A Fluorescent Probe for Imaging Sirtuin Activity in Living Cells,Based on One‐Step Cleavage of the Dabcyl Quencher

Sirtuins (SIRTs) are a family of NAD⁺‐dependent histone deacetylases. In mammals, dysfunction of SIRTs is associated with age‐related metabolic diseases and cancers, so SIRT modulators are considered attractive therapeutic targets. However, current screening methodologies are problematic, and no tools for imaging endogenous SIRT activity in living cells have been available until now. In this work we present a series of simple and highly sensitive new SIRT activity probes. Fluorescence of these probes is activated by SIRT‐mediated hydrolytic release of a 4‐(4‐dimethylaminophenylazo)benzoyl (Dabcyl)‐based FRET quencher moiety from the ?‐amino group of lysine in a nonapeptide derived from histone H3K9 and bearing a C‐terminal fluorophore. The probe SFP3 detected activities of SIRT1, ‐2, ‐3, and ‐6, which exhibit deacylase activities towards long‐chain fatty acyl groups. We then truncated the molecular structure of SFP3 in order to improve both its stability to peptidases and its membrane permeability, and developed probe KST‐F, which showed specificity for SIRT1 over SIRT2 and SIRT3. We show that KST‐F can visualize endogenous SIRT1 activity in living cells.     

A Molecular Perspective on Sirtuin Activity

The protein acetylation of either the α-amino groups of amino-terminal residues or of internal lysine or cysteine residues is one of the major posttranslational protein modifications that occur in the cell with repercussions at the protein as well as at the metabolome level. The lysine acetylation status is determined by the opposing activities of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs), which add and remove acetyl groups from proteins, respectively. A special group of KDACs, named sirtuins, that require NAD⁺ as a substrate have received particular attention in recent years. They play critical roles in metabolism, and their abnormal activity has been implicated in several diseases. Conversely, the modulation of their activity has been associated with protection from age-related cardiovascular and metabolic diseases and with increased longevity. The benefits of either activating or inhibiting these enzymes have turned sirtuins into attractive therapeutic targets, and considerable effort has been directed toward developing specific sirtuin modulators. This review summarizes the protein acylation/deacylation processes with a special focus on the current developments in the sirtuin research field.     

Activity‐Based Probes for Monitoring Postproline Protease Activity

Postproline proteases constitute a subset of serine proteases involved in the regulation of many signaling events and are emerging as promising therapeutic targets for prevalent diseases, such as diabetes and cancer. Therefore, monitoring their activity in different tissues and diverse physiological states would certainly facilitate the elucidation of their physiological role and the establishment of new therapeutic targets. Here, we have synthesized a dipeptidyl phosphonate activity‐based probe that has proved to be highly selective for a specific postproline protease, prolyl oligopeptidase (POP). Its high sensitivity allows the detection of the endogenous activity of POP both by in‐gel analysis and mass spectrometry. The evidence provided by mass spectrometry for the high selectivity of the synthesized probe opens the possibility of using dipeptidyl phosphonates not only for activity‐based profiling (ABP), but also for other ABP applications like substrate‐based protease identification.     

Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

Aminoacyl‐tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl‐tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic‐code‐expansion strategy to site‐specifically incorporate N^?‐acetyl‐l ‐lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5‐related N‐acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl‐CoA or acetyl‐phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.     

Phospha‐Michael Addition as a New Click Reaction for Protein Functionalization

A new type of click reaction between an alkyl phosphine and acrylamide was developed and applied for site‐specific protein labeling in vitro and in live cells. Acrylamide is a small electrophilic olefin that readily undergoes phospha‐Michael addition with an alkyl phosphine. Our kinetic study indicated a second‐order rate constant of 0.07 m ^?1 s^?1 for the reaction between tris(2‐carboxyethyl)phosphine and acrylamide at pH 7.4. To demonstrate its application in protein functionalization, we used a dansyl–phosphine conjugate to successfully label proteins that were site‐specifically installed with N^?‐acryloyl‐l ‐lysine and employed a biotin–phosphine conjugate to selectively probe human proteins that were metabolically labeled with N‐acryloyl‐galactosamine.     

