Remarkable Effect of Chalcogen Substitution on an Enzyme Mimetic for Deiodination of Thyroid Hormones

Iodothyronine deiodinases are selenoenzymes which regulate the thyroid hormone homeostasis by catalyzing the regioselective deiodination of thyroxine (T4). Synthetic deiodinase mimetics are important not only to understand the mechanism of enzyme catalysis, but also to develop therapeutic agents as abnormal thyroid hormone levels have implications in different diseases, such as hypoxia, myocardial infarction, critical illness, neuronal ischemia, tissue injury, and cancer. Described herein is that the replacement of sulfur/selenium atoms in a series of deiodinase mimetics by tellurium remarkably alters the reactivity as well as regioselectivity toward T4. The tellurium compounds reported in this paper represent the first examples of deiodinase mimetics which mediate sequential deiodination of T4 to produce all the hormone derivatives including T0 under physiologically relevant conditions.     

Substrate mimetics in protease catalysis: characteristics,kinetics, and synthetic utility

This article reviews the latest developments in protease-catalyzed peptide synthesis focusing on the use of substrate mimetics. The substrate mimetics approach takes advantage of the characteristic of this novel type of substrates to direct the enzyme to recognize an alternative site on the acyl donor, i.e. the site-specific ester leaving group, mediating the acceptance of originally poorly reactive acyl moieties. At first the kinetics and catalytic mechanism of substrate mimetics-mediated reactions are discussed on the basis of hydrolysis, peptide synthesis, protein-ligand docking, and molecular dynamics studies. By the example of the Glu-specific V8 protease and the aromatic amino acid-specific chymotrypsin both the empirical and computer-aided design of specific substrate mimetics is described. The influence of the leaving group specifically recognized by the enzyme is also considered. The benefits of these artificial substrates over common acyl donor components are illustrated by selected synthesis reactions of small peptides, peptide isosteres, non-peptidic carboxylic acid amides, and the coupling of peptide fragments at non-specific ligation sites resulting in biologically active peptide products. Finally, this review focuses on critical syntheses that uses specific-amino acid-containing peptides as the reactants of ligation. Based on these, the restrictions of the substrate mimetics approach is critically discussed and techniques to their overcoming are presented.     

Fluorescent Mimetics of CMP‐Neu5Ac Are Highly Potent,Cell‐Permeable Polarization Probes of Eukaryotic and Bacterial Sialyltransferases and Inhibit Cellular Sialylation

Oligosaccharides of the glycolipids and glycoproteins at the outer membranes of human cells carry terminal neuraminic acids, which are responsible for recognition events and adhesion of cells, bacteria, and virus particles. The synthesis of neuraminic acid containing glycosides is accomplished by intracellular sialyl transferases. Therefore, the chemical manipulation of cellular sialylation could be very important to interfere with cancer development, inflammations, and infections. The development and applications of the first nanomolar fluorescent inhibitors of sialyl transferases are described herein. The obtained carbohydrate‐nucleotide mimetics were found to bind all four commercially available and tested eukaryotic and bacterial sialyl transferases in a fluorescence polarization assay. Moreover, it was observed that the anionic mimetics intruded rapidly and efficiently into cells in vesicles and translocated to cellular organelles surrounding the nucleus of CHO cells. The new compounds inhibit cellular sialylation in two cell lines and open new perspectives for investigations of cellular sialylation.     

Biaryl amino acid templates in place of D-Pro-L-Pro in cyclic beta-hairpin cationic antimicrobial peptidomimetics

The turn-forming D-Pro-L-Pro template has been frequently used to promote regular beta-hairpin conformations in cyclic protein epitope mimetics. Here the use of three isomeric biaryl templates has been studied as alternatives to D-Pro-L-Pro in the preparation of beta-hairpin peptidomimetics. The o,o'- o,m'- and m,m'-isomers of carboxymethyl- and aminomethyl-substituted biaryl templates have been incorporated into novel macrocyclic mimics of the naturally occurring cationic antimicrobial peptide protegrin I. The presence of the o-carboxymethyl-o'-aminomethyl-biaryl template within the macrocyclic peptide resulted in the appearance of slowly interconverting atropisomers. Although none of the resulting mimetics adopted stable beta-hairpin structures in aqueous solution, they all nevertheless retained a significant antimicrobial activity against Gram positive and Gram negative bacteria. These mimetics provide interesting starting points for an optimization program in the search for potent and novel antimicrobial compounds.     

