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Graphical abstract, Highlights • A novel thermophilic esterase discovered from hot-spring metagenomic library. • EstD11 shows broad substrate specificity including substrates of industrial interest. • Atomic resolution crystallographic complexes reveal hot-spots in the active site. • High-T structures provide unique evidence on cap dynamics as occurs in vivo. • Met zipper at active site essential in thermo-stability and substrate promiscuity., A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the α/β-hydrolase superfamily. The canonical α/β-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.

The stability of binary mixtures of several protic ionic liquids (ethylammonium nitrate, ethylammonium acetate and ethylammonium tetrafluoroborate) with polyethylene oxide is studied by means of molecular dynamics simulations. The solubility range is seen to be wider for ethylammonium acetate, and the structure and single-particle dynamics of its ternary mixtures with lithium acetate are then studied. The structure of liquid mixtures of lithium acetate with the ionic liquid is seen to be seldom modified by the addition of the polymer, with very limited hydrogen bonding between the ionic liquid and the polymer taking place. Moreover, lithium is seen to be solvated in the liquid phase forming [Li(ACE)4]−3 tetrahedral complexes irrespective of the presence of the polymer, with very limited binding of metal cations to oxygen atoms in the polymer backbone. Hence, the registered single particle dynamics and lithium transport takes place in practically the same way as in the liquid phase with almost no interference of the polymer, contrarily to previously reported results for other ionic liquids.

The synthesis of highly functionalized bicyclic and cyclic β-amino acids from β-nitrosugars is reported. Specifically, our strategy for the synthesis of polyhydroxylated cyclopentane β-amino acids via the intramolecular C-alkylation of 6-nitro-2-O-triflates of furanosides has been applied to the preparation of the first two examples of a novel class of bicyclic β-amino acids and a novel cyclopentene β-amino acid. Also, our Henry reaction mediated strategy for the synthesis of polyhydroxylated cyclohexane β-amino acids has been extended to a divergent, stereoselective synthesis of new polysubstituted cyclohexane and cyclopentane β-amino acids.

Intrigued by the not fully extended hairpin monomeric structure of the previously reported cyclo-(αβ3αβ 2α)2 peptide 2, as well as its nanochannel crystallographic assembly, we here investigate the structural properties of a series of turn derivatives (3-17). Five crystallographic monomeric structures of the symmetric and asymmetric cyclo- (αβ3αβ2α)2 peptides 3-17 are found; the novel saddlelike (4 and 16) and the twisted hairpin (6) conformers, as well as the not fully extended hairpins 7 and 14. The pentafluorophenyl/1-naphthyl and pentafluorophenyl/9-phenanthryl derivatives 7 and 14, respectively, adopt the anticipated hexagon-shaped crystalline nanotube assemblies, resembling the crystal packing of the parent peptide 2. The structural analysis of the compounds as described here can serve as a basis for biological applications, such as the design of β-sheet mimics or for the development of functional nanomaterials. © 2013 American Chemical Society.

The structural and dynamical properties of bulk mixtures of long-chained primary and secondary alcohols (propanol, butanol, and 2-pentanol) with protic ionic liquids (ethylammonium and butylammonium nitrate) were studied by means of molecular dynamics simulations and small angle X-ray scattering (SAXS). Changes in the structure with the alcohol concentration and with the alkyl chain length of the alcohol moieties were found, showing variations in the radial distribution function and in the number of hydrogen bonds in the bulk liquids. Moreover, the structural behaviour of the studied mixtures is further clarified with the spatial distribution functions. The global picture in the local scale is in good agreement with the nanostructured solvation paradigm [T. Mendez-Morales et al. Phys. Chem. B 118, 761 (2014)], according to which alcohols are accommodated into the hydrogen bonds’ network of the ionic liquid instead of forming clusters in the bulk. Indeed, our study reveals that the alcohol molecules are placed with their polar heads at the interfaces between polar and nonpolar nanodomains in the ionic liquid, with their alkyl chains inside the nonpolar organic nanodomains. The influence of alcohol chain length in the single-particle dynamics of the mixtures is also reported calculating the velocity autocorrelation function and vibrational densities of states of the different species in the ionic liquid-alcohol mixtures, and a weak caging effect for the ethylammonium cations independent of the chain size of the alcohols was found. However, the SAXS data collected for the studied mixtures show an excess of the scattering intensities which indicates that there are also some structural heterogeneities at the nanoscale.

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. © 2012 Elsevier Ltd. All rights reserved.

