Automated Measurements of Key Morphological Features of Human Embryos for IVF.

A major challenge in clinical In-Vitro Fertilization (IVF) is selecting the highest quality embryo to transfer to the patient in the hopes of achieving a pregnancy. Time-lapse microscopy provides clinicians with a wealth of information for selecting embryos. However, the resulting movies of embryos are currently analyzed manually, which is time consuming and subjective. Here, we automate feature extraction of time-lapse microscopy of human embryos with a machine-learning pipeline of five convolutional neural networks (CNNs). Our pipeline consists of (1) semantic segmentation of the regions of the embryo, (2) regression predictions of fragment severity, (3) classification of the developmental stage, and object instance segmentation of (4) cells and (5) pronuclei. Our approach greatly speeds up the measurement of quantitative, biologically relevant features that may aid in embryo selection.

The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) Inhibitor.

The profound efficacy, yet associated toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (>100-fold) inhibition of a subset of the eight bromodomains is enticing, but challenging given the close homology. Herein, we describe the X-ray crystal structure-directed optimization of a novel weak fragment ligand with a pan-second bromodomain (BD2) bias, to potent and highly BD2 selective inhibitors. A template hopping approach, enabled by our parallel research into an orthogonal template (15, GSK046), was the basis for the high selectivity observed. This culminated in two tool molecules, 20 (GSK620) and 56 (GSK549), which showed an anti-inflammatory phenotype in human whole blood, confirming their cellular target engagement. Excellent broad selectivity, developability, and in vivo oral pharmacokinetics characterize these tools, which we hope will be of broad utility to the field of epigenetics research.

Discovery of an Orally Bioavailable Pan αv Integrin Inhibitor for Idiopathic Pulmonary Fibrosis.

The heterodimeric transmembrane αv integrin receptors have recently emerged as potential targets for the treatment of idiopathic pulmonary fibrosis. Herein, we describe how subtle modifications of the central aromatic ring of a series of phenylbutyrate-based antagonists of the vitronectin receptors αvß3 and αvß5 significantly change the biological activities against αvß6 and αvß8. This resulted in the discovery of a pan αv antagonist (compound 39, 4-40 nM for the integrin receptors named above) possessing excellent oral pharmacokinetic properties in rats (with a clearance of 7.6 mL/(min kg) and a bioavailability of 97%).

Thermal and photochemical annulation of vinyl azides to 2-aminoimidazoles.

2-Aminoimidazoles represent useful synthons for incorporation into medicinal compounds. They provide hydrogen bonding loci, water solubilizing properties and convenient handles for further synthetic elaboration. The rapid and facile generation of diverse 2-aminoimidazoles via tandem addition cyclization reaction of vinyl azides and cyanamide has been investigated. These reactions proceeded through either thermal or photochemical activation of vinyl azides and demonstrated wide substrate scope. In the photochemical reaction, blue light (456 nm) alone triggered photolysis of the azide without the addition of a photocatalyst. Possible reaction mechanisms in the context of substrate reactivity are discussed.

Identification of GSK3186899/DDD853651 as a Preclinical Development Candidate for the Treatment of Visceral Leishmaniasis.

The leishmaniases are diseases that affect millions of people across the world, in particular visceral leishmaniasis (VL) which is fatal unless treated. Current standard of care for VL suffers from multiple issues and there is a limited pipeline of new candidate drugs. As such, there is a clear unmet medical need to identify new treatments. This paper describes the optimization of a phenotypic hit against Leishmania donovani, the major causative organism of VL. The key challenges were to balance solubility and metabolic stability while maintaining potency. Herein, strategies to address these shortcomings and enhance efficacy are discussed, culminating in the discovery of preclinical development candidate GSK3186899/DDD853651 (1) for VL.

Discovery of Novel 1-Cyclopentenyl-3-phenylureas as Selective, Brain Penetrant, and Orally Bioavailable CXCR2 Antagonists.