Site‐Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin

Expansion of the structural diversity of peptide antibiotics was performed through two different methods. Supplementation‐based incorporation (SPI) and stop‐codon suppression (SCS) approaches were used for co‐translational incorporation of isostructural and orthogonal noncanonical amino acids (ncAAs) into the lasso peptide capistruin. Two ncAAs were employed for the SPI method and five for the SCS method; each of them probing the incorporation of ncAAs in strategic positions of the molecule. Evaluation of the assembly by HR‐ESI‐MS proved more successful for the SCS method. Bio‐orthogonal chemistry was used for post‐biosynthetic modification of capistruin congener Cap_Alk10 containing the ncAA Alk (Nε‐Alloc‐L ‐lysine) instead of Ala. A second‐generation Hoveyda–Grubbs catalyst was used for an in vitro metathesis reaction with Cap_Alk10 and an allyl alcohol, which offers options for post‐biosynthetic modifications. The use of synthetic biology allows for the in vivo production of new peptide‐based antibiotics from an expanded amino acid repertoire.     

3‐Substituted Indazoles as Configurationally Locked 4EGI‐1 Mimetics and Inhibitors of the eIF4E/eIF4G Interaction

4EGI‐1, the prototypic inhibitor of eIF4E/eIF4G interaction, was identified in a high‐throughput screening of small‐molecule libraries with the aid of a fluorescence polarization assay that measures inhibition of binding of an eIF4G‐derived peptide to recombinant eIF4E. As such, the molecular probe 4EGI‐1 has potential for the study of molecular mechanisms involved in human disorders characterized by loss of physiological restraints on translation initiation. A hit‐to‐lead optimization campaign was carried out to overcome the configurational instability in 4EGI‐1, which stems from the E‐to‐Z isomerization of the hydrazone function. We identified compound 1 a , in which the labile hydrazone was incorporated into a rigid indazole scaffold, as a promising rigidified 4EGI‐1 mimetic lead. In a structure–activity relationship study directed towards probing the structural latitude of this new chemotype as an inhibitor of eIF4E/eIF4G interaction and translation initiation we identified 1 d , an indazole‐based 4EGI‐1 mimetic, as a new and improved lead inhibitor of eIF4E/eIF4G interaction and a promising molecular probe candidate for elucidation of the role of cap‐dependent translation initiation in a host of pathophysiological states.     

Radiofluorinated Pyrimidine‐2,4,6‐triones as Molecular Probes for Noninvasive MMP‐Targeted Imaging

Matrix metalloproteinases (MMPs) are zinc‐ and calcium‐dependent endopeptidases. Representing a subfamily of the metzincin superfamily, MMPs are involved in the proteolytic degradation of components of the extracellular matrix. Unregulated MMP expression, MMP dysregulation and locally increased MMP activity are common features of various diseases, such as cancer, atherosclerosis, stroke, arthritis, and others. Therefore, activated MMPs are suitable biological targets for the specific visualization of such pathologies, in particular by using radiolabeled MMP inhibitors (MMPIs). The aim of this work was to develop a radiofluorinated molecular probe for noninvasive in vivo imaging for the detection of up‐regulated levels of activated MMPs in the living organism. Fluorinated MMPIs ( 26 , 31 and 38 ) based on the pyrimidine‐2,4,6‐trione lead structure RO 28‐2653 ( 1 ) were synthesized, and their MMP inhibition potency was evaluated in vitro. The radiosynthesis and the in vivo biodistribution of the first ¹⁸F‐labeled prototype, MMP‐targeted tracer [¹⁸F] 26 , suitable for molecular imaging by means of positron emission tomography (PET) were realized.     

Evolving the N‐Terminal Domain of Pyrrolysyl‐tRNA Synthetase for Improved Incorporation of Noncanonical Amino Acids

By evolving the N‐terminal domain of Methanosarcina mazei pyrrolysyl‐tRNA synthetase (PylRS) that directly interacts with tRNA^Pyl, a mutant clone displaying improved amber‐suppression efficiency for the genetic incorporation of N^?‐(tert‐butoxycarbonyl)‐l ‐lysine threefold more than the wild type was identified. The identified mutations were R19H/H29R/T122S. Direct transfer of these mutations to two other PylRS mutants that were previously evolved for the genetic incorporation of N^?‐acetyl‐l ‐lysine and N^?‐(4‐azidobenzoxycarbonyl)‐l ‐δ,?‐dehydrolysine also improved the incorporation efficiency of these two noncanonical amino acids. As the three identified mutations were found in the N‐terminal domain of PylRS that was separated from its catalytic domain for charging tRNA^Pyl with a noncanonical amino acid, they could potentially be introduced to all other PylRS mutants to improve the incorporation efficiency of their corresponding noncanonical amino acids. Therefore, it represents a general strategy to optimize the pyrrolysine incorporation system‐based noncanonical amino‐acid mutagenesis.     