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. Triclosan, a broad-range antibacterial agent, binds to ENR, inhibiting fatty-acid synthesis. As humans do not have an ENR enzyme, they are not affected. Here, high-resolution structures of Thermus thermophilus (Tth) ENR in the apo form, bound to NAD(+) and bound to NAD(+) plus triclosan are reported. Differences from and similarities to other known ENR structures are reported; in general, the structures are very similar. The cofactor-binding site is also very similar to those of other ENRs and, as reported for other species, triclosan leads to greater ordering of the loop that covers the cofactor-binding site, which, together with the presence of triclosan itself, presumably provides tight binding of the dinucleotide, preventing cycling of the cofactor. Differences between the structures of Tth ENR and other ENRs are the presence of an additional β-sheet at the N-terminus and a larger number of salt bridges and side-chain hydrogen bonds. These features may be related to the high thermal stability of Tth ENR.

The first stereocontrolled nitro sugar-mediated synthesis of polyhydroxylated β-amino acids and their incorporation into peptides is described. The key steps of this approach are a Michael addition of the lithium salt of tris(phenylthio)methane (a carboxyl synthetic equivalent) to sugar nitro olefins, and the reduction of the nitro group to an amino group. Specifically, two glyceraldehyde-based β-amino acids and a polyhydroxylated cyclohexyl β-amino acid were prepared. The latter, which could act as a water-soluble mimic of the proline-glycine δ-turn, was easily transformed into the corresponding 5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetraol, a novel amino-carbasugar. However, this did not show significant glycosidase inhibiting properties. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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. The derivative containing the pyranoid SAA is slightly less hydrophobic and displays a diminished haemolytic activity, but has similar antimicrobial properties as GS.

The synthesis of new analogues of the cationic antimicrobial peptide gramicidin S, having a modified D-phenylalanine residue, their antibacterial properties against several Gram positive and negative strains, as well as their hemolytic activity is reported. (C) 2009 Elsevier Ltd. All rights reserved.

The natural product Gramicidin S is a promising scaffold for novel oligopeptide-based bisphosphine ligands, combining the advantageous rigid chiral backbone with the close proximity of phosphine substituents. The required unnatural, phosphine-containing, amino acid building blocks were synthesized by means of a novel protocol that involves the enantioselective alkylation of a chiral nickel Schiff base template. Three Ni complexes were prepared with different alkyl chains between the phosphine group and the α-carbon atom of the incorporated glycine; the absolute stereochemistry of two of them was determined by single-crystal X-ray structure analysis. By detaching the template, enantiopure L-phosphine amino acids resulted enabling the solid-phase, stepwise construction of a linear sequence of the phosphine-modified oligopeptides. On cyclization three bisphosphine-substituted Gramicidin S analogues resulted, differing only in the size and shape of the linkage between the phosphine groups and the oligopeptides backbone. Their crystal structures suggest these species to have potential as chelating ligands. © 2009 Wiley-VCH Verlag GmbH & Co.

A stereocontrolled synthesis of the methyl ester of (2 S )-3-amino-2-((4′ S )-2′,2′-dimethyl-1′,3′-dioxolan-4′-yl)propanoic acid from d -glyceraldehyde is described for the first time. This method involves the stereoselective Michael addition of the lithium salt of tris(phenylthio)methane to ( S )-2,2-dimethyl-4-(( E )-2-nitrovinyl)-1,3-dioxolane followed by hydrolysis of the resulting (4 S )-2,2-dimethyl-4-((2′ S )-3′-nitro-1′,1′,1′-tris(phenylthio)propan-2′-yl)-1,3-dioxolane to (2 S )-methyl 2-((4′ S )-2′,2′-dimethyl-1′,3′-dioxolan-4′-yl)-3-nitropropanoate, which was finally reduced to the target compound. A similarly stereocontrolled transformation of l -glyceraldehyde into (2 R )-methyl 3-amino-2-((4′ R )-2′,2′-dimethyl-1′,3′-dioxolan-4′-yl)propanoate is also described.

Structural and computational studies to explore the WAT1 binding pocket in the structure-based design of inhibitors against the type II dehydroquinase (DHQ2) enzyme are reported. The crystal structures of DHQ2 from M. tuberculosis in complex with four of the reported compounds are described. The electrostatic interaction observed between the guanidinium group of the essential arginine and the carboxylate group of one of the inhibitors in the reported crystal structures supports the recently suggested role of this arginine as the residue that triggers the release of the product from the active site. The results of the structural and molecular dynamics simulation studies revealed that the inhibitory potency is favored by promoting interactions with WAT1 and the residues located within this pocket and, more importantly, by avoiding situations where the ligands occupy the WAT1 binding pocket. The new insights can be used to advantage in the structure-based design of inhibitors Financial support from the Spanish Ministry of Science and Innovation (Grant SAF2010-15076) and the Xunta de Galicia (Grant GRC2013/041) is gratefully acknowledged. B.B. and A.P. thank the Spanish Ministry of Education for their respective FPU fellowships. A.S. thanks the Spanish Ministry of Economy and Competitiveness for her FPI fellowship. J.M.O. thanks the Xunta de Galicia for a Plan I2C postdoctoral fellowship SI

