Recognition of anion-water clusters by peptide-based supramolecular capsules.

The biological and technological importance of anion-mediated processes has made the development of improved methods for the selective recognition of anions one of the most relevant research topics today. The hydration sphere of anions plays an important role in the functions performed by anions by forming a variety of cluster complexes. Here we describe a supramolecular capsule that recognizes hydrated anion clusters.

Sugar-based synthesis of an enantiomorphically pure zeolite.

Zeolites, well-known by their high selectivities in catalytic and separation processes due to their porous nature, play a crucial role in various applications. One significant long-term objective is the synthesis of enantiopure zeolites, potentially enabling enantioselective processes. Earlier attempts result in partial success, yielding some enantiomorphically enriched zeolites.

Low temperature glass/crystal transition in ionic liquids determined by H-bond coulombic strength.

Self-assembled ionic liquid crystals are anisotropic ionic conductors, with potential applications in areas as important as solar cells, battery electrolytes and catalysis. However, many of these applications are still limited by the lack of precise control over the variety of phases that can be formed (nematic, smectic, or semi/fully crystalline), determined by a complex pattern of different intermolecular interactions. Here we report the results of a systematic study of crystallization of several imidazolium salts in which the relative contribution of isotropic coulombic and directional H-bond interactions is carefully tuned.

A novel amyloid designable scaffold and potential inhibitor inspired by GAIIG of amyloid beta and the HIV-1 V3 loop.

The GAIIG sequence, common to the amyloid beta peptide (residues 29-33) and to the HIV-1 gp120 (residues 24-28 in a typical V3 loop), self-assembles into amyloid fibrils, as suggested by theory and the experiments presented here. The longer YATGAIIGNII sequence from the V3 loop also self-assembles into amyloid fibrils, of which the first three and the last two residues are outside the amyloid GAIIG core. We postulate that this sequence, with suitably selected modifications at the flexible positions, can serve as a designable scaffold for novel amyloid-based materials.

[(CH)NH]PbX (X = Cl and Br), 2D-Perovskite Related Hybrids with Dielectric Transitions and Broadband Photoluminiscent Emission.

We have prepared two new lead halides with the novel general formula of DMAPbX (DMA = [(CH)NH] and X = Cl or Br) by using an easy route under mild conditions at room temperature. These compounds exhibit an unprecedented crystal structure, are formed by layers of distorted [PbX] octahedra, which share corners and faces, and contain intercalated DMA cations. Very interestingly, they display dielectric transitions, which are related to a partial order-disorder process of the DMA cations between 160 and 260 K.

Phase Transition, Dielectric Properties, and Ionic Transport in the [(CH)NH]PbI Organic-Inorganic Hybrid with 2H-Hexagonal Perovskite Structure.

In this work, we focus on [(CH)NH]PbI, a member of the [AmineH]PbI series of hybrid organic-inorganic compounds, reporting a very easy mechanosynthesis route for its preparation at room temperature. We report that this [(CH)NH]PbI compound with 2H-perovskite structure experiences a first-order transition at ≈250 K from hexagonal symmetry P6/mmc (HT phase) to monoclinic symmetry P2/c (LT phase), which involves two cooperative processes: an off-center shift of the Pb cations and an order-disorder process of the N atoms of the DMA cations. Very interestingly, this compound shows a dielectric anomaly associated with the structural phase transition.

Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.

Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding.

A Covalent Organic Helical Cage with Remarkable Chiroptical Amplification.

Purely organic shape-persistent chiral cages are designed through the use of rigid chiral axes. Covalent dimerization of a tripodal fragment bearing chiral allenes forms a molecular twisted prism with loop-like lateral edges presenting 10-fold chiroptical amplification compared to its isolated building blocks. The expected geometry of covalent organic helical cage (M,M)3 -1 was confirmed by X-ray crystal structure analysis.

Preparation and characterization of a halogen-bonded shape-persistent chiral alleno-acetylenic inclusion complex.

A chiral bidentate inclusion complex has been formed by halogen-bond interaction between the pyridyl moieties of a pyridoallenoacetylenic host and octafluorodiiodobutane. X-ray crystallography showed that the guest adopts a chiral conformation inside the molecular channels formed by stacking of the host units. A 10 ppm shielding of the (15)N NMR resonance for the pyridil units provided evidence of the formation of the halogen-bond complex in solution.

Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover.

Shikimate kinase (SK) is an essential enzyme in several pathogenic bacteria and does not have any counterpart in human cells, thus making it an attractive target for the development of new antibiotics. The key interactions of the substrate and product binding and the enzyme movements that are essential for catalytic turnover of the Mycobacterium tuberculosis shikimate kinase enzyme (Mt-SK) have been investigated by structural and computational studies. Based on these studies several substrate analogs were designed and assayed.

Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids.

The structural changes caused by the substitution of the aromatic moiety in (2S)-2-benzyl-3-dehydroquinic acids and its epimers in C2 by electron-withdrawing or electron-donating groups in type II dehydroquinase enzyme from M. tuberculosis and H. pylori has been investigated by structural and computational studies.

High-resolution structures of Thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with NAD+ and in complex with NAD+ and triclosan.

Enoyl-acyl carrier protein reductase (ENR; the product of the fabI gene) is an important enzyme that is involved in the type II fatty-acid-synthesis pathway of bacteria, plants, apicomplexan protozoa and mitochondria. Harmful pathogens such as Mycobacterium tuberculosis and Plasmodium falciparum use the type II fatty-acid-synthesis system, but not mammals or fungi, which contain a type I fatty-acid-synthesis pathway consisting of one or two multifunctional enzymes. For this reason, specific inhibitors of ENR are attractive antibiotic candidates.

'Inverted' analogs of the antibiotic gramicidin S with an improved biological profile.

