Lonafarnib reduces the resistance of primitive quiescent CML cells to imatinib mesylate in vitro.

Recent studies indicate that a rare population of primitive quiescent BCR-ABL(+) cells are innately insensitive to imatinib mesylate (IM) and persist after IM therapy of patients with chronic myeloid leukemia (CML). New approaches to the eradication of these cells are therefore likely to be crucial to the development of curative therapies for CML. We have now found that Ara-C, LY294002 (a PI-3 (phosphatidylinositol-3' kinase) kinase inhibitor), 17AAG (a heat-shock protein (HSP)-90 antagonist) and lonafarnib (a farnesyltransfease inhibitor) all enhance the toxicity of IM on K562 cells and on the total CD34(+) leukemic cell population from chronic phase CML patients. However, for quiescent CD34(+) leukemic cells, this was achieved only by concomitant exposure of the cells to lonafarnib. Ara-C or LY294002 alone blocked the proliferation of these cells but did not kill them, and Ara-C, LY294002 or 17AAG in combination with IM enhanced the cytostatic effect of IM but did not prevent the subsequent regrowth of the surviving leukemic cells. These studies demonstrate the importance of in vitro testing of novel agents on the subset of primary leukemic cells most likely to determine long-term treatment outcomes in vivo.

Mini-fingerprints for virtual screening: design principles and generation of novel prototypes based on information theory.

Binary fingerprint representations of molecular structure and properties are convenient computational tools for similarity searching in compound databases and virtual screening (VS). We are investigating the design of relatively simple fingerprints for the identification of molecules having similar biological activity and recognition of remote similarity relationships. Since our designs are considerably shorter than other fingerprints used in VS, we have previously termed them "mini-fingerprints" (MFPs). A key aspect of the design strategy is the identification of suitable molecular descriptors. Whereas our initial fingerprint designs have relied on descriptor combinations that performed well in compound classification according to biological activity, second generation MFPs encode combinations of descriptors with high information content in large compound databases and high frequency of occurrence in drug-like molecules. Thus, the design of these new fingerprints does not depend on the analysis of specific classes of bioactive compounds, but rather on descriptor information content in large compound databases. Systematic evaluation of fingerprint performance in VS test calculations demonstrates that these new prototypes perform better than previously generated MFPs. The analysis described herein provides an example for the development of search tools for VS.

Differential Shannon Entropy as a sensitive measure of differences in database variability of molecular descriptors.

A method termed Differential Shannon Entropy (DSE) is introduced to compare differences in information content and variance of molecular descriptors between compound databases. The analysis is based on histograms recording the individual and grouped distributions of molecular descriptors and calculation of Shannon entropy (SE), a formalism originally applied to digital communication. We have recently shown that SE values reflect the nonparametric variability of descriptor settings. Now the analysis has been advanced to assess differences in information content of 143 molecular descriptors in databases containing synthetic compounds, natural products, or drug-like molecules. The DSE metric captures the degree to which descriptor distributions complement or duplicate information contained in molecular databases. In our analysis, we observe significant differences for a number of descriptors and rank them according to their associated DSE values. Using DSE calculations, relative information content of different types of descriptors can be quantified, even if differences are subtle.

Fingerprint scaling increases the probability of identifying molecules with similar activity in virtual screening calculations.

Results of systematic virtual screening calculations using a structural key-type fingerprint are reported for compounds belonging to 14 activity classes added to randomly selected synthetic molecules. For each class, a fingerprint profile was calculated to monitor the relative occupancy of fingerprint bit positions. Consensus bit patterns were determined consisting of all bits that were always set on in compounds belonging to a specific activity class. In virtual screening calculations, scale factors were applied to each consensus bit position in fingerprints of query molecules. This technique, called "fingerprint scaling", effectively increases the weight of consensus bit positions in fingerprint comparisons. Although overall prediction accuracy was satisfactory using unscaled calculations, scaling significantly increased the number of correct predictions but only slightly increased the rate of false positives. These observations suggest that fingerprint scaling is an attractive approach to increase the probability of identifying molecules with similar activity by virtual screening. It requires the availability of a series of related compounds and can be easily applied to any keyed fingerprint representation that associates bit positions with specific molecular features.

Mini-fingerprints detect similar activity of receptor ligands previously recognized only by three-dimensional pharmacophore-based methods.