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. Both compounds are reversible competitive inhibitors of this enzyme, which is essential in these pathogenic bacteria. The crystal structures of M. tuberculosis and H. pylori in complex with (2S)-2-(4-methoxy)benzyl- and (2S)-2-perfluorobenzyl-3-dehydroquinic acids have been solved at 2.0, 2.3, 2.0, and 1.9 Å, respectively. The crystal structure of M. tuberculosis in complex with (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid is also reported at 1.55 Å. These crystal structures reveal key differences in the conformation of the flexible loop of the two enzymes, a difference that depends on the presence of electron-withdrawing or electron-donating groups in the aromatic moiety of the inhibitors. This loop closes over the active site after substrate binding, and its flexibility is essential for the function of the enzyme. These differences have also been investigated by molecular dynamics simulations in an effort to understand the significant inhibition potency differences observed between some of these compounds and also to obtain more information about the possible movements of the loop. These computational studies have also allowed us to identify key structural factors of the H. pylori loop that could explain its reduced flexibility in comparison to the M. tuberculosis loop, specifically by the formation of a key salt bridge between the side chains of residues Asp18 and Arg20 Financial support from the Xunta de Galicia (10PXIB2200122PR and GRC2010/12) and the Spanish Ministry of Science and Innovation (SAF2010-15076 to CGB and BFU2008-01588/BMC to M.J.vR.) is gratefully acknowledged. L.T., A.P., and V.F.V.P. thank the Spanish Ministry of Science and Innovation for FPU fellowships and the Portuguese Fundaca̧o para a Ciencia e a Tecnologia for an FCT fellowship, respectively. J.M.O. thanks the Xunta de Galicia and Spanish Ministry of Science and Innovation for “Ángeles Alvariño” and “José Castillejo” fellowships, respectively SI

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. The crystal structure of Mt-SK in complex with ADP and one of the most potent inhibitors has been solved at 2.15 Å. These studies reveal that the fixation of the diaxial conformation of the C4 and C5 hydroxyl groups recognized by the enzyme or the replacement of the C3 hydroxyl group in the natural substrate by an amino group is a promising strategy for inhibition because it causes a dramatic reduction of the flexibility of the LID and shikimic acid binding domains. Molecular dynamics simulation studies showed that the product is expelled from the active site by three arginines (Arg117, Arg136, and Arg58). This finding represents a previously unknown key role of these conserved residues. These studies highlight the key role of the shikimic acid binding domain in the catalysis and provide guidance for future inhibitor designs Financial support from ́ the Spanish Ministry of Economy and Competitiveness (SAF2010-15076 to CGB and BFU2011-24843 to M.J.vR.) and the Xunta de Galicia (10PXIB2200122PR and GRC2010/ 12) is gratefully acknowledged. B.B. thanks the Spanish Ministry of Education for her FPU fellowship. V.P. and C.G.D. thank the Spanish Ministry of Economy and Competitiveness for their respective FPI fellowships. J.M.O. thanks the Xunta de Galicia for a Plan I2C postdoctoral fellowship SI

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. The results show that an aromatic substituent on C2 prevents the closure of the active site by impeding the hydrogen-bonding interaction of Arg108 with the essential Tyr24 of the flexible loop, the residue that initiates catalysis. Chemical modifications of the reported acids were also carried out to improve internalization into Mycobacterium tuberculosis through an ester prodrug approach. Propyl esters proved to be the most efficient in achieving optimal in vitro activities.

