Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

Review: Modelling the pathology and behaviour of frontotemporal dementia.

Frontotemporal dementia (FTD) encompasses a collection of clinically and pathologically diverse neurological disorders. Clinical features of behavioural and language dysfunction are associated with neurodegeneration, predominantly of frontal and temporal cortices. Over the past decade, there have been significant advances in the understanding of the genetic aetiology and neuropathology of FTD which have led to the creation of various disease models to investigate the molecular pathways that contribute to disease pathogenesis. The generation of in vivo models of FTD involves either targeting genes with known disease-causative mutations such as GRN and C9orf72 or genes encoding proteins that form the inclusions that characterize the disease pathologically, such as TDP-43 and FUS. This review provides a comprehensive summary of the different in vivo model systems used to understand pathomechanisms in FTD, with a focus on disease models which reproduce aspects of the wide-ranging behavioural phenotypes seen in people with FTD. We discuss the emerging disease pathways that have emerged from these in vivo models and how this has shaped our understanding of disease mechanisms underpinning FTD. We also discuss the challenges of modelling the complex clinical symptoms shown by people with FTD, the confounding overlap with features of motor neuron disease, and the drive to make models more disease-relevant. In summary, in vivo models can replicate many pathological and behavioural aspects of clinical FTD, but robust and thorough investigations utilizing shared features and variability between disease models will improve the disease-relevance of findings and thus better inform therapeutic development.

Subtypes of anhedonia and facial electromyography response to negative affective pictures in non-psychiatric adults.

INTRODUCTION: Flat/constricted affect and anhedonia are symptoms found in several psychiatric disorders such as depression and schizophrenia. However, there are very few studies on the relationships between specific anhedonia subtypes and objectively assessed flat affect, and it appears that none of the existing studies examined potential moderation by sex. METHODS: Forty-seven undergraduate students (60% male) completed self-report questionnaires assessing three subtypes of anhedonia - non-social consummatory (CON) and anticipatory (ANT) anhedonia, and overall social anhedonia. Participants viewed 15 pictures (5 neutral and 10 negative) from the International Affective Picture System, whereas facial muscle reaction was recorded using electromyography (EMG). RESULTS: Male participants reporting a greater level of overall social or non-social CON anhedonia showed a greater EMG activity increase in the corrugator supercilii muscle to negative (vs. neutral) pictures. In females, the relationship was only found with social anhedonia and was opposite in direction, as increased social anhedonia related to less EMG activity change in the corrugator muscle. CONCLUSIONS: The relationship between anhedonia and flat affect varied as a function of sex and anhedonia subtype. These findings may help explain discrepancies in the sparse existing literature examining this relationship in psychiatric populations and have implications for assessment and treatment of these symptoms across psychiatric disorders.

Dissolution enhancement of poorly water-soluble APIs processed by hot-melt extrusion using hydrophilic polymers.

The aim of this study was to investigate the efficiency of hydrophilic polymers to enhance the dissolution rate of poorly water-soluble active pharmaceutical ingredients (APIs) processed by hot-melt extrusion (HME). Indomethacin (INM) and famotidine (FMT) were selected as model active substances while polyvinyl caprolactam graft copolymer, soluplus (SOL) and vinylpyrrolidone-vinyl acetate copolymer grades, Kollidon VA64 (VA64) and Plasdone S630 (S630) were used as hydrophilic polymeric carriers. For the purpose of the study, drug-polymer binary blends at various ratios were processed by a Randcastle single screw extruder. The physicochemical properties and the morphology of the extrudates were evaluated through X-ray diffraction (XRD), differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). Increased drug loadings of up to 40% were achieved in the extruded formulations for both drugs. INM and FMT exhibited strong plasticization effects with increasing concentrations and were found to be molecularly dispersed within the polymer blends. The in vitro dissolution studies showed increased INM/FMT release rates for all formulations compared to that of pure APIs alone.

Synaptotagmin C2A loop 2 mediates Ca2+-dependent SNARE interactions essential for Ca2+-triggered vesicle exocytosis.

