Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors

Poly ADP-ribose polymerase 1 (PARP1) is an attractive therapeutic target for cancer treatment. Machine-learning scoring functions constitute a promising approach to discovering novel PARP1 inhibitors. Cutting-edge PARP1-specific machine-learning scoring functions were investigated using semi-synthetic training data from docking activity-labelled molecules: known PARP1 inhibitors, hard-to-discriminate decoys property-matched to them with generative graph neural networks and confirmed inactives. We further made test sets harder by including only molecules dissimilar to those in the training set. Comprehensive analysis of these datasets using five supervised learning algorithms, and protein-ligand fingerprints extracted from docking poses and ligand only features revealed one highly predictive scoring function. This is the PARP1-specific support vector machine-based regressor, when employing PLEC fingerprints, which achieved a high Normalized Enrichment Factor at the top 1% on the hardest test set (NEF1% = 0.588, median of 10 repetitions), and was more predictive than any other investigated scoring function, especially the classical scoring function employed as baseline.

Coordinating activation of endo-lysosomal two-pore channels and TRP mucolipins

Two-pore channels and TRP mucolipins are ubiquitous endo-lysosomal cation channels of pathophysiological relevance. Both are Ca2+-permeable and regulated by phosphoinositides, principally PI(3,5)P2. Accumulating evidence has uncovered synergistic channel activation by PI(3,5)P2 and endogenous metabolites such as the Ca2+ mobilizing messenger NAADP, synthetic agonists including approved drugs and physical cues such as voltage and osmotic pressure. Here, we provide an overview of this coordination.

The role of the nucleus pulposus in intervertebral disc recovery: Towards improved specifications for nucleus replacement devices

Nucleus replacement devices (NRDs) have potential to treat degenerated or herniated intervertebral discs (IVDs). However, IVD height loss is a post-treatment complication. IVD height recovery involves the nucleus pulposus (NP), but the mechanism of this in response to physiological loads is not fully elucidated. This study aimed to characterise the non-linear recovery behaviour of the IVD in intact, post-nuclectomy, and post-NRD treatment states, under physiological loading. 36 bovine IVDs (12 intact, 12 post-nuclectomy, 12 post-treatment) underwent creep-recovery protocols simulating Sitting, Walking or Running, followed by 12 h of recovery. A rheological model decoupled the fluid-independent (elastic, fast) and fluid-dependent (slow) recovery phases. In post-nuclectomy and post-treatment groups, nuclectomy efficiency (ratio of NP removed to remaining NP) was quantified following post-test sectioning. Relative to intact, post-nuclectomy recovery significantly decreased in Sitting (-0.3 ± 0.4 mm, p < 0.05) and Walking (-0.6 ± 0.3 mm, p < 0.001) coupled with significant decreases to the slow response (p < 0.05). Post-nuclectomy, the fast and slow responses negatively correlated with nuclectomy efficiency (p < 0.05). In all protocols, the post-treatment group performed significantly worse in recovery (-0.5 ± 0.3 mm, p < 0.01) and the slow response (p < 0.05). Results suggest the NP mainly facilitates slow-phase recovery, linearly dependent on the amount of NP present. Failure of this NRD to recover is attributed to poor fluid imbibition. Additionally, unconfined NRD performance cannot be extrapolated to the in vitro response. This knowledge informs NRD design criteria to provide high osmotic pressure, and encourages testing standards to incorporate long-term recovery protocols.

Unraveling the Behavior of Intrinsically Disordered Protein c-Myc: A Study Utilizing Gaussian-Accelerated Molecular Dynamics

The protein c-Myc is a transcription factor that remains largely intrinsically disordered and is known to be involved in various biological processes and is overexpressed in various cancers, making it an attractive drug target. However, intrinsically disordered proteins such as c-Myc do not show funnel-like basins in their free-energy landscapes; this makes their druggability a challenge. For the first time, we propose a heterodimer model of c-Myc/Max in full length in this work. We used Gaussian-accelerated molecular dynamics (GaMD) simulations to explore the behavior of c-Myc and its various regions, including the transactivation domain (TAD) and the basic helix-loop-helix-leucine-zipper (bHLH-Zipper) motif in three different conformational states: (a) monomeric c-Myc, (b) c-Myc when bound to its partner protein, Max, and (c) when Max was removed after binding. We analyzed the GaMD trajectories using root-mean-square deviation (RMSD), radius of gyration, root-mean-square fluctuation, and free-energy landscape (FEL) calculations to elaborate the behaviors of these regions. The results showed that the monomeric c-Myc structure showed a higher RMSD fluctuation as compared with the c-Myc/Max heterodimer in the bHLH-Zipper motif. This indicated that the bHLH-Zipper motif of c-Myc is more stable when it is bound to Max. The TAD region in both monomeric and Max-bound states showed similar plasticity in terms of RMSD. We also conducted residue decomposition calculations and showed that the c-Myc and Max interaction could be driven mainly by electrostatic interactions and the residues Arg299, Ile403, and Leu420 seemed to play important roles in the interaction. Our work provides insights into the behavior of c-Myc and its regions that could support the development of drugs that target c-Myc and other intrinsically disordered proteins.

