BEERS2: RNA-Seq simulation through high fidelity in silico modeling.

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

Bora-Diaza-Indacene Based Fluorescent Probes for Simultaneous Visualisation of Lipid Droplets and Endoplasmic Reticulum.

Organelle selective fluorescent probes, especially those capable of concurrent detection of specific organelles, are of benefit to the research community in delineating the interplay between various organelles and the impact of such interaction in maintaining cellular homeostasis and its disruption in the diseased state. Although very useful, such probes are synthetically challenging to design due to the stringent lipophilicity requirement posed by different organelles, and hence, the lack of such probes being reported so far. This work details the synthesis, photophysical properties, and cellular imaging studies of two bora-diaza-indacene based fluorescent probes that can specifically and simultaneously visualise lipid droplets and endoplasmic reticulum; two organelles suggested having close interactions and implicated in stress-induced cellular dysfunction and disease progression.

Involvement of the tumour necrosis factor receptor system in glioblastoma cell death induced by palbociclib-heptamethine cyanine dye conjugate.

Glioblastoma is the most common and aggressive primary brain tumour in adults. The development of anti-brain cancer agents are challenged by the blood-brain barrier and the resistance conferred by the local tumour microenvironment. Heptamethine cyanine dyes (HMCDs) are a class of near-infrared fluorescence compounds that have recently emerged as promising agents for drug delivery. We conjugated palbociclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, to an HMCD, MHI-148, and conducted drug activity analysis on primary patient-derived glioblastoma cell lines. In addition to the expected cytostatic activity, our in vitro studies revealed that palbociclib-MHI-148 conjugate resulted in an almost 100-fold increase in cytotoxicity compared to palbociclib alone. This shift of palbociclib from cytostatic to cytotoxic when conjugated to MHI-148 was due to increased DNA damage, as indicated by an increase in γH2AX foci, followed by an increased expression of key extrinsic apoptosis genes, including TP53, TNFR1, TRAIL, FADD and caspase 8. In addition, we observed a time-dependent increase in the cell surface expression of TNFR1, consistent with an observed increase in the secretion TNFα, followed by TNFR1 endocytosis at 48 h. The treatment of patient GBM cells with the palbociclib-MHI-148 conjugate prevented TNFα-induced NFκB translocation, suggesting conjugate-induced TNFR1 signalling favoured the TNFR1-mediated apoptotic response rather than the pro-inflammatory response pathway. Notably, pharmacological inhibition of endocytosis of TNFR1, and siRNA-knockdown of TNFR1 reversed the palbociclib-MHI-148-induced cell death. These results show a novel susceptibility of glioblastoma cells to TNFR1-dependent apoptosis, dependent on inhibition of canonical NFκB signalling using our previously reported palbociclib-HMCD conjugate. Video Abstract.

Measurement of Complement Activation via Plasma-Soluble C5b-9 Comparison with Terminal Complement Complex Staining in a Series of Kidney Biopsies.

INTRODUCTION: With the emergence of therapeutic complement inhibitors, there is a need to identify patients with complement-driven inflammation. C5b-9 is the terminal product of the three complement pathways and therefore a marker of total complement activation. We present a pilot study which aims to assess whether plasma soluble C5b-9 (sC5b-9) correlates with terminal complement complex (TCC) staining in kidney tissue. The secondary aim was to assess the utility of plasma sC5b-9 as part of routine workup in kidney patients undergoing kidney biopsy. METHODS: Thirty-seven patients undergoing kidney biopsy had plasma sC5b-9 and TCC staining on kidney tissue performed. Additional blood markers including creatinine, haemoglobin, CRP, factor H, factor I, and midkine levels were also taken. These parameters were correlated with the histological diagnoses. Patients were divided into a diseased group (n = 31) and a control group (n = 6) consisting of transplanted kidneys with minor or no changes. Of the biopsies in the control group, 50% were performed as per protocol, and the other 50% were performed due to clinical need. RESULTS: There was no correlation found between plasma sC5b-9 and TCC kidney staining. Elevated sC5b-9 levels were found in a heterogeneous group of patients but were associated with higher CRP and lower haemoglobin levels. Overall, there was more TCC kidney staining in the diseased group compared with the control group, and a trend was observed of diabetic, primary membranous nephropathy, and amyloidosis patients having more intense glomerular and peritubular/interstitial staining. CONCLUSION: Plasma sC5b-9 as a marker of total complement activation does not correlate with TCC kidney staining. This discordance suggests that plasma sC5b-9 and TCC staining are distinct markers of disease. TCC staining reflects chronicity and tissue deposition of complement over time. Conversely, plasma sC5b-9 concentrations change rapidly and reflect systemic complement activation. Complement activation was present in a heterogeneous group of kidney disease, indicating the underlying role of complement in many disorders.