Mini-fingerprints (MFPs) are short binary bit string representations of molecular structure and properties, composed of few selected two-dimensional (2D) descriptors and a number of structural keys. MFPs were specifically designed to recognize compounds with similar activity. Here we report that MFPs are capable of detecting similar activities of some druglike molecules, including endothelin A antagonists and alpha(1)-adrenergic receptor ligands, the recognition of which was previously thought to depend on the use of multiple point three-dimensional (3D) pharmacophore methods. Thus, in these cases, MFPs and pharmacophore fingerprints produce similar results, although they define, in terms of their complexity, opposite ends of the spectrum of methods currently used to study molecular similarity or diversity. For each of the studied compound classes, comparison of MFP bit settings identified a consensus or signature pattern. Scaling factors can be applied to these bits in order to increase the probability of finding compounds with similar activity by virtual screening.

'Like a possession of the devil'. The diffusion of Nightingale nursing and Anglo-Australian relations.

The main focus of this paper is on the difficulties Lucy Osburn experienced in transferring British ideals of Nightingale nursing to an Australian colony. Neither Nightingale nor Osburn allowed for the impact of colonial culture and politics on the nurses in Sydney. In particular, the improved economic and social prospects of the five nurses who accompanied Osburn had a profound impact on their behaviour. As well, the political ambitions of the two men responsible for the invitation to the Nightingale nurses, Henry Parkes and Alfred Roberts, remained dominant. Nightingale, on the other side of the world, could do little but acquiesce to colonial opinion. The paper describes how the endeavour in Australia progressed, what became of the careers and lives of the central participants and the impact it had on the development of nursing in both countries.

A "lamentable failure"? The founding of Nightingale nursing in Australia, 1868-1884.

Florence Nightingale's private assessment was that Lucy Osburn failed in her attempt to found Nightingale nursing in Australia. This assessment is directly at odds with those of historians who have unquestioningly accepted Osburn's success. An alternative narrative of the founding of Nightingale nursing in Australia is provided through examining why Nightingale thought Osburn failed. The judgment of failure had little to do with nursing practice or care. Nightingale's judgment was based on the personal characteristics she expected of the Nightingale nurse and her fear of public exposure of problems at the Nightingale School of Nursing at St Thomas's Hospital.

Defining relationships and limiting power: two leaders of Australian nursing, 1868-1904.

This paper analyses aspects of the relationship between nursing and medicine during 1868-1904, in terms of power, gender and authority. A biographical approach is used with a focus on two leading nurses in Australia and their relationship with two leading medical practitioners. The first nurse is Lucy Osburn, the figurehead of the first generation of Nightingale nursing in Australia. The second nurse represents the second generation when Nightingale nursing had largely won acceptance and was firmly established in Australian hospitals: she is Susan McGahey. Their main medical antagonists were Dr Alfred Roberts and Dr Anderson Stuart. A struggle over the control of nursing is evident in these relationships. The outcome transcended personalities, greatly influenced the structure of modern nursing, and marked the rising tide of medical domination in Australia.

Evaluation of descriptors and mini-fingerprints for the identification of molecules with similar activity.

Combinations of 65 preferred 1D/2D molecular descriptors and 143 single structural keys were evaluated for their performance in compound classification focused on biological activity. The analysis was based on principal component analysis of descriptor combinations and facilitated by use of a genetic algorithm and different scoring functions. In these calculations, several descriptor combinations with greater than 95% prediction accuracy were identified. A set of 40 preferred structural keys was incorporated into a small binary fingerprint designed to search databases for compounds with biological activity similar to query molecules. The performance of mini-fingerprints was tested by systematic similarity search calculations in a database consisting of compounds belonging to seven biological activity classes, which had not been used to select effective descriptors. In these blind test calculations, mini-fingerprints correctly identified approximately 54% of compounds sharing similar biological activity and with 1% false positives. Thus, although the design of mini-fingerprints is conceptually simple, they perform well in activity-oriented similarity searching.

Distinguishing between natural products and synthetic molecules by descriptor Shannon entropy analysis and binary QSAR calculations.

Molecular descriptors were identified by Shannon entropy analysis that correctly distinguished, in binary QSAR calculations, between naturally occurring molecules and synthetic compounds. The Shannon entropy concept was first used in digital communication theory and has only very recently been applied to descriptor analysis. Binary QSAR methodology was originally developed to correlate structural features and properties of compounds with a binary formulation of biological activity (i.e., active or inactive) and has here been adapted to correlate molecular features with chemical source (i.e., natural or synthetic). We have identified a number of molecular descriptors with significantly different Shannon entropy and/or "entropic separation" in natural and synthetic compound databases. Different combinations of such descriptors and variably distributed structural keys were applied to learning sets consisting of natural and synthetic molecules and used to derive predictive binary QSAR models. These models were then applied to predict the source of compounds in different test sets consisting of randomly collected natural and synthetic molecules, or, alternatively, sets of natural and synthetic molecules with specific biological activities. On average, greater than 80% prediction accuracy was achieved with our best models. For the test case consisting of molecules with specific activities, greater than 90% accuracy was achieved. From our analysis, some chemical features were identified that systematically differ in many naturally occurring versus synthetic molecules.

