Identification of 2-Aryl-Quinolone Inhibitors of Cytochrome bd and Chemical Validation of Combination Strategies for Respiratory Inhibitors against Mycobacterium tuberculosis

Mycobacterium tuberculosis cytochrome bd quinol oxidase (cyt bd), the alternative terminal oxidase of the respiratory chain, has been identified as playing a key role during chronic infection and presents a putative target for the development of novel antitubercular agents. Here, we report confirmation of successful heterologous expression of M. tuberculosis cytochrome bd. The heterologous M. tuberculosis cytochrome bd expression system was used to identify a chemical series of inhibitors based on the 2-aryl-quinolone pharmacophore. Cytochrome bd inhibitors displayed modest efficacy in M. tuberculosis growth suppression assays together with a bacteriostatic phenotype in time-kill curve assays. Significantly, however, inhibitor combinations containing our front-runner cyt bd inhibitor CK-2-63 with either cyt bcc-aa₃ inhibitors (e.g., Q203) and/or adenosine triphosphate (ATP) synthase inhibitors (e.g., bedaquiline) displayed enhanced efficacy with respect to the reduction of mycobacterium oxygen consumption, growth suppression, and in vitro sterilization kinetics. In vivo combinations of Q203 and CK-2-63 resulted in a modest lowering of lung burden compared to treatment with Q203 alone. The reduced efficacy in the in vivo experiments compared to in vitro experiments was shown to be a result of high plasma protein binding and a low unbound drug exposure at the target site. While further development is required to improve the tractability of cyt bd inhibitors for clinical evaluation, these data support the approach of using small-molecule inhibitors to target multiple components of the branched respiratory chain of M. tuberculosis as a combination strategy to improve therapeutic and pharmacokinetic/pharmacodynamic (PK/PD) indices related to efficacy.

Industrial scale high-throughput screening delivers multiple fast acting macrofilaricides

Nematodes causing lymphatic filariasis and onchocerciasis rely on their bacterial endosymbiont, Wolbachia, for survival and fecundity, making Wolbachia a promising therapeutic target. Here we perform a high-throughput screen of AstraZeneca’s 1.3 million in-house compound library and identify 5 novel chemotypes with faster in vitro kill rates (<2 days) than existing anti-Wolbachia drugs that cure onchocerciasis and lymphatic filariasis. This industrial scale anthelmintic neglected tropical disease (NTD) screening campaign is the result of a partnership between the Anti-Wolbachia consortium (A∙WOL) and AstraZeneca. The campaign was informed throughout by rational prioritisation and triage of compounds using cheminformatics to balance chemical diversity and drug like properties reducing the chance of attrition from the outset. Ongoing development of these multiple chemotypes, all with superior time-kill kinetics than registered antibiotics with anti-Wolbachia activity, has the potential to improve upon the current therapeutic options and deliver improved, safer and more selective macrofilaricidal drugs.

Parasitic nematodes causing onchocerciasis and lymphatic filariasis rely on a bacterial endosymbiont, Wolbachia, which is a validated therapeutic target. Here, Clare et al. perform a high-throughput screen of 1.3 million compounds and identify 5 chemotypes with faster kill rates than existing anti-Wolbachia drugs.

Design and Synthesis of Irreversible Analogues of Bardoxolone Methyl for the Identification of Pharmacologically Relevant Targets and Interaction Sites

Semisynthetic triterpenoids such as bardoxolone methyl (methyl-2-cyano 3,12-dioxooleano-1,9-dien-28-oate; CDDO-Me) (4) are potent inducers of antioxidant and anti-inflammatory signaling pathways, including those regulated by the transcription factor Nrf2. However, the reversible nature of the interaction between triterpenoids and thiols has hindered attempts to identify pharmacologically relevant targets and characterize the sites of interaction. Here, we report a shortened synthesis and SAR profiling of 4, enabling the design of analogues that react irreversibly with model thiols, as well as the model protein glutathione S-transferase P1, in vitro. We show that one of these analogues, CDDO-epoxide (13), is comparable to 4 in terms of cytotoxicity and potency toward Nrf2 in rat hepatoma cells and stably modifies specific cysteine residues (namely, Cys-257, -273, -288, -434, -489, and -613) within Keap1, the major repressor of Nrf2, both in vitro and in living cells. Supported by molecular modeling, these data demonstrate the value of 13 for identifying site(s) of interaction with pharmacologically relevant targets and informing the continuing development of triterpenoids as novel drug candidates.