Synthetic studies towards isomeric pyrazolopyrimidines as potential ATP synthesis inhibitors of Mycobacterium tuberculosis. Structural correction of reported N-(6-(2-(dimethylamino)ethoxy)-5-fluoropyridin-3-yl)-2-(4-fluorophenyl)-5-(trifluoromethyl)pyrazolo[1,5-α]pyrimidin-7-amine.

During our studies into preparing analogues of pyrazolopyrimidine as ATP synthesis inhibitors of Mycobacterium tuberculosis, a regiospecific condensation reaction between ethyl 4,4,4-trifluoroacetoacetate and 3-(4-fluorophenyl)-1H-pyrazol-5-amine was observed which was dependent on the specific reaction conditions employed. This work identifies optimized reaction conditions to access either the pyrazolo[3,4-ß]pyridine or the pyrazolo[1,5-α]pyrimidine scaffold. This has led to the structural confirmation of the previously reported pyrazolopyrimidine 17b which was reported as pyrazolo[1,5-α]pyrimidine structure 2 which was corrected to pyrazolo[3,4-ß]-pyrimidine 19.

Proximal humeral fracture-dislocations: which patterns can be reduced in the emergency department?

BACKGROUND: Shoulder fracture-dislocations can represent a challenging management scenario in the emergency department (ED) because of concern for the presence of occult fractures that may displace during a reduction attempt. The alternative, a closed reduction attempt in the operating room, has the benefit of full paralysis but requires additional resource utilization. There is limited guidance in the literature about the risks of an initial reduction attempt in the ED as a function of fracture pattern to help guide physicians with this decision. METHODS: This was a retrospective case review of adult patients with shoulder dislocations and fracture-dislocations seen in the ED at a level 1 trauma center over a 10-year period. Imaging and medical records were reviewed to evaluate whether the reduction attempt was successful, unsuccessful without worsening, or unsuccessful with worsening alignment of any fractures, as well as the ultimate clinical outcome. RESULTS: We identified 165 patients with fracture-dislocations and 484 patients with simple dislocations during the same period. Of the patients with fracture-dislocations, 103 had greater tuberosity fractures, 12 had nondisplaced surgical neck fractures, and 50 had displaced surgical neck fractures. None of the patients with simple dislocations had displacement during an ED reduction attempt, including 100 patients aged >65 years. Of the 103 patients with greater tuberosity fracture-dislocations, only 1 had displacement of a humeral shaft fracture during ED reduction. Displacement occurred in 6 of 8 patients with nondisplaced neck fractures who underwent an initial ED reduction attempt vs. 1 of 4 patients who underwent the initial reduction attempt in the operating room. ED reduction was attempted in 25 of the 50 displaced humeral neck fracture-dislocations and was successful in 10 of these (40%). CONCLUSIONS: For patients with greater tuberosity fracture-dislocations, there is a low rate of displacement with a reduction attempt in the ED, but an ED reduction attempt in nondisplaced neck fractures is not recommended because of the high rate of displacement. For displaced neck fractures, closed reduction can be successful in select patients. Finally, these data confirm prior reports that closed reduction of simple shoulder dislocations in patients aged >65 years is safe in the ED.

Conjugation of Palbociclib with MHI-148 Has an Increased Cytotoxic Effect for Breast Cancer Cells and an Altered Mechanism of Action.

The CDK4/6 inhibitor palbociclib, combined with endocrine therapy, has been shown to be effective in postmenopausal women with estrogen receptor-positive, HER2-negative advanced or metastatic breast cancer. However, palbociclib is not as effective in the highly aggressive, triple-negative breast cancer that lacks sensitivity to chemotherapy or endocrine therapy. We hypothesized that conjugation of the near-infrared dye MHI-148 with palbociclib can produce a potential theranostic in triple-negative, as well as estrogen receptor-positive, breast cancer cells. In our study, the conjugate was found to have enhanced activity in all mammalian cell lines tested in vitro. However, the conjugate was cytotoxic and did not induce G1 cell cycle arrest in breast cancer cells, suggesting its mechanism of action differs from the parent compound palbociclib. The study highlights the importance of investigating the mechanism of conjugates of near-infrared dyes to therapeutic compounds, as conjugation can potentially result in a change of mechanism or target, with an enhanced cytotoxic effect in this case.