Synaptotagmins contain tandem C2 domains and function as Ca(2+) sensors for vesicle exocytosis but the mechanism for coupling Ca(2+) rises to membrane fusion remains undefined. Synaptotagmins bind SNAREs, essential components of the membrane fusion machinery, but the role of these interactions in Ca(2+)-triggered vesicle exocytosis has not been directly assessed. We identified sites on synaptotagmin-1 that mediate Ca(2+)-dependent SNAP25 binding by zero-length cross-linking. Mutation of these sites in C2A and C2B eliminated Ca(2+)-dependent synaptotagmin-1 binding to SNAREs without affecting Ca(2+)-dependent membrane binding. The mutants failed to confer Ca(2+) regulation on SNARE-dependent liposome fusion and failed to restore Ca(2+)-triggered vesicle exocytosis in synaptotagmin-deficient PC12 cells. The results provide direct evidence that Ca(2+)-dependent SNARE binding by synaptotagmin is essential for Ca(2+)-triggered vesicle exocytosis and that Ca(2+)-dependent membrane binding by itself is insufficient to trigger fusion. A structure-based model of the SNARE-binding surface of C2A provided a new view of how Ca(2+)-dependent SNARE and membrane binding occur simultaneously.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.

Semi-quantitative analysis of the monomer composition in co-polymer microgels using solid state Raman and NMR spectroscopy.

A series of colloidal microgels have been prepared by surfactant-free emulsion polymerisation (SFEP) based on the N-isopropylacrylamide (NIPAM) monomer. 4-Vinylpyridine (4-VP) and butylacrylate (BuA) have been used as co-monomers. Co-polymer poly(NIPAM/4-VP) and poly(NIPAM/BuA) have been prepared with various monomer ratios, ranging from pure poly(NIPAM) to pure poly(BuA)/poly(4-VP). Freeze-dried samples of the microgels have been analysed by solid state (ss) Raman and NMR (Nuclear Magnetic Resonance) spectroscopy to investigate the monomer composition in the co-polymer microgels. Spectral data have been analysed graphically and also statistically. Spectroscopic measurements have shown that co-polymerization has occurred. The graphical and statistical analysis of the spectroscopic data for both co-polymer microgels, enables the semi-quantitative measurement of the percentage incorporation of co-monomers (4-VP/BuA) in the co-polymer microgels. A good correlation exists between the Raman and NMR results, however, Raman spectroscopy is much less time consuming (Raman spectral acquisition time is less than 10 minutes) and the measurements are easy to make and very small quantities (less than 1 mg) of the sample are required. This compares with the experimental measurements of approximately 72 hours and 100-200 mg of sample that are required for the NMR experiments.

Effects of crystal habit on the sticking propensity of ibuprofen-A case study.

This study demonstrates the effect of active pharmaceutical ingredient (API) particle habit on the sticking propensity of ibuprofen. Four diverse crystal habits with similar physico chemical properties are reported and the sticking propensity was found to increase with shape regularity. The surface energy of the extreme habits were shown to be different where particles that were more regular in shape exhibited surface energies of 9mJ/m2 higher than those that were needle-like in habit. Computational and experimental data reveals that the increase in surface energy of the regular shaped particles can be attributed to the increase in the specific (polar) component, which is due to greater presence of faces which contain the carboxylic acid functionality at the surface. The increase in the specific energy component is shown to correlate with the sticking propensity of ibuprofen. It is proposed that investigation of the chemical causality of sticking, for this API and others, using the techniques demonstrated in this paper will be of increasing importance.

Bioactive glass fillers reduce bacterial penetration into marginal gaps for composite restorations.

OBJECTIVE: Bioactive glass (BAG) is known to possess antimicrobial and remineralizing properties; however, the use of BAG as a filler for resin based composite restorations to slow recurrent caries has not been studied. Accordingly, the objective of this study was to investigate the effect of adding 15wt% BAG to a resin composite on bacterial biofilms penetrating into marginal gaps of simulated tooth fillings in vitro during cyclic mechanical loading. METHODS: Human molars were machined into approximately 3mm thick disks of dentin and 1.5-2mm deep composite restorations were placed. A narrow 15-20 micrometer wide dentin-composite gap was allowed to form along half of the margin by not applying dental adhesive to that region. Two different 72wt% filled composites were used, one with 15wt% BAG filler (15BAG) and the balance silanated strontium glass and one filled with aerosol silica and silanated strontium glass without BAG (0BAG-control). Samples of both groups had Streptococcus mutans biofilms grown on the surface and were tested inside a bioreactor for two weeks while subjected to periods of cyclic mechanical loading. After post-test biofilm viability was confirmed, each specimen was fixed in glutaraldehyde, gram positive stained, mounted in resin and cross-sectioned to reveal the gap profile. Depth of biofilm penetration for 0BAG and 15BAG was quantified as the fraction of gap depth. The data were compared using a Student's t-test. RESULTS: The average depth of bacterial penetration into the marginal gap for the 15BAG samples was significantly smaller (∼61%) in comparison to 0BAG, where 100% penetration was observed for all samples with the biofilm penetrating underneath of the restoration in some cases. SIGNIFICANCE: BAG containing resin dental composites reduce biofilm penetration into marginal gaps of simulated tooth restorations. This suggests BAG containing composites may have the potential to slow the development and propagation of secondary tooth decay at restoration margins.

