bluuebunny/crossref_metadata_2025 huggingface dataset:
PNA zipper as a dimerization tool: Development of a bZip mimic
Authors: Pensato Soccorsa , Renda Mario , Leccia Felicia , Saviano Michele , D'Andrea Luca D. , Pedone Carlo , Pedone Paolo V. , Romanelli Alessandra
Published: November 2009

The article describes the use of a PNA duplex (PNA zipper) as a tool to dimerize or bring in close proximity two polypeptides or protein domains. The amino acid sequence to be dimerized is covalently bound to complementary PNA sequences. Annealing of the PNA strands results in dimer formation. To test the ability of the “PNA‐zipper” as a dimerization tool, we designed a GCN4 mimetic, where the leucine‐zipper dimerization domain was replaced by the PNA zipper, whereas the basic DNA‐binding domain was covalently attached to the PNA. The molecule was assembled by chemical ligation of the peptide corresponding to the DNA‐binding domain of GCN4 modified with a succinyl thioester with two complementary PNAs harboring a cysteine residue. Electromobility‐shift experiments show the ability of the PNA zipper‐GCN4 to bind selected DNA duplexes. The PNA zipper‐GCN4 binds both the TRE and CRE DNA sites, but it does not bind TRE and CRE mutants containing even a single base mutation, as the native GCN4. The ability to fold upon complexation with DNA was investigated by CD. A good correlation between the ability of the PNA zipper‐GCN4 to fold into α helices and the ability to bind DNA was found. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 434–441, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Australasian Laparoscopic Colon Cancer Study shows that elderly patients may benefit from lower postoperative complication rates following laparoscopic versus open resection
Authors: Allardyce R A , Bagshaw P F , Frampton C M , Frizelle F A , Hewett P J , Rieger N A , Smith J S , Solomon M J , Stevenson A R L
Published: November 2009

Background

A retrospective analysis of age-related postoperative morbidity in the Australia and New Zealand prospective randomized controlled trial comparing laparoscopic and open resection for right- and left-sided colonic cancer is presented.

Methods

A total of 592 eligible patients were entered and studied from 1998 to 2005.

Results

Data from 294 patients who underwent laparoscopic and 298 who had open colonic resection were analysed; 266 patients were aged less than 70 years and 326 were 70 years or older (mean(s.d.) 70·3(11·0) years). Forty-three laparoscopic operations (14·6 per cent) were converted to an open procedure. Fewer complications were reported for intention-to-treat laparoscopic resections compared with open procedures (P = 0·002), owing primarily to a lower rate in patients aged 70 years or more (P = 0·002). Fewer patients in the laparoscopic group experienced any complication (P = 0·035), especially patients aged 70 years or above (P = 0·019).

Conclusion

Treatment choices for colonic cancer depend principally upon disease-free survival; however, patients aged 70 years or over should have rigorous preoperative investigation to avoid conversion and should be considered for laparoscopic colonic resection. Registration number: NCT00202111 (http://www.clinicaltrials.gov).
Disease recurrence patterns after R0 resection of hilar cholangiocarcinoma
Authors: Kobayashi A , Miwa S , Nakata T , Miyagawa S
Published: November 2009

Background

There is little information regarding the clinical behaviour of hilar cholangiocarcinoma after curative resection.

Methods

A retrospective study was undertaken of 79 consecutive patients with hilar cholangiocarcinoma who had undergone major hepatectomy (three or more Couinaud segments) concomitant with caudate lobectomy, and had negative resection margins. Sites of initial disease recurrence were classified as locoregional (porta hepatis) or distant (intrahepatic, peritoneal, para-aortic lymph nodal or extra-abdominal). Univariable and multivariable analyses were performed to determine the factors potentially related to recurrence.

Results

Disease recurrence was observed in 42 (53 per cent) of the 79 patients. Cumulative recurrence rates at 3 and 4 years after surgery were 52 and 56 per cent respectively. Locoregional recurrence alone was observed in eight (10 per cent) and distant metastasis in 34 (43 per cent) of the 79 patients after R0 resection. Positive nodal involvement and high International Union Against Cancer tumour (T) stage were independent prognostic factors associated with distant metastasis.

Conclusion

Distant metastases are more common than locoregional recurrence after R0 resection for hilar cholangiocarcinoma, and associated with nodal involvement and high T stage.
Randomized clinical trial of perianal surgery performed under spinal saddle block versus total intravenous anaesthesia
Authors: Schmittner M D , Schreiber H , Janke A , Weiss C , Blunk J , Bussen D G , Luecke T
Published: November 2009

Background

The aim of this randomized clinical trial was to determine whether spinal saddle block (SSB) is superior to total intravenous anaesthesia (TIVA) in perianal surgery.

Methods

Suitable patients aged 18–75 years (American Society of Anesthesiologists grade I or II) scheduled to undergo perianal surgery were randomized to SSB (1·0 ml 0·5 per cent hyperbaric bupivacaine) or TIVA with propofol and fentanyl by means of a laryngeal mask. Cumulative consumption of analgesics within 24 h after surgery was recorded, and postoperative recovery and patient satisfaction were evaluated.