Cytoprotective agent troxipide-cyanine dye conjugate with cytotoxic and antiproliferative activity in patient-derived glioblastoma cell lines.

Cytoprotective agents are mainly used to protect the gastrointestinal tract linings and in the treatment of gastric ulcers. These agents are devoid of appreciable cytotoxic or cytostatic effects, and medicinal chemistry efforts to modify them into anticancer agents are rare. A drug repurposing campaign initiated in our laboratory with the primary focus of discovering brain cancer drugs resulted in drug-dye conjugate 1, a combination of the cytoprotective agent troxipide and heptamethine cyanine dye MHI 148. The drug-dye conjugate 1 was evaluated in three different patient-derived adult glioblastoma cell lines, commercially available U87 glioblastoma, and one paediatric glioblastoma cell line. In all cases, the conjugate 1 showed potent cytotoxic activity with nanomolar potency (EC50: 267 nM). Interestingly, troxipide alone does not show any cytotoxic and cytostatic activity in the above cell lines. We also observe a synergistic effect of 1 with temozolomide (TMZ), the standard drug used for glioblastoma treatment, even though the cell lines we used in this study were resistant to TMZ treatment. Herein we disclose the synthesis and in vitro activity of drug-dye conjugate 1 for treatment of difficult-to-treat brain cancers such as glioblastoma.

Factors associated with participation in colorectal cancer screening: A population-based study of 7200 individuals.

OBJECTIVE: This study aimed to evaluate how the knowledge and perception towards colorectal cancer (CRC) screening had been changed in a large population, and identified factors associated with its participation based on factors pertinent to the Health Belief Model (HBM). METHODS: Data from 3600 screening participants and 3600 non-participants were collected through a telephone survey via simple random sampling of telephone numbers in a territory-wide directory from December 2016 to November 2018. Sociodemographic factors; the enabling factors of screening as well as the barriers of screening were collected. The changes in these factors were evaluated by Pearson's chi-square trend test. A logistic regression model was constructed to identify the association between the above factors and CRC screening participation. RESULTS: The knowledge level (67.9% to 85.4%, p < 0.001), perceived severity of having CRC (37.7%-42.8%, p < 0.01), perceived benefits of screening (54.9%-72.1%, p < 0.001), and reductions in barriers (14.1%-5.1%, p < 0.001) of CRC screening significantly improved among the non-users. Subjects with older age (adjusted odds ratio (AOR): 2.01, p < 0.001), higher knowledge level of screening methods (AOR: 6.68, p < 0.001), greater perceived severity (AOR: 2.04, p < 0.001) and coverage of insurance (AOR: 1.22, p < 0.01) were more likely to participate. In contrast, more affluent subjects (AOR: 0.69, p < 0.001), female individuals (AOR: 0.63, p < 0.001), higher level of perceived psychological (AOR: 0.54, p < 0.001) and access barriers (AOR: 0.55, p < 0.001) were associated with poorer participation. CONCLUSION: These findings demonstrated a substantial increase in the enabling factors of CRC screening, including knowledge, perceived severity and perceived benefits. The study also identified the target groups such as younger individuals, females and more affluent people among whom more intensive educational initiatives are needed to enhance their participation.

Global Prevalence of Colorectal Neoplasia: A Systematic Review and Meta-Analysis.

