Towards Profiles of Resistance Development and Toxicity for the Small Cationic Hexapeptide RWRWRW-NH2.

RWRWRW-NH2 (MP196) is an amphipathic hexapeptide that targets the bacterial cytoplasmic membrane and inhibits cellular respiration and cell wall synthesis. In previous studies it showed promising activity against Gram-positive bacteria and no significant cytotoxicity or hemolysis. MP196 is therefore used as lead structure for developing more potent antibiotic derivatives.

Rational design of supramolecular hemin/G-quadruplex-dopamine aptamer nucleoapzyme systems with superior catalytic performance.

The rational design of a set of hemin/G-quadruplex (hGQ)-dopamine binding aptamer (DBA) conjugates, acting as nucleoapzymes, is described. The nucleoapzyme constructs consist of a hGQ DNAzyme as a catalytic unit and DBA as a substrate binding unit that are brought into spatial proximity by a duplex scaffold composed of complementary oligonucleotide strands. When the hGQ unit is linked to the duplex scaffold a single-strand DNA tether of variable length, the resulting nucleoapzymes reveal a moderate catalytic enhancement toward the HO-mediated oxidation of dopamine to aminochrome as compared to the process stimulated by the separated hGQ and DBA units (5-7 fold enhancement).

Supramolecular micelle-based nucleoapzymes for the catalytic oxidation of dopamine to aminochrome.

Lipidated DNAzymes or a lipidated Cu(II)-complex and lipidated aptamer sequences form supramolecular assemblies of micellar nucleoapzymes for the enhanced oxidation of dopamine to aminochrome. The catalytic functions of the micellar nucleoapzymes are attributed to the concentration of the substrate, using the aptamer units, in close proximity to the active sites.

Nucleoapzymes: Hemin/G-Quadruplex DNAzyme-Aptamer Binding Site Conjugates with Superior Enzyme-like Catalytic Functions.

A novel concept to improve the catalytic functions of nucleic acids (DNAzymes) is introduced. The method involves the conjugation of a DNA recognition sequence (aptamer) to the catalytic DNAzyme, yielding a hybrid structure termed "nucleoapzyme". Concentrating the substrate within the "nucleoapzyme" leads to enhanced catalytic activity, displaying saturation kinetics.

Influence of lipidation on the mode of action of a small RW-rich antimicrobial peptide.

Antimicrobial peptides are a potent class of antibiotics. In the Gram-positive model organism Bacillus subtilis the synthetic peptide RWRWRW-NH2 integrates into the bacterial membrane and delocalizes essential peripheral membrane proteins involved in cell wall biosynthesis and respiration. A lysine residue has been added to the hexapeptide core structure, either C or N-terminally.

Programmed Synthesis by Stimuli-Responsive DNAzyme-Modified Mesoporous SiO2 Nanoparticles.

DNAzyme-capped mesoporous SiO2 nanoparticles (MP SiO2 NPs) are applied as stimuli-responsive containers for programmed synthesis. Three types of MP SiO2 NPs are prepared by loading the NPs with Cy3-DBCO (DBCO=dibenzocyclooctyl), Cy5-N3 , and Cy7-N3 , and capping the NP containers with the Mg(2+) , Zn(2+) , and histidine-dependent DNAzyme sequences, respectively. In the presence of Mg(2+) and Zn(2+) ions as triggers, the respective DNAzyme-capped NPs are unlocked, leading to the "click" reaction product Cy3-Cy5.

Computational docking simulations of a DNA-aptamer for argininamide and related ligands.

The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes.

Aptasensors based on supramolecular structures of nucleic acid-stabilized Ag nanoclusters.

Two-sized luminescent nucleic acid-functionalized Ag nanoclusters (NCs) are implemented for the analysis and multiplexed detection of adenosine monophosphate, AMP, and of cocaine using aptamer-ligand complexes.

Multiplexed analysis of genes using nucleic acid-stabilized silver-nanocluster quantum dots.