CXCR2 has emerged as a therapeutic target for not only peripheral inflammatory diseases but also neurological abnormalities in the central nervous system (CNS). Herein, we describe the discovery of a novel 1-cyclopentenyl-3-phenylurea series as potent and CNS penetrant CXCR2 antagonists. Extensive SAR studies, wherein molecules' property forecast index (PFI) was carefully optimized for overall balanced developability profiles, led to the discovery of the advanced lead compound 68 with a desirable PFI. Compound 68 demonstrated good in vitro pharmacology with excellent selectivity over CXCR1 and other chemokine receptors. Rat and dog pharmacokinetics (PK) revealed good oral bioavailability, high oral exposure, and desirable elimination half-life of the compound in both species. In addition, the compound demonstrated dose-dependent efficacy in the in vivo pharmacology neutrophil infiltration "air pouch" model in rodents after oral administration. Further, compound 68 is a CNS penetrant molecule with high unbound fraction in brain tissue.

Conversion of a Benzofuran Ester to an Amide through an Enamine Lactone Pathway: Synthesis of HCV Polymerase Inhibitor GSK852A.

HCV NS5B polymerase inhibitor GSK852A (1) was synthesized in only five steps from ethyl 4-fluorobenzoylacetate (3) in 46% overall yield. Key to the efficient route was the synthesis of the highly functionalized benzofuran core 15 from the ß-keto ester in one pot and the efficient conversion of ester 6 to amide 19 via enamine lactone 22. Serendipitous events led to identification of the isolable enamine lactone intermediate 22. Single crystal X-ray diffraction and NMR studies supported the intramolecular hydrogen bond shown in enamine lactone 22. The hydrogen bond was considered an enabler in the proposed pathway from ester 6 to enamine lactone 22 and its rearrangement to amide 19. GSK852A (1) was obtained after reductive amination and mesylation with conditions amenable to the presence of the boronic acid moiety which was considered important for the desirable pharmacokinetics of 1. The overall yield of 46% in five steps was a significant improvement to the previous synthesis from the same ß-keto ester in 5% yield over 13 steps.

The scars of time: the disappearance of peptic ulcer-related pyloric stenosis through the 20th century.

BACKGROUND: The changing pattern of haemorrhage and perforation from peptic ulcer disease is well documented but little is known about pyloric stenosis, the third complication of the disease. METHODS: We reviewed records relating to definitive operations (with intent to cure) for peptic ulcer disease carried out in York, UK from 1929-1997. We categorised the patients as pyloric stenosis and no pyloric stenosis based on findings at operation and examined the change in total number of cases with pyloric stenosis and proportion of cases with pyloric stenosis, by year of operation and by decade of birth. To place our results in perspective, we reviewed world literature to examine rates of pyloric stenosis as a percentage of operative cases reported in other case series in the 20th century. RESULTS: 4178 patients were included in the analysis; 3697 without pyloric stenosis and 481 with pyloric stenosis (11.5%). Analysis by birth cohort showed that the proportion found to have pyloric stenosis at surgery fell from 17% in the first cohort (birth 1880-89) to only 2.9% in the last cohort (birth 1950-59; p<0.001). Mean age at operation fell more steeply for those with pyloric stenosis: 74 to 30 years vs. 65 to 28 years (p <0.001). The trend of final decline started before the introduction of modern medical treatment. Review of similar case series from across the world shows a similar decline in the proportion of peptic ulcer cases showing pyloric stenosis at operation. CONCLUSION: The reduction in pyloric stenosis over the last several decades is disproportionately greater than the change seen in peptic ulcer disease requiring surgery. Our findings suggest that this reduction in pyloric stenosis is largely the result of the changing natural history of the disease rather than due to the introduction of acid-suppressing medication.

Solid-state NMR analysis of a complex crystalline phase of ronacaleret hydrochloride.

A crystalline phase of the pharmaceutical compound ronacaleret hydrochloride is studied by solid-state nuclear magnetic resonance (SSNMR) spectroscopy and single-crystal X-ray diffraction. The crystal structure is determined to contain two independent cationic molecules and chloride anions in the asymmetric unit, which combine with the covalent structure of the molecule to yield complex SSNMR spectra. Experimental approaches based on dipolar correlation, chemical shift tensor analysis, and quadrupolar interaction analysis are employed to obtain detailed information about this phase. Density functional theory (DFT) calculations are used to predict chemical shielding and electric field gradient (EFG) parameters for comparison with experiment. (1)H SSNMR experiments performed at 16.4 T using magic-angle spinning (MAS) and homonuclear dipolar decoupling provide information about hydrogen bonding and molecular connectivity that can be related to the crystal structure. (19)F and (13)C assignments for the Z' = 2 structure are obtained using DFT calculations, (19)F homonuclear dipolar correlation, and (13)C-(19)F heteronuclear dipolar correlation experiments. (35)Cl MAS experiments at 16.4 T observe two chlorine sites that are assigned using calculated chemical shielding and EFG parameters. SSNMR dipolar correlation experiments are used to extract (1)H-(13)C, (1)H-(15)N, (1)H-(19)F, (13)C-(19)F, and (1)H-(35)Cl through-space connectivity information for many positions of interest. The results allow for the evaluation of the performance of a suite of SSNMR experiments and computational approaches as applied to a complex but typical pharmaceutical solid phase.