Results

A total of 201 patients were randomized. Supplemental analgesia within 24 h after surgery was required by 31 of 101 patients having SSB and 58 of 100 who had TIVA (P < 0·001). Median monitoring time in the recovery room was 5 (range 1–45) min for SSB versus 44 (4–148) min for TIVA (P < 0·001). Patients in the SSB group were able to eat and drink more quickly, although times to mobilization and micturition were not significantly different. Patients having SSB were more likely to describe the anaesthesia as ‘better than expected’.

Conclusion

SSB is superior to TIVA in patients undergoing perianal surgery in terms of analgesic consumption within 24 h after surgery and aspects of postoperative recovery. Registration number: ISRCTN41981381 (http://www.controlled-trials.com).
Randomized clinical trial of laparoscopic versus open donor nephrectomy
Authors: Nicholson M L , Kaushik M , Lewis G R R , Brook N R , Bagul A , Kay M D , Harper S J , Elwell R , Veitch P S
Published: November 2009

Background

This randomized controlled trial was designed to determine the safety and efficacy of laparoscopic donor nephrectomy (LDN) in comparison with short-incision open donor nephrectomy (ODN).

Methods

Eighty-four live kidney donors were randomized in a 2 : 1 ratio to LDN (56 patients) or short-incision ODN without rib resection (28). Primary endpoints were pain relief and duration of inpatient stay.

Results

There was no donor death or allograft thrombosis in either group. The first warm ischaemic time median (range) 4 (2–7) versus 2 (1–5) min; P = 0·001) and the duration of operation (160 (110–250) versus 150 (90–200); P = 0·004) were longer for LDN. LDN led to a reduction in parenteral morphine requirement 59 (6–136) versus 90 (35–312) mg; P = 0·001) and hospital stay (4 (2–6) versus 6 (2–9) days; P = 0·001), and earlier return to employment (42 (14–84) versus 66·5 (14–112) days; P = 0·004). Postoperative respiratory function was improved after LDN. There were more postoperative complications per donor in the ODN group (0·6(0·7) versus 0·3(0·5); P = 0·033). At a median follow-up of 74 months, there were no differences in renal function or allograft survival between the groups.

Conclusion

LDN removes some of the disincentives to live donation without compromising the outcome of the recipient transplant.
PCR cloning of partial nbs sequences from grape (Vitis aestivalis Michx)
Authors: Chang Ming‐Mei , DiGennaro Peter , Macula Anthony
Published: November 2009

Plants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide‐binding site (NBS) and leucine‐rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R genes. Here, we report a 4‐week undergraduate laboratory exercise that mimics the research environment to PCR‐clone partial nbs sequences using degenerate primers corresponding to the phosphate‐binding loop (P‐loop) and GLPL motifs within the NBS domain of potential R gene products from the North American grape, Vitis aestivalis Michx. Students were able to complete the laboratory procedures successfully and obtained four different clones, among which three are new. Through the laboratory exercise, students learned a variety of important molecular techniques including genomic DNA isolation, DNA quantification, PCR, agarose gel electrophoresis, DNA extraction from agarose gel, ligation, bacterial transformation, and plasmid DNA isolation and purification. They also used currently available web‐based bioinformatic programs for sequence analysis. The laboratory exercise provides students the hands‐on experience on PCR cloning and shows them how it is done in a research environment. The clones obtained may be further tested for their potential use as markers to differentiate resistant cultivars from the susceptible ones, a useful tool in breeding programs.
Using Pseudomonas putida xylE gene to teach molecular cloning techniques for undergraduates
Authors: Dong Xu , Xin Yi , Ye Li , Ma Yufang
Published: November 2009

We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. Pseudomonas putida xylE gene, encoding catechol 2, 3‐dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students a chance to mimic real research and product development by connecting separated techniques. This serial experiment helped students set up intact idea of molecular biology and to understand the relation of each individual operation.
Algorithm for writing a scientific manuscript
Authors: O'Connor Timothy R. , Holmquist Gerald P.
Published: November 2009

We present an algorithm for the construction of a strong initial draft. It is designed to overcome writer's block and to assist scientists who are not native English speakers. The writing starts with making figures and tables. These suggest several terse summary statements, the few major conclusions or observations the author will present to the scientific community. After identification of the audience, the specific community addressed, materials and methods are written to explain how the tables and figures were generated. Results are initially restricted to describing the logical data relations in each table and figure. The discussion then converts each data relationship into mechanistic cause‐and‐effect interpretations suitable for the abstract. A brief epilogue deals with the submission and the fate of the final manuscript once submitted. Although other models for the initial draft exist, this model has worked for us and new researchers in our laboratories and addresses problems we encountered while editing manuscripts.
Detergent‐based isolation of yeast membrane rafts
Authors: Willhite D. Grant , Wright Stephen E.
Published: November 2009