BACKGROUND & AIMS: Most colorectal cancers (CRC) arise from colorectal adenomas, yet there is not enough information on global prevalence to inform health care policy. We examined the prevalence of any type of adenomas, advanced adenomas (AADs), and CRC according to age, sex, ethnicity, geographic regions, and anatomic location (proximal vs distal). METHODS: MEDLINE and Embase were searched from their inception through May 1, 2018, to identify population-based, observational studies that reported the prevalence of colorectal neoplasia. Studies on participants 15 years or older, with a sample size of 500 persons or more, were included. Metaprop (College Station, TX) was used to model within-study variability by binomial distribution and Freeman-Tukey Double Arcsine Transformation to stabilize the variances. The prevalence figures were presented by proportions and their 95% CIs using random-effects models. RESULTS: Our meta-analysis included 70 studies involving 637,414 individuals. The overall prevalence rates of adenoma (23.9%; 95% CI, 22.2%-25.8%), AAD (4.6%; 95% CI, 3.8%-5.5%), and CRC (0.4%, 95% CI, 0.3%-0.5%) were calculated. Subgroup analysis indicated that prevalence values (adenomas, AADs, and CRCs) were higher among men (29.7%, 6.5%, and 0.8%, respectively) than women (19.3%, 3.8% and 0.4%, respectively), among older adults (25.9%, 5.2%, and 0.6%, respectively) than younger adults (14.6%, 1.6%, and 0.1%, respectively), among Caucasians (23.7%, 6.6%, and 0.5%, respectively) than other ethnicities, in European countries (25.9%, 8.4%, and 0.8%, respectively) than other countries, and among patients with proximal (25.9%, 5.3%, and 0.1%, respectively) vs distal neoplasia. CONCLUSIONS: In a systematic review and meta-analysis, we found a high prevalence of colorectal neoplasia among some populations. This indicates a need to expand CRC screening programs for these groups. The pooled prevalence estimates can be used as quality indicators for established CRC screening programs.

Heptamethine Cyanine Dye Mediated Drug Delivery: Hype or Hope.

This review covers the application of heptamethine cyanine dye (HMCD) mediated drug delivery. A relatively small number of HMCDs possess tumor targeting abilities, and this has spurred interest from research groups to explore them as drug delivery systems. Their tumor selectivity is primarily attributed to their uptake by certain isoforms of organic anion transporting polypeptides (OATPs) which are overexpressed in cancer tissues, although there are other possible mechanisms for the observed selectivity still under investigation. This specificity is confirmed using various cancer cell lines and is accompanied by moderate cytotoxicity. Their retention in tumor tissue is facilitated by the formation of albumin adducts as revealed by published mechanistic studies. HMCDs are also organelle selective dyes with specificity toward mitochondria and lysosomes, and with absorption and emission in the near-infrared region. This makes them valuable tools for biomedical imaging, especially in the field of fluorescence-guided tumor surgery. Furthermore, conjugating antitumor agents to HMCDs is providing novel drugs that await clinical testing. HMCD development as theranostic agents with dual tumor targeting and treatment capability signals a new approach to overcome drug resistance (mediated through evasion of efflux pumps) and systemic toxicity, the two parameters which have long plagued drug discovery.

PARP inhibitor cyanine dye conjugate with enhanced cytotoxic and antiproliferative activity in patient derived glioblastoma cell lines.

We describe the synthesis and in vitro activity of drug-dye conjugate 1, which is a combination of the PARP inhibitor rucaparib and heptamethine cyanine dye IR-786. The drug-dye conjugate 1 was evaluated in three different patient-derived glioblastoma cell lines and showed strong cytotoxic activity with nanomolar potency (EC50: 128 nM), which was a 780 fold improvement over rucaparib itself. We also observe a synergistic effect of 1 with temozolomide (TMZ), the standard drug for treatment for glioblastoma even though these cell lines were resistant to TMZ treatment. We envisage such conjugates to be worth exploring for their utility in the treatment of various brain cancers.

Variations in the C-unit of bedaquiline provides analogues with improved biology and pharmacology.

Analogues of the anti-tuberculosis drug bedaquiline, bearing a 3,5-dimethoxy-4-pyridyl C-unit, retain high anti-bacterial potency yet exert less inhibition of the hERG potassium channel, in vitro, than the parent compound. Two of these analogues (TBAJ-587 and TBAJ-876) are now in preclinical development. The present study further explores structure-activity relationships across a range of related 3,5-disubstituted-4-pyridyl C-unit bedaquiline analogues of greatly varying lipophilicity (clogP from 8.16 to 1.89). This broader class shows similar properties to the 3,5-dimethoxy-4-pyridyl series, being substantially more potent in vitro and equally active in an in vivo (mouse) model than bedaquiline, while retaining a lower cardiovascular risk profile through greatly attenuated hERG inhibition.

Synthesis and structure-activity relationships for tetrahydroisoquinoline-based inhibitors of Mycobacterium tuberculosis.