Vacancy‐Engineered Nanoceria: Enzyme Mimetic Hotspots for the Degradation of Nerve Agents

Organophosphorus‐based nerve agents, such as paraoxon, parathion, and malathion, inhibit acetylcholinesterase, which results in paralysis, respiratory failure, and death. Bacteria are known to use the enzyme phosphotriesterase (PTE) to break down these compounds. In this work, we designed vacancy‐engineered nanoceria (VE CeO₂ NPs) as PTE mimetic hotspots for the rapid degradation of nerve agents. We observed that the hydrolytic effect of the nanomaterial is due to the synergistic activity between both Ce³⁺ and Ce⁴⁺ ions located in the active site‐like hotspots. Furthermore, the catalysis by nanoceria overcomes the product inhibition generally observed for PTE and small molecule‐based PTE mimetics.     

Design and synthesis of alpha-helical peptides and mimetics

The alpha-helix is the most abundant secondary structural element in proteins and is an important structural domain for mediating protein-protein and protein-nucleic acid interactions. Strategies for the rational design and synthesis of alpha-helix mimetics have not matured as well as other secondary structure mimetics such as strands and turns. This perspective will focus on developments in the design, synthesis and applications of alpha-helices and mimetics, particularly in the last 5 years. Examples where synthetic compounds have delivered promising biological results will be highlighted as well as opportunities for the design of mimetics of the type I alpha-helical antifreeze proteins.     

Enzymatic coupling of specific peptides at nonspecific ligation sites: effect of Asp189Glu mutation in trypsin on substrate mimetic-mediated reactions

Two main drawbacks seriously restrict the synthetic value of proteases as reagents in peptide fragment coupling: (i) native proteolytic activity and, thus, risk of undesired peptide cleavage; (ii) limited enzyme specificities restricting the amino acid residues between which a peptide bond can be formed. While the latter can be overcome by the use of substrate mimetics achieving peptide bond formation at nonspecific ligation sites, the risk of proteolytic cleavage still remains and hinders the wide acceptance of this powerful strategy for peptide coupling. This paper reports on the effect of the trypsin point mutant Asp189Glu on substrate mimetic-mediated reactions. The effect of this mutation on the steady-state hydrolysis of substrate mimetics of the 4-guanidinophenyl ester type and on trypsin-specific Lys- and Arg-containing peptides was investigated. The results were confirmed by enzymatic coupling reactions using substrate mimetics as the acyl donor and specific amino acid-containing peptides as the acyl acceptor. The competition assay verifies the predicted shift in substrate preference from Lys and Arg to the substrate mimetics and, thus, from cleavage to synthesis of peptide bonds. The combination of results obtained qualifies the trypsin mutant D189E as the first substrate mimetic-specific peptide ligase.     

Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA

A method is described for the NMR-based screening for the discovery of aminoglycoside mimetics that bind to Escherichia coli A-site RNA. Although aminoglycosides are clinically useful, they exhibit high nephrotoxicity and ototoxicity, and their overuse has led to the development of resistance to important microbial pathogens. To identify a new series of aminoglycoside mimetics that could potentially overcome the problems associated with toxicities and resistance development observed with the aminoglycosides, we have prepared large quantities of E. coli 16 S A-site RNA and conducted an NMR-based screening of our compound library in search for small-molecule RNA binders against this RNA target. From these studies, several classes of compounds were identified as initial hits with binding affinities in the range of 70 microM to 3 mM. Lead optimization through synthetic modifications of these initial hits led to the discovery of several small-molecule aminoglycoside mimetics that are structurally very different from the known aminoglycosides. Structural models of the A-site RNA/ligand complexes were prepared and compared to the three-dimensional structures of the RNA/aminoglycoside complexes.     

树状多肽的合成及应用

树状多肽作为树枝状大分子的一种,具有不同于链状多肽的独特理化特性,在生物学领域中具有广泛的应用.本文简要综述了树状多肽的合成方法,及其在诱导免疫反应、生物分子模拟、免疫诊断试剂、人工酶、药物及基因载体等方面的应用.     

From Cycloolefins to Linear C2-Symmetrical 1,4-Diamino-2,3-diol Building Blocks—Peptide Mimetics,Biocatalysis, and Pinacol Coupling of α-Amino Aldehydes

Technical olefins and azodicarbonic ester are the starting materials for C₂-symmetrical C₁₆ and C₁₂ 1,4-diamino-2,3-diol building blocks (see structure), which are of interest for a variable access to potentially bioactive compounds (peptide mimetics, enzyme inhibitors). MOM = methoxymethyl.     