Luminescent nucleic acid-stabilized Ag nanoclusters (Ag NCs) are applied for the optical detection of DNA and for the multiplexed analysis of genes. Two different sensing modules including Ag NCs as luminescence labels are described. One sensing module involves the assembly of a three-component sensing module composed of a nucleic acid-stabilized Ag NC and a quencher-modified nucleic acid hybridized with a nucleic acid scaffold that is complementary to the target DNA.

Multifunctional, defect-engineered metal-organic frameworks with ruthenium centers: sorption and catalytic properties.

A mixed-linker solid-solution approach was employed to modify the metal sites and introduce structural defects into the mixed-valence Ru(II/III) structural analogue of the well-known MOF family [M3(II,II)(btc)2] (M=Cu, Mo, Cr, Ni, Zn; btc=benzene-1,3,5-tricarboxylate), with partly missing carboxylate ligators at the Ru2 paddle-wheels. Incorporation of pyridine-3,5-dicarboxylate (pydc), which is the same size as btc but carries lower charge, as a second, defective linker has led to the mixed-linker isoreticular derivatives of Ru-MOF, which display characteristics unlike those of the defect-free framework. Along with the creation of additional coordinatively unsaturated sites, the incorporation of pydc induces the partial reduction of ruthenium.

Small cationic antimicrobial peptides delocalize peripheral membrane proteins.

Short antimicrobial peptides rich in arginine (R) and tryptophan (W) interact with membranes. To learn how this interaction leads to bacterial death, we characterized the effects of the minimal pharmacophore RWRWRW-NH2. A ruthenium-substituted derivative of this peptide localized to the membrane in vivo, and the peptide also integrated readily into mixed phospholipid bilayers that resemble Gram-positive membranes.

C-Terminal acetylene derivatized peptides via silyl-based alkyne immobilization.

A new Silyl-based Alkyne Modifying (SAM)-linker for the synthesis of C-terminal acetylene-derivatized peptides is reported. The broad scope of this SAM2-linker is illustrated by manual synthesis of peptides that are side-chain protected, fully deprotected, and disulfide-bridged. Synthesis of a 14-meric (KLAKLAK)2 derivative by microwave-assisted automated SPPS and a one-pot cleavage click procedure yielding protected 1,2,3-triazole peptide conjugates are also described.

Short antibacterial peptides with significantly reduced hemolytic activity can be identified by a systematic L-to-D exchange scan of their amino acid residues.

High systemic toxicity of antimicrobial peptides (AMPs) limits their clinical application to the treatment of topical infections; in parenteral systemic application of AMPs the problem of hemolysis is one of the first to be tackled. We now show that the selectivity of lipidated short synthetic AMPs can be optimized substantially by reducing their hemolytic activity without affecting their activity against methicillin resistant Staphylococcus aureus (MRSA). In order to identify the optimized peptides, two sets of 32 diastereomeric H-(D)Arg-WRWRW-(L)Lys(C(O)CnH2n+1)-NH2 (n = 7 or 9) peptides were prepared using a split-split procedure to perform a systematic L-to-D exchange scan on the central WRWRW-fragment.

Structural and biological implications of the binding of Leu-enkephalin and its metal derivatives to opioid receptors.

Binding of Leu-enkephalin and [Rh(III)(η(5)-Cp*)(η(6)-Tyr(1))]Leu-enkephalin to the recently published crystal structures of the μ- and δ-opioid receptor is studied. Docking of free Leu-enkephalin reveals two preferred conformations, one of which suggests an alternative binding site for the tyrosine residue. Furthermore, the three-dimensional solution structure of [Rh(III)(η(5)-Cp*)(η(6)-Tyr(1))]Leu-enkephalin was solved by using 2D NMR spectroscopic techniques.

Tuning the activity of a short arg-trp antimicrobial Peptide by lipidation of a C- or N-terminal lysine side-chain.

