Exploring the Translational Gap of a Novel Class of Escherichia coli IspE Inhibitors

Discovery of novel antibiotics needs multidisciplinary approaches to gain target enzyme and bacterial activities while aiming for selectivity over mammalian cells. Here, we report a multiparameter optimisation of a fragment-like hit that was identified through a structure-based virtual-screening campaign on Escherichia coli IspE crystal structure. Subsequent medicinal-chemistry design resulted in a novel class of E. coli IspE inhibitors, exhibiting activity also against the more pathogenic bacteria Pseudomonas aeruginosa and Acinetobacter baumannii. While cytotoxicity remains a challenge for the series, it provides new insights on the molecular properties for balancing enzymatic target and bacterial activities simultaneously as well as new starting points for the development of IspE inhibitors with a predicted new mode of action.

1-deoxy-D-xylulose-5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding

The ESKAPE bacteria are the six highly virulent and antibiotic-resistant pathogens that require the most urgent attention for the development of novel antibiotics. Detailed knowledge of target proteins specific to bacteria is essential to develop novel treatment options. The methylerythritol-phosphate (MEP) pathway, which is absent in humans, represents a potentially valuable target for the development of novel antibiotics. Within the MEP pathway, the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) catalyzes a crucial, rate-limiting first step and a branch point in the biosynthesis of the vitamins B1 and B6. We report the high-resolution crystal structures of DXPS from the important ESKAPE pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae in both the co-factor-bound and the apo forms. We demonstrate that the absence of the cofactor thiamine diphosphate results in conformational changes that lead to disordered loops close to the active site that might be important for the design of potent DXPS inhibitors. Collectively, our results provide important structural details that aid in the assessment of DXPS as a potential target in the ongoing efforts to combat antibiotic resistance.

Role of Ommaya Reservoir in Pediatric Hydrocephalus: Experience in Bangladesh Medical College Hospital from 2019-2021

The goal of this study was to analyze the efficacy of the Ommaya reservoir within all the different types of hydrocephalus in pediatric patients. At the same time, it's safe for repeated aspirations or long-term retention of the reservoir in the body. This retrospective, cross-sectional study was performed from January 2019 to December 2021, 33 consecutive cases of reservoir implantation were taken into the study irrespective of the etiology of hydrocephalus in the Neurosurgery Department of Bangladesh Medical College Hospital, Dhaka, Bangladesh. These were mostly placed along with endoscopic third ventriculostomy and some were placed as an intermediary procedure to combat shunt complications in emaciated infants. Cerebrospinal fluid (CSF) aspiration was done in case of failed endoscopic third ventriculostomy and the frequency of aspiration depended upon the production of cerebrospinal fluid. Acetazolamide was routinely administered in each patient to reduce the frequency of aspiration. Most of the patients required ventriculo-peritoneal (VP) shunt while they had sufficient body weight and few required no surgery. The average age at presentation was 76.88 days. All the neonates and infants had less weight in terms of their age. 42.4% of babies needed aspiration 2 times per week. Among all cases, 9.1% developed reservoir complications. Complications were not related to the number and volume of aspiration or duration of the reservoir in the body. Two (2) patients died after one year of reservoir implantation due to unknown etiology. Out of the 31 survivors, 3 patients did not need any further aspiration and 19 patients needed a ventriculo-peritoneal shunt, but the reservoir was kept in situ for a future emergency. The rest of them is waiting for a definitive shunt procedure. Other findings include low socioeconomic group was more prone to low birth weight and they carried the burden of congenital hydrocephalus and meningomyelocele. Most affected babies had their prenatal period in arsenic-affected areas in Bangladesh. Overall folic acid supplementation was started after the formation of the neural tube irrespective of socioeconomic status. Ommaya reservoir placement along with endoscopic third ventriculostomy plays a vital role in delaying shunt in endoscopic third ventriculostomy failure. It is a 'time buying' procedure until the baby has sufficient weight for successful shunt surgery. It has been found very effective intermediary intervention for managing shunt infection and it also helps revive a channel in shunt obstruction.