Lead identification and structure-activity relationships of heteroarylpyrazole arylsulfonamides as allosteric CC-chemokine receptor 4 (CCR4) antagonists.

A knowledge-based library of aryl 2,3-dichlorophenylsulfonamides was synthesised and screened as human CCR4 antagonists, in order to identify a suitable hit for the start of a lead-optimisation programme. X-ray diffraction studies were used to identify the pyrazole ring as a moiety that could bring about intramolecular hydrogen bonding with the sulfonamide NH and provide a clip or orthogonal conformation that was believed to be the preferred active conformation. Replacement of the core phenyl ring with a pyridine, and replacement of the 2,3-dichlorobenzenesulfonamide with 5-chlorothiophenesulfonamide provided compound 33 which has excellent physicochemical properties and represents a good starting point for a lead optimisation programme. Electronic structure calculations indicated that the preference for the clip or orthogonal conformation found in the small molecule crystal structures of 7 and 14 was in agreement with the order of potency in the biological assay.

Solid-state NMR analysis of a boron-containing pharmaceutical hydrochloride salt.

A novel crystalline form of the boron-containing antibacterial drug (S)-3-(aminomethyl)-7-(3-hydroxypropoxy)benzo[c] [1,2]oxaborol-1(3H)-ol hydrochloride is studied by solid-state nuclear magnetic resonance (SSNMR) and single-crystal X-ray diffraction techniques. After determination of the crystal structure by X-ray diffraction, SSNMR spectroscopy of this form is performed to obtain structural information using experimental approaches based on dipolar correlation, chemical shift analysis, and quadrupolar interaction analysis. 1H SSNMR experiments at 16.4 T using magic-angle spinning (MAS) and homonuclear dipolar decoupling, 2D SSNMR experiments based on (1)H­(13)C and (1)H­(11)B dipolar heteronuclear correlation, and density functional theory (DFT) calculations are combined in a novel approach to obtain a nearly complete assignment of the (1)H spectrum of this crystalline phase. (11)B and (35)Cl chemical shift and quadrupolar parameters are obtained using the analysis of MAS spectra and are found to be accurately reproduced using DFT calculations. NMR chemical shielding and electric field gradient parameters obtained using these methods are related to hydrogen-bonding trends in the crystal structure. The results illustrate the increasing capability of SSNMR techniques involving (1)H, (11)B, and (35)Cl SSNMR in the analysis of the crystal structure of a pharmaceutical compound containing covalently bonded boron.

Synthesis and structure-activity relationships of indazole arylsulfonamides as allosteric CC-chemokine receptor 4 (CCR4) antagonists.

A series of indazole arylsulfonamides were synthesized and examined as human CCR4 antagonists. Methoxy- or hydroxyl-containing groups were the more potent indazole C4 substituents. Only small groups were tolerated at C5, C6, or C7, with the C6 analogues being preferred. The most potent N3-substituent was 5-chlorothiophene-2-sulfonamide. N1 meta-substituted benzyl groups possessing an α-amino-3-[(methylamino)acyl]-group were the most potent N1-substituents. Strongly basic amino groups had low oral absorption in vivo. Less basic analogues, such as morpholines, had good oral absorption; however, they also had high clearance. The most potent compound with high absorption in two species was analogue 6 (GSK2239633A), which was selected for further development. Aryl sulfonamide antagonists bind to CCR4 at an intracellular allosteric site denoted site II. X-ray diffraction studies on two indazole sulfonamide fragments suggested the presence of an important intramolecular interaction in the active conformation.

Mortality in Barrett's esophagus: three decades of experience at a single center.