Lipid rafts have been implicated in numerous cellular processes including cell signaling, endocytosis, and even viral infection. Isolation of these lipid rafts often involves detergent treatment of the membrane to dissolve nonraft components followed by separation of raft regions in a density gradient. We present here an inquiry‐based lab series using these techniques to isolate membrane rafts from yeast cells designed for the upper division biochemistry or cell biology course laboratory. The co‐localization of a common raft‐associated protein with lipid rafts is then followed. This lab series involves undergraduate cell biology or biochemistry students in each step of the scientific process from experimental design to dissemination of their results. Additionally, this lab series reinforces concepts in membrane structure while exposing undergraduates to common techniques in cell biology and biochemistry.
Problem‐solving test: The effect of synonymous codons on gene expression
Authors: Szeberényi József
Published: November 2009

Terms to be familiar with before you start to solve the test: the genetic code, codon, degenerate codons, protein synthesis, aminoacyl‐tRNA, anticodon, antiparallel orientation, wobble, unambiguous codons, ribosomes, initiation, elongation and termination of translation, peptidyl transferase, translocation, degenerate oligonucleotides, green fluorescent protein, expression plasmid, cDNA, electron microscopy, fluorescence microscopy, phase contrast microscopy, bacteriophage, promoter, gene library, Northern blotting, Western blotting, in silico analysis, and hairpin structures.
Sustainable development and intangibles: building sustainable intellectual capital
Authors: López‐Gamero María D. , Zaragoza‐Sáez Patrocinio , Claver‐Cortés Enrique , Molina‐Azorín José F.
Published: November 2009

Sustainable intellectual capital is a promising starting‐point for the incorporation of environmental aspects into the general management system of a firm. This paper examines how sustainable intellectual capital helps to overcome the shortcomings of conventional approaches to environmental management systems. It does this by extending the concept of sustainability from relational capital to the three pillars of intellectual capital: human, structural and relational intellectual capital. A multiple case study was carried out with Spanish firms characterized by their high level of environmental leadership. The findings indicated that sustainable human intellectual capital, environmental training, information and awareness sessions help in the accumulation and utilization of knowledge. As for sustainable structural intellectual capital, the environmental technology portfolio is improved and new environmental departments are created. Regarding sustainable relational intellectual capital, the firm–environment link is very important. In the primary and secondary sectors suppliers become involved to a greater extent in the environmental management process, whereas in the service sector it is the customer who becomes more involved. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.
Effects of defendant and victim race on perceptions of juvenile sex offenders
Authors: Stevenson Margaret C. , Sorenson Katlyn M. , Smith Amy C. , Sekely Ady , Dzwairo Rukudzo A.
Published: November 2009

We investigated effects of defendant race, victim race, and juror gender on public perceptions of a juvenile sex offense. We predicted that participants, particularly men, would support registering a juvenile defendant as a sex offender more when he was Black than White and that participants, particularly women, would support registering the defendant more when the female crime victim was portrayed as White than as Black. We also expected that support for registration would be higher when the defendant and victim were different races than when they were the same race. As expected, women (but not men) recommended registration more when the victim was White than Black. Further, participants supported registration more when the defendant and the victim were different races than when they were the same race. These effects were mediated by retributive goals to punish the offender—not by utilitarian goals to protect society. Explanations and implications are discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Differential correlates to self‐report and parent‐report of callous–unemotional traits in a sample of juvenile sexual offenders
Authors: White Stuart F. , Cruise Keith R. , Frick Paul J.
Published: November 2009

The association of callous–unemotional (CU) traits with violence and severe antisocial behavior has led to a recent focus on the association between CU traits and sexual offending behavior. When assessing juveniles with sexual offenses, practice standards recommend that multiple sources of data are considered. However, the differential correlates of parent‐report versus self‐report of CU traits in juvenile sex offenders have not been investigated. A sample of 94 detained male youth (mean age = 15.22, SD = 1.48) was administered both youth and parent versions of the Inventory of Callous–Unemotional Traits (ICU), a general delinquency risk assessment tool (YLS), and a sexual offending risk assessment tool (J‐SOAP‐II) to investigate concordance between self‐report and parent‐report of CU traits as well as association with general and sex‐specific risk factors. Both parent‐report and self‐report of CU traits were significantly related to higher general delinquency risk scores, with parent‐report showing stronger correlations than self‐report. Both parent‐report and self‐report were related to sex‐specific risk factors. However, only parent‐report significantly predicted static sexual risk, while self‐report significantly predicted dynamic sexual risk scores. Evidence supports the importance of including both parent‐ and self‐report of CU traits in the comprehensive assessment of sexually offending youth. Copyright © 2009 John Wiley & Sons, Ltd.
Assessment of embryonic growth in chicken eggs by means of visible transmission spectroscopy
Authors: Kemps Bart J. , Bamelis Flip R. , Mertens Kristof , Decuypere Eddy M. , De Baerdemaeker Josse G. , De Ketelaere Bart
Published: November 2009