The influence of geometry on intervertebral disc stiffness

Geometry plays an important role in intervertebral disc (IVD) mechanics. Previous computational studies have found a link between IVD geometry and stiffness. However, few experimental studies have investigated this link, possibly due to difficulties in non-destructively quantifying internal geometric features. Recent advances in ultra-high resolution MRI provides the opportunity to visualise IVD features in unprecedented detail. This study aimed to quantify 3D human IVD geometries using 9.4 T MRIs and to investigate correlations between geometric variations and IVD stiffness. Thirty human lumbar motion segments (fourteen non-degenerate and sixteen degenerate) were scanned using a 9.4 T MRI and geometric parameters were measured. A 1kN compressive load was applied to each motion segment and stiffness was calculated. Degeneration caused a reduction (p < 0.05) in IVD height, a decreased nucleus-annulus area ratio, and a 1.6 ± 3.0 mm inward collapse of the inner annulus. The IVD height, anteroposterior (AP) width, lateral width, cross-sectional area, nucleus-annulus boundary curvature, and nucleus-annulus area ratio had a significant (p < 0.05) influence on IVD stiffness. Linear relationships (p < 0.05, r > 0.47) were observed between these geometric features and IVD compressive stiffness and a multivariate regression model was generated to enable stiffness to be predicted from features observable on clinical imaging (stiffness, N/mm = 6062 - (61.2 × AP width, mm) - (169.2 × IVD height, mm)). This study advances our understanding of disc structure-function relationships and how these change with degeneration, which can be used to both generate and validate more realistic computational models.

Combination of QSAR Modeling and Hybrid-Based Consensus Scoring to Identify Dual-Targeting Inhibitors of PLK1 and p38γ

Polo-like kinase 1 (PLK1) and p38γ mitogen-activated protein kinase (p38γ) play important roles in cancer pathogenesis by controlling cell cycle progression and are therefore attractive cancer targets. The design of multitarget inhibitors may offer synergistic inhibition of distinct targets and reduce the risk of drug-drug interactions to improve the balance between therapeutic efficacy and safety. We combined deep-learning-based quantitative structure-activity relationship (QSAR) modeling and hybrid-based consensus scoring to screen for inhibitors with potential activity against the targeted proteins. Using this combination strategy, we identified a potent PLK1 inhibitor (compound 4) that inhibited PLK1 activity and liver cancer cell growth in the nanomolar range. Next, we deployed both our QSAR models for PLK1 and p38γ on the Enamine compound library to identify dual-targeting inhibitors against PLK1 and p38γ. Likewise, the identified hits were subsequently subjected to hybrid-based consensus scoring. Using this method, we identified a promising compound (compound 14) that could inhibit both PLK1 and p38γ activities. At nanomolar concentrations, compound 14 inhibited the growth of human hepatocellular carcinoma and hepatoblastoma cells in vitro. This study demonstrates the combined screening strategy to identify novel potential inhibitors for existing targets.

Convergent activation of Ca2+ permeability in two-pore channel 2 through distinct molecular routes

TPC2 is a pathophysiologically relevant lysosomal ion channel that is activated directly by the phosphoinositide PI(3,5)P2 and indirectly by the calcium ion (Ca2+)-mobilizing molecule NAADP through accessory proteins that associate with the channel. TPC2 toggles between PI(3,5)P2-induced, sodium ion (Na+)-selective and NAADP-induced, Ca2+-permeable states in response to these cues. To address the molecular basis of polymodal gating and ion-selectivity switching, we investigated the mechanism by which NAADP and its synthetic functional agonist, TPC2-A1-N, induced Ca2+ release through TPC2 in human cells. Whereas NAADP required the NAADP-binding proteins JPT2 and LSM12 to evoke endogenous calcium ion signals, TPC2-A1-N did not. Residues in TPC2 that bind to PI(3,5)P2 were required for channel activation by NAADP but not for activation by TPC2-A1-N. The cryptic voltage-sensing region of TPC2 was required for the actions of TPC2-A1-N and PI(3,5)P2 but not for those of NAADP. These data mechanistically distinguish natural and synthetic agonist action at TPC2 despite convergent effects on Ca2+ permeability and delineate a route for pharmacologically correcting impaired NAADP-evoked Ca2+ signals.

Human soluble CD39 displays substrate inhibition in a substrate-specific manner

CD39 (ectonucleoside triphosphate diphosphohydrolase-1; ENTPD1) metabolizes extracellular ATP and ADP to AMP. AMP is subsequently metabolized by CD79 to adenosine. CD39 activity is therefore a key regulator of purinergic signalling in cancer, thrombosis, and autoimmune diseases. In this study we demonstrate that soluble, recombinant CD39 shows substrate inhibition with ADP or ATP as the substrate. Although CD39 activity initially increased with increasing substrate concentration, at high concentrations of ATP or ADP, CD39 activity was markedly reduced. Although the reaction product, AMP, inhibits CD39 activity, insufficient AMP was generated under our conditions to account for the substrate inhibition seen. In contrast, inhibition was not seen with UDP or UTP as substrates. 2-methylthio-ADP also showed no substrate inhibition, indicating the nucleotide base is an important determinant of substrate inhibition. Molecular dynamics simulations revealed that ADP can undergo conformational rearrangements within the CD39 active site that were not seen with UDP or 2-methylthio-ADP. Appreciating the existence of substrate inhibition of CD39 will help the interpretation of studies of CD39 activity, including investigations into drugs that modulate CD39 activity.