Design of a probe based on poly(glycidyl methacrylate‐co‐vinylferrocene)‐coated Pt electrode for electrochemical detection of PTEN gene in PCR amplified samples from prostate tissues

In this study, a new probe based on immobilization of amino linked oligonucleotide (NH₂‐linked DNA) on poly(glycidyl methacrylate‐co‐vinylferrocene)‐coated Pt electrode was fabricated for the electrochemical detection of PTEN gene from human prostate tissues. The experimental parameters such as DNA immobilization time, DNA concentration, and target concentration were optimized. The selectivity of the NH₂‐linked DNA probe was assessed with mismatch (MM) and noncomplementary (NC) sequences. The applicability of the NH₂‐linked DNA probe to the PCR amplified samples correspond to PTEN gene from prostate tissues was evaluated. The immobilization of DNA on the copolymer was confirmed by FTIR, AFM, CV and DPV analysis. The PCR products were also identified by using agarose gel electrophoresis. The prepared probe indicated a linear range (10–100 μg mL^?1) with a detection limit (4.7 μg mL^?1) and a good selectivity of the NH₂‐linked DNA probe toward target DNA sequence. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40638.     

Synthesis and Evaluation of a Series of Long‐Acting Glucagon‐Like Peptide‐1 (GLP‐1) Pentasaccharide Conjugates for the Treatment of Type 2 Diabetes

The present study details the development of a family of novel D ‐Ala⁸ glucagon‐like peptide‐1 (GLP‐1) peptide conjugates by site specific conjugation to an antithrombin III (ATIII) binding carrier pentasaccharide through tetraethylene glycol linkers. All conjugates were found to possess potent insulin‐releasing activity. Peptides with short linkers (<25 atoms) conjugated at Lys³⁴ and Lys³⁷ displayed strong GLP‐1 receptor (GLP‐1‐R) binding affinity. All D ‐Ala⁸GLP‐1 conjugates exhibited prominent glucose‐lowering action. Biological activity of the Lys³⁷ short‐linker peptide was evident up to 72 h post‐injection. In agreement, the pharmacokinetic profile of this conjugate (t_1/2, 11 h) was superior to that of the GLP‐1‐R agonist, exenatide. Once‐daily injection of the Lys³⁷ short‐linker peptide in ob/ob mice for 21 days significantly decreased food intake and improved HbA_1c and glucose tolerance. Islet size was decreased, with no discernible change in islet number. The beneficial effects of the Lys³⁷ short‐linker peptide were similar to or better than either exenatide or liraglutide, another GLP‐1‐R agonist. In conclusion, GLP‐1 peptides conjugated to an ATIII binding carrier pentasaccharide have a substantially prolonged bioactive profile compatible for possible once‐weekly treatment of type 2 diabetes in humans.     

Preparation of block copolymers via metal‐free visible‐light‐induced ATRP for the detection of lead ions

Polyacrylamide‐b‐poly(methacrylic acid) was prepared on the surface of Au electrode (Au/PAM/PMAA) for Pb²⁺ ion electrochemical sensing via metal‐free visible‐light‐induced atom transfer radical polymerization, which was very simple, convenient, and environmentally friendly. Au/PAM/PMAA was carefully examined by cyclic voltammetry, electrochemical impedance spectroscopy, and X‐ray photoelectron spectroscopy. Further, Au/PAM/PMAA was successfully used for the determination of Pb²⁺ ion by differential pulse anodic stripping voltammetry. Under the optimal conditions, a linear response from 1.0 × 10^?11 to 1.0 × 10^?4 mol/L with detection limit of 2.5 × 10^?12 mol/L (S/N = 3) was achieved from the results of experiments. Comparing with similar Pb²⁺ sensors, the broader linear range and lower detection limit suggested the promising prospect of Au/PAM/PMAA. In a word, the work of this article had an important significance for the polymer‐modified electrodes and the sensitive detection of Pb²⁺. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018 , 135, 45863.     