A series of 5,8-disubstituted tetrahydroisoquinolines were shown to be effective inhibitors of M. tb in culture and modest inhibitors of M. tb ATP synthase. There was a broad general trend of improved potency with higher lipophilicity. Large substituents (e.g., Bn) at the tetrahydroquinoline 5-position were well-tolerated, while N-methylpiperazine was the preferred 8-substituent. Structure-activity relationships for 7-linked side chains showed that the nature of the 7-linking group was important; -CO- and -COCH2- linkers were less effective than -CH2- or -CONH- ones. This suggests that the positioning of a terminal aromatic ring is important for target binding. Selected compounds showed much faster rates of microsomal clearance than did the clinical ATP synthase inhibitor bedaquiline, and modest inhibition of mycobacterial ATP synthase.

Seroprevalence of Torque Teno Virus in hemodialysis and renal transplant patients in Australia: A cross-sectional study.

INTRODUCTION: Torque teno virus (TTV) is a non-pathogenic anellovirus commonly found in the blood of human beings. Emerging data suggest that TTV viral load is proportional to the degree of immunosuppression, but its seroprevalence is unknown in Australia. We aimed to determine the seroprevalence of TTV in an Australian population of renal patients. METHODS: We developed a real-time PCR to measure TTV viral load, using the TaqMan platform and previously published primers and probes. Following ethics approval and informed consent, we collected blood from hemodialysis patients not receiving immunosuppression, and renal transplant patients. All patients were recruited from a single teaching hospital in New South Wales. RESULTS: We enrolled 50 hemodialysis and 30 renal transplant patients. 56 (70%) were males, and the mean (sd) age was 61 (16) years. TTV was detectable in plasma of 40/50 (80%) of hemodialysis patients and 28/30 (93%) of transplant patients. The mean TTV viral load was higher in transplant patients than in dialysis patients (6.3 log versus 5.0 log copies/ml, P = .001). CONCLUSIONS: Torque teno virus is prevalent in Australian renal patients and thus may be a useful novel marker to help tailor immunosuppressive therapy in renal transplant patients. Further work is needed to establish TTV seroprevalence in other regions and patient groups, and to investigate whether there is correlation with clinically important events (infection and rejection episodes) in longitudinal studies.

Feasibility of Online Haemodiafiltration in Sleep Apnoea: A Randomized Crossover Study.

BACKGROUND: Sleep apnoea is prevalent in dialysis patients. Previous studies identified excessive inflammation in -patients with sleep apnoea. Online haemodiafiltration -(OL-HDF) may reduce systematic inflammation through better clearance of middle molecules. We aimed to determine the feasibility of OL-HDF in sleep apnoea management. METHODS: Eligible dialysis patients were screened for risk of sleep apnoea by nocturnal oximetry followed by a diagnostic sleep study to assess apnoea-hypopnea index (AHI). Patients with AHI ≥15/h were invited to a randomized crossover trial. The intervention was 2-month high-flux haemodialysis (HF-HD) followed by 2-month OL-HDF or vice versa with 1-month washout via HF-HD. Feasibility was assessed by patient recruitment and the primary outcome, severity of sleep apnoea (AHI). Secondary outcomes were pro-inflammatory cytokines, patient-reported daytime sleepiness, quality of sleep and health-related quality of life. RESULTS: Of 65 participants at risk of sleep apnoea, only 15 were consented and randomized (mean age 70 years, 80% male, mean AHI 42.2/h). AHI was not statistically different between OL-HDF versus HF-HD (55.6/h vs. 48.3/h, p = 0.134); however, when sleep apnoea was stratified into obstructive and central apnoea, patients had less obstructive episodes after treated by OL-HDF (23.2/h vs. 18.6/h, p = 0.178); a sensitivity analysis was performed excluding outliers, and the treatment effect for obstructive episodes was found to be statistically significant (11.1 vs. 18.2/h, p = 0.019). Pro-inflammatory biomarkers and patient-reported outcomes were similar between OL-HDF and HF-HD. CONCLUSION: Patient recruitment was a major challenge in this feasibility study. OL-HDF may reduce obstructive sleep apnoea; however, the result needs to be confirmed by larger studies.

Synthetic Studies to Help Elucidate the Metabolism of the Preclinical Candidate TBAJ-876-A Less Toxic and More Potent Analogue of Bedaquiline.