During this work, it was investigated whether spectral measurements can be used to monitor embryonic growth. An experiment was conducted in which both the transmission spectra and embryonic weight were determined on 240 eggs (Cobb, 37 weeks) between Day 5 and Day 10 of incubation. The spectral data were linked to embryonic weight by means of a partial least squares analysis. Different preprocessing procedures were compared during this work, that is, smoothing, multiplicative scatter correction (MSC), and first‐ and second‐order derivative. Compared to the remainder of the preprocessing procedures, MSC leads to a considerable improvement of the prediction capability of the embryonic weight. The ratio of performance to deviation obtained for the MSC spectra equaled 4.5 indicating that a very accurate prediction of embryonic weight is feasible based on the VIS/NIR transmission measurements. Important regions for the prediction are situated around 685–740 nm. It is suggested that the spectral changes in these spectral regions result from the displacement of carotenoids from the yolk into the blood circuitry. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Understanding the key factors for enzymatic conversion of pretreated lignocellulose by partial least square analysis
Authors: Huang Renliang , Su Rongxin , Qi Wei , He Zhimin
Published: November 2009

The relationship between the physicochemical properties of lignocellulosic substrates and enzyme digestion is still not well known. After different pretreatments, cellulase hydrolysis and measurements of physicochemical characteristics by column solute exclusion, particle size analysis, X‐ray diffraction, Fourier transform infrared spectroscopy and solid state 13C nuclear magnetic resonance were performed in this study. Partial least squares was then applied to seek the key factors limiting the rate and extent of cellulose digestion. According to the PLS results, the most important factor for cellulose digestion was accessible interior surface area, followed by delignification and the destruction of the hydrogen bonds. The cellulose digestion at 2 and 24 hr were improved with the increased accessibility of interior surface area to the reporter molecules of 5.1‐nm diameter. Removal of lignin and breaking of hydrogen bonds were also found to significantly promote cellulose conversion. Other properties, including the breakdown of intramolecular hydrogen bonds, cellulose crystallinity, and hemicellulose content, had less effect on the efficiency of enzymatic hydrolysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Mimic of a large‐scale diafiltration process by using ultra scale‐down rotating disc filter
Authors: Ma Guijun , Aucamp Jean , Gerontas Spyridon , Eardley‐Patel Ranna , Craig Alan , Hoare Mike , Zhou Yuhong
Published: November 2009

Ultra scale‐down (USD) approach is a powerful tool to predict large‐scale process performance by using very small amounts of material. In this article, we present a method to mimic flux and transmission performance in a labscale crossflow operation by an USD rotating disc filter (RDF). The Pellicon 2 labscale system used for evaluation of the mimic can readily be related to small pilot and industrial scale. Adopted from the pulsed sample injection technique by Ghosh and Cui (J Membr Sci. 2000;175:5‐84), the RDF has been modified by building in inserts to allow the flexibility of the chamber volume, so that only 1.5 mL of processing material is required for each diafiltration experiment. The reported method enjoys the simplicity of dead‐end mode operation with accurate control of operation conditions that can mimic well the crossflow operation in large scale. Wall shear rate correlations have been established for both the labscale cassette and the USD device, and a mimic has been developed by operating both scales under conditions with equivalent averaged shear rates. The studies using E. coli lysate show that the flux vs. transmembrane pressure profile follows a first‐order model, and the transmission of antibody fragment (Fab′) is independent of transmembrane pressure. Predicted flux and transmission data agreed well with the experimental results of a labscale diafiltration where the cassette resistance was considered. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Disposal and simple living: exploring the circulation of goods and the development of sacred consumption
Authors: Cherrier Hélène
Published: November 2009

This study examines how consumers who engage in voluntary simplicity experience disposal in relation to changes in their values, identity, and lifestyle. The hermeneutic analysis shows disposal organized around three main themes: “desire for emancipation,” “sacrificing the surplus,” and “moving toward the sacred.” Each theme offers insights on disposal as a transcendental experience during which consumers relocate consumption meanings from the profane to the sacred. On the one hand, the practice of disposal symbolizes a distance from the profane marketplace and its constraining norms and on the other hand, it leads consumers to participate in the life of objects and to construct sacred consumption. Here, goods are removed from the profane commerce and transferred to sacredness with an eternal life of transit between hands and ownership. As such, goods can be regarded as alive, physically moving from one person to another. This article concludes that voluntary disposal can be seen as a form of empowerment. Through disposal, consumers participate in the life of objects. By contributing to the circulation of the material, consumers have the power to transform an act of pure elimination into a transcendental experience that prefigures the death of profane consumption and the birth of sacred consumption.

