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Irreversible inhibition of the enzyme type I dehydroquinase (DHQ1), a promising target for anti-virulence drug development, has been explored by enhancing the electrophilicity of specific positions of the ligand towards covalent lysine modification. For ligand design, we made use of the advantages offered by the intrinsic acid-base properties of the amino substituents introduced in the quinate scaffold, namely compounds 6–7 (R configuration at C3), to generate a potential leaving group, as well as the recognition pattern of the enzyme. The reactivity of the C2–C3 bond (Re face) in the scaffold was also explored using compound 8. The results of the present study show that replacement of the C3 hydroxy group of (–)-quinic acid by a hydroxyamino substituent (compound 6) provides a time-dependent irreversible inhibitor, while compound 7, in which the latter functionality was substituted by an amino group, and the introduction of an oxirane ring at C2–C3 bond, compound 8, do not allow covalent modification of the enzyme. These outcomes were supported by resolution of the crystal structures of DHQ1 from Staphylococcus aureus (Sa-DHQ1) and Salmonella typhi (St-DHQ1) chemically modified by 6 at a resolution of 1.65 and 1.90 Å, respectively, and of St-DHQ1 in the complex with 8 (1.55 Å). The combination of these structural studies with extensive molecular dynamics simulation studies allowed us to understand the molecular basis of the type of inhibition observed. This study is a good example of the importance of achieving the correct geometry between the reactive center of the ligand (electrophile) and the enzyme nucleophile (lysine residue) to allow selective covalent modification. The outcomes obtained with the hydroxyamino derivative 6 also open up new possibilities in the design of irreversible inhibitors based on the use of amino substituents.

We report the structure and charge transport properties of a novel solid-state proton conductor obtained by acid-base chemistry via proton transfer from 12-tungstophosphoric acid to imidazole. The resulting material (henceforth named Imid3WP) is a solid salt hydrate that, at room temperature, includes four water molecules per structural unit. To our knowledge, this is the first attempt to tune the properties of a heteropolyacid-based solid-state proton conductor by means of a mixture of water and imidazole, interpolating between water-based and ionic liquid-based proton conductors of high thermal and electrochemical stability. The proton conductivity of Imid3WP·4H2O measured at truly anhydrous conditions reads 0.8 × 10-6 S cm-1 at 322 K, which is higher than the conductivity reported for any other related salt hydrate, despite the lower hydration. In the pseudoanhydrous state, that is, for Imid3WP·2H2O, the proton conductivity is still remarkable and, judging from the low activation energy (Ea = 0.26 eV), attributed to structural diffusion of protons. From complementary X-ray diffraction data, vibrational spectroscopy, and solid-state NMR experiments, the local structure of this salt hydrate was resolved, with imidazolium cations preferably orienting flat on the surface of the tungstophosphate anions, thus achieving a densely packed solid material, and water molecules of hydration that establish extremely strong hydrogen bonds. Computational results confirm these structural details and also evidence that the path of lowest energy for the proton transfer involves primarily imidazole and water molecules, while the proximate Keggin anion contributes with reducing the energy barrier for this particular pathway.

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 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.

The first example of an ammonium derivative that causes a specific modification of the active site of type I dehydroquinase (DHQ1), a dehydratase enzyme that is a promising target for antivirulence drug discovery, is described. The resolution at 1.35 Å of the crystal structure of DHQ1 from Salmonella typhi chemically modified by this ammonium derivative revealed that the ligand is covalently attached to the essential Lys170 through the formation of an amine. The detection by mass spectroscopy of the reaction intermediates, in conjunction with the results of molecular dynamics simulations, allowed us to explain the inhibition mechanism and the experimentally observed differences between S. typhi and Staphylococcus aureus enzymes. The results presented here reveal that the replacement of Phe225 in St-DHQ1 by Tyr214 in Sa-DHQ1 and its hydrogen bonding interaction with the conserved water molecule observed in several crystal structures protects the amino adduct against further dehydration/aromatization reactions. In contrast, for the St-DHQ1 enzyme, the carboxylate group of Asp114, with the assistance of this water molecule, would trigger the formation of a Schiff base that can undergo further dehydration reactions until full aromatization of the cyclohexane ring is achieved. Moreover, in vitro antivirulence studies showed that the reported compound is able to reduce the ability of Salmonella Enteritidis to kill A459 respiratory cells. These studies have identified a good scaffold for the design of irreversible inhibitors that can be used as drugs and has opened up new opportunities for the development of novel antivirulence agents by targeting the DHQ1 enzyme Financial support from the Spanish Ministry of Science and Innovation (SAF2013-42899-R), Xunta de Galicia (GRC2013-041), and the European Regional Development Fund (ERDF) is gratefully acknowledged. E.L. thanks the Xunta de Galicia for his postdoctoral fellowship. A.B. thanks the Miguel Servet Programme ISCIII-FEDER (CP13/00226) and the ISCIIIGeneral Subdirection of Assesment and Promotion of the Research (PI14/00059) for financial support SI

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.

