer mechanism to prepare compounds that are unattainable with current commercially available linkers. A dual linker system, exploiting the hyper-acid labile Sieber amide linker as part of the construct, enabled the initial reductive alkylation reactions of hindered amines and their subsequent acylation with a range of carboxylic acids with varying stereoelectronic properties to be monitored. Simple acylation conditions (HBTU/HOBt/NMM) sufficed to provide near quantitative reaction of test acids with support-bound hindered amines, reaction conditions which failed when commercial linkers were used.     

Trinuclear adducts of cobalt diketonates based on di-<Emphasis Type="Italic">o</Emphasis>-quinone with a bis(chelate) linker: Computational search for spin qubits

Computer modeling (DFT UB3LYP*/6-311++G(d,p)) of trinuclear cobalt diketonate adducts based on di-o-quinone containing a bis(chelate) linker has been performed. Calculations predict the stability of the compounds to dissociation into the initial molecules. It has been demonstrated that rational choice of the metal atom of the bis(chelate) linker and the type of ancillary ligand of the terminal moieties makes it possible to find a system exhibiting the properties of logical elements of quantum computers—spin qubits.