Searching for molecules with similar biological activity: analysis by fingerprint profiling.

We have recently developed a mini-fingerprint (MFP) representation for small molecules that performs well in database searches for compounds with similar biological activity. The MFP consists of only 54 bit positions that account for numerical ranges of three two-dimensional (2D) descriptors or the presence or absence of defined structural fragments. Here we present an analysis method, termed fingerprint profiling, to systematically compare bit patterns of compounds belonging to different biological activity classes. Some but not all bit positions were variably occupied in seven different activity classes and responsible for the detection of structure-activity differences. The analysis has made it possible to rank bit positions and encoded molecular descriptors according to their importance for our similarity search calculations. Fingerprint profiling can be applied to any keyed bit string representation and should be helpful, for example, to analyze descriptor distributions in large compound databases.

Database searching for compounds with similar biological activity using short binary bit string representations of molecules.

In an effort to identify biologically active molecules in compound databases, we have investigated similarity searching using short binary bit strings with a maximum of 54 bit positions. These "minifingerprints" (MFPs) were designed to account for the presence or absence of structural fragments and/or aromatic character, flexibility, and hydrogen-bonding capacity of molecules. MFP design was based on an analysis of distributions of molecular descriptors and structural fragments in two large compound collections. The performance of different MFPs and a reference fingerprint was tested by systematic "one-against-all" similarity searches of molecules in a database containing 364 compounds with different biological activities. For each fingerprint, the most effective similarity cutoff value was determined. An MFP accounting for only 32 structural fragments showed less than 2% false positive similarity matches and correctly assigned on average approximately 40% of the compounds with the same biological activity to a query molecule. Inclusion of three numerical two-dimensional (2D) molecular descriptors increased the performance by 15%. This MFP performed better than a complex 2D fingerprint. At a similarity cutoff value of 0.85, the 2D fingerprint totally eliminated false positives but recognized less than 10% of the compounds within the same activity class.

Melanoma cell-derived factor stimulation of fibroblast glycosaminoglycan synthesis--the role of platelet-derived growth factor.

The hyaluronan-rich matrix surrounding many tumours may facilitate tumour growth, invasion and angiogenesis, with the majority of this hyaluronan apparently being synthesised by normal fibroblasts, stimulated to do so by tumour cell-derived factors. Melanoma cell-conditioned medium (CM) stimulates up to a 6-fold increase in fibroblast glycosaminoglycan (GAG) synthesis, with the active factors being present in tumour CM ultrafiltration fractions > 30 kDa and < 1 kDa. These fractions are poorly active individually, but when recombined, the activity is substantially greater than the additive effect. The objective of this study was to identify the factors present in the ultrafiltration fraction > 30 kDa that produce a greater than additive effect with the fraction < 1 kDa in stimulating the incorporation of 3H glucosamine into fibroblast GAGs. A number of factors including basic fibroblast growth factor (bFGF), interleukin (IL)-1 beta, pleiotrophin, platelet-derived growth factor (PDGF), transforming growth factor-beta (TGF-beta), tumour necrosis factor-alpha (TNF-alpha) and vascular endothelial growth factor (VEGF) failed to stimulate any significant increase in GAG synthesis, but when added to the < 1 kDa tumour CM fraction, both PDGF and to a lesser extent, bFGF, exhibited potent stimulating activities. Neutralising antibodies to PDGF and bFGF added to the melanoma CM decreased the fibroblast GAG-stimulating activity by 29% and 40%, respectively, in C8161 melanoma CM and by 47% and 45%, respectively, in Hs294T melanoma CM. The activities of PDGF-AA and PDGF-BB isoforms were indistinguishable, suggesting the PDGF-alpha receptor plays a role in the GAG-stimulatory response. Western analysis following treatment with PDGF, bFGF or melanoma CM revealed banding patterns for PDGF and melanoma CM that were similar. Immunoprecipitation of the PDGF-alpha receptor revealed it to be phosphorylated in fibroblasts treated with PDGF and melanoma CM, but not with control fibroblast CM. These studies suggest that PDGF plays an important role in the GAG-stimulating activity of the melanoma CM, but requires the presence of an as yet unidentified novel low molecular weight factor for full activity.