Copyright © 2009 John Wiley & Sons, Ltd.
Not moving things along: hoarding, clutter and other ambiguous matter
Authors: Maycroft Neil
Published: November 2009

Disposition and disposal are intriguing terms for, while they share the same roots, disposition is not usually understood popularly as a synonym of disposal. However, all disposal involves disposition as a prelude to destruction, reuse, recycling or redistribution of some sort. Here, however, disposition is considered in another sense; the relocation of an object without the attendant continuation of the disposal process. In particular, the paper considers the phenomena of the domestic hoarding of goods. Hoarding will be considered in relation to both opportunities for disposition and other types of ‘ambiguous’ stuff including clutter. Following this, hoarding as behaviour in relation to the spatial ‘disordering’ of material culture will be examined. Finally, the material nature of the hoard itself will be addressed. It is concluded that hoarding is an ambiguous concept without clear agreement as to its causes, characteristics, scope or significance. Its affinities with other forms of collecting, storing and ‘arranging’ matter also demand further attention. Finally, the paper calls for more empirical research as both adjunct and potential counterweight to its theoretical orientation.

Copyright © 2009 John Wiley & Sons, Ltd.
From trash to treasure and beyond: the meaning of voluntary disposition
Authors: Albinsson Pia A. , Perera B. Yasanthi
Published: November 2009

Extant consumer research literature focuses on the subtleties, multiplicity of meanings, and values consumers attach to acquisition of personal possessions. Researchers have devoted less attention to consumers' disposition behaviors, including factors that influence disposition decisions. This paper explores voluntary disposition using data gathered through participant observations and in‐depth interviews with a range of consumers, including those involved in clothing exchange (CE) events. The findings provide support for the a priori themes of values and consumption patterns, extending the life of self and goods, and consumers' self‐concept. Additionally, the findings yield emergent themes of role transitions, role models and family patterns, and shared community. Utilizing our findings, and extant literature, we propose a conceptual Framework of Voluntary Disposition that can be utilized to analyze further meanings of consumer disposition patterns in different contexts.

Copyright © 2009 John Wiley & Sons, Ltd.
Improving Compound Quality through in vitro and in silico Physicochemical Profiling
Authors: van de Waterbeemd Han
Published: November 2009

Many compounds entering clinical studies do not survive the numerous hurdles for a good pharmacological lead to a drug on the market. The reasons for attrition have been widely studied which resulted in more early attention to compound quality related to physical chemistry, drug metabolism and pharmacokinetics (DMPK), and toxicology/safety. This paper will briefly review current physicochemical in vitro assays and in silico predictions to support compound and library design through to lead optimization. The most important physicochemical properties include lipophilicity (log P/D), pKa, solubility, and permeability. These drive key ADMET properties such as absorption, cell penetration, access to the brain, volume of distribution, plasma protein binding, metabolism, and toxicity, as well as biopharmaceutical behavior. Much data are now available from medium‐ to high‐throughput physchem and ADMET in vitro assays, either in the public domain (see, e.g., PubChem, PubMed) or in drug companies' in‐house databases. Such data are increasingly being computer‐modelled and used in predictive chemistry. New pipelining technology makes it easier to build and update QSAR models so that such models can use the latest available data to produce robust local and global predictive in silico ADMET models.
Large‐Scale Evaluation of log P Predictors: Local Corrections May Compensate Insufficient Accuracy and Need of Experimentally Testing Every Other Compound
Authors: Tetko Igor V. , Poda Gennadiy I. , Ostermann Claude , Mannhold Raimund
Published: November 2009

A large variety of log P calculation methods failed to produce sufficient accuracy in log P prediction for two in‐house datasets of more than 96000 compounds contrary to their significantly better performances on public datasets. The minimum Root Mean Squared Error (RMSE) of 1.02 and 0.65 were calculated for the Pfizer and Nycomed datasets, respectively, in the ‘out‐of‐box’ implementation. Importantly, the use of local corrections (LC) implemented in the ALOGPS program based on experimental in‐house log P data significantly reduced the RMSE to 0.59 and 0.48 for the Pfizer and Nycomed datasets, respectively, instantly without retraining the model. Moreover, more than 60% of molecules predicted with the highest confidence in each set had a mean absolute error (MAE) less than 0.33 log units that is only ca. 10% higher than the estimated variation in experimental log P measurements for the Pfizer dataset. Therefore, following this retrospective analysis, we suggest that the use of the predicted log P values with high confidence may eliminate the need of experimentally testing every other compound. This strategy could reduce the cost of measurements for pharmaceutical companies by a factor of 2, increase the confidence in prediction at the analog design stage of drug discovery programs, and could be extended to other ADMET properties.
Membrane Permeability in the Gastrointestinal Tract: The Interplay between Microclimate pH and Transporters
Authors: Kristl Albin
Published: November 2009