Not Every Hit-Identification Technique Works on 1-Deoxy-d-Xylulose 5-Phosphate Synthase (DXPS): Making the Most of a Virtual Screening Campaign

In this work, we demonstrate how important it is to investigate not only on-target activity but to keep antibiotic activity against critical pathogens in mind. Since antimicrobial resistance is spreading in bacteria such as Mycobacterium tuberculosis, investigations into new targets are urgently needed. One promising new target is 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. We have recently solved the crystal structure of truncated M. tuberculosis DXPS and used it to perform a virtual screening in collaboration with Atomwise Inc. using their deep convolutional neural network-based AtomNet® platform. Of 94 virtual hit compounds only one showed interesting results in binding and activity studies. We synthesized 30 close derivatives using a straightforward synthetic route that allowed for easy derivatization. However, no improvement in activity was observed for any of the derivatives. Therefore, we tested them against a variety of pathogens and found them to be good inhibitors against Escherichia coli.

Bulking for stress urinary incontinence in men: A systematic review

AIMS

An updated literature review on outcomes in men treated with currently commercially available bulking agents was performed to determine whether this is a reasonable option in selected patients.

METHODS

The review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework of systematic reviews. A comprehensive search of PubMed, Medline, and Embase was undertaken. Abstracts were independently screened by two investigators to include men with stress urinary incontinence treated with a peri-urethral injection of bulking agents currently available in the market.

RESULTS

Only eight original articles met the inclusion criteria. The bulking agents used were Macroplastique in five studies (total 123 patients), Opsys, Durasphere, and Urolastic in one study each (10, 7, and 2 patients, respectively). Only one study was randomized; Macroplastique vs AUS in men with mild or total incontinence. The included populations were heterogeneous and encompassed endoscopic, perineal, abdominal and laparoscopic prostate surgery as well as spinal cord injuries and urethral sphincter insufficiency. Significant dissimilarity was evident for the duration of incontinence (9-108 months), mean volume of bulking agent used (2.3-13.5 mL), number of cushions (1-5), depth and position of the cushions. The outcomes varied significantly, with reported dry rates between 0% and 83%. Outcomes were limited by relatively short follow-up in most studies.

CONCLUSION

Following initial enthusiasm and then dismay with collagen-based compounds, sparse and heterogeneous literature data were produced on newer non-migrating and nonabsorbable bulking agents. Some studies have suggested encouraging, if short term outcomes, however, future studies are needed in this field to support recommendations for widespread use.

Increased Anion Gap Metabolic Acidosis as a Result of 5- Oxoproline (Pyroglutamic Acid) in Pregnancy: A Case Report

Accumulation of 5- Oxoproline (pyroglutamic acid) is a rare cause of severe, high anion gap metabolic acidosis in adults. A 21 year old lady presented at 39 weeks gestation in her first pregnancy with 2 weeks history of shortness of breath. Arterial blood gas showed metabolic acidosis. Urine and serum samples were taken which showed an increase in the serum level of 5- Oxoproline -creatinine ratio indicating pyroglutamic metabolic acidosis. Metabolic acidosis that is caused by 5- oxoproline results from disruption of the gamma glutamyl cycle. Glutamile synthetase (GS) deficiency is an autosomol recessive disorder. With GS deficiency, reduced glutathione levels increases gamma glutamile synthetase activity, and the resulting gamma - glutamile cystine levels are converted to 5-oxoproline.Suspicion for 5-oxoproline-associated high anion gap metabolic acidosis should be made when the cause of high anion gap metabolic acidosis remains poorly defined. DOI: http://www.dx.doi.org/10.3126/njog.v7i2.11144   Nepal Journal of Obstetrics and Gynaecology / Vol 7 / No. 2 / Issue 14 / July-Dec, 2012 / 47-49

Tined lead versus percutaneous nerve evaluation for sacral nerve stimulator assessment

Purpose:

We compared the outcomes of percutaneous nerve evaluation (PNE) with first-stage tined lead placement (FSTLP) for the testing phase of sacral nerve neuromodulation (SNM), and we assessed the outcomes of these two techniques following implantation of a (second-stage) permanent sacral nerve stimulator (SNS).