The role of the locus coeruleus in corticotropin-releasing hormone and stress-induced suppression of pulsatile luteinizing hormone secretion in the female rat.

Despite a wealth of evidence for CRH mediating stress-induced suppression of the hypothalamic GnRH pulse generator, and hence reproductive dysfunction, the site and mechanism of action remains elusive. The locus coeruleus (LC), a prominent noradrenergic brain stem nucleus, is innervated by CRH neurons, mediates several behavioral stress responses, and is implicated in the control of pulsatile LH secretion. The aim of this study was to test the hypothesis that LC CRH has a critical role in mediating stress-induced suppression of pulsatile LH secretion in the rat. Ovariectomized rats with 17beta-estradiol or oil-filled s.c. capsules were implanted with bilateral LC and i.v. cannulae. Central administration of CRH (10 ng to 1 microg) resulted in a dose-dependent suppression of LH pulses, which was reversed by a CRH receptor antagonist (alpha-helical CRF(9-41), 1 microg). The induction of c-fos expression in glutamic acid decarboxylase67 immunostained neurons in the preoptic area suggests activation of the secretion of gamma-aminobutyric acid in response to intracoerulear administration of CRH; 17beta-estradiol further increased the percentage of glutamic acid decarboxylase67-positive neurons that expressed fos and augmented suppression of LH pulses. Furthermore, intracoerulear administration of alpha-helical CRF(9-41) completely blocked restraint stress-induced suppression of LH pulses, without affecting the inhibitory response to hypoglycemia. These results suggest that CRH innervation of the LC may play a pivotal, but differential, role in the normal physiological response of stress-induced suppression of the GnRH pulse generator and hence the reproductive system.

Physical chemical evidence of structural weakness in coronary arterial calcification.

Physical-chemical properties of calcified human coronary arteries were obtained through 857 electron probe microanalyses of samples of endarterectomy tissue from 12 patients and by X-ray and electron diffraction from separate samples. The calcific phase exhibited a weight percentage calcium to phosphorus ratio of 2.5 (SEM 0.15), a density of 2.95 (0.02) g.cm-3, and a crystalline unit cell volume of 530 (0.5) A3, or 53 (0.05) nm3. The phase has been characterised as a phosphorus deficient dahllite variant of apatite in which the crystal structure has been weakened by the incorporation of water molecules and tetrahedral hydroxyl groups in isomorphic substitution conforming with the McConnell-type defect. Isomorphic substitution within the apatitic cell appears sufficient to suggest that the crystal structure of the mineral deposit is weakened to the extent that means might be sought to attack the early formation of the pathological deposition.

Cyclic mechanical loading promotes bacterial penetration along composite restoration marginal gaps.

OBJECTIVES: Secondary caries is the most common reason for composite restoration replacement and usually forms between dentin and the filling. The objective of this study was to investigate the combined effect of cyclic loading and bacterial exposure on bacterial penetration into gaps at the interface between dentin and resin composite restorative material using a novel bioreactor system and test specimen design. METHODS: Human molars were machined into 3mm thick disks with 2mm deep × 5 mm diameter cavity preparations into which composite restorations were placed. A ∼ 15-30 µm (small) or ∼ 300 µm wide (large) marginal gap was introduced along half of the interface between the dentin and restoration. Streptococcus mutans UA 159 biofilms were grown on each sample prior to testing each in a bioreactor both with and without cyclic loading. Both groups of samples were tested for 2 weeks and post-test biofilm viability was confirmed with a live-dead assay. Samples were fixed, mounted and cross-sectioned to reveal the gaps and observe the depth of bacterial penetration. RESULTS: It was shown that for large gap samples the bacteria easily penetrated to the full depth of the gap independent of loading or non-loading conditions. The results for all cyclically loaded small gap samples show a consistently deep bacterial penetration down 100% of the gap while the average penetration depth was only 67% for the non-loaded samples with only two of six samples reaching 100%. SIGNIFICANCE: A new bioreactor was developed that allows combining cyclic mechanical loading and bacterial exposure of restored teeth for bacterial biofilm and demineralization studies. Cyclic loading was shown to aid bacterial penetration into narrow marginal gaps, which could ultimately promote secondary caries formation.