The β3-subunit modulates the effect of venom peptides ProTx-II and OD1 on NaV 1.7 gating

The voltage-gated sodium channel NaV 1.7 is involved in various pain phenotypes and is physiologically regulated by the NaV -β3-subunit. Venom toxins ProTx-II and OD1 modulate NaV 1.7 channel function and may be useful as therapeutic agents and/or research tools. Here, we use patch-clamp recordings to investigate how the β3-subunit can influence and modulate the toxin-mediated effects on NaV 1.7 function, and we propose a putative binding mode of OD1 on NaV 1.7 to rationalise its activating effects. The inhibitor ProTx-II slowed the rate of NaV 1.7 activation, whilst the activator OD1 reduced the rate of fast inactivation and accelerated recovery from inactivation. The β3-subunit partially abrogated these effects. OD1 induced a hyperpolarising shift in the V1/2 of steady-state activation, which was not observed in the presence of β3. Consequently, OD1-treated NaV 1.7 exhibited an enhanced window current compared with OD1-treated NaV 1.7-β3 complex. We identify candidate OD1 residues that are likely to prevent the upward movement of the DIV S4 helix and thus impede fast inactivation. The binding sites for each of the toxins and the predicted location of the β3-subunit on the NaV 1.7 channel are distinct. Therefore, we infer that the β3-subunit influences the interaction of toxins with NaV 1.7 via indirect allosteric mechanisms. The enhanced window current shown by OD1-treated NaV 1.7 compared with OD1-treated NaV 1.7-β3 is discussed in the context of differing cellular expressions of NaV 1.7 and the β3-subunit in dorsal root ganglion (DRG) neurons. We propose that β3, as the native binding partner for NaV 1.7 in DRG neurons, should be included during screening of molecules against NaV 1.7 in relevant analgesic discovery campaigns.

Identification of Potential p38γ Inhibitors via In Silico Screening, In Vitro Bioassay and Molecular Dynamics Simulation Studies

Protein kinase p38γ is an attractive target against cancer because it plays a pivotal role in cancer cell proliferation by phosphorylating the retinoblastoma tumour suppressor protein. Therefore, inhibition of p38γ with active small molecules represents an attractive alternative for developing anti-cancer drugs. In this work, we present a rigorous and systematic virtual screening framework to identify potential p38γ inhibitors against cancer. We combined the use of machine learning-based quantitative structure activity relationship modelling with conventional computer-aided drug discovery techniques, namely molecular docking and ligand-based methods, to identify potential p38γ inhibitors. The hit compounds were filtered using negative design techniques and then assessed for their binding stability with p38γ through molecular dynamics simulations. To this end, we identified a promising compound that inhibits p38γ activity at nanomolar concentrations and hepatocellular carcinoma cell growth in vitro in the low micromolar range. This hit compound could serve as a potential scaffold for further development of a potent p38γ inhibitor against cancer.

Quantal leaps in understanding Ca 2+ signaling: A “Taylored” approach

On 2 September 2022, about 85 scientists gathered in person at Queens’ College in Cambridge, UK, for a scientific meeting to celebrate the career of Colin W. Taylor of Cambridge University upon his retirement. The meeting was organized by the authors, who are all former graduate students in the Taylor laboratory, which has been at the forefront of Ca 2+ signaling for more than 30 years.

The inositol 5-phosphatase INPP5B regulates B cell receptor clustering and signaling

Upon antigen binding, the B cell receptor (BCR) undergoes clustering to form a signalosome that propagates downstream signaling required for normal B cell development and physiology. BCR clustering is dependent on remodeling of the cortical actin network, but the mechanisms that regulate actin remodeling in this context remain poorly defined. In this study, we identify the inositol 5-phosphatase INPP5B as a key regulator of actin remodeling, BCR clustering, and downstream signaling in antigen-stimulated B cells. INPP5B acts via dephosphorylation of the inositol lipid PI(4,5)P2 that in turn is necessary for actin disassembly, BCR mobilization, and cell spreading on immobilized surface antigen. These effects can be explained by increased actin severing by cofilin and loss of actin linking to the plasma membrane by ezrin, both of which are sensitive to INPP5B-dependent PI(4,5)P2 hydrolysis. INPP5B is therefore a new player in BCR signaling and may represent an attractive target for treatment of B cell malignancies caused by aberrant BCR signaling.

Electrophysiology of Endolysosomal Two-Pore Channels: A Current Account

Two-pore channels TPC1 and TPC2 are ubiquitously expressed pathophysiologically relevant proteins that reside on endolysosomal vesicles. Here, we review the electrophysiology of these channels. Direct macroscopic recordings of recombinant TPCs expressed in enlarged lysosomes in mammalian cells or vacuoles in plants and yeast demonstrate gating by the Ca2+-mobilizing messenger NAADP and/or the lipid PI(3,5)P2. TPC currents are regulated by H+, Ca2+, and Mg2+ (luminal and/or cytosolic), as well as protein kinases, and they are impacted by single-nucleotide polymorphisms linked to pigmentation. Bisbenzylisoquinoline alkaloids, flavonoids, and several approved drugs demonstrably block channel activity. Endogenous TPC currents have been recorded from a number of primary cell types and cell lines. Many of the properties of endolysosomal TPCs are recapitulated upon rerouting channels to the cell surface, allowing more facile recording through conventional electrophysiological means. Single-channel analyses have provided high-resolution insight into both monovalent and divalent permeability. The discovery of small-molecule activators of TPC2 that toggle the ion selectivity from a Ca2+-permeable (NAADP-like) state to a Na+-selective (PI(3,5)P2-like) state explains discrepancies in the literature relating to the permeability of TPCs. Identification of binding proteins that confer NAADP-sensitive currents confirm that indirect, remote gating likely underpins the inconsistent observations of channel activation by NAADP.