Bedaquiline is a novel drug approved in 2012 by the FDA for treatment of drug-resistant tuberculosis (TB). Although it shows high efficacy towards drug-resistant forms of TB, its use has been limited by the potential for significant side effects. In particular, bedaquiline is a very lipophilic compound with an associated long terminal half-life and shows potent inhibition of the cardiac potassium hERG channel, resulting in QTc interval prolongation in humans that may result in cardiac arrhythmia. To address these issues, we carried out a drug discovery programme to develop an improved second generation analogue of bedaquiline. From this medicinal chemistry program, a candidate (TBAJ-876) has been selected to undergo further preclinical evaluation. During this evaluation, three major metabolites arising from TBAJ-876 were observed in several preclinical animal models. We report here our synthetic efforts to unequivocally structurally characterize these three metabolites through their independent directed synthesis.

The synthesis of a novel Crizotinib heptamethine cyanine dye conjugate that potentiates the cytostatic and cytotoxic effects of Crizotinib in patient-derived glioblastoma cell lines.

We describe the synthesis of drug-dye conjugate 1 between anaplastic lymphoma kinase inhibitor Crizotinib and heptamethine cyanine dye IR-786. The drug-dye conjugate 1 was evaluated in three different patient-derived glioblastoma cell lines and showed potent cytotoxic activity with nanomolar potency (EC50: 50.9 nM). We also demonstrate evidence for antiproliferative activity of 1 with single digit nanomolar potency (IC50: 4.7 nM). Furthermore, the cytotoxic effects conveyed a dramatic, 110-fold improvement over Crizotinib. This improvement was even more pronounced (492-fold) when 1 was combined with Temozolomide, the standard drug for treatment for glioblastoma. This work lays the foundation for future exploration of similar tyrosine kinase inhibitor drug-dye conjugates for the treatment of glioblastoma.

3,5-Dialkoxypyridine analogues of bedaquiline are potent antituberculosis agents with minimal inhibition of the hERG channel.

Bedaquiline is a new drug of the diarylquinoline class that has proven to be clinically effective against drug-resistant tuberculosis, but has a cardiac liability (prolongation of the QT interval) due to its potent inhibition of the cardiac potassium channel protein hERG. Bedaquiline is highly lipophilic and has an extremely long terminal half-life, so has the potential for more-than-desired accumulation in tissues during the relatively long treatment durations required to cure TB. The present work is part of a program that seeks to identify a diarylquinoline that is as potent as bedaquiline against Mycobacterium tuberculosis, with lower lipophilicity, higher clearance, and lower risk for QT prolongation. Previous work led to the identification of compounds with greatly-reduced lipophilicity compounds that retain good anti-tubercular activity in vitro and in mouse models of TB, but has not addressed the hERG blockade. We now present compounds where the C-unit naphthalene is replaced by a 3,5-dialkoxy-4-pyridyl, demonstrate more potent in vitro and in vivo anti-tubercular activity, with greatly attenuated hERG blockade. Two examples of this series are in preclinical development.

Structure-activity relationships for unit C pyridyl analogues of the tuberculosis drug bedaquiline.

The ATP-synthase inhibitor bedaquiline is effective against drug-resistant tuberculosis but is extremely lipophilic (clogP 7.25) with a very long plasma half-life. Additionally, inhibition of potassium current through the cardiac hERG channel by bedaquiline, is associated with prolongation of the QT interval, necessitating cardiovascular monitoring. Analogues were prepared where the naphthalene C-unit was replaced with substituted pyridines to produce compounds with reduced lipophilicity, anticipating a reduction in half-life. While there was a direct correlation between in vitro inhibitory activity against M. tuberculosis (MIC90) and compound lipophilicity, potency only fell off sharply below a clogP of about 4.0, providing a useful lower bound for analogue design. The bulk of the compounds remained potent inhibitors of the hERG potassium channel, with notable exceptions where IC50 values were at least 5-fold higher than that of bedaquiline. Many of the compounds had desirably higher rates of clearance than bedaquiline, but this was associated with lower plasma exposures in mice, and similar or higher MICs resulted in lower AUC/MIC ratios than bedaquiline for most compounds. The two compounds with lower potency against hERG exhibited similar clearance to bedaquiline and excellent efficacy in vivo, suggesting further exploration of C-ring pyridyls is worthwhile.