Allelic Variation of Cytochrome P450s Drives Resistance to Bednet Insecticides in a Major Malaria Vector

Scale up of Long Lasting Insecticide Nets (LLINs) has massively contributed to reduce malaria mortality across Africa. However, resistance to pyrethroid insecticides in malaria vectors threatens its continued effectiveness. Deciphering the detailed molecular basis of such resistance and designing diagnostic tools is critical to implement suitable resistance management strategies. Here, we demonstrated that allelic variation in two cytochrome P450 genes is the most important driver of pyrethroid resistance in the major African malaria vector Anopheles funestus and detected key mutations controlling this resistance. An Africa-wide polymorphism analysis of the duplicated genes CYP6P9a and CYP6P9b revealed that both genes are directionally selected with alleles segregating according to resistance phenotypes. Modelling and docking simulations predicted that resistant alleles were better metabolizers of pyrethroids than susceptible alleles. Metabolism assays performed with recombinant enzymes of various alleles confirmed that alleles from resistant mosquitoes had significantly higher activities toward pyrethroids. Additionally, transgenic expression in Drosophila showed that flies expressing resistant alleles of both genes were significantly more resistant to pyrethroids compared with those expressing the susceptible alleles, indicating that allelic variation is the key resistance mechanism. Furthermore, site-directed mutagenesis and functional analyses demonstrated that three amino acid changes (Val¹⁰⁹Ile, Asp³³⁵Glu and Asn³⁸⁴Ser) from the resistant allele of CYP6P9b were key pyrethroid resistance mutations inducing high metabolic efficiency. The detection of these first DNA markers of metabolic resistance to pyrethroids allows the design of DNA-based diagnostic tools to detect and track resistance associated with bednets scale up, which will improve the design of evidence-based resistance management strategies.

Scale up of Long Lasting Insecticide Nets has massively reduced malaria mortality across Africa. However, resistance to pyrethroid insecticides in malaria vectors threatens its continued effectiveness. Here, we established that allelic variation in two CYP450s is the most important driver of pyrethroid resistance in the major African vector Anopheles funestus and detected key mutations controlling this resistance. The duplicated P450s CYP6P9a and CYP6P9b are directionally selected across Africa with alleles segregating according to resistance phenotypes. Alleles from resistant mosquitoes present significantly higher metabolic activities toward pyrethroids compared with alleles from susceptible mosquitoes. Furthermore, transgenic flies over-expressing resistant alleles of both genes were significantly more resistant to pyrethroids. Three amino acid changes from the resistant CYP6P9b allele are the key pyrethroid resistance mutations which induce high metabolic efficiency. The detection of these first DNA markers of metabolic resistance to pyrethroids allows the design of diagnostic tools to detect and track resistance.

Routine phasing of coiled-coil protein crystal structures with AMPLE

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallo-graphic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE

Molecular Replacement (MR) is an increasingly popular route to protein structure solution. AMPLE[1] is a software pipeline that uses either cheaply obtained ab inito protein models, or NMR structures to extend the scope of MR, allowing it to solve entirely novel protein structures in a completely automated pipeline on a standard desktop computer. AMPLE employs a cluster-and-truncate approach, combined with multiple modes of side chain treatment, to analyse the candidate models and extract the consensual features most likely to solve the structure. The search models generated in this way are screened by MrBump using Phaser and Molrep and correct solutions are detected using main chain tracing and phase modification with Shelxe. AMPLE proved capable of processing rapidly obtained ab initio structure predictions into successful search models and more recently proved effective in assembling NMR structures for MR[2]. Coiled-coil proteins are a distinct class of protein fold whose structure solution by MR is not typically straightforward. We show here that AMPLE can quickly and routinely solve most coiled-coil structures using ab initio predictions from Rosetta. The predictions are generally not globally accurate, but by encompassing different degrees of truncation of clustered models, AMPLE succeeds by sampling across a range of search models. These sometimes succeed through capturing locally well-modelled conformations, but often simply contain small helical units. Remarkably, the latter regularly succeed despite out-of-register placement and poor MR statistics. We demonstrate that single structures derived from successful ensembles perform less well, and comparable ideal helices solve few targets. Thus, both modelling of distortions from ideal helical geometry and the ensemble nature of the search models contribute to success. AMPLE is a framework applicable to any set of input structures in which variability is correlated with inaccuracy. We also present preliminary data demonstrating structure solution of transmembrane helical structures using Rosetta modelling. We finally consider future sources of starting models which offer the hope that MR with AMPLE, in the absence of close homology between a known structure and the target, may soon be possible with larger proteins.

Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1

MuRF1 is an E3 ubiquitin ligase central to muscle catabolism. It belongs to the TRIM protein family characterized by a tripartite fold of RING, B-box and coiled-coil (CC) motifs, followed by variable C-terminal domains. The CC motif is hypothesized to be responsible for domain organization in the fold as well as for high-order assembly into functional entities. But data on CC from this family that can clarify the structural significance of this motif are scarce. We have characterized the helical region from MuRF1 and show that, contrary to expectations, its CC domain assembles unproductively, being the B2- and COS-boxes in the fold (respectively flanking the CC) that promote a native quaternary structure. In particular, the C-terminal COS-box seemingly forms an α-hairpin that packs against the CC, influencing its dimerization. This shows that a C-terminal variable domain can be tightly integrated within the conserved TRIM fold to modulate its structure and function. Furthermore, data from transfected muscle show that in MuRF1 the COS-box mediates the in vivo targeting of sarcoskeletal structures and points to the pharmacological relevance of the COS domain for treating MuRF1-mediated muscle atrophy.

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computedab initiomodels. Corrigendum

The article by Bibbyet al.[(2012),Acta Cryst.D68, 1622–1631] is corrected.

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models

Protein ab initio models predicted from sequence data alone can enable the elucidation of crystal structures by molecular replacement. However, the calculation of such ab initio models is typically computationally expensive. Here, a computational pipeline based on the clustering and truncation of cheaply obtained ab initio models for the preparation of structure ensembles is described. Clustering is used to select models and to quantitatively predict their local accuracy, allowing rational truncation of predicted inaccurate regions. The resulting ensembles, with or without rapidly added side chains, solved 43% of all test cases, with an 80% success rate for all-α proteins. A program implementing this approach, AMPLE, is included in the CCP4 suite of programs. It only requires the input of a FASTA sequence file and a diffraction data file. It carries out the modelling using locally installed Rosetta, creates search ensembles and automatically performs molecular replacement and model rebuilding.

Formal modeling and analysis of the MAL-associated biological regulatory network: insight into cerebral malaria

The discrete modeling formalism of René Thomas is a well known approach for the modeling and analysis of Biological Regulatory Networks (BRNs). This formalism uses a set of parameters which reflect the dynamics of the BRN under study. These parameters are initially unknown but may be deduced from the appropriately chosen observed dynamics of a BRN. The discrete model can be further enriched by using the model checking tool HyTech along with delay parameters. This paves the way to accurately analyse a BRN and to make predictions about critical trajectories which lead to a normal or diseased response. In this paper, we apply the formal discrete and hybrid (discrete and continuous) modeling approaches to characterize behavior of the BRN associated with MyD88-adapter-like (MAL)--a key protein involved with innate immune response to infections. In order to demonstrate the practical effectiveness of our current work, different trajectories and corresponding conditions that may lead to the development of cerebral malaria (CM) are identified. Our results suggest that the system converges towards hyperinflammation if Bruton's tyrosine kinase (BTK) remains constitutively active along with pre-existing high cytokine levels which may play an important role in CM pathogenesis.

Cytochrome P450 6M2 from the malaria vector Anopheles gambiae metabolizes pyrethroids: Sequential metabolism of deltamethrin revealed

Resistance to pyrethroid insecticides in the malaria vector Anopheles gambiae is a major threat to malaria control programmes. Cytochome P450-mediated detoxification is an important resistance mechanism. CYP6M2 is over-expressed in wild populations of permethrin resistant A. gambiae but its role in detoxification is not clear. CYP6M2 was expressed in Escherichia coli and a structural model was produced to examine its role in pyrethroid metabolism. Both permethrin and deltamethrin were metabolized. Rates were enhanced by A. gambiae cytochrome b(5) with kinetic parameters of K(M)=11±1μM and k(cat)=6.1±0.4 per min for permethrin (1:1 cis-trans) and K(M)=2.0±0.3μM and k(cat)=1.2±0.1 per min for deltamethrin. Mass spectrometry and NMR analysis identified 4'-hydroxy deltamethrin and hydroxymethyl deltamethrin as major and minor deltamethrin metabolites respectively. Secondary breakdown products included cyano(3-hydroxyphenyl)methyl deltamethrate and deltamethric acid. CYP6M2 was most highly transcribed in the midgut and Malpighian tubules of adult A. gambiae, consistent with a role in detoxification. Our data indicates that CYP6M2 plays an important role in metabolic resistance to pyrethroids and thus an important target for the design of new tools to combat malaria.