In-silico discovery of inhibitors against human papillomavirus E1 protein

High-risk (HR) Human papillomavirus (e.g. HPV16 and HPV18) causes approximately two-thirds of all cervical cancers in women. Although the first and second-generation vaccines confer some protection against individuals, there are no approved drugs to treat HR-HPV infections to-date. The HPV E1 protein is an attractive drug target because the protein is highly conserved across all HPV types and is crucial for the regulation of viral DNA replication. Hence, we used the Random Forest algorithm to construct a Quantitative-Structure Activity Relationship (QSAR) model to predict the potential inhibitors against the HPV E1 protein. Our QSAR classification model achieved an accuracy of 87.5%, area under the receiver operating characteristic curve of 1.00, and F-measure of 0.87 when evaluated using an external test set. We conducted a drug repurposing campaign by deploying the model to screen the Drugbank database. The top three compounds, namely Cinalukast, Lobeglitazone, and Efatutazone were analyzed for their cell membrane permeability, toxicity, and carcinogenicity. Finally, these three compounds were subjected to molecular docking and 200 ns-long Molecular Dynamics (MD) simulations. The predicted binding free energies for the candidates were calculated using the MM-GBSA method. The binding free energies for Cinalukast, Lobeglitazone, and Efatutazone were -37.84 kcal/mol, -25.30 kcal/mol, and -29.89 kcal/mol respectively. Therefore, we propose their chemical scaffolds for future rational design of E1 inhibitors.Communicated by Ramaswamy H. Sarma.

Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors

Lipoteichoic acid synthase (LtaS) is a key enzyme for the cell wall biosynthesis of Gram-positive bacteria. Gram-positive bacteria that lack lipoteichoic acid (LTA) exhibit impaired cell division and growth defects. Thus, LtaS appears to be an attractive antimicrobial target. The pharmacology around LtaS remains largely unexplored with only two small-molecule LtaS inhibitors reported, namely "compound 1771" and the Congo red dye. Structure-based drug discovery efforts against LtaS remain unattempted due to the lack of an inhibitor-bound structure of LtaS. To address this, we combined the use of a molecular docking technique with molecular dynamics (MD) simulations to model a plausible binding mode of compound 1771 to the extracellular catalytic domain of LtaS (eLtaS). The model was validated using alanine mutagenesis studies combined with isothermal titration calorimetry. Additionally, lead optimization driven by our computational model resulted in an improved version of compound 1771, namely, compound 4 which showed greater affinity for binding to eLtaS than compound 1771 in biophysical assays. Compound 4 reduced LTA production in S. aureus dose-dependently, induced aberrant morphology as seen for LTA-deficient bacteria, and significantly reduced bacteria titers in the lung of mice infected with S. aureus. Analysis of our MD simulation trajectories revealed the possible formation of a transient cryptic pocket in eLtaS. Virtual screening (VS) against the cryptic pocket led to the identification of a new class of inhibitors that could potentiate β-lactams against methicillin-resistant S. aureus. Our overall workflow and data should encourage further drug design campaign against LtaS. Finally, our work reinforces the importance of considering protein conformational flexibility to a successful VS endeavor.

Nutrition adequacy, gastrointestinal and hepatic function during extracorporeal membrane oxygenation in critically ill adults: a retrospective observational study

AIMS

To identify clinical and biochemical markers associated with nutrition adequacy and gastrointestinal and liver dysfunction in adults on extracorporeal membrane oxygenation (ECMO).

METHODS

A retrospective, observational, study was conducted at 2 centres in Australia. Adult patients who received ECMO from July 2011 to June 2015 were included. Mode of ECMO used, fluid balance, number of systemic inflammatory response syndrome (SIRS) criteria present, vasoactive-inotropic scores (VIS) and liver function tests (LFTs) were collected for the duration of ECMO until 7 days after ECMO cessation. Multiple regression models were used to determine if the collected variables were associated with nutrition adequacy. The mean LFTs during ECMO were also compared to mean LFTs post ECMO cessation.

RESULTS

During the first 5 days of ECMO commencement, mean nutrition adequacy was 10% higher in the veno-venous (VV) ECMO group than in the veno-arterial (VA) group (95% confidence interval [CI], 2% to 17%). For every 5,000 ml increase of fluid balance, an associated decrease in nutrition adequacy was observed (-8%, 95% CI, -15% to -2%). A doubling of bilirubin and VIS were associated with a mean reduction in nutrition adequacy of -5% (CI -8% to -2%) and -2% (CI, -3% to -1%), respectively.