Methods:

Seventy consecutive patients had either PNE ( n = 35) or FSTLP ( n = 35) evaluation, and conversion to a permanent SNS implant according to response. Primary outcomes were assessed using frequency-volume charts, pad testing, ICIQ/EQ5D questionnaires and global health perception visual analogue scale (VAS). Success was considered if they achieved greater than 50% improvement in their urinary symptoms. Success and failure rates were compared during the test phase and after implantation of the SNS.

Results:

Mean follow-up for the FSTLP group was 14 months (nine to 20) and for the PNE group was 22 months (eight to 27). Sixteen (46%) of the PNE tests and 20 (57%) of the FSTLP patients were converted to permanent implant. A significant correlation was noted between patients’ general health (VAS score) and a successful test phase ( r = 0.297, p = 0.013). Eighteen of 19 (95%) of tined lead patients have successful SNS implants, whereas five of 16 (31%) of PNE evaluations failed to convert test efficacy to the permanent SNS implant ( p = 0.042). Furthermore, two of PNE-SNS patients were successfully salvaged by the implantation of a second tined lead.

Conclusions:

FSTLP-SNS has a significantly higher success rate than PNE-SNS in converting the test phase to SNS implantation. This may be due in part to difficulties retaining accurate lead placement with the two-lead (PNE-SNS) approach. These findings have important cost and logistical implications for SNS services.

Sub-50 fs Yb-doped laser with anomalous-dispersion photonic crystal fiber

We report on the generation of 42 fs pulses at 1 μm in a completely fiber-integrated format, which are, to the best of our knowledge, the shortest from all-fiber-integrated Yb-doped fiber lasers to date. The ring fiber cavity incorporates anomalous-dispersion, solid-core photonic crystal fiber with low birefringence, which acts as a broadband, in-fiber Lyot filter to facilitate mode locking. The oscillator operates in the stretched-pulse regime under slight normal net cavity dispersion. The cavity generates 4.7 ps long pulses with a spectral bandwidth of 58.2 nm, which are dechirped to 42 fs via a grating pair compressor outside of the cavity. Relative intensity noise (RIN) of the laser is characterized, with the integrated RIN found to be 0.026% in the 3 Hz-250 kHz frequency range.

Congenital Descending Colonic Stenosis with Perforation of Transverse Colon in a Neonate: A Case Report

Colonic atresia and stenosis are rare causes of intestinal obstruction in the infant. Only 10 cases have been reported in Literature since 1966 and only one late-onset case has been reported in Literature until now. We describe the case of a 3 day old baby presenting with abdominal distension, failure to pass meconium and vomiting. X-ray of the abdomen showed dilated gut loops. Exploratory laparotomy was performed. At the junction of descending and sigmoid colon a stenosis was found, laparotomy also revealed a perforation of transverse colon. Transverse colostomy and a mucous fistula of sigmoid colon was performed after resecting stenosing segment and colon distal to perforation site upto stenosing site. Diagnosis was confirmed on histopathology. Colostomy was close after six weaks with uneventful recovery. Considering both the Literature and our case, congenital colonic stenosis should be considered one of the rare differential diagnoses in a neonate presenting as complete or partial intestinal obstruction. Key words: Colonic Stenosis; Perforation; Obstruction DOI: http://dx.doi.org/10.3126/jnps.v32i1.5446   J. Nepal Paediatr. Soc. Vol.32(1) 2012 73-75  

Transcripts from a novel BMPR2 termination mutation escape nonsense mediated decay by downstream translation re-initiation: implications for treating pulmonary hypertension

Bone morphogenetic protein receptor type 2 (BMPR2) gene mutations are a major risk factor for heritable pulmonary arterial hypertension (HPAH), an autosomal dominant fatal disease. We have previously shown that BMPR2 transcripts that contain premature termination codon (PTC) mutations are rapidly and nearly completely degraded through nonsense mediated decay (NMD). Here we report a unique PTC mutation (W13X) that did not behave in the predicted manner. We found that patient-derived cultured lymphocytes (CLs) contained readily detectable levels of the PTC-containing transcript. Further analysis suggested that this transcript escaped NMD by translational re-initiation at a downstream Kozak sequence, resulting in the omission of 173 amino acids. Treatment of CLs containing the PTC with an aminoglycoside decreased the truncated protein levels, with a reciprocal increase in full-length BMPR2 protein and, importantly, BMPR-II signaling. This is the first demonstration of aminoglycoside-mediated 'repair' of a BMPR2 mutation at the protein level in patient-derived cells and has obvious implications for treatment of HPAH where no disease-specific treatment options are available. Our data also suggest the need for a more thorough characterization of mutations prior to labeling them as haploinsufficient or dominant negative based simply on sequencing data.