The influence of replacing the d-phenylalanine residue with substituted and unsubstituted azoles on the structure and biological activity of the antibiotic gramicidinS 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 gramicidinS, 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, gramicidinS. In general for the triazole series, the hemolytic activity could be correlated with the antibacterial activity, that is, the higher the antibacterial activity, the higher the toxicity towards blood cells. Interestingly, its imidazole counterpart showed high antibacterial activity, combined with significantly diminished hemolytic activity. Turning circles! A series of substituted and unsusbstituted azole derivatives of gramicidinS were synthesised, analysed and tested against a range of bacteria and against erythrocytes. The compound where R=H and X=N exhibited high antibacterial and lower hemolytic activities, while a considerable loss of antibacterial activity was observed for the triazole derivative (R=H; X=CH). © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Restriction is good for inhibition! Tetrahydrobenzothiophene-derived rigid mimics of the typeII dehydroquinase (DHQ2)-catalyzed reaction intermediate are reported. These derivatives fix the interaction with the tyrosine, the base that initiates the enzymatic reaction, in an inappropriate orientation for catalysis. Two competitive inhibitors in the series, 2-propenyl derivative 5e and 2-cyclopropylethyl compound 5i (shown), were crystallized in complex with DHQ2 from Helicobacter pylori, and the X-ray structures were determined at 1.95A and 1.85A, respectively. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BACE-1 is one of the aspartic proteases involved in the cleavage of beta amyloid peptide, an initial step in the formation of amyloid plaques whose toxicity induces neuron death in Alzheimer's disease patients. One of the central issues in the search of novel BACE-1 inhibitors is the optimum pH for the binding of inhibitors to the enzyme. It is known that the enzyme has optimal catalytic activity at acidic pH, while cell active inhibitors may bind optimally at higher pH. In this work we determine the effect of the pH on the affinities of a set of inhibitors, with a variety of chemical motifs, for the ectodomain region of BACE-1 by a surface plasmon resonance (SPR) biosensor based assay. In order to understand the molecular interactions that underlie the diverse optimum pH for the binding of the various inhibitors as observed experimentally, we have calculated the titration curves for a set of BACE-1 ligand complexes. The results indicate that the pK(a) values of the titratable residues of the protein depend on the nature of the ligand involved, in disagreement with previous work. The enzyme-inhibitor structures with the resulting protonation states at pH values 4.5 and 7.4 served as the starting point for the prediction of the pH-dependent binding ranking. Our calculations reproduced the entire affinity ranking observed upon pH increase and most of the binding trends among inhibitors, especially at low pH. Finally, our cell-based assays indicate a possible correlation between high inhibitor affinity at both acidic and neutral pH values, with optimal cell response, a result that may open new venues for the search of potent BACE-1 inhibitors that are active at the cellular level.

et al., 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 β-hairp0in 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). We show that compound 8, containing the dipeptide isostere trans-MAA 4, has an apparent high structural resemblance with GS and that its antibacterial activity against a panel of Gram positive and -negative bacterial strains is better than the derivatives 6, 7 and 9. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA., Este trabajo ha sido financiado por una beca del Leiden Institute of Chemistry y por la subvención BFU2008-01588/BMC del Ministerio español de Ciencia e Innovación. José M. Otero ha sido apoyado económicamente por un contratro “Angeles Alvariño” de la Xunta de Galicia.

The shikimic acid pathway is essential to many pathogens but absent in mammals. Enzymes in its pathway are therefore appropriate targets for the development of novel antibiotics. Dehydroquinase is the third enzyme of the pathway, catalyzing the reversible dehydratation of 3-dehydroquinic acid to form 3-dehydroshikimic acid. Here we present the synthesis of novel inhibitors with high affinity for Helicobacter pylori type II dehydroquinase and efficient inhibition characteristics. The structure of Helicobacter pylori type II dehydroquinase in complex with the most potent inhibitor shows that the aromatic functional group interacts with the catalytic Tyr22 by π-stacking, expelling the Arg17 side chain, which is essential for catalysis, from the active site. The structure therefore explains the favorable properties of the inhibitor and will aid in design of improved antibiotics. © 2009 American Chemical Society., This work was supported by the Spanish Ministry of Science and Innovation (under Projects SAF2007-63533 to C.G.B., BFU2005-02974/BMC and BFU2008-01588/ BMC to M.J.v.R.), CSIC (Grant 488IE7 to M.J.v.R.), and the Xunta de Galicia (Grants PGIDT07PXIB209080PR and GRC2006/132 to C.G.B.). V.F.V.P., J.M.O., L.T., and P.G.-C. thank the Portuguese Fundaçao para a Ciência e a Tecnología for a FCT fellowship, the Xunta de Galicia for a “Angeles Alvariño” contract, and the Spanish Ministry of Science and Innovation for FPU fellowships, respectively. Data collection at EMBL/DESY was supported by the European Community FP6 Research Infrastructure Action “Structuring the European Research Area”, Contract No. RII3/CT/2004/5060008.

et al., 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. This peptide acts against both Gram-negative and Gram-positive bacteria, including several MRSA strains, and represents an interesting lead for the development of a broadly applicable antibiotic. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim., Trabajo financiado por el Ministerio de España de Educación y Ciencia (número de concesión: BFU2008–01588) y Xunta de Galicia.