CONCLUSIONS

In the first 5 days of ECMO commencement, higher nutrition adequacy was associated with the VV mode of ECMO and reduced nutrition adequacy with increased fluid balance, more vasopressor and inotropic support and raised bilirubin. Prospective investigation is required to confirm whether these associations have a causal relationship.

Q94 is not a selective modulator of proteinase-activated receptor 1 (PAR1) in platelets

Thrombin is a potent platelet activator, acting through proteinase-activated receptors -1 and -4 (PAR1 and PAR4). Of these, PAR-1 is activated more rapidly and by lower thrombin concentrations. Consequently, PAR-1 has been extensively investigated as a target for anti-platelet drugs to prevent myocardial infarction. Q94 has been reported to act as an allosteric modulator of PAR1, potently and selectively inhibiting PAR1-Gαq coupling in multiple cell lines, but its effects on human platelet activation have not been previously studied. Platelet Ca²⁺ signaling, integrin α_IIbβ₃ activation and α-granule secretion were monitored following stimulation by a PAR1-activating peptide (PAR1-AP). Although Q94 inhibited these responses, its potency was low compared to other PAR1 antagonists. In addition, α_IIbβ₃ activation and α-granule secretion in response to other platelet activators were also inhibited with similar potency. Finally, in endothelial cells, Q94 did not inhibit PAR1-dependent Ca²⁺ signaling. Our data suggest that Q94 may have PAR1-independent off-target effects in platelets, precluding its use as a selective PAR1 allosteric modulator.

Increasing TB/HIV Case Notification through an Active Case-Finding Approach among Rural and Mining Communities in Northwest Tanzania

While Tanzania is among the high TB burden countries to reach the WHO's End TB 2030 milestones, 41% of the people estimated to have had TB in 2020 were not diagnosed and notified. As part of the response to close the TB treatment coverage gap, SHDEPHA+ Kahama conducted a TB REACH active case-finding (ACF) intervention among rural and mining communities in Northwest Tanzania to increase TB/HIV case notification from July 2017 to June 2020. The intervention successfully linked marginalized mining communities with integrated TB/HIV screening, diagnostic, and referral services, screening 144,707 people for TB of whom 24,200 were tested for TB and 4,478 were tested for HIV, diagnosing 1,499 people with TB and 1,273 people with HIV (including at least 154 people with TB/HIV coinfection). The intervention revealed that community-based ACF can ensure high rates of linkage to care among hard-to-reach populations for TB. Providing integrated TB and HIV screening and diagnostic services during evening hours (Moonlight Events) in and around mining settlements can yield a large number of people with undiagnosed TB and HIV. For TB, this is true not only amongst miners but also FSW living in the same communities, who appear to be at similar or equally high risk of infection. Local NGOs can help to bridge the TB treatment coverage gap and to improve TB and HIV health outcomes by linking these marginalized groups with public sector services. Capturing the number of referrals arriving at CTCs is an important next step to identify how well the integrated TB/HIV outreach services operate and how they can be strengthened.

Repurposing FDA-approved drugs as HIV-1 integrase inhibitors: an in silico investigation

The Human Immunodeficiency Virus (HIV) infection is a global pandemic that has claimed 33 million lives to-date. One of the most efficacious treatments for naïve or pretreated HIV patients is the HIV integrase strand transfer inhibitors (INSTIs). However, given that HIV treatment is life-long, the emergence of HIV strains resistant to INSTIs is an imminent challenge. In this work, we showed two best regression QSAR models that were constructed using a boosted Random Forest algorithm (r² = 0.998, q²_10CV = 0.721, q²_{external_test} = 0.754) and a boosted K* algorithm (r² = 0.987, q²_10CV = 0.721, q²_{external_test} = 0.758) to predict the pIC₅₀ values of INSTIs. Subsequently, the regression QSAR models were deployed against the Drugbank database for drug repositioning. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies and accelerated Molecular Dynamics simulation. Lastly, their potential as INSTIs were also evaluated from our literature search. Our study offers the first example of a large-scale regression QSAR modelling effort for discovering highly active INSTIs to combat HIV infection.Communicated by Ramaswamy H. Sarma.

Acid-sensing ion channel 3: An analgesic target

Acid-sensing ion channel 3 (ASIC3) belongs to the epithelial sodium channel/degenerin (ENaC/DEG) superfamily. There are 7 different ASIC subunits encoded by 5 different genes. Most ASIC subunits form trimeric ion channels that upon activation by extracellular protons mediate a transient inward current inducing cellular excitability. ASIC subunits exhibit differential tissue expression and biophysical properties, and the ability of subunits to form homo- and heteromeric trimers further increases the complexity of currents measured and their pharmacological properties. ASIC3 is of particular interest, not only because it exhibits high expression in sensory neurones, but also because upon activation it does not fully inactivate: a transient current is followed by a sustained current that persists during a period of extracellular acidity, i.e. ASIC3 can encode prolonged acidosis as a nociceptive signal. Furthermore, certain mediators sensitize ASIC3 enabling smaller proton concentrations to activate it and other mediators can directly activate the channel at neutral pH. Moreover, there is a plethora of evidence using transgenic mouse models and pharmacology, which supports ASIC3 as being a potential target for development of analgesics. This review will focus on current understanding of ASIC3 function to provide an overview of how ASIC3 contributes to physiology and pathophysiology, examining the mechanisms by which it can be modulated, and highlighting gaps in current understanding and future research directions.

