Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target

With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.

Spirocycle MmpL3 Inhibitors with Improved hERG and Cytotoxicity Profiles as Inhibitors of Mycobacterium tuberculosis Growth

With the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, there is a pressing need for new oral drugs with novel mechanisms of action. A number of scaffolds with potent anti-tubercular in vitro activity have been identified from phenotypic screening that appear to target MmpL3. However, the scaffolds are typically lipophilic, which facilitates partitioning into hydrophobic membranes, and several contain basic amine groups. Highly lipophilic basic amines are typically cytotoxic against mammalian cell lines and have associated off-target risks, such as inhibition of human ether-à-go-go related gene (hERG) and IKr potassium current modulation. The spirocycle compound 3 was reported to target MmpL3 and displayed promising efficacy in a murine model of acute tuberculosis (TB) infection. However, this highly lipophilic monobasic amine was cytotoxic and inhibited the hERG ion channel. Herein, the related spirocycles (1-2) are described, which were identified following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis. The novel N-alkylated pyrazole portion offered improved physicochemical properties, and optimization led to identification of a zwitterion series, exemplified by lead 29, with decreased HepG2 cytotoxicity as well as limited hERG ion channel inhibition. Strains with mutations in MmpL3 were resistant to 29, and under replicating conditions, 29 demonstrated bactericidal activity against M. tuberculosis. Unfortunately, compound 29 had no efficacy in an acute model of TB infection; this was most likely due to the in vivo exposure remaining above the minimal inhibitory concentration for only a limited time.

Diastereoselective synthesis of trifluoromethylated 1,3-dioxanes by intramolecular oxa-Michael reaction

A highly diastereoselective synthesis of trifluoromethylated 1,3-dioxanes is described. The reaction proceeds by an addition/oxa-Michael sequence and works efficiently under mild reaction conditions, with a good substrate scope and acceptable to good yields.

Effect of small-scale woodland clearing and thinning on vertebrate fauna in a largely intact tropical savanna mosaic

Context Habitat degradation and fragmentation of vegetation can transform and deplete local wildlife populations, and is a key threatening process globally. In northern Australian tropical savannas, clearing is relatively rare across the biome, although it is slowly intensifying as a result of increasing agricultural development. However, the terrestrial vertebrates in these largely intact landscapes are undergoing current population declines because of a variety of land-management changes, one of which is increasing land clearing; therefore, there is a need to understand the relative effect of small-scale land clearing the fauna. Aims The present study examined the variation in abundance of birds, mammals and reptiles in intact, thinned and cleared Eucalyptus woodlands in a tropical savanna bioregion. Methods The vertebrate fauna were sampled in 88 sites over two general geographic locations within the Desert Uplands in 2005 and 2006. Standardised 1-ha surveys were employed in a single vegetation type and across three treatments. As two discrete locations were examined, linear mixed models were used in the analysis. Key results The fauna composition varied significantly across the intact, thinned and cleared sites. Bird species richness reduced from intact to thinned and cleared sites, and reptile richness and abundance declined in cleared sites, but was largely unaffected by thinning. Seventeen bird species recorded significant variation in abundance across the three vegetation structural types, with 12 most abundant in the intact sites. Mammals on the whole were recorded in very low abundances and in few sites. For reptiles, two were most abundant in thinned sites and three in intact sites. Conclusions In the present study, we have demonstrated that small-scale clearing and vegetation manipulation via thinning, even within largely intact tropical savanna woodland, can cause localised depletion of some species, although most notably where the vegetation disruption was most severe (i.e. clearing). Birds are most affected, and many species that declined in abundance are the same as those that suffered severe population reductions as a result of broad-scale clearing in south-eastern Australia. Implications The proposed increase in the intensity of agricultural land use in northern Australia will result in incremental landscape change as a result of clearing. Understanding how the gradual reduction of vegetation cover and habitat will change the faun assemblage is important for pre-emptive conservation planning. This is vital to avoid the mistakes of extensive landscape change in southern Australia that has left a legacy of a permanently depleted fauna.

Home range and habitat use of a low-density population of greater gliders, Petauroides volans (Pseudocheiridae: Marsupialia), in a hollow-limiting environment