Characterization of inhibitors and substrates of Anopheles gambiae CYP6Z2

Three CYP6Z genes are linked to a major pyrethroid resistance locus in the mosquito Anopheles gambiae. We have expressed CYP6Z2 in Escherichia coli and produced a structural model in order to examine its role in detoxification. E. coli membranes co-expressing CYP6Z2 and An. gambiae P450 reductase (AgCPR) catalysed the dealkylation of benzyloxyresorufin with kinetic parameters K(m) = 0.13 microM; K(cat) = 1.5 min(-1). The IC(50) values of a wide range of compounds were measured. Pyrethroids cypermethrin and permethrin produced low IC(50) values, but were not metabolized. Plant flavanoids were the most potent inhibitors. Several compounds were shown to be substrates, suggesting that CYP6Z2 has broad substrate specificity and plays an important chemo-protective role during the herbivorous phase of the life-cycle.

Tension-free vaginal tape for primary genuine stress incontinence: a two-centre follow-up study

OBJECTIVE

To assess the safety and efficacy of the tension-free vaginal tape procedure in the treatment of primary genuine stress incontinence.

PATIENTS AND METHODS

A two-centre follow-up study was conducted on 40 women with urodynamically confirmed primary genuine stress incontinence who had a tension-free vaginal tape inserted under local anaesthesia with sedation. Operative details were recorded and all patients followed up both subjectively, and objectively with repeat urodynamic studies and pad testing.

RESULTS

The mean (range) age of the women was 51.1 (33-86) years, the median parity 2 (0-4) and mean body mass index 25.1 (19-35). The mean anaesthesia and operative duration was 42 (25-65) min; 93% of the women resumed immediate spontaneous voiding with no need for catheterization. The mean inpatient stay was 2.2 (2-4) days (where 2 days is equivalent to one night in hospital). The follow-up was conducted at a mean interval of 12.3 (6-24) months. Subjectively, 80% of women were cured and 17.5% significantly improved; objectively, genuine stress incontinence was cured in 95%. Symptomatic postoperative detrusor instability was found in 15% of women and symptoms of voiding dysfunction identified in 5% of women. There were no defects in healing or tape rejection.

CONCLUSION

The tension-free vaginal tape procedure is a promising new technique that, in this short-term analysis, appears to be safe and effective. Intra-operative complications are uncommon and both hospital stay and recovery are short. Voiding complications are rare but symptomatic postoperative detrusor instability had an incidence of 15%.

Evidence-based practice. Guiding lights

Traditional methods of implementing clinical guidelines and changing professional practice endure despite evidence that they are ineffective. The increasing demand for guideline implementation will have to be met within existing resources. Work in one health authority, which marries the methods of changing practice shown to be effective with the limited resources available, is already showing dividends.

Prevalence of HPV cervical infection in a family planning clinic determined by polymerase chain reaction and dot blot hybridisation

The overall prevalence of human papillomavirus (HPV) cervical infection in 131 women attending a family planning clinic was 7% (HPV 6/11, 16, 18, 31) by dot blot hybridisation, 53% (HPV 11, 16, 31) by polymerase chain reaction (PCR), and 56% by the two methods combined. HPV 16 and 18 were the commonest types (4% each) by dot blot, HPV 16 (39%) by PCR. Fifteen percent of subjects had mildly abnormal cervical cytology (grades 1A, 2A, or 3). There was no significant correlation between cytological abnormality and HPV positivity, or between cytological or HPV status and other postulated risk factors for cervical neoplasia. It is concluded that PCR is considerably more sensitive than dot blot DNA hybridisation in detecting HPV cervical infection in such a "low risk" setting, where HPV copy number may be low. Firm conclusions cannot be drawn from our results regarding a causal role for HPV or other factors in the development of cervical neoplasia.

