β-Peptides incorporating polyhydroxylated cyclohexane β-amino acid: synthesis and conformational study

We describe the synthesis of trihydroxylated cyclohexane β-amino acids from (-)-shikimic acid, in their cis and trans configuration, and the incorporation of the trans isomer into a trans-2-aminocyclohexanecarboxylic acid peptide chain. Subsequently, the hydroxyl groups were partially or totally deprotected. The structural study of the new peptides by FTIR, CD, solution NMR and DFT calculations revealed that they all fold into a 14-helix secondary structure, similarly to the homooligomer of trans-2-aminocyclohexanecarboxylic acid. This means that the high degree of substitution of the cyclohexane ring of the new residue is compatible with the adoption of a stable helical secondary structure and opens opportunities for the design of more elaborate peptidic foldamers with oriented polar substituents at selected positions of the cycloalkane residues.

Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight

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.

Hydroxylammonium derivatives for selective active-site lysine modification in the anti-virulence bacterial target DHQ1 enzyme

The first example of a hydroxylammonium derivative that causes a specific covalent modification of the active-site lysine residue of an aldolase enzyme, which is a promising target for anti-bacterial drug discovery, is reported.

Irreversible covalent modification of type I dehydroquinase with a stable Schiff base

Structural and computational studies carried out with two epoxides provide insight into the irreversible inhibition of type I dehydroquinase.

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. 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.

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. 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.

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. 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.

[Morbidity and mortality in a series of patients suffering from intraperitoneal neoplasia treated with peritoneal cytoreduction and hyperthermic intraperitoneal chemotherapy at the Fundación Santa Fe de Bogotá Teaching Hospital (ONCOLGroup--ATIA study)]

BACKGROUND

The procedure of radical peritonectomy followed by hyperthermic intraperitoneal chemotherapy (HIPEC) is considered the standard treatment for peritoneal cancers.

AIMS

To evaluate various outcomes in a cohort of patients with peritoneal tumors treated with HIPEC.

METHODS

Twenty-four patients consecutively treated with radical peritonectomy plus HIPEC within the time frame of November 2007 to July 2010 were enrolled; 15 (62%) had tumors of appendicular origin, 4 (16.7%) had primary peritoneal tumors, 2 had ovarian carcinomas and there was one case of colon cancer, one carcinosarcoma and one hemangioendothelioma. Mean age was 53 years (range: 26-68) and median follow-up was 14.2 months (range: 1-32). Demographic data, histology, peritoneal cancer index (PCI), surgical procedure characteristics, recurrence-free survival (RFS), and overall survival (OS) were all evaluated. Short-term morbidity and mortality were also determined.

RESULTS

Complete cytoreduction was achieved in 18 patients (75%). Mean PCI was 15 (<10: 41% and >10: 58%), and the median (range) for surgery duration, length of stay in the Intensive Care Unit, parenteral nutritional support, and hospital stay were 12,5 (7-20) hours, 11,4 (2-74) days, 13,8 (12-65) days, and 29,1 (10-90) days, respectively. One patient (4%) died 6 months after the procedure, due to multiple associated complications. Considerable morbidity was seen in 52% of cases, including thromboembolic events (41%), catheter-related bacteremia (29%), fistulas (29%), and nephrotoxicity (25%). Six patients (25%) recurred after a median of 21 months of RFS.

CONCLUSIONS

Cytoreductive surgery plus HIPEC in well-selected patients presenting with tumors that affect the peritoneum is a procedure that can be carried out in Colombia with an adequate safety and effectiveness profile. Mortality was similar to that reported in the international literature.

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

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.

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. Using this backbone structure as our benchmark we prepared a small series of ring-extended GS analogues featuring sugar amino acid dipeptide isosteres of varied hydrophobicity at the turn region. We show that via this approach hydrophobicity of extended GS analogues can be tuned without affecting the secondary structure (as observed from NMR and CD spectra). Biological evaluation reveals that hydrophobicity correlates to cell toxicity, but still bacteriolysis is induced with GS analogues that are too hydrophilic to efficiently lyse human red blood cells.

Preliminary Studies on the Transformation of Nitrosugars into Branched Chain Iminosugars: Synthesis of 1,4-Dideoxy-4-C-hydroxymethyl- 1,4-imino-pentanols

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].

Regression of symptomatic syringomyelia after resection of posterior fossa tumour

Syringomyelia associated with posterior fossa tumours is a very infrequent combination of pathological entities. The few cases which have been reported generally were asymptomatic in respect of the spinal cavitations. The authors report on a 36-year-old woman with a large extradural posterior fossa epidermoid tumour with a concomitant holocord symptomatic syringomyelia. Some of her symptoms were clearly attributed to the intraspinal cavitation. The lesions were both diagnosed by magnetic resonance imaging (MR). The patient did well after surgery of the brain lesion, with an objective improvement in her neurological status and a complete resolution of the syrinx documented by the MR 7 months after tumour removal. Syringomyelia in this case could be explained by blockage of the cerebrospinal fluid (CSF) circulation at the foramen magnum which in turn resulted in cranio-spinal pressure dissociation. This led to an accumulation of extracellular fluid (ECF) in the central canal, starting cavitation. Consequently, the syrinx was slowly expanded by the long-standing "slosh" effect of the systolic pressure waves. However, also via a distortion mechanism within the posterior fossa a pathologically plugged obex could have contributed to syrinx formation by means of preventing drainage of fluid from the ventricular CSF system.