Molecular scaffold-based design and comparison of combinatorial libraries focused on the ATP-binding site of protein kinases.

Compound libraries were designed to target specifically the ATP cofactor-binding site in protein kinases by combining knowledge- and diversity-based design elements. A key aspect of the approach is the identification of molecular building blocks or scaffolds that are compatible with the binding site and therefore capture some aspects of target specificity. Scaffolds were selected on the basis of docking calculations and analysis of known inhibitors. We have generated 75 molecular scaffolds and applied different strategies to compute diverse compounds from scaffolds or, alternatively, to screen compound databases for molecules containing these scaffolds. The resulting libraries had a similar degree of molecular diversity, with at most 12% of the compounds being identical. However, their scaffold distributions differed significantly and a small number of scaffolds dominated the majority of compounds in each library.

Managing the patient with a chest drain: a review.

This article describes a preliminary review of the literature on the nursing management of patients with chest drains before pursuing a systematic review of the evidence. Current evidence is patchy and the answers to basic questions are not easily identified. It is clear that further evidence must be gathered and critically appraised before definitive recommendations can be made.

Evaluation of docking strategies for virtual screening of compound databases: cAMP-dependent serine/threonine kinase as an example.

In an effort to establish efficient docking routines for computational screening of compound databases on protein structures, cAMP-dependent protein kinase has been selected as a test case and a variety of docking options and scoring functions were compared. These included rigid-body and flexible docking and scoring based on surface complementarity and/or force field energy. Inhibitors were removed from complex crystal structures and added to compound libraries in their binding conformations and, in addition, deliberately modified conformations. Rigid-body docking and contact scoring well reproduced two of three experimental enzyme-inhibitor complexes. Ligand docking with flexible torsional angles failed to do so but anchored search of some inhibitors converged near to experimental structures, however, only when energy scoring was applied.

Effect of retinoic acid on melanoma cell-derived factor stimulation of fibroblast glycosaminoglycan synthesis.

The hyaluronan-rich matrix that surrounds many tumours and facilitates tumour cell growth and invasion is thought to be predominantly synthesized by normal stromal cells stimulated by tumour cell-derived factors. This study examines the possibility that the production of tumour cell-derived factors that stimulate fibroblast glycosaminoglycan (GAG) synthesis may be blocked by exposure to differentiation-inducing agents such as retinoic acid. We have demonstrated that Hs294T, C8161 and A375 human melanoma cell lines release factors into their medium that stimulate normal fibroblast GAG synthesis. Exposure of these melanoma cells to retinoic acid failed to mediate any significant reduction in growth over a 7-day period. Retinoic acid failed to block the tumour cell production of GAG-stimulating activities and even enhanced the activities produced by the C8161 cell line, particularly at low retinoic acid concentrations (48% stimulation at 10(-9) M retinoic acid; P < 0.02). Addition of retinoic acid directly to fibroblast cultures exposed to fibroblast-conditioned medium resulted in an inhibition of GAG synthesis with a 33% inhibition observed at 10(-5) M. Addition of retinoic acid to fibroblast cultures exposed to the tumour cell-conditioned medium failed to inhibit the stimulation of GAG synthesis. Other differentiation-inducing agents, such as hexamethylene-bis-acetamide and butyrate, also failed to block the production of tumour cell-derived GAG-stimulating activities. These results demonstrate that retinoic acid and other differentiation-inducing agents fail to inhibit melanoma cell production of fibroblast GAG synthesis-stimulating factors or their action upon fibroblasts.

Partial characterisation of human melanoma cell-derived factors that stimulate fibroblast glycosaminoglycan synthesis.

Glycosaminoglycans (GAGs), and in particular hyaluronan, are known to play a role in tumour cell migration, invasion and metastasis. Conditioned medium from two human metastatic melanoma cell lines (Hs294T and C8161) shows potent fibroblast GAG-synthesis-stimulating activities which are active in fibroblast cultures derived from different anatomical sites. This ability is not specific to melanoma cells and is observed in several carcinoma cell lines. Initial characterisation studies have demonstrated that the GAG-stimulating activities in the medium conditioned with melanoma cells show a degree of heat and trypsin resistance. Fractionation of the conditioned medium with Amicon ultrafiltration membranes of various molecular weight cut-offs, ranging from 1 to 30 kD, resulted in a total loss of activity. Activity could be regained by recombination of the concentrated fraction with the filtrate, suggesting more than one factor to be involved in GAG stimulation, with a degree of interdependence between the individual fractions. The fraction greater than 30 kD and that less than 1 kD appear to contain the majority of the GAG-stimulating activity.