Greater gliders, Petauroides volans, were radio-tracked within a large tract of forest in the dry inland of southern Queensland. This forest has been commercially logged for timber for more than 100 years. Home-range estimates ranged from 1.4 ha (female) to 19.3 ha (male). Minimum convex polygon (MCP) estimates were larger for males (average, 11.5 ha) than females (average, 3.3 ha) and combined (6.8 ha, sexes pooled) were larger than estimates from other Australian populations. Gliders were located foraging in myrtaceous tree species only, using mostly Eucalyptus moluccana, E. fibrosa and Corymbia citriodora. E. moluccana was used for foraging more frequently than would be expected on the basis of its availability in the forest. E. fibrosa and C. citriodora were used in proportion to their availability in the forest. Gliders were not seen foraging in non-myrtaceous species or myrtaceous trees <20 cm diameter at breast height (dbh), preferring trees in 30–70-cm dbh classes and as ‘mature’ and ‘over-mature’ classified according to growth-stage characteristics. Den tree species included the same species used for foraging as well as dead trees (16% of den trees). E. fibrosa and E. tereticornis were preferred significantly more than expected by their availability in the forest. Non-myrtaceous species were not used as live den trees. Large (dbh >50 cm) and old living trees (in deteriorating and senescent condition: ‘late mature’ and ‘over-mature’ categories) were primarily used as den trees. Individual gliders utilised 4–20 den trees. Females utilised more den trees per unit area of home range (3.8 den trees ha–1, maximum) than males (0.9 den trees ha–1, maximum). Fewer den trees were used per unit area of home range than by gliders at a coastal location with approximately the same latitude. The density of live stems containing hollows suitable as dens is currently lower than 1 tree ha–1 in some parts of the study forest. Gliders were two and half times less likely to be observed during standardised spotlighting surveys in the study area than elsewhere in southern Queensland. It is likely that low availability of den trees is contributing to large home ranges and the apparent low population density observed in this study.

Active learning with support vector machines in the drug discovery process

We investigate the following data mining problem from computer-aided drug design: From a large collection of compounds, find those that bind to a target molecule in as few iterations of biochemical testing as possible. In each iteration a comparatively small batch of compounds is screened for binding activity toward this target. We employed the so-called "active learning paradigm" from Machine Learning for selecting the successive batches. Our main selection strategy is based on the maximum margin hyperplane-generated by "Support Vector Machines". This hyperplane separates the current set of active from the inactive compounds and has the largest possible distance from any labeled compound. We perform a thorough comparative study of various other selection strategies on data sets provided by DuPont Pharmaceuticals and show that the strategies based on the maximum margin hyperplane clearly outperform the simpler ones.

Arterial embolectomy in the leg: results in a referral hospital

A review of 66 patients undergoing femoral embolectomy showed that 38 (58%) obtained a good final outcome (discharge from hospital with viable limb) while 28 (42%) died or required amputation prior to discharge. The major association with poor final outcome was pre-operative life-threatening cardiac disease which occurred in 17 (61%) of those patients who later died or underwent amputation and in six (16%) of those who were discharged with viable limbs (p less than 0.001). Age, sex, source of embolus, duration of ischaemia and pre-existing vascular disease had little effect on final outcome. Surgical dissatisfaction, at the time of operation, with the result of attempted revascularisation was of major prognostic significance in terms of future amputation or death.

Arachidonic acid metabolites mediate early burn edema

Standard burns were sequentially produced on the backs of Sprague-Dawley rats at 0, 1, 2, and 2 1/2 hr, followed by the IV injection of Evans blue dye. All animals were killed at 3 hr, and burns evaluated by wet/dry weight ratios, and Evans blue extravasation scored 1-4 by two observers. Five groups of rats were compared to controls. Rats made neutropenic by exposure to 137cesium showed no significant difference in wet/dry weight ratio or Evans blue extravasation compared to controls. At 1 1/2 hr four other groups were treated with various inhibitors of arachidonic acid metabolism including ibuprofen, a cyclo-oxygenase inhibitor; FPL 55712, a leukotriene (LT) receptor antagonist; ketoconazole, an inhibitor of thromboxane (Tx) synthetase; and lodoxamide, a calcium channel inhibitor. All treated groups showed significant reduction of Evans blue dye extravasation. Wet/dry weight ratios were significantly reduced in rats treated with FPL 55712 and ketoconazole before or after burning. These data support the postulate that oxygenation products of arachidonic acid, particularly Tx and LT, are important mediators in early burn edema.

A prospective study of the development of hypertension and renal stone disease in subjects with increased blood urate

The results of a prospective study of the development of hypertension and renal stone disease in subjects with increased blood urate are reported and compared with matched controls. None of the 14 patients on Allopurinol developed a renal stone but one untreated control did. For male patients there was a significant difference (p less than 0.01) in diastolic blood pressure between the 2 groups over the 5-year study period, with treated patients having higher blood pressures than untreated controls. This suggests that Allopurinol has had no effect on lowering diastolic blood pressure. Long-term therapy with Allopurinol was effective in reducing mean blood urate levels. It is suggested that blood urate levels are more relevant in predicting renal stone formation and of less value in assessing the therapy and prognosis in hypertension.

Randomized controlled trial of physiotherapy for postoperative pulmonary complications

A prospective randomized controlled trial was conducted in patients undergoing elective cholecystectomy to assess the value of routine chest physiotherapy. One hundred and two patients entered the study: 47 patients developed no pulmonary complications, 29 had pulmonary atelectasis and a further 26 developed chest infection. The pattern of changes in arterial oxygen tension in the period after operation supported the clinical allocation of the patients. Of 51 patients not receiving physiotherapy, 11 developed atelectasis and 19 chest infection. Of 51 treated patients, 18 developed atelectasis and seven chest infection. Routine prophylactic postoperative chest physiotherapy decreased significantly the frequency of chest infection (P less than 0.02).