The attachment of lipids to C- or N-terminally positioned lysine side-chain amino groups increases the activity of a short synthetic (Arg-Trp)3 antimicrobial peptide significantly, making these peptides even active against pathogenic Gram-negative bacteria. Thus, a peptide with strong activity against S. aureus (1.

Modulating the activity of short arginine-tryptophan containing antibacterial peptides with N-terminal metallocenoyl groups.

A series of small synthetic arginine and tryptophan containing peptides was prepared and analyzed for their antibacterial activity. The effect of N-terminal substitution with metallocenoyl groups such as ferrocene (FcCO) and ruthenocene (RcCO) was investigated. Antibacterial activity in different media, growth inhibition, and killing kinetics of the most active peptides were determined.

Silyl-based alkyne-modifying linker for the preparation of C-terminal acetylene-derivatized protected peptides.

A novel linker for the synthesis of C-terminal acetylene-functionalized protected peptides is described. This SAM1 linker is applied in the manual Fmoc-based solid-phase peptide synthesis of Leu-enkephalin and in microwave-assisted automated synthesis of Maculatin 2.1, an antibacterial peptide that contains 18 amino acid residues.

Proteomic response of Bacillus subtilis to lantibiotics reflects differences in interaction with the cytoplasmic membrane.

Mersacidin, gallidermin, and nisin are lantibiotics, antimicrobial peptides containing lanthionine. They show potent antibacterial activity. All three interfere with cell wall biosynthesis by binding lipid II, but they display different levels of interaction with the cytoplasmic membrane.

The chemoselective reactions of tyrosine-containing G-protein-coupled receptor peptides with [Cp*Rh(H2O)3](OTf)2, including 2D NMR structures and the biological consequences.

The bioconjugation of organometallic complexes with peptides has proven to be a novel approach for drug discovery. We report the facile and chemoselective reaction of tyrosine-containing G-protein-coupled receptor (GPCR) peptides with [Cp*Rh(H(2)O)(3)](OTf)(2), in water, at room temperature, and at pH 5-6. We have focused on three important GPCR peptides; namely, [Tyr(1)]-leu-enkephalin, [Tyr(4)]-neurotensin(8-13), and [Tyr(3)]-octreotide, each of which has a different position for the tyrosine residue, together with competing functionalities.

Trivalent ultrashort lipopeptides are potent pH dependent antifungal agents.

The activity of antimicrobial peptides (AMPs) that contain a large proportion of histidine residues (pK(a) ∼ 6) depends on the physiological pH environment. Advantages of these AMPs include high activity in slightly acidic areas of the human body and relatively low toxicity in other areas. Also, many AMPs are highly active in a multivalent form, but this often increases toxicity.

Triazacyclophane (TAC)-scaffolded histidine and aspartic acid residues as mimics of non-heme metalloenzyme active sites.

We describe the synthesis and coordination behaviour to copper(II) of two close structural triazacyclophane-based mimics of two often encountered aspartic acid and histidine containing metalloenzyme active sites. Coordination of these mimics to copper(I) and their reaction with molecular oxygen leads to the formation of dimeric bis(μ-hydroxo) dicopper(II) complexes.

TAC-scaffolded tripeptides as artificial hydrolytic receptors: a combinatorial approach toward esterase mimics.

In this report, we present the first library of tripodal synthetic receptor molecules containing three different, temporarily N-terminal protected peptide arms capable of performing hydrolytic reactions. To construct this library, the orthogonally protected triazacyclophane (TAC)-scaffold was used in the preparation of a split-mix library of 19 683 resin bound tripodal receptor molecules. For the construction of the peptide arms, three different sets of amino acids were used, each focused on one part of the catalytic triad as found in several families of hydrolytic enzymes.

Scaffolded amino acids as a close structural mimic of type-3 copper binding sites.

We report the use of triazacyclophane (TAC)-scaffolded amino acids as a structural mimic for 3-histidine metal-binding sites in metalloproteins, especially for the mimicry of type-3 copper binding sites as are present in hemocyanin, tyrosinase and catechol oxidase.