Novel and Convenient Method for the Preparation of Phosphonate Peptides and Phosphonamidate Peptides

Phosphonate and phosphonamidate peptides are phosphorus analogues of natural peptides. They have been great used as stable mimetics of tetrahedral transition states as enzyme inhibitors and as haptens for catalytic antibody research in recent years. Although several methods are available for the preparation of phosphonate peptides and phosphonamidate peptides, all of them use phosphonic acid derivatives as starting materials. The overall yields from the synthesis of phosphonic acid derivatives to desired peptides are not satisfactory in most cases.     

On the rational design of substrate mimetics: The function of docking approaches for the prediction of protease specificities

The behaviour of substrate mimetics in mediating the acceptance of nonspecific acyl moieties by proteases has been investigated as a direct function of their site-specific ester leaving groups. In this contribution we report on a computational approach to rationalise this interplay and to predict the power of a potential ester moiety to act as a suitable substrate mimetic for a given enzyme by means of an automated docking procedure. Investigations with seven distinct substrate mimetics and two proteases, subtilisin and chymotrypsin, show a clear correlation between the theoretically calculated binding energies DeltaE and the specificity constants k(cat)KM(-1) obtained from parallel hydrolysis kinetic studies. These results prove the general function of the docking approach as a rational model not only in predicting the general acceptance of a substrate mimetic in a qualitative manner, but also to provide reliable information on its individual specificity towards proteases.     

Peroxidase activity of new mixed‐valence cobalt complexes with ligands derived from pyridoxal

New mixed‐valence cobalt complexes with ligands derived from pyridoxal were synthesized and characterized, and their application as mimetics of the peroxidase enzyme was investigated. Single‐crystal X‐ray diffraction was used to analyze all complex structures in the solid state and their electrochemical behavior was investigated. A reactivity pattern was observed in the complex synthesis regarding the cobalt compounds from which analogous zwitterionic derivatives were obtained. The importance of these compounds lies in understanding their behavior in an oxidizing environment and evaluating whether they can activate hydrogen peroxide to oxidize phenolic compounds. In nature, enzymes called peroxidases, which efficiently oxidize phenolic compounds, trigger many reactions involving the activation of hydrogen peroxide to oxidize organic substrates. However, these enzymes present several disadvantages, including denaturation and elevated costs. Therefore, these limitations can be overcome by expanding research into the study of synthetic catalysts for the oxidation of phenolic compounds using hydrogen peroxide, which is a highly relevant field of bioinorganic chemistry.     

Synthesis and photophysical characterization of 1- and 4-(purinyl)triazoles

Fluorescent adenine mimetics are useful tools for studying DNA, RNA and enzyme functions. Herein we describe the synthesis of eight 1-(purinyl)triazoles and two 4-(purinyl)triazoles utilizing the 1,4-regioselective copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction as the key step. The fluorescence properties of five of the synthesized 1-(purinyl)triazoles are also presented. The five measured compounds displayed low quantum yields. The results, when compared to previously published data, suggest a high influence of the substitution pattern of the triazole on the fluorescence properties.     

Solid-phase synthesis and biochemical studies of O-boranophosphopeptides and O-dithiophosphopeptides

Signal transduction cascades maintain control over important cellular processes such as cell growth and differentiation by orchestrating protein phosphorylation and dephosphorylation. Specific control of these processes in vivo and in vitro can be achieved with peptide analogues that mimic the binding properties of phosphoproteins. We present here the solid-phase synthesis of two novel classes of phosphopeptide mimetics, O-boranophosphopeptides and O-dithiophosphopeptides, derivatized on tyrosine, serine, and threonine. The use of H-phosphonate and H-phosphonothioate monoesters containing the base labile 9-fluorenemethyl protecting group was key to the synthesis of both phosphopeptide mimetics. O-Boranophosphopeptides were synthesized by condensing O-(9-fluorenemethyl)-H-phosphonate to the peptide hydroxylic component (tyr, ser, or thr) followed by oxidation with borane complexes. Similarly, the synthesis of O-dithiophosphopeptides used the O-(9-fluorenemethyl)-H-phosphonothioate synthon and oxidation with elemental sulfur. Base elimination of the Fmol protecting group and cleavage from the solid support with concentrated ammonium hydroxide afforded the boranophosphopeptide and dithiophosphopeptide target compounds. Ac-YIIPLPG-NH2, having either dithiophosphoryl tyrosine or boranophosphoryltyrosine but no sequence specificity for Yersinia protein tyrosine phosphatase (PTP), was found to competitively inhibit this enzyme with KI values of 430 +/- 50 and 670 +/- 50 microM, respectively. In addition, both phosphopeptide analogues were resistant toward Yersinia PTP enzymatic hydrolysis. Under conditions (pH 8.0) where the phosphopeptide was rapidly dephosphorylated, the boranophosphopeptide hydrolyzed slowly (t1/2 = 15 h) and the dithiophosphopeptide was completely stable over 24 h.     