BACKGROUND AND STUDY AIMS: There is a view that the majority of deaths in patients with Barrett's esophagus are from causes other than esophageal adenocarcinoma (EAC). The aim of this analysis was to establish the pattern of mortality for a number of causes in patients with Barrett's esophagus. PATIENTS AND METHODS: This was a single-center prospective cohort study of patients from Rotherham District General Hospital, which is a secondary referral center. The cohort consisted of 1239 patients who were diagnosed with Barrett's esophagus between April 1978 and March 2009.  Follow-up for mortality was undertaken by "flagging" the patients with the NHS Information Center. Causes of death were compared with UK Office of National Statistics age- and sex-specific mortality data for 1999, the median year of diagnosis. Analysis was by a "person - years at risk" calculation from date of diagnosis. RESULTS: The ratio of observed deaths from EAC compared with those expected in this cohort was 25.02 - a very large excess. There was no difference in mortality from colorectal cancer or circulatory disease and there were fewer deaths from cancers other than esophageal adenocarcinoma and colon cancer compared with national statistics. There was a small statistically significant difference in mortality from all causes but this disappeared completely when deaths from esophageal adenocarcinoma were excluded. CONCLUSIONS: Overall, mortality in Barrett's esophagus is increased significantly but only as a result of the large excess of deaths from EAC. This strengthens the case for endoscopic surveillance if successful interventions can be undertaken in patients with Barrett's esophagus to prevent development of esophageal adenocarcinoma.

One-phase crystal disorder in pharmaceutical solids and its implication for solid-state stability.

Solid-state disorders of active pharmaceutical ingredients have been characterized by means of X-ray diffraction techniques and solid-state nuclear magnetic resonance spectroscopy. The results determined that the pleuromutilin-derivative, I, displays a unique continuous conformational disorder while retaining its long-range crystalline structure. The propionic acid (PA) version of this compound displayed partial crystalline order and site disorder of PA, depending on the quantity of PA incorporated in the structure. Thus, I is a unique example of one-phase crystalline-amorphous model. Physical and chemical stability data was acquired on these disordered systems and discussed in relation with the characterized disorder present in the crystal systems. Analysis of the results showed that in contrast to phase-separated amorphous, restrained disorders do not influence the stability.

A United Kingdom inflammatory bowel disease database: making the effort worthwhile.

BACKGROUND: Inflammatory bowel disease (IBD), a paradigm of chronic illness, requires for its safe clinical management ready access to complete information, not always possible using paper records. AIM: To develop an IBD database (DB) for both individual patient management and collating information across centres. METHODS: Access® based, with a minimum dataset. RESULTS: Prospectively collected data for 11,432 patients from 21 centres. PROFILE DIAGNOSIS: Ulcerative colitis (UC) 56%, Crohn's disease (CD) 40%, indeterminate colitis 4%. M:F ratio: UC 1.08:1, CD 0.72:1. Median age at diagnosis: UC 39, CD 30 years. Operated: UC 16%, CD 47%. Thiopurine use: UC 16%, CD 29%. IBD related mortality: 0.74%. DISCUSSION: A snapshot of this large IBD cohort shows the disease profile across the UK is similar to other large series. Unexpected gaps, sometimes large emerged (e.g. data on smoking and immunosuppression) highlighting the need for clear definition, consistency and completeness of data collection. Clinical management is made easier by the 'at a glance' summary, automated clinic letters, and facility for monitoring and audit, but the time required limited its 'real-time' use. CONCLUSION: Our experience shows it is possible to collect data from centres across the country which truly reflects clinical practice. We have learned as much from the process itself as from the data, principally, information needs to be well defined, validated at entry, and updated at every visit, a time consuming sequence which we had underestimated. Our lessons learned may help inform the development of a national database, and support national IBD standards and audit.

Studying the origin of the antiferromagnetic to spin-canting transition in the beta-p-NCC6F4CNSSN* molecular magnet.