Activity of α‐Aminoadipate Reductase Depends on the N‐Terminally Extending Domain

L ‐α‐Aminoadipic acid reductases catalyze the ATP‐ and NADPH‐dependent reduction of L ‐α‐aminoadipic acid to the corresponding 6‐semialdehyde during fungal L ‐lysine biosynthesis. These reductases resemble peptide synthetases with regard to their multidomain composition but feature a unique domain of elusive function—now referred to as an adenylation activating (ADA) domain—that extends the reductase N‐terminally. Truncated enzymes based on NPS3, the L ‐α‐aminoadipic acid reductase of the basidiomycete Ceriporiopsis subvermispora, lacking the ADA domain either partially or entirely were tested for activity in vitro, together with an ADA‐adenylation didomain and the ADA domainless adenylation domain. We provide evidence that the ADA domain is required for substrate adenylation: that is, the initial step of the catalytic turnover. Our biochemical data are supported by in silico modeling that identified the ADA domain as a partial peptide synthetase condensation domain.     

Liposome‐Based in Vitro Evolution of Aminoacyl‐tRNA Synthetase for Enhanced Pyrrolysine Derivative Incorporation

Methanosarcina species pyrrolysyl‐tRNA synthetase (PylRS) attaches Pyl to its cognate amber suppressor tRNA. The introduction of two mutations (Y384F and Y306A) into PylRS was previously shown to generate a mutant, designated LysZ‐RS, that was able to attach N‐benzyloxycarbonyl‐L ‐lysine (LysZ) to its cognate tRNA. Despite the potential of LysZ derivatives, further LysZ‐RS engineering has not been performed; consequently, we aimed to generate LysZ‐RS mutants with improved LysZ incorporation activity through in vitro directed evolution. Using a liposome‐based in vitro compartmentalization (IVC) approach, we screened a randomly mutagenized gene library of LysZ‐RS and obtained a mutant that showed increased LysZ incorporation activity both in vitro and in vivo. The ease and high flexibility of liposome‐based IVC should enable the evolution of not only LysZ‐RS that can attach various LysZ derivatives but also of other enzymes involved in protein translation.     

Versatile Substrates and Probes for IgA1 Protease Activity

Bacterial meningitis is a severe infectious disease with high mortality. Gram‐positive and Gram‐negative bacteria that cause meningitis secrete immunoglobulin A1 (IgA1) proteases to assist in mucosal colonization, invasion, and immune evasion. IgA1 proteases have unique selectivity, with few reported substrates other than IgA1 from human tissue. Here we describe the design, characterization, and application of peptide substrates for diverse IgA1 proteases from Neisseria, Haemophilus, and Streptococcus bacteria. IgA1 proteases from diverse strains showed unexpected selectivity profiles among peptide substrates derived from autoproteolytic sites. A fluorescence probe derived from one of these peptides was used to quantitate IgA1 protease activity in buffer and in human cerebrospinal fluid; it was able to detect recombinant Haemophilus influenzae type 1 IgA1 protease at less than 1 μg mL^?1. We also used the probe to establish the first high‐throughput screen for IgA1 protease inhibitors. This work provides tools that will help investigate the roles of IgA1 proteases in bacterial colonization, immune evasion, and infection.     

Expanding the Applicability of the Metal Labeling of Biomolecules by the RIKEN Click Reaction: A Case Study with Gallium‐68 Positron Emission Tomography

Radiolabeled biomolecules with short half‐life times are of increasing importance for positron emission tomography (PET) imaging studies. Herein, we demonstrate an improved and generalized method for synthesizing a [radiometal]‐unsaturated aldehyde as a lysine‐labeling probe that can be easily conjugated into various biomolecules through the RIKEN click reaction. As a case study, ⁶⁸Ga‐PET imaging of U87MG xenografted mice is demonstrated by using the ⁶⁸Ga‐DOTA‐RGDyK peptide, which is selective to α_Vβ₃ integrins.     