Structure, Function and Regulation of a Second Pyruvate Kinase Isozyme in Pseudomonas aeruginosa

Pseudomonas aeruginosa (PA) depends on the Entner-Doudoroff pathway (EDP) for glycolysis. The main enzymatic regulator in the lower half of the EDP is pyruvate kinase. PA contains genes that encode two isoforms of pyruvate kinase, denoted PykAPA and PykFPA. In other well-characterized organisms containing two pyruvate kinase isoforms (such as Escherichia coli) each isozyme is differentially regulated. The structure, function and regulation of PykAPA has been previously characterized in detail, so in this work, we set out to assess the biochemical and structural properties of the PykFPA isozyme. We show that pykF PA expression is induced in the presence of the diureide, allantoin. In spite of their relatively low amino acid sequence identity, PykAPA and PykFPA display broadly comparable kinetic parameters, and are allosterically regulated by a very similar set of metabolites. However, the x-ray crystal structure of PykFPA revealed significant differences compared with PykAPA. Notably, although the main allosteric regulator binding-site of PykFPA was empty, the "ring loop" covering the site adopted a partially closed conformation. Site-directed mutation of the proline residues flanking the ring loop yielded apparent "locked on" and "locked off" allosteric activation phenotypes, depending on the residue mutated. Analysis of PykFPA inter-protomer interactions supports a model in which the conformational transition(s) accompanying allosteric activation involve re-orientation of the A and B domains of the enzyme and subsequent closure of the active site.

Immune infiltration and prognostic and diagnostic use of LGALS4 in colon adenocarcinoma and bladder urothelial carcinoma

Colon adenocarcinoma (COAD) is a common tumor of the gastrointestinal tract with a high mortality rate. Current research has identified many genes associated with immune infiltration that play a vital role in the development of COAD. In this study, we analysed the prognostic and diagnostic features of such immune-related genes in the context of colonic adenocarcinoma (COAD). We analysed 17 overlapping gene expression profiles of COAD and healthy samples obtained from TCGA-COAD and public single-cell sequencing resources, to identify potential therapeutic COAD targets. We evaluated the abundance of immune infiltration with those genes using the TIMER (Tumor Immune Estimation Resource) deconvolution method. Subsequently, we developed predictive and survival models to assess the prognostic value of these genes. The LGALS4 (Galectin-4) gene was found to be significantly (P<0.05) downregulated in COAD and bladder urothelial carcinoma (BLCA) compared to healthy samples. We identified LGALS4 as a prognostic and diagnostic marker for multiple cancer types, including COAD and BLCA. Our analysis reveals a series of novel candidate drug targets, as well as candidate molecular markers, that may explain the pathogenesis of COAD and BLCA. LGALS4 gene is associated with multiple cancer types and is a possible prognostic, as well as diagnostic, marker of COAD and BLCA.

A plastid two-pore channel essential for inter-organelle communication and growth of Toxoplasma gondii

Two-pore channels (TPCs) are a ubiquitous family of cation channels that localize to acidic organelles in animals and plants to regulate numerous Ca²⁺-dependent events. Little is known about TPCs in unicellular organisms despite their ancient origins. Here, we characterize a TPC from Toxoplasma gondii, the causative agent of toxoplasmosis. TgTPC is a member of a novel clad of TPCs in Apicomplexa, distinct from previously identified TPCs and only present in coccidians. We show that TgTPC localizes not to acidic organelles but to the apicoplast, a non-photosynthetic plastid found in most apicomplexan parasites. Conditional silencing of TgTPC resulted in progressive loss of apicoplast integrity, severely affecting growth and the lytic cycle. Isolation of TPC null mutants revealed a selective role for TPCs in replication independent of apicoplast loss that required conserved residues within the pore-lining region. Using a genetically-encoded Ca²⁺ indicator targeted to the apicoplast, we show that Ca²⁺ signals deriving from the ER but not from the extracellular space are selectively transmitted to the lumen. Deletion of the TgTPC gene caused reduced apicoplast Ca²⁺ uptake and membrane contact site formation between the apicoplast and the ER. Fundamental roles for TPCs in maintaining organelle integrity, inter-organelle communication and growth emerge.

A Comparative Study between Magnetic Resonance Imaging and Clinical FIGO Criteria in Different Stages of Carcinoma Cervix