Mimetics of the Selenoenzyme Glutathione Peroxidase: Novel Structures and Unusual Catalytic Mechanisms

Glutathione peroxidase (GPx) mimetics comprise an important class of selenium-containing antioxidants that catalyze the destruction of biologically harmful peroxides in the presence of stoichiometric thiol reductants. The synthesis of two novel cyclic selenium compounds and their evaluation as GPx mimetics was achieved. The first is a cyclic seleninate ester that is formed in situ from the oxidation of allyl 3-hydroxypropyl selenide. The second is a spirodioxyselenurane that is similarly formed from di(3-hydroxypropyl) selenide. Both compounds were shown to be remarkably active catalysts in an assay based on the reduction of t-butyl hydroperoxide with benzyl thiol. The mechanisms of the catalytic cycles of the two novel selenium compounds were elucidated and were found to be distinct from each other and from that of GPx.     

Design, synthesis, and bioactivity of the first nonsteroidal mimetics of brassinolide

Ten novel compounds, each consisting of two subunits and a linker, were designed with the aid of molecular modeling to resemble the natural steroidal phytohormone brassinolide. The mimetics were synthesized and subjected to the rice leaf lamina inclination bioassay to test for brassinosteroid activity. Most of the mimetics displayed very weak or no bioactivity, but two were strongly active when coapplied with the auxin indole-3-acetic acid (IAA), which synergizes the activity of brassinosteroids. Thus, 1-(4,6 alpha,7 alpha-trihydroxy-5,6,7,8-tetrahydronaphthyl)-2-(6 alpha',7 alpha'-dihydroxy-5',6',7',8'-tetrahydronaphthyl)ethyne (4) and (E)-1,2-bis[trans-(4a alpha,8a beta)-4-oxo-6 alpha,7 alpha-dihydroxy-4a,5,6,7,8,8a-hexahydro-(3H)-naphthyl]ethylene (11) showed exceptional activity at doses as low as 0.01 ng and 0.001 ng/plant, respectively. These compounds are the first biologically active nonsteroidal brassinolide mimetics.     

A Modular Synthesis of Teraryl‐Based α‐Helix Mimetics,Part 1: Synthesis of Core Fragments with Two Electronically Differentiated Leaving Groups

Teraryl‐based α‐helix mimetics have proven to be useful compounds for the inhibition of protein–protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl‐based α‐helix mimetics. Central to our strategy is the use of a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd‐catalyzed cross‐coupling used for terphenyl assembly. With the halogen/diazonium route and the halogen/triflate route, two strategies have successfully been established. The synthesis of core building blocks with aliphatic (Ala, Val, Leu, Ile), aromatic (Phe), polar (Cys, Lys), hydrophilic (Ser, Gln), and acidic (Glu) amino acid side chains are reported.     

High-throughput turbidimetric screening for heparin-neutralizing agents and low-molecular-weight heparin mimetics

Safer heparin-neutralizing agents are currently required to replace protamine, the use of which causes adverse effects such as anaphylaxia. Low-molecular-weight (LMW) heparin mimetics that potentiate antithrombin III (AT) action are also valuable as anti-thrombotics. This paper describes a high-throughput assay for both heparin-neutralizing agents and LMW heparin mimetics without the use of blood preparations. The assay is based on turbidimetric measurement of a solution of collagen, heparin, and a test compound. Native collagen molecules spontaneously form insoluble fibrils when transferred to a physiological buffer, and this process is inhibited by heparin. In the presence of a heparin-neutralizing agent or an LMW heparin mimetic, the inhibitory effect of heparin is canceled and turbidity increase is retrieved. We demonstrated that this assay is effective in detecting potential agents with high reliability (Z' factor=0.9). The screening of a chemical library (34400 compounds) was further performed in a 384-well format, and led to the identification of a novel heparin-neutralizing agent. Since this assay protocol is feasible for an automated high-throughput screening (HTS) system, it could enhance the lead seeking process for drugs related to heparin/heparan sulfate (HS) functions.     

A new scaffold for the stereoselective synthesis of alpha-O-linked glycopeptide mimetics

alpha-O-Linked glycohomoglutamates are obtained as diastereomerically pure compounds by chemo-, regio-, and stereoselective cycloadditions between glycals and aspartic acid derivatives. The latter constitute orthogonally functionalized scaffolds for glycopeptide mimetics.