A series of gramicidin S derivatives 4-15 are presented that have four ornithine residues as polar protonated side chains and two central hydrophobic amino acids with unaltered turn regions. These peptides were screened against human erthrocytes and our standard panel of Gram negative- and Gram positive bacteria, including four MRSA strains. Based on the antibacterial- and hemolytic data, peptides 13 and 14 have an improved biological profile compared to the clinically applied topical antibiotic gramicidin S.

Rotation-locked 2,6-pyrido-allenophanes: characterization of all stereoisomers.

New 2,6-disubstituted pyrido-allenophanes with locked rotation of aromatic spacers were designed and synthesized. The synthesis was accomplished by Pd-catalyzed C(sp(2))-C(sp) Sonogashira cross-coupling reaction between 1,3-diethynylallene (DEA) and 2,6-dibromopyridine followed by an intermolecular ring closure. Because racemic DEA was employed, pyrido-allenophanes were obtained as mixtures of stereoisomers that were resolved by preparative HPLC.

A prodrug approach for improving antituberculosis activity of potent Mycobacterium tuberculosis type II dehydroquinase inhibitors.

The synthesis of high-affinity reversible competitive inhibitors of Mycobacterium tuberculosis type II dehydroquinase, an essential enzyme in Mycobacterium tuberculosis bacteria, is reported. The inhibitors reported here are mimics of the enol intermediate and the effect of substitution on C2 was studied. The crystal structures of Mycobacterium tuberculosis type II dehydroquinase in complex with three of the reported inhibitors are also described.

Synthesis and evaluation of strand and turn modified ring-extended gramicidin S derivatives.

In this paper, we describe the crystal structure of previously reported ring-extended gramicidin S (GS) derivative 2 (GS14K4), containing a d-amino acid residue in one of the β-strand regions. This structure is in agreement with a previously reported modeling study of the same molecule. The polar side chain of the additional d-amino acid residue is positioned at the same face of the molecule as the hydrophobic side chains, and we believe that because of this compound 2 is considerably less hydrophobic than extended GS derivatives in which the strand regions are exclusively composed of l-amino acids.

Evaluation of readily accessible azoles as mimics of the aromatic ring of D-phenylalanine in the turn region of gramicidin S.

The influence of replacing the d-phenylalanine residue with substituted and unsubstituted azoles on the structure and biological activity of the antibiotic gramicidin S was investigated against a representative panel of Gram-positive and Gram-negative bacteria strains. Substituted triazole derivatives, obtained using a convergent synthetic strategy, are as active as gramicidin S, provided that any substituent on the triazole moiety is not too large. The unsubstituted triazole derivative was biologically less active than the parent natural product, gramicidin S.

Exploring the conformational and biological versatility of β-turn-modified gramicidin S by using sugar amino acid homologues that vary in ring size.

Monobenzylated sugar amino acids (SAAs) that differ in ether ring size (containing an oxetane, furanoid, and pyranoid ring) were synthesized and incorporated in one of the β-turn regions of the cyclo-decapeptide gramicidin S (GS). CD, NMR spectroscopy, modeling, and X-ray diffraction reveal that the ring size of the incorporated SAA moieties determines the spatial positioning of their cis-oriented carboxyl and aminomethyl substituents, thereby subtly influencing the amide linkages with the adjacent amino acids in the sequence. Unlike GS itself, the conformational behavior of the SAA-containing peptides is solvent dependent.

Structure of the bacteriophage T4 long tail fiber receptor-binding tip.

Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers.

An adamantyl amino acid containing gramicidin S analogue with broad spectrum antibacterial activity and reduced hemolytic activity.

The cyclic cationic antimicrobial peptide gramicidin S (GS) is an effective topical antibacterial agent that is toxic for human red blood cells (hemolysis). Herein, we present a series of amphiphilic derivatives of GS with either two or four positive charges and characteristics ranging between very polar and very hydrophobic. Screening of this series of peptide derivatives identified a compound that combines effective antibacterial activity with virtually no toxicity within the same concentration range.

Understanding the key factors that control the inhibition of type II dehydroquinase by (2R)-2-benzyl-3-dehydroquinic acids.

The binding mode of several substrate analogues, (2R)-2-benzyl-3-dehydroquinic acids 4, which are potent reversible competitive inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by structural and computational studies. The crystal structures of Mycobacterium tuberculosis and Helicobacter pylori DHQ2 in complex with one of the most potent inhibitor, p-methoxybenzyl derivative 4 a, have been solved at 2.40 Å and 2.

Crystallographic structure of porcine adenovirus type 4 fiber head and galectin domains.

Adenovirus isolate NADC-1, a strain of porcine adenovirus type 4, has a fiber containing an N-terminal virus attachment region, shaft and head domains, and a C-terminal galectin domain connected to the head by an RGD-containing sequence. The crystal structure of the head domain is similar to previously solved adenovirus fiber head domains, but specific residues for binding the coxsackievirus and adenovirus receptor (CAR), CD46, or sialic acid are not conserved. The structure of the galectin domain reveals an interaction interface between its two carbohydrate recognition domains, locating both sugar binding sites face to face.

Gramicidin S derivatives containing cis- and trans-morpholine amino acids (MAAs) as turn mimetics.

The cyclic decapeptide gramicidin S (GS) was used as a model for the evaluation of four turn mimetics. For this purpose, one of the D-Phe-Pro two-residue turn motifs in the rigid cyclic beta-hairpin structure of GS was replaced with morpholine amino acids (MAA 2-5), differing in stereochemistry and length of the side-chain. The conformational properties of the thus obtained GS analogues (6-9) was assessed by using NMR spectroscopy and X-ray crystallography, and correlated with their biological properties (antimicrobial and hemolytic activity).