Plasma concentrations of prostaglandins during late human pregnancy: influence of normal and preterm labor

Highly sensitive and specific RIA procedures have been used to measure prostaglandin concentrations in the peripheral circulation of late pregnant and parturient women. The concentrations of prostaglandin E (PGE) and prostaglandin F (PGF) in plasma samples assayed within 4 weeks of collection were not significantly different among the groups studied, the levels (mean +/- SEM, picograms per ml) were: late pregnancy (n = 13): PGE, 4.8 +/- 1.0; PGF, 6.2 +/- 0.5; early term labor (n = 5): PGE, 6.8 +/- 1.5; PGF, 7.9 +/- 0.7; late term labor (n = 5): PGE, 5.4 +/- 2.2; PGF, 12.4 +/- 3.5; and preterm labor (n = 7): PGE, 4.4 +/- 0.4; PGF, 6.9 +/- 1.4. The concentration of 13,14-dihydro-15-keto-prostaglandin F (PGFM) in late pregnancy was 59.0 +/- 7.8 pg/ml. During spontaneous term labor, the concentration of PGFM was significantly elevated (P less than 0.01) to 142.8 +/- 32.3 pg/ml in early labor and 282.7 +/- 55.3 pg/ml in late labor. The concentration of PGFM in plasma from patients in preterm labor (62.7 +/- 17.4 pg/ml) was not significantly different from that found during late pregnancy, but was significantly lower than levels found at term during early labor (P less than 0.05). The concentration of PGE increased significantly in frozen plasma samples stored for more than 4 weeks in all groups studied; the concentration of PGF was significantly elevated after storage only in the late pregnancy group (P less than 0.01). The plasma concentration of PGFM in all groups studied was unaffected by storage. It is concluded that measurement of PGFM concentrations is the most reliable method available of monitoring prostaglandins in the peripheral circulation and that great care must be exercised in the assay and interpretation of prostaglandin levels in human plasma.

Specific production of prostaglandin E by human amnion in vitro

Prostaglandin production by intra-uterine human tissues has been investigated using a method of tissue superfusion. Tissues were obtained at elective Caesarean section and after spontaneous vaginal delivery. It was found that all the tissues studied (amnion, chorion, decidua and placenta) produced more prostaglandin E (PGE) and 13,14-dihydro-15-keto-prostaglandin F (PGFM - the major circulating metabolite of prostaglandin F) than prostaglandin F (PGF). Amnion produced significantly more PGE (but not PGF or PGFM) than any other tissue. Prostaglandin production by each tissue was similar whether it was taken at elective Caesarean section or after spontaneous vaginal delivery.

Prostaglandins in the human umbilical circulation at birth

Prostaglandin E (PGE), prostaglandin F (PGF) and 13, 14-dihydro-15-keto-prostaglandin F (PGFM) have been measured in umbilical cord plasma obtained immediately after delivery of the baby before clampiing of the cord. In general the prostaglandin levels followed the pattern PGFM greater than PGE greater than PGF. A significant arterio-venous difference was demonstrated only for PGE with raised venous levels (P less than 0.01). In cord blood samples obtained from infants whose mothers had received epidural anaesthesia, no arterio-venous difference for PGE could be demonstrated although the mean levels were not significantly different from controls. The concentrations of prostaglandins in umbilical cord plasma proximal to the placenta were found to rise continuously from the time of delivery of the baby with no significant changes after cord clamping or placental delivery. The possible physiological significance of these findings is discussed.

Rapid increases in plasma prostaglandin concentrations after vaginal examination and amniotomy

Peripheral plasma concentrations of 13,14-dihydro-15-keto prostaglandin F (PGFM) were measured in three groups of women after the 37th week of pregnancy. Samples were taken before and five minutes after (a) amniotomy, (b) vaginal examination with sweeping of the fetal membranes, or (c) vaginal examination without sweeping of the membranes. Each procedure significantly raised the circulating PGFM levels, although amniotomy and vaginal examination with membrane sweep were more potent stimuli than vaginal examination alone. These findings suggest that there is a considerable potential for rapid increases in prostaglandin production during late pregnancy and provide a possible explanation for the fact that amniotomy and vaginal examination with membrane sweep often initiate labour.