A strategy for the synthesis of the novel (6b R ,7 R ,8 S ,9 S ,10 S ,10a R )-8-(benzyloxy)-7,9,10-trihydroxy-6b,7,8,9,10,10a-hexahydro-11 H -benzo[ a ]carbazole-5,6-dione is reported. The key steps were the Michael addition of 2-hydroxy-1,4-naphthoquinone to 1-nitrocyclohexene or 3- O -benzyl-5,6-dideoxy-1,2- O -isopropylidene-6-nitro-α- d - xylo -hex-5-enefuranose and the diastereoselective intramolecular Henry reaction of 3- O -benzyl-5,6-dideoxy-5-C-(3′-hydroxy-1′,4′-naphthoquinon-2′-yl)-1,2- O -isopropylidene-6-nitro-α- d -glucofuranose to give the key (1 S ,2 S ,3 S ,4 R ,5 R ,6 R )-3-(benzyloxy)-1,2,4-trihydroxy-5-(3′-hydroxy-1′,4′-naphthoquinon-2′-yl)-6-nitrocyclohexane. When 2-hydroxy-1,4-naphthoquinone was replaced by (1,4-dimethoxynaphthalen-2-yl)lithium, the novel (1 R ,2 S ,3 S ,4 R ,4a S ,11b S )-2-(benzyloxy)-1,3,4-trihydroxy-1,2,3,4,4a,5-hexahydro-11b H -benzo[ b ]carbazole-6,11-dione was obtained.

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.

A novel promising strategy for the transformation of nitrosugars into branched pyrrolidines, based on double Henry reaction with formaldehyde followed by reductive ring closure, allowed the first enantiospecific synthesis of a 4-C-hydroxymethyl branched derivative of the well-known glycosidase inhibitor 1,4-dideoxy-1,4-imino-pentanol. This strategy also afforded a new route to some other interesting derivatives, such as N-hydroxy, N-propyloxy, and imino derivatives, a new kind of compounds with promising biological properties. [reaction: see text].

The irreversible inhibition of type I dehydroquinase (DHQ1), the third enzyme of the shikimic acid pathway, is investigated by structural, biochemical and computational studies. Two epoxides, which are mimetics of the natural substrate, were designed as irreversible inhibitors of the DHQ1 enzyme and to study the binding requirements of the linkage to the enzyme. The epoxide with the S configuration caused the covalent modification of the protein whereas no reaction was obtained with its epimer. The first crystal structure of DHQ1 from Salmonella typhi covalently modified by the S epoxide, which is reported at 1.4 Å, revealed that the modified ligand is surprisingly covalently attached to the essential Lys170 by the formation of a stable Schiff base. The experimental and molecular dynamics simulation studies reported here highlight the huge importance of the conformation of the C3 carbon of the ligand for covalent linkage to this type of aldolase I enzyme, revealed the key role played by the essential His143 as a Lewis acid in this process and show the need for a neatly closed active site for catalysis Financial support from the Spanish Ministry of Science and Innovation (SAF2013-42899-R), Xunta de Galicia (GRC2013-041) and the European Regional Development Fund (ERDF) is gratefully acknowledged. LT, AP and MM thank the Spanish Ministry of Education for their respective FPU fellowships. EL and JMO thank and the Xunta de Galicia for their respective postdoctoral fellowships SI

Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonella typhi in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, was solved at 1.5 Å. The present study reveals a previously unknown key role for conserved Glu, Phe and Met and Gln, Pro and Ala residues, with the latter three being located in the flexible substrate-covering loop. Glu was shown to be responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 was found to be key in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis. The present study could be useful in the rational design of inhibitors of this challenging and recognized target for the development of novel herbicides and antimicrobial agents This work was supported by the Spanish Ministry of Science and Innovation (grant number SAF2010-15076) and via FPU fellowships to M.M. and A.P., the Xunta de Galicia (grant number GRC2013/041) and via postdoctoral fellowships to E.L. and J.M.O., and by the European Regional Development Fund (ERDF) SI

In Alzheimer's disease, amyloid-β (Aβ) peptides aggregate into extracellular fibrillar deposits. Although these deposits may not be the prime cause of the neurodegeneration that characterizes this disease, inhibition or dissolution of amyloid fibril formation by Aβ peptides is likely to affect its development. ThT fluorescence measurements and AFM images showed that the natural antibiotic gramicidin S significantly inhibited Aβ amyloid formation in vitro and could dissolve amyloids that had formed in the absence of the antibiotic. In silico docking suggested that gramicidin S, a cyclic decapeptide that adopts a β-sheet conformation, binds to the Aβ peptide hairpin-stacked fibril through β-sheet interactions. This may explain why gramicidin S reduces fibril formation. Analogues of gramicidin S were also tested. An analogue with a potency that was four-times higher than that of the natural product was identified.

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

15 pags, 9 figs, One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA-binding J-binding protein 1 domain essential for biosynthesis and maintenance of DNA base-J (β-D-glucosyl-hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae. © 2011 Wiley-Liss, Inc., Grant sponsor: Spanish Ministry of Education and Science; Grant number: BFU2008-01588; Grant sponsor: European Commission; Grant number: NMP4-CT-2006-033256; Grant sponsor: Spanish Ministry of Education and Science (José Castillejo fellowship); Grant sponsor: Xunta de Galicia (Angeles Alvariño fellowship); Grant sponsor: National Institutes of Health; Grant numbers: K22-CA124517 (D.E.C.); R01-GM090161 (C.K.) GM074942; GM094585; Grant sponsor: U. S. Department of Energy, Office of Biological and Environmental Research; Grant number: DE-AC02-06CH11357 (to A.J.); Grant sponsor: Foundation for Polish Science (to K.M.); Grant sponsor: NSF; Grant number: DBI 0829586.

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.

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.