A short-term longitudinal study of impulsivity and antisocial behavior

This study analyzes the relationships between impulsivity and antisocial behavior in a noninstitutionalized sample, taking into account the multidimensional nature of impulsivity and the diversity of types of antisocial behavior. Data were obtained in 1989 and 1990 from 1,226 adolescents aged 12-18 years (583 boys and 643 girls) as part of a longitudinal study of risk factors for drug abuse and delinquency. The patterns of stability or change of the various dimensions of antisocial behavior (rule breaking, vandalism, theft, aggression, and drug taking) in relation to impulsivity were investigated. The results support that self-report measures of impulsivity are closely correlated with antisocial behavior among adolescents. The longitudinally oriented analysis of this work also shows that impulsivity is associated with a future increase in antisocial behavior.

A short-term longitudinal study of impulsivity and antisocial behavior

This study analyzes the relationships between impulsivity and antisocial behavior in a noninstitutionalized sample, taking into account the multidimensional nature of impulsivity and the diversity of types of antisocial behavior. Data were obtained in 1989 and 1990 from 1,226 adolescents aged 12-18 years (583 boys and 643 girls) as part of a longitudinal study of risk factors for drug abuse and delinquency. The patterns of stability or change of the various dimensions of antisocial behavior (rule breaking, vandalism, theft, aggression, and drug taking) in relation to impulsivity were investigated. The results support that self-report measures of impulsivity are closely correlated with antisocial behavior among adolescents. The longitudinally oriented analysis of this work also shows that impulsivity is associated with a future increase in antisocial behavior.

Comparison among various methods of assessment of impulsiveness

The current confused status of the research on impulsivity may be attributed to the lack of precise definitions, the reliance of most operationalizations on a single index, and inconsistency among different measures of the construct. Empirical measurements of impulsivity by self-reports, rating scales, or performance tasks suggest that the instruments employed measure aspects that have very little in common, a finding that throws serious doubts on the validity of the construct and implies a need for further research. To clarify this topic, we applied four different measures of impulsivity to 46 7th-grade (12 to 13 years old) schoolchildren. The children were rated by their teachers on an impulsivity behavior scale and were administered Kagan's Matching Familiar Figures Test, Version MFF-20, and two self-report forms, the Eysenck Impulsiveness Questionnaire, and the Barratt Impulsiveness Scale. Although the results confirmed the lack of convergence among these measures, high latencies on matching were associated with the cognitive aspect of the self-report scales. Treating impulsivity as a multidimensional construct is discussed.

Management of 50 spontaneous cerebellar haemorrhages. Importance of obstructive hydrocephalus

The records of 50 cerebellar haemorrhages were reviewed retrospectively. In this series the most important factor for clinical development, management and mortality was the presence of obstructive hydrocephalus (p < 0.01). Slowly progressive (type 1) and abruptly developing (type 2) deterioration of consciousness was significantly related to high mortality; this holds also true for the combination of hydrocephalus with an haematoma diameter > 3 cm. Larger haematomas had a higher mortality but this relation, analyzed alone, did not reach statistical significance (p > 0.05). In cases with hydrocephalus mortality could significantly be reduced by surgical evacuation of the haematoma (p < 0.01). The treatment of cerebellar haemorrhages must be directed at resolving obstructive hydrocephalus.

Population, labour force and unemployment in Andalusia: prospects for 1993

"This paper is concerned with forecasting population, employment, labour force and unemployment in Andalusia [Spain] to 1993. For this purpose, a block-recursive demoeconomic model is presented. The demographic submodel is based on the component-cohort method of forecasting population by age and sex. The economic submodel uses econometric and time series analysis to forecast employment both in the medium and short-term. In the labour market part, the labour force is forecasted taking into account the encouraged-discouraged worker effects of changes in the demand for labour."

Operant escape learning in decerebrate duck embryos

Peking duck embryos were trained in an operant escape task on Day 25 of incubation (total incubation period = 27 days) following decerebration on Day 24 of incubation. Experimental embryos successfully acquired the operant response, which involved the performance of a discrete foot flexion in order to terminate a shock applied to the wing. The decerebrate embryos resembled normal, unoperated embryos of this age in their acquisition of the operant behavior. This study demonstrates that this form of learning can be acquired without benefit of telencephalic structures, at least at this point in development. Differences in the consequences of decerebration during prenatal or neonatal versus adult stages are discussed.