The objective of this study was to determine whether Magnetic Resonance Imaging is a sensitive and specific alternative method to clinical FIGO criteria in the staging of cervical carcinoma. This prospective cross-sectional study was conducted in the Department of Radiology and Imaging, BSMMU, Dhaka during the period of September 2018 to August 2020. A total of 60 patients were selected purposively and all are staged clinically by EUA. Then all samples underwent MRI in Department of Radiology and Imaging, BSMMU. Images of uterine cervix, corpus, vagina and parametrium were taken with a prefixed standard protocol (TIWI axial, T2WI axial and sagittal, DWI axial & DCE) and reporting was done by Radiologist. Comparison was done between the MRI and clinical FIGO criteria of staging of cervical carcinoma. P value <0.05 was considered as significant. Sensitivity & specificity of the MRI was measured. Data were analyzed by using Statistical Package for Social Sciences (SPSS) software version 23.0 for Windows (SPSS Inc., Chicago, Illinois, USA). Out of 60 patients in this study the mean age was found 47.5±10.1 years with range from 22 to 60 years. Positive correlation (r=0.993; p=0.001) between histopathological size and MRI size of tumour. Positive correlation (r=0.950; p=0.001) between histopathological size and FIGO size of tumour. MRI findings more correlates with histopathology than clinically detected tumor size. The sensitivity, specificity, accuracy, positive and negative predictive values of MRI diagnosis evaluation for vaginal extension was 100.00%, 95.20%, 100.00%, 98.30% and 97.50% respectively. Sensitivity, specificity, accuracy, positive and negative predictive values of MRI diagnosis evaluation for parametrial invasion was 100.00%, all. In this study we observed that MRI staging was more likely to be concordant with pathological stage in comparison to the clinical stage. There was a concordance rate of 95.00% in MRI and 65.00% in clinical staging respectively. Out of 3 non-concordant cases in MRI, 2 were upstaged and 1 case was down staged in histopathology. FIGO staging concurred with histopathology in 39(65.00%) cases and differed in 21(35.00%) cases. Magnetic resonance imaging (MRI) is a sensitive and specific modality for accurate staging of cervical carcinoma in comparison with clinical FIGO criteria considering histopathology as gold standard.

Clinical Risk Index for Babies II Score as a Predictor of Neonatal Death among Preterm Low Birth Weight Babies

Clinical risk index for babies II (CRIB II) score is simple, validated and widely used risk-adjustment instrument for predicting mortality among preterm low birth weight babies. To assess the efficacy of CRIB II score as a tool to predict the risk for neonatal death among the preterm and LBW babies admitted in NICU of BSMMU, a tertiary care hospital in Bangladesh. This prospective observational study was conducted in Department of Neonatology in BSMMU from September 2016 to August 2017. Inborn preterm neonates with gestational age ≤34 weeks admitted were enrolled in the study. CRIB-II score was calculated for each infant within 1 hour of birth from birth weight, gestational age, sex, admission temperature and base excess. The primary outcome measured in the study was neonatal death or survival up to 28 days. Total 112 patients were finally analyzed in this study. Mean CRIB II score was significantly higher in the non-survivor group compared to the survivor group (p-value <0.0001). Receiver operating characteristic (ROC) curve analysis for mortality prediction by CRIB II score, gestational age and birth weight showed AUC 0.87 (95% CI 0.76-0.97), 0.76 (95% CI 0.63-0.88) and 0.79 (95% CI 0.66-0.92) respectively. ROC curve analysis also revealed that the most suitable cut-off points for predicting mortality were 5 for CRIB II score, 32 weeks for gestational age and 1250 gram for birth weight. Using these most suitable cut-off points, CRIB II score had the highest sensitivity and specificity followed by birth weight and gestational age. In this study, CRIB II score was found to be an effective tool for predicting neonatal death among preterm LBW babies. It predicted outcome more accurately than birth weight or gestational age alone.

Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology

The cardiac troponin T variations have often been used as an example of the application of clinical genotyping for prognostication and risk stratification measures for the management of patients with a family history of sudden cardiac death or familial cardiomyopathy. Given the disparity in patient outcomes and therapy options, we investigated the impact of variations on the intermolecular interactions across the thin filament complex as an example of an unbiased systems biology method to better define clinical prognosis to aid future management options. We present a novel unbiased dynamic model to define and analyse the functional, structural and physico-chemical consequences of genetic variations among the troponins. This was subsequently integrated with clinical data from accessible global multi-centre systematic reviews of familial cardiomyopathy cases from 106 articles of the literature: 136 disease-causing variations pertaining to 981 global clinical cases. Troponin T variations showed distinct pathogenic hotspots for dilated and hypertrophic cardiomyopathies; considering the causes of cardiovascular death separately, there was a worse survival in terms of sudden cardiac death for patients with a variation at regions 90–129 and 130–179 when compared to amino acids 1–89 and 200–288. Our data support variations among 90–130 as being a hotspot for sudden cardiac death and the region 131–179 for heart failure death/transplantation outcomes wherein the most common phenotype was dilated cardiomyopathy. Survival analysis into regions of high risk (regions 90–129 and 130–180) and low risk (regions 1–89 and 200–288) was significant for sudden cardiac death (p = 0.011) and for heart failure death/transplant (p = 0.028). Our integrative genomic, structural, model from genotype to clinical data integration has implications for enhancing clinical genomics methodologies to improve risk stratification.

Recent progress on the prospective application of machine learning to structure-based virtual screening

As more bioactivity and protein structure data become available, scoring functions (SFs) using machine learning (ML) to leverage these data sets continue to gain further accuracy and broader applicability. Advances in our understanding of the optimal ways to train and evaluate these ML-based SFs have introduced further improvements. One of these advances is how to select the most suitable decoys (molecules assumed inactive) to train or test an ML-based SF on a given target. We also review the latest applications of ML-based SFs for prospective structure-based virtual screening (SBVS), with a focus on the observed improvement over those using classical SFs. Finally, we provide recommendations for future prospective SBVS studies based on the findings of recent methodological studies.