The crystal structure of the spin-canted antiferromagnet beta-p-NCC(6)F(4)CNSSN* at 12 K (reported in this work) was found to adopt the same orthorhombic space group as that previously determined at 160 K. The change in the magnetic properties of these two crystal structures has been rigorously studied by applying a first-principles bottom-up procedure above and below the magnetic transition temperature (36 K). Calculations of the magnetic exchange pathways on the 160 K structure reveal only one significant exchange coupling (J(d1)=-33.8 cm(-1)), which generates a three-dimensional diamond-like magnetic topology within the crystal. The computed magnetic susceptibility, chi(T), which was determined by using this magnetic topology, quantitatively reproduces the experimental features observed above 36 K. Owing to the anisotropic contraction of the crystal lattice, both the geometry of the intermolecular contacts at 12 K and the microscopic J(AB) radical-radical magnetic interactions change: the J(d1) radical-radical interaction becomes even more antiferromagnetic (-43.2 cm(-1)) and two additional ferromagnetic interactions appear (+7.6 and +7.3 cm(-1)). Consequently, the magnetic topologies of the 12 and 160 K structures differ: the 12 K magnetic topology exhibits two ferromagnetic sublattices that are antiferromagnetically coupled. The chi(T) curve, computed below 36 K at the limit of zero magnetic field by using the 12 K magnetic topology, reproduces the shape of the residual magnetic susceptibility (having subtracted the contribution to the magnetization arising from spin canting). The evolution of these two ferromagnetic J(AB) contributions explains the change in the slope of the residual magnetic susceptibility in the low-temperature region.

Elucidating the pathways of degradation of denagliptin.

Stress testing or forced degradation studies of denagliptin (1) tosylate in solution and solid-state, its blends with excipients, and capsules were conducted in order to elucidate degradation pathways, aid formulation development, and generate data to support regulatory filings. In solution, denagliptin was stressed in acid, water, and base using organic cosolvents. In the solid-state, denagliptin was stressed under heat, humidity, and light. Blends of denagliptin with various excipients were stressed under heat and humidity in order to evaluate whether tablet was a viable dosage form. Capsules were stressed under heat, humidity, and light. It was found that denagliptin was stable in the solid-state, but degraded in solution, in blends with all excipients, and in capsules predominantly by cyclization to (3S,7S,8aS) amidine (2), which epimerized to (3S,7S,8aR) amidine (3). (3S,7S,8aR) amidine (3) subsequently hydrolyzed to the corresponding diketopiperazine (4). The purpose of this manuscript is to discuss the results of stress testing studies conducted during the development of denagliptin and the elucidation of its key degradation pathway.

An investigation into the electrophilic cyclisation of N-acyl-pyrrolidinium ions: a facile synthesis of pyrrolo-tetrahydroisoquinolones and pyrrolo-benzazepinones.

The triflic acid-mediated cyclisation of N-arylmethyl- and N-arylethyl-acylpyrrolidinium ions gave moderate to good yields of pyrrolo-tetrahydroisoquinolones and pyrrolo-benzazepinones respectively. Electron-donating R substituents enhanced the rate of reaction and gave higher yields than electron-withdrawing substituents. Substituents on the methyl or ethyl chain in general enhanced the reaction, unless sterically encumbered. The equivalent acylpiperidinium ions cyclised much slower and in lower yield.

Time, change and peptic ulcer disease in Rotherham, UK.

BACKGROUND AND AIM: We have documented the changing pattern of peptic ulcer disease in our centre in the last quarter of the 20th century and speculate on the reasons thereof. PATIENTS AND METHODS: The profile of peptic ulcer disease patients presenting newly to our centre (population 250,000) from 1977 to 2001 was examined. All patients were prospectively followed and detailed records kept. Results are presented in 5-year periods. RESULTS: Seven thousand five hundred and ninety new peptic ulcer disease patients (5564 duodenal ulcer+2026 gastric ulcer) were seen, peaking in 1982-1986 but declining thereafter, and with a falling male preponderance. Patients with gastric ulcer were older than those with duodenal ulcer; were older than duodenal ulcer, the mean age of both increased over time and the age gap from the general population widened. The numbers presenting with perforation changed little but haemorrhage increased, particularly amongst the elderly. Ulcers refractory to H2 receptor antagonists declined even before proton pump inhibitors were introduced. Elective surgery, already declining before H2 receptor antagonists, had virtually disappeared by 1992-1996. DISCUSSION AND CONCLUSION: Peptic ulcer disease affects an older population, an increasing proportion of whom present with haemorrhage. Refractoriness to H2 receptor antagonists and the need for elective operation was declining even before the emergence of modern treatment. We suggest the changes observed result not only from modern therapy but also substantially from a changing natural history.