Alterations in oestrogen metabolism: implications for higher penetrance of familial pulmonary arterial hypertension in females

Mutations in bone morphogenetic protein receptor type 2 (BMPR2) cause familial pulmonary arterial hypertension (FPAH), but the penetrance is reduced and females are significantly overrepresented. In addition, gene expression data implicating the oestrogen-metabolising enzyme CYP1B1 suggests a detrimental role of oestrogens or oestrogen metabolites. We examined genetic and metabolic markers of altered oestrogen metabolism in subjects with a BMPR2 mutation. Genotypes for CYP1B1 Asn453Ser (N453S) were determined for 140 BMPR2 mutation carriers (86 females and 54 males). Nested from those subjects, a case-control study of urinary oestrogen metabolite levels (2-hydroxyoestrogen (2-OHE) and 16alpha-hydroxyoestrone (16alpha-OHE(1))) was conducted in females (five affected mutation carriers versus six unaffected mutation carriers). Among females, there was four-fold higher penetrance among subjects homozygous for the wild-type genotype (N/N) than those with N/S or S/S genotypes (p = 0.005). Consistent with this finding, the 2-OHE/16alpha-OHE(1) ratio was 2.3-fold lower in affected mutation carriers compared to unaffected mutation carriers (p = 0.006). Our findings suggest that variations in oestrogens and oestrogen metabolism modify FPAH risk. Further investigation of the role of oestrogens in this disease with profound sex bias may yield new insights and, perhaps, therapeutic interventions.

Clinical picture of craniopharyngioma in childhood

This cross sectional and observational study was carried out among the admitted patients of the department of Neurosurgery, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka during the period of 1st March 2004 to 31st March 2005. Among the all intracranial tumours, 2.5-04% are Craniopharyngiomas. Although there is a bi-modal age distribution-1st peak at 5-10 years and the 2nd peak at 55-65 years, the common patients are children (9% of childhood tumour). A typical child with Craniopharyngioma (CP) is short, obese and half blind and has a poor school record. The study has been undertaken to know in details, how child patients with Craniopharyngiomas in Bangladesh present their disease at the hospital. Earlier diagnosis and management may improve the quality of life and longivity. The average age of the patients was 13 years ranging from 07 to 17 years. The vast majority patients were admitted with visual problems as their presenting complaints. Among the patients 33% had total blindness of which 03 had primary optic atrophy and 1 has secondary optic atrophy. Among the remaining 08 patients, 75% were found to have field defect. All patients showed fundal changes ranging from early papilloedema to optic atrophy. We found major endocrinological deficiency in child patients with Craniopharyngioma in 17% cases. Raised Prolactin level may not be significant, because it could be due to stalk effect. Although 25% patients were of short stature, their hormonal profile was within normal range according to age and sex.

Long-term urological outcomes in paediatric spinal cord injury

STUDY DESIGN

Retrospective review.

OBJECTIVE

This retrospective review observes the evolution of bladder management by time and reports adult urological outcomes and complications in paediatric onset spinal cord injury (SCI).

SETTING

Spinal Injuries Unit RNOH Stanmore.

METHOD

In total, 10 traumatic SCI patients with mean age at injury of 13.6 years underwent treatment, for a mean period of 13.1 years. Characteristics of injury were noted. Two diagnostic subgroups, neurogenic detrusor overactivity (NDO), and acontractile detrusor were made. Complications, treatment changes, operative procedures with follow-up were noted.