Some examples of pH‐ and transporter‐dependent permeability, determined in side‐by‐side diffusion cells, are summarized. We investigated the polarized transport in the mucosal‐to‐serosal direction of monocarboxylic acid‐type drugs through the excised rat jejunal tissue and an artificial membrane. We established that,in vitro, these substances are most probably not transported by monocarboxylate transporter 1, but by passive pH‐dependent transport. We also studied various influences on the permeability of fluorescein, a low permeability marker, through isolated rat intestinal segments, Caco‐2 cell monolayers, and an artificial membrane. Polarized transport of fluorescein in the serosal‐to‐mucosal direction through the rat jejunum by multidrug resistance‐associated protein was triggered by the addition ofD‐glucose to the mucosal side, while the pH‐dependent increase of fluorescein influx is presumably the consequence of a monocarboxylate transporter and a member of the organic‐anion transporting polypeptide family. With permeability experiments through the excised segments of rat small intestine, we ascertained that ciprofloxacin is a low‐permeability drug and has higher and pH‐dependent transport in the mucosal‐to‐serosal direction than in the opposite direction. We also established that neither the permeability of fluoroquinolones nor their solubility in different buffers was influenced by the interactions with metal cations.
Miniaturization of Powder Dissolution Measurement and Estimation of Particle Size
Authors: Avdeef Alex , Tsinman Konstantin , Tsinman Oksana , Sun Na , Voloboy Dmytro
Published: November 2009

The objective was to investigate the applicability and limitations of an approach for estimating particle size from powder dissolution measurement using as little as 50 μg of sample in 1 ml of buffer solutions. The powder dissolution profiles of five sparingly‐soluble drugs (hydrochlorothiazide, phenazopyridine hydrochloride, 2‐naphthoic acid, indomethacin, and dipyridamole) were evaluated with a novel biexponential spherical particle equation and also the Wang–Flanagan spherical particle non‐sink equation. The results were compared to particle sizing based on measured specific surface area by the Brunauer–Emmett–Teller (BET) method, and also based on Coulter counting. With the exception of hydrochlorothiazide, the model compounds indicated some agglomeration in the dissolution media. The dry‐state specific surface area was larger than expected from either the Coulter method or the powder‐dissolution data, especially for phenazopyridine hydrochloride. The particle radii estimated by the powder dissolution method ranged from 10 to 68 μm, with equilibrium solubilities spanning from 5 μg/ml (dipyridamole) to 911 μg/ml (hydrochlorothiazide). Powder dissolution data collected with the miniaturized apparatus can be used to determine particle size, with estimated values agreeing reasonably with those measured by the Coulter counter method.
Addressing Central Nervous System (CNS) Penetration in Drug Discovery: Basics and Implications of the Evolving New Concept
Authors: Reichel Andreas
Published: November 2009

Despite enormous efforts, achieving a safe and efficacious concentration profile in the brain remains one of the big challenges in central nervous system (CNS) drug discovery and development. Although there are multiple reasons, many failures are due to underestimating the complexity of the brain, also in terms of pharmacokinetics (PK).

To this day, PK support of CNS drug discovery heavily relies on improving the blood–brain barrier (BBB) permeabilityin vitroand/or the brain/plasma ratio (Kp)in vivo, even though neither parameter can be reliably linked to pharmacodynamic (PD) and efficacy readouts. While increasing BBB permeability may shorten the onset of drug action, an increase in the total amount in brain may not necessarily increase the relevant drug concentration at the pharmacological target. Since the traditionalKpratio is based on a crude homogenization of brain tissue, it ignores the compartmentalization of the brain and an increase favors non‐specific binding to brain lipids rather than free drug levels.

To better link exposure/PK to efficacy/PD and to delineate key parameters, an integrated approach to CNS drug discovery is emerging which distinguishes total from unbound brain concentrations. As the complex nature of the brain requires different compartments to be considered when trying to understand and improve new compounds, several complementary parameters need to be measuredin vitroandin vivo, and integrated into a coherent model of brain penetration and distribution.

The new paradigm thus concentrates on finding drug candidates with the right balance between free fraction in plasma and brain, and between rate and extent of CNS penetration. Integrating this data into a coherent model of CNS distribution which can be linked to efficacy will allow it to design compounds with an optimal mix in physicochemical, pharmacologic, and pharmacokinetic properties, ultimately mitigating the risk for failures in the clinic.
Prodrug Approaches for Enhancing the Bioavailability of Drugs with Low Solubility
Authors: Müller Christa E.
Published: November 2009

Low water solubility and low bioavailability are frequent problems in drug development, particularly in the area of central nervous system (CNS) drugs. This short review describes selected prodrug approaches which have been developed to enhance the bioavailability of drugs, especially that of poorly soluble drugs. Some of the most successful drugs on the market are prodrugs. With a better understanding of active‐transport processes at cell membranes in the gut as well as at the blood–brain barrier, the importance of prodrug approaches will further increase in the future. Prodrug approaches will already be considered in the early phase of drug discovery.
The Unstirrable Water Layer Is Unstirrable because It Does Not Exist
Authors: Scherrer Robert A.
Published: November 2009