End-stage renal failure in juvenile diabetes mellitus: a 5-year follow-up of treatment.

A group of 43 juvenile diabetic patients accepted for renal transplantation and followed up for as long as 5 years was studied. The cumulative survivial of the group was 66% at 1 year and 58% at 5 years. The 1-year survival of those receiving cadaveric renal allografts (65%) or of those on dialysis alone (55%) was less than the survival of those after living related donor transplantation (88%). The major morbid sequelae included retinopathy, neuropathy, and peripheral vascular disease. While patients were on dialysis, blindness increased, with 44% of the bilateral blindness and 27% of the unilateral blindness representing new cases. After transplantation, permanent unilateral or bilateral blindness developed in an additional 12% of the patients. Severe neuropathy progressed rapidly in patients on dialysis and improved after transplantation in all. Fifty percent of the patients who survived transplantation 1 year or more required amputation of one or more extremities. Only 25% of the patients who survived 1 year after transplantation were without blindness, severe peripheral vascular problems, or both.

Serum lipids in chronic renal failure.

The serum lipids and lipoprotein patterns in 100 adult patients with nonnephrotic chronic renal failure were analyzed retrospectively. Hypertriglyceridemia was found in 43% of these patients. Forty-nine of the 100 had a normal lipoprotein pattern, whereas 42 had type IV hyperlipoproteinemia. This abnormal lipoprotein pattern could not be correlated with the degree of renal impairment, the type of renal disease, or with the patient's age, sex, weight, or diet.

Chronic peritoneal dialysis in juvenile-onset diabetes mellitus: a comparison with hemodialysis.

Fourteen juvenile-onset diabetic patients accepted for renal transplantation and maintained on chronic peritoneal dialysis during a 3-year period were compared with a similar group of 43 patients accepted for renal transplantation and maintained on hemodialysis. The 1-year survival in each group was similar (52% on chronic peritoneal dialysis; 55% on hemodialysis), but there was a striking difference in progressive morbidity. Seven patients on chronic peritoneal dialysis were blind in one or both eyes at the onset, and visual acuity improved in two, including one bilaterally blind patient who achieved 20/35 vision bilaterally; none worsened. In the hemodialysis group, 12 patients were totally blind in one or both eyes and 11 additional patients became blind or had severe deterioration in vision; none improved. Neuropathy progressed in only 1 patient on chronic peritoneal dialysis, whereas it worsened in 17 patients on hemodialysis--9 to the extent that they needed braces or canes or were nonambulatory. All patients on chronic peritoneal dialysis were home trained and were dialyzed at night, with seven being able to work full or part time; virtually none of the patients on hemodialysis were able to work. Chronic peritoneal dialysis was relatively free of technical complication, and no significant difficulty was encountered in diabetic control, in the anephric state, or during abdominal surgery. Chronic peritoneal dialysis appears to have less associated morbidity than does hemodialysis in the treatment of chronic renal failure of juvenile-onset diabetes mellitus.

Hemosiderosis in a dialysis patient: treatment with hemofiltration and deferoxamine chelation therapy.

Although the highly permeable membranes utilized in hemofiltration are theoretically more permeable to deferoxamine-chelated iron than the standard cuprophan membranes used in conventional hemodialysis, no clinical data support this contention. Ours are the first published results of a preliminary short-term trial of combined therapy with deferoxamine and hemofiltration in a dialysis patient with hemosiderosis. An average of 15.3 mg of iron was mobilized with a 19.5-liter exchange over only 4 1/2 hours of postdilution hemofiltration. This compares favorable with previous reports in which 8 to 12 hours of dialysis were performed with Kiil dialyzers, and also with the 24-hour urinary excretion of chelated iron in iron-overloaded patients with normal renal function. We conclude that combined therapy with deferoxamine and hemofiltration offers promises as an effective means of iron mobilization in dialysis patients with hemosiderosis.