RESULTS

In group 1 (6/10 patients) with NDO, five had DSD. Initial bladder management was reflex/urge voiding (n=4), suprapubic catheterisation (SPC), (n=1) and self-intermittent catheterisation (SIC), (n=1). Two patients had multiple upper tract complications with decreased renal function, two recurrent symptomatic urinary infections and one; bladder calculus. In total, 12 operative procedures were performed to treat complications and change bladder management to, SIC+oxybutynin (n=3), ileal conduit (n=1), sacral anterior root stimulator implant (SARSI), (n=1), voiding on urge (n=1). In group 2 (4/10 patients) with a-contractile detrusor two had low compliance. Initial bladder management was SIC (n=3) and voiding on urge/straining (n=1). Two patients converted from SIC to permanent catheter drainage and reported complications. Incidental kidney stone was diagnosed in one. A total of four interventions were carried out with final management of SIC (n=2), voiding on urge/straining (n=1) and Mitrofanoff+ileocystoplasty (n=1).

CONCLUSION

Bladder management in paediatric SCI is dependent on neurological level and type of injury; it changes with growth and is affected by changes in bladder management.

Effects of repeated ejaculations on semen characteristics following spinal cord injury

STUDY DESIGN

Prospective randomised controlled study.

OBJECTIVE

To evaluate the effects of repeated ejaculation on semen characteristics following spinal cord injury (SCI) in a prospective randomised controlled study.

SETTING

Spinal Research Centre, Stanmore, UK and Institute of Urology and Nephrology, London, UK.

METHODS

A total of 74 patients with SCI above T10 were tested by vibro-ejaculation using a Ferticare penile vibrator (Multicept A/S Horsholm, Denmark) using a standardised technique. The ejaculate was examined according to WHO protocol. The successfully vibro-ejaculated subjects (n = 32) were randomised into a study group (n = 18) and a control group (n = 14). The patients in the study group vibro-ejaculated weekly for 3 months with semen analysis performed at baseline and then monthly. The control group vibro-ejaculated at baseline and at the end of the 3-month period. Two experienced observers performed the semen analysis independently. All measures were compared for statistical significance across the two groups at the beginning and at the end of the 3-month period using a two-tailed student t-test. Significance was determined at the 95% confidence interval (P < 0.05).

RESULTS

In total, 10 patients in the study group and nine in the control group have completed the study so far. Six patients have dropped out of the study group and three from the control group for varied reasons. Two patients are currently enrolled in the study and control groups. The morphology and forward progression of sperm shows a statistically significant increase in the study group. The motility improves but is not statistically significant in the study group. No significant adverse effects were reported.

CONCLUSIONS

We have shown in this unique randomised controlled study that repeated ejaculation does improve the sperm characteristics in SCI patients. It is suggested that SCI men should undergo repeated ejaculation for at least 3 months before trying intravaginal or intrauterine insemination techniques. If this fails then in vitro fertilisation can be used. This method promotes natural conception, is intimate and cost effective.

Long-term efficacy of AMS 800 artificial urinary sphincter in male patients with urodynamic stress incontinence due to spinal cord lesion

STUDY DESIGN

Retrospective analysis.

OBJECTIVES

To evaluate long-term efficacy and complications of AMS 800 (American Medical Systems) artificial urinary sphincter (AUS) in treatment of urodynamic stress incontinence (USI) in male patients with spinal cord lesion (SCL).

SETTING

London Spinal Injuries Unit, Stanmore, UK and Institute of Urology and Nephrology, London, UK.

PATIENTS AND METHODS

A retrospective analysis identified nine males with SCL (five thoracic, three lumbar, one cervical) with USI, who underwent AMS 800 AUS implantation by a single surgeon at a specialist spinal injuries unit. The mean age was 38.2 years (range 27-47 years), with the mean time since injury of 13.8 years (range 6-26 years). In all, seven were complete and two were incomplete SCL (traumatic spinal injury eight, tranverse myelitis one). All implants were inserted with the urethral cuff around the bulbar urethra with a 61-70 cm water pressure reservoir in the retropubic space. Implant activation was carried out at 6 weeks postoperatively. All patients were regularly followed up in outpatient clinics at the interval of 3 months, 6 months and yearly thereafter. An ultrasound examination for the upper tracts and a video-cystometrogram (VCMG) was carried out at 3 months postsurgery and then yearly.