A number of membrane‐permeation models require the incorporation of an unstirred or unstirrable water layer (UWL). An example occurs in PAMPA models when the effective permeation rate of lipophilic acids and bases, Pe, falls behind the expected permeation rate, Pm, at pH values providing a high concentration of unionized species in the donor phase. In such cases, the compound has an apparent pKa of a weaker acid or base. The explanation is that an UWL adjacent to the membrane provides a rate‐limiting diffusion barrier for such compounds. The thickness of the UWL is correlated with the difference between the aqueous pKa and the apparent pKa (pK$\rm{ {_{a}^{flux}}}$). Here, we provide an explanation for the pK$\rm{ {_{a}^{flux}}}$ term that requires no UWL. It comes from the fact that, in the process of passing into a membrane, an ionizable compound undergoes a change in pKa. At some point along its path into the membrane, the compound attains a maximum free energy, at which point it is as likely to continue into the membrane, as it is to return to the donor phase. This is the transition state for absorption. The pK$\rm{ {_{a}^{flux}}}$ is the pKa of the compound at the transition state. This is a testable hypothesis (see text). The relevance of absorption to permeation depends on the rate‐limiting step of permeation.
An Expert System Approach to the Assessment of Hepatotoxic Potential
Authors: Marchant Carol A. , Fisk Lilia , Note Reine R. , Patel Mukesh L. , Suárez Diana
Published: November 2009

Hepatotoxicity is a major cause of pharmaceutical drug attrition and is also a concern within other chemical industries. In silico approaches to the prediction of hepatotoxicity are an important tool in the early identification of adverse effects in the liver associated with exposure to a chemical. Here, we describe work in progress to develop an expert system approach to the prediction of hepatotoxicity, focussing particularly on the identification of structural alerts associated with its occurrence. The development of 74 such structural alerts based on public‐domain literature and proprietary data sets is described. Evaluation results indicate that, whilst these structural alerts are effective in identifying the hepatotoxicity of many chemicals, further research is needed to develop additional structural alerts to account for the hepatotoxicity of a number of chemicals which is not currently predicted. Preliminary results also suggest that the specificity of the structural alerts may be improved by the combined use of applicability domains based on physicochemical properties such as log P and molecular weight. In the longer term, the performance of predictive models is likely to benefit from the further integration of diverse data and prediction model types.
Predicting Ligand Interactions with ABC Transporters in ADME
Authors: Demel Michael A. , Krämer O. , Ettmayer Peter , Haaksma Eric E. J. , Ecker Gerhard F.
Published: November 2009

ABC‐type drug efflux pumps, e.g., ABCB1 (=P‐glycoprotein, =MDR1), ABCC1 (=MRP1), and ABCG2 (=MXR, =BCRP), confer a multi‐drug resistance (MDR) phenotype to cancer cells. Furthermore, the important contribution of ABC transporters for bioavailability, distribution, elimination, and blood–brain barrier permeation of drug candidates is increasingly recognized.

This review presents an overview on the different computational methods and models pursued to predict ABC transporter substrate properties of drug‐like compounds. They encompass ligand‐based approaches ranging from ‘simple rule’‐based efforts to sophisticated machine learning methods. Many of these models show excellent performance for the data sets used. However, due to the complex nature of the applied methods, useful interpretation of the models that can be directly translated into chemical structures by the medicinal chemist is rather difficult.

Additionally, very recent and promising attempts in the field of structure‐based modeling of ABC transporters, which embody homology modeling as well as recently published X‐ray structures of murine ABCB1, will be discussed.
Beyond Profiling: Using ADMET Models to Guide Decisions
Authors: Segall Matthew , Champness Edmund , Obrezanova Olga , Leeding Chris
Published: November 2009

ADMET Models, whether in silico or in vitro, are commonly used to ‘profile’ molecules, to identify potential liabilities or filter out molecules expected to have undesirable properties. While useful, this is the most basic application of such models. Here, we will show how models may be used to go ‘beyond profiling’ to guide key decisions in drug discovery. For example, selection of chemical series to focus resources with confidence or design of improved molecules targeting structural modifications to improve key properties.

To prioritise molecules and chemical series, the success criteria for properties and their relative importance to a project's objective must be defined. Data from models (experimental or predicted) may then be used to assess each molecule's balance of properties against those requirements. However, to make decisions with confidence, the uncertainties in all of the data must also be considered. In silico models encode information regarding the relationship between molecular structure and properties. This is used to predict the property value of a novel molecule. However, further interpretation can yield information on the contributions of different groups in a molecule to the property and the sensitivity of the property to structural changes. Visualising this information can guide the redesign process. In this article, we describe methods to achieve these goals and drive drug‐discovery decisions and illustrate the results with practical examples.
Galectin‐1–Asialofetuin Interaction Is Inhibited by Peptides Containing the Tyr‐Xxx‐Tyr Motif Acting on the Glycoprotein
Authors: Wéber Edit , Hetényi Anasztázia , Váczi Balázs , Szolnoki Éva , Fajka‐Boja Roberta , Tubak Vilmos , Monostori Éva , Martinek Tamás A.
Published: November 2009