Continuous ambulatory peritoneal dialysis. Three years' experience at the Mayo Clinic.

From January 1979 through January 1982, 69 patients with end-stage renal failure of various causes were treated by continuous ambulatory peritoneal dialysis. The dialysis was adequate and stable in all except four patients; two of these four became irreversibly uremic, and the other two had inadequate ultrafiltration. Hemoglobin levels increased initially and remained stable in all but two patients. In our experience, metabolic problems included control of secondary hyperparathyroidism, adequate protein nutrition, progressive neuropathy, abnormal lipoprotein profiles, and excessive weight gain. Technical problems included recurrent peritonitis, maintenance of adequate peritoneal access, and development of abdominal hernias. In general, all but two patients remained enthusiastic about this type of therapy despite inherent problems. The long-term potential of continuous ambulatory peritoneal dialysis remains uncertain at this point, but for most patients, adequate short-term treatment by this method is a reasonable alternative to hemodialysis.

Results of treatment of center hemodialysis patients.

Four hundred eighty-three patients were maintained by hemodialysis in an outpatient hemodialysis center at the Mayo Clinic between 1963 and 1977. Although only 18 patients had experienced a myocardial infarction and 6 had had a cerebral infarction before beginning dialysis, 30 subsequently had acute myocardial infarction and 45 had a stroke. These two complications accounted for 48 of the 98 deaths that occurred during maintenance dialysis. Despite such complications, 183 patients were employed, 124 remained active at home or at school, and 115 were totally disabled. Survival of patients maintained solely by dialysis was 52% at 5 years. For the group as a whole, including patients who received their first allograft, the survival rate at 5 years was 65%.

Results of treatment of renal failure by means of home hemodialysis.

Of 630 patients who began hemodialysis treatment for chronic renal failure between 1965 and 1977, 147 successfully completed training for home hemodialysis. Patient compliance was satisfactory, as reflected by the results of monthly blood chemical values, hematocrits, and weight gain between dialysis. Although only 15 patients had previous myocardial infarctions and 4 had had strokes before beginning dialysis, 9 patients subsequently experienced acute myocardial infarctions and 14 had strokes. Of the 45 patients who died while being maintained by hemodialysis, 24 had cardiopulmonary complications and 6 had strokes. Despite such complications, 70 patients were gainfully employed and 32 were active at home or at school, whereas 29 were totally disabled. At last follow-up, 74 remained on home hemodialysis, 53 had functioning renal allografts, and the rest of the patients were being maintained in our dialysis center, had transferred elsewhere, or were being maintained by peritoneal dialysis. The overall estimated 5-year survival rate was 56%, whereas the estimated 5-year survival rate for those maintained by home hemodialysis alone was 52%.

Differential effects of repeated restraint stress on pulsatile lutenizing hormone secretion in female Fischer, Lewis and Wistar rats.

Stress activates the hypothalamic-pituitary-adrenocortical (HPA) axis and can suppress pulsatile luteinizing hormone (LH) secretion, resulting in reproductive dysfunction. The histocompatible inbred Fischer and Lewis rat strains exhibit marked phenotypic differences in the activity of the HPA axis, the former being more reactive. Using Fischer, Lewis and Wistar rats, we assessed effects of repeated restraint stress on pulsatile LH secretion. Adult rats were ovariectomized and fitted with cardiac catheters. Blood samples were collected at 5-min intervals for 3-5 h for detection of LH. Less frequent samples were collected for corticosterone measurement. After 2 h, rats were restrained for 60 min. The same regimen was repeated four times at 6-day intervals. The mean peak corticosterone levels achieved during the first restraint in Fischer rats were significantly higher than those in Lewis and Wistar rats. By the time of the fourth episode of restraint, there had been some adaptation of the corticosterone response in the Fischer, but not in the Lewis or Wistar rats. LH pulses were interrupted during the 1st restraint in all experimental groups, although only Fischer rats showed suppression of LH pulses during the subsequent 2-h postrestraint period. During the fourth restraint, LH pulse frequency was still reduced in Wistar, but not in Fischer and Lewis rats, both of which showed a complete habituation. These results suggest that differential control mechanisms underlie the response of the HPA and HPG axes to repeated restraint stress.