A fluorescent chemosensor based on optically active 2,2′‐binaphtho‐20‐crown‐6 for metal ions

A chiral conjugated polymer can be obtained by the polymerization of (S)‐6,6′‐dibromo‐2,2′‐binaphtho‐20‐crown‐6 and 1,4‐divinyl‐2,5‐dibutoxybenzene via a palladium‐catalyzed Heck cross‐coupling reaction. The chiral conjugated polymer shows strong green‐blue fluorescence. The responsive properties of the chiral polymer to metal ions were investigated using fluorescence and UV‐visible absorption spectra. K⁺, Pb²⁺, Cd²⁺ and Ba²⁺ enhance the fluorescence of the polymer; in contrast, Hg²⁺ causes effective quenching of the fluorescence of the polymer. The obvious influences on the fluorescence indicate that the 2,2′‐binaphtho‐20‐crown‐6 moiety plays an important role in fluorescence recognition for Hg²⁺ due to the effective photo‐induced electron transfer or charge transfer between the conjugated polymer backbone and the receptor ions. The responsive properties of the polymer to metal ions show that the chiral conjugated polymer incorporating 2,2′‐binaphtho‐20‐crown‐6 moieties in the main‐chain backbone as recognition sites can act as an excellent fluorescent probe for the sensitive detection of Hg²⁺. Copyright © 2010 Society of Chemical Industry     

Cashew nut shell liquid based t‐BOC protected alternating “high ortho” copolymer as a possible e‐beam resist: Characterization using multi‐dimensional NMR spectroscopy

A cardanol/m‐cresol‐based copolymer was esterified using di‐tert‐butyl dicarbonate (t‐BOC), which makes it a suitable candidate as a possible e‐beam resists. This work reports a full characterization of the product using the techniques of FTIR and UV–Visible spectroscopy, one dimensional ¹H NMR, ¹³C NMR, DEPT‐135. Two dimensional NMR experiments such as, COSY, HSQC, and HMBC have been employed for exhaustive probing of the microstructural details of this derivatized copolymer. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Non‐natural Peptide Triazole Antagonists of HIV‐1 Envelope gp120

We investigated the derivation of non‐natural peptide triazole dual receptor site antagonists of HIV‐1 Env gp120 to establish a pathway for developing peptidomimetic antiviral agents. Previously we found that the peptide triazole HNG‐156 [R‐I‐N‐N‐I‐X‐W‐S‐E‐A‐M‐M‐CONH₂, in which X=ferrocenyltriazole‐Pro (FtP)] has nanomolar binding affinity to gp120, inhibits gp120 binding to CD4 and the co‐receptor surrogate mAb 17b, and has potent antiviral activity in cell infection assays. Furthermore, truncated variants of HNG‐156, typified by UM‐24 (Cit‐N‐N‐I‐X‐W‐S‐CONH₂) and containing the critical central stereospecific ^LX‐^LW cluster, retain the functional characteristics of the parent peptide triazole. In the current work, we examined the possibility of replacing natural with unnatural residue components in UM‐24 to the greatest extent possible. The analogue with the critical “hot spot” residue Trp 6 replaced with L ‐3‐benzothienylalanine (Bta) (KR‐41), as well as a completely non‐natural analogue containing D ‐amino acid substitutions outside the central cluster (KR‐42, ^DCit‐^DN‐^DN‐^DI‐X‐Bta‐^DS‐CONH₂), retained the dual receptor site antagonism/antiviral activity signature. The results define differential functional roles of subdomains within the peptide triazole and provide a structural basis for the design of metabolically stable peptidomimetic inhibitors of HIV‐1 Env gp120.     

Rational Design of a Ratiometric Fluorescent Probe Based on Arene–Metal‐Ion Contact for Endogenous Hydrogen Sulfide Detection in Living Cells

We report the design and development of a fluorescent Cd^II ion complex that is capable of the ratiometric detection of H₂S in living cells. This probe exploits the metal‐ion‐induced emission red shift resulting from direct contact between the aromatic ring of a fluorophore and a metal ion (i.e., arene–metal‐ion or “AM” contact). The Cd^II complex displays a large emission blue shift upon interaction with H₂S as the Cd^II‐free ligand is released by the formation of cadmium sulfide. Screening of potential ligands and fluorophores led to the discovery of a pyronine‐type probe, 6? Cd^II, that generated a sensitive and rapid ratio value change upon interaction with H₂S, without interference from the glutathione that is abundant in the cell. The membrane‐impermeable 6? Cd^II was successfully translocated into live cells by using an oligo‐arginine peptide and pyrenebutylate as carriers. As such, 6? Cd^II was successfully applied to the ratiometric detection of both exogenous and endogenous H₂S produced by the enzymes in living cells, thus demonstrating the utility of 6? Cd^II in biological fluorescence analysis.