Galectin‐1 (Gal‐1), a ubiquitous β‐galactoside‐binding protein expressed by various normal and pathological tissues, has been implicated in cancer and autoimmune/inflammatory diseases in consequence of its regulatory role in adhesion, cell viability, proliferation, and angiogenesis. The functions of Gal‐1 depend on its affinity for β‐galactoside‐containing glycoconjugates; accordingly, the inhibition of sugar binding blocks its functions, hence promising potential therapeutic tools. The Tyr‐Xxx‐Tyr peptide motifs have been reported to be glycomimetic sequences, mainly on the basis of their inhibitory effect on the Gal‐1–asialofetuin (ASF) interaction. However, the results regarding the efficacy of the Tyr‐Xxx‐Tyr motif as a glycomimetic inhibitor are still controversial. The present STD and trNOE NMR experiments reveal that the Tyr‐Xxx‐Tyr peptides studied do not bind to Gal‐1, whereas their binding to ASF is clearly detected. 15N,1H HSQC titrations with 15N‐labeled Gal‐1 confirm the absence of any peptide–Gal‐1 interaction. These data indicate that the Tyr‐Xxx‐Tyr peptides tested in this work are not glycomimetics as they interact with ASF via an unrevealed molecular linkage.
Electro‐Oxidation of Methanol on PtRu Nanostructured Catalysts Electrodeposited onto Electroactivated Carbon Fiber Materials
Authors: Sieben Juan M. , Duarte Marta M. E. , Mayer C. E.
Published: November 2009

The surface of different carbon substrates, such as glassy carbon (GC), graphite cloth (GC‐10), graphite felt (GF‐S2), and carbon fiber paper (CFP) was modified by electrochemical treatment to generate high concentrations of oxygenated functional groups. These activated carbons were used as substrates for the simultaneous electrodeposition of Pt and Ru by a double potentiostatic pulse program. The different catalyst/carbon systems were evaluated as electrodes for methanol oxidation in acid solution. Comparing the results for the oxidized and nonoxidized substrates, the oxidation of the different carbon materials prior to the catalyst deposition was found to lead to an increase in the electrode activity for methanol oxidation. This enhancement could be associated with a remarkable improvement of metal dispersion, reduction of particle size, and a higher active surface area of the catalyst. The electrodes prepared with oxidized graphite felt exhibited the greatest catalytic activity.
Tetrabrominated Lead Naphthalocyanine for Optical Power Limiting
Authors: Dini Danilo , Meneghetti Moreno , Calvete Mario J. F. , Arndt Thomas , Liddiard Colin , Hanack Michael
Published: November 2009

The complex 2,(3)‐tetrabromo‐3,(2)‐tetra[(3,5‐di‐tert‐butyl)phenyloxy]‐naphthalocyaninato lead [Br4(tBu2C6H3O)4NcPb, 1] has been prepared and its optical limiting properties for ns light pulses have been measured. Complex 1 behaves as a reverse saturable absorber within the spectral range 440–720 nm with a limiting threshold of 0.1 J cm−2 at 532 nm. The lifetime of the absorbing triplet excited state has been evaluated as 3.8×10−7 s and the quantum yield of triplet formation has been measured as 0.07 in toluene. The nonlinear optical transmission properties of complex 1 have also been determined in Plexiglas [naphthalocyanine content: 5.0×10−4 M (0.1 % by weight)]. A reversible nonlinear absorption was again observed for a fluence above 0.4 J cm−2, but through different excited‐state dynamics. This may be rationalized in terms of aggregation of the molecule in the polymer matrix.
Synthesis of Enantiopure Sulfonimidamides and Elucidation of Their Absolute Configuration by Comparison of Measured and Calculated CD Spectra and X‐Ray Crystal Structure Determination
Authors: Worch Christin , Atodiresei Iuliana , Raabe Gerhard , Bolm Carsten
Published: November 2009

Straightforward syntheses of enantiopure N‐benzoyl‐ and N‐tert‐butyloxycarbonyl‐protected sulfonimidamides, which can be used as building blocks in newly designed catalysts, are presented. Key synthetic step is a dynamic resolution of a racemic sulfinic acid sodium salt. All subsequent transformations proceed stereospecifically. The absolute configurations at the sulfur atoms of both sulfonimidamides were determined by comparison of measured and calculated CD spectra. An X‐ray crystal structure determination of a sulfonimidoylguanidine derivative confirmed this result.
On the Scope of Trimethylaluminium‐Promoted 1,2‐Additions of ArZnX Reagents to Aldehydes
Authors: Glynn Daniel , Shannon Jonathan , Woodward Simon
Published: November 2009

A practical asymmetric 1,2‐addition of functionalised arylzinc halides to aromatic and aliphatic aldehydes is described by the use of aminoalcohol catalysis in the presence of AlMe3. The process is simple to carry out, uses only commercially available reagents/ligands and provides moderate to good (80–96 %ee) enantioselectivities for a wide range of substrates. Either commercial ArZnX reagents or those prepared in situ from low cost aryl bromides can be used. In the latter case electrophilic functional groups are tolerated (CO2Et, CN). The reaction relies on rapid exchange between ArZnX and AlMe3to generate mixed organometallic species that lead to the formation of a key intermediate that is distinctly different from the classic “anti” transition states of Noyori. NMR monitoring and related experiments have been used to probe the validity of the proposed selective transition state.