RESULTS

The follow-up ranged from 3 to 133 months (mean 70.2 months). All implants were activated successfully with no intra- or immediate-postoperative complications. At activation all patients reported total urinary continence with seven out of nine implants (77%) currently working well. Two patients reported significant recurrent incontinence at 3 month follow-up, one of whom underwent a removal of the entire implant at the end of 3 months and the other was continent after a pump and cuff revision. The implant removed at 3 months was due to erosion and infection while the second was removed at 24 months due to secondary implant infection. Three out of seven (43%) successful implants required one revision each. One patient continues to report minimal leakage only during transfers with no leak demonstrated on postoperative VCMG. One patient with indwelling urethral catheter, two with suprapubic catheter and one voiding on urge have changed their bladder management to intermittent catheterisations postoperatively. All removals and revision procedures were carried out in the first 53 months of follow-up and four out of seven implants (57%) required no revisions.

CONCLUSION

On a long term, AMS 800 is a viable option to treat USI in men with SCL. Mechanical revisions are frequent but effective. Strict patient selection, optimum preoperative bladder management and regular follow-up ensure low complication and high efficacy rates in the long term.

Stress urinary incontinence: current understanding

Many new concepts were introduced in epidemiology, a etiopathology and treatment of stress urinary incontinence. This review gives a short account of these concepts and compares the results of commonly used treatment options with new ones recently introduced.

Stress urinary incontinence: current understanding

Many new concepts were introduced in epidemiology, a etiopathology and treatment of stress urinary incontinence. This review gives a short account of these concepts and compares the results of commonly used treatment options with new ones recently introduced.

Comparison of alamar blue and MTT assays for high through-put screening

The performance of alamar blue and 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT) cell viability assays in a high through-put format were compared. A total of 117 drugs chosen for their wide range of therapeutic areas were screened at 10 microM using both assays in human hepatoma cell line HepG2. Except for terfenadine and astemizole, which performed consistently in both assays, the alamar blue assay was slightly more sensitive than the MTT assay for most compounds. The MTT assay was less sensitive detecting an effect for daunorubicin and trifluoperazine. Seven drugs, astemizole, daunorubicin, ellipticine, fluphenazine, terfenadine, thioridazine and trifluoperazine, had percent viability results of 55% or less in the alamar blue assay at the single point screen. These were re-tested in both assays for reconfirmation of cytotoxicity and determination of the EC50 values. Except for daunorubicin, the EC50 values were comparable in both assays. Based on these results and the Z'-factor assessment of assay quality, both assays provided useful information to identify in vitro cytotoxic drugs at early stages of drug candidate selection. However, careful interpretation of data is warranted due to the possibility of false positive or negative results caused by inducers and/or inhibitors of metabolic enzymes that are responsible for transformation of cell toxicity end points, as we demonstrated using dicumarol.

Intratesticular cysts and malignant potential: conservative management is an option

Benign intratesticular cysts are rare, but recognition is essential to prevent unnecessary surgical intervention. The diagnostic dilemma is to differentiate these cysts from testicular malignancy. As they are extremely uncommon, experience of their management is limited and controversial. We present a case of a simple intratesticular cyst and discuss the diagnostic and management principles.

Penile erosion in spinal cord injury – an important lesson

STUDY DESIGN

A case report of the complications of a spinal cord injury (SCI) patient alternating between indwelling urethral catheter and a condom drainage system for bladder management.

OBJECTIVE

To highlight the importance of penile care for bladder drainage following SCI.

SETTING

Spinal Injuries Unit, Stanmore, UK.

SUBJECT

A 39-year-old male who sustained a lumbar level SCI in December 2000. He presented acutely with leakage of urine around his condom drainage device.

MAIN OUTCOME MEASURE

The examination revealed an eroded area on the ventral aspect of the proximal penile shaft, which corresponded to the site of condom attachment. An indwelling urethral catheter was inserted as a temporary measure before reconstruction.

RESULT

At operation, in addition to the preoperatively observed area of erosion, the penile urethra was found to be cleaved for almost its entire length.

CONCLUSIONS

The patient had suffered two complications from a combination of two types of bladder management, and surgery was successful in treating both the urethral cleavage and the skin erosion.