Clinical Course and Cardiac Complications of Hospitalized COVID-19 Patients

Purpose

We describe the hospitalization course, cardiac complications and echocardiographic findings in a subset of acutely ill hospitalized patients with COVID-19.

Methods

Patients admitted to a large academic hospital in Ontario, Canada from March-June 2020 with COVID-19 and who had an echocardiogram within 4-weeks of their diagnosis were included in this study. Their demographics, hospitalization details and echocardiographic findings were analyzed.

Results

76 patients are included in our study, 83% of whom required ICU. Mean age was 58.9 years (+/-15.7 years). Cardiovascular comorbidities were common: diabetes (35.5%), hypertension (50%), CKD (11.8%), prior CAD (13.2%) or stroke (11.8%). Median length of admission was 25.5 days (IQR 22days). Overall, in-hospital mortality was high at 35.5%, with increased mortality in the ICU vs. non-ICU group (32.9% vs. 15.4%). A large number of patients required invasive support: intubation (77.6%), Extracorporeal life support (23.7%), or renal replacement therapy (19.7%). Cardiac complications included new AF (13.2%), hemodynamically significant VT (3.9%), moderate or more pericardial effusion (2.6%) and acute stroke (9.2%). Echocardiographic analysis demonstrated that 7.9% of patients developed moderate or more LV dysfunction on visual assessment. RV dysfunction was more common (27.6%) with 11.8% being visually classified as moderate or greater in severity. High sensitivity troponin was elevated in 59.2% of patients and was statistically higher in patients experiencing cardiac complications (Chi-Square 0.005). Although not achieving significance, there was a trend towards elevated troponin and development of moderate or greater LV/RV dysfunction (Chi-square 0.30).

Conclusion

In acute patients hospitalized with COVID-19, there was a high prevalence of cardiovascular co-morbidities. Troponin elevations was common and associated with a significantly increased risk of cardiovascular events and a trend towards moderate or greater ventricular dysfunction.

Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease

The ongoing coronavirus pandemic has been a burden on the worldwide population, with mass fatalities and devastating socioeconomic consequences. It has particularly drawn attention to the lack of approved small-molecule drugs to inhibit SARS coronaviruses. Importantly, lessons learned from the SARS outbreak of 2002-2004, caused by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), can be applied to current drug discovery ventures. SARS-CoV-1 and SARS-CoV-2 both possess two cysteine proteases, the main protease (Mpro) and the papain-like protease (PLpro), which play a significant role in facilitating viral replication, and are important drug targets. The non-covalent inhibitor, GRL-0617, which was found to inhibit replication of SARS-CoV-1, and more recently SARS-CoV-2, is the only PLpro inhibitor co-crystallised with the recently solved SARS-CoV-2 PLpro crystal structure. Therefore, the GRL-0617 structural template and pharmacophore features are instrumental in the design and development of more potent PLpro inhibitors. In this work, we conducted scaffold hopping using GRL-0617 as a reference to screen over 339,000 ligands in the chemical space using the ChemDiv, MayBridge, and Enamine screening libraries. Twenty-four distinct scaffolds with structural and electrostatic similarity to GRL-0617 were obtained. These proceeded to molecular docking against PLpro using the AutoDock tools. Of two compounds that showed the most favourable predicted binding affinities to the target site, as well as comparable protein-ligand interactions to GRL-0617, one was chosen for further analogue-based work. Twenty-seven analogues of this compound were further docked against the PLpro, which resulted in two additional hits with promising docking profiles. Our in silico pipeline consisted of an integrative four-step approach: (1) ligand-based virtual screening (scaffold-hopping), (2) molecular docking, (3) an analogue search, and, (4) evaluation of scaffold drug-likeness, to identify promising scaffolds and eliminate those with undesirable properties. Overall, we present four novel, and lipophilic, scaffolds obtained from an exhaustive search of diverse and uncharted regions of chemical space, which may be further explored in vitro through structure-activity relationship (SAR) studies in the search for more potent inhibitors. Furthermore, these scaffolds were predicted to have fewer off-target interactions than GRL-0617. Lastly, to our knowledge, this work contains the largest ligand-based virtual screen performed against GRL-0617.

Novel Small-Molecule Scaffolds as Candidates against the SARS Coronavirus 2 Main Protease: A Fragment-Guided in Silico Approach

The ongoing pandemic caused by the novel coronavirus has been the greatest global health crisis since the Spanish flu pandemic of 1918. Thus far, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 1 million deaths, and there is no cure or vaccine to date. The recently solved crystal structure of the SARS-CoV-2 main protease has been a major focus for drug-discovery efforts. Here, we present a fragment-guided approach using ZINCPharmer, where 17 active fragments known to bind to the catalytic centre of the SARS-CoV-2 main protease (SARS-CoV-2 M^pro) were used as pharmacophore queries to search the ZINC databases of natural compounds and natural derivatives. This search yielded 134 hits that were then subjected to multiple rounds of in silico analyses, including blind and focused docking against the 3D structure of the main protease. We scrutinised the poses, scores, and protein-ligand interactions of 15 hits and selected 7. The scaffolds of the seven hits were structurally distinct from known inhibitor scaffolds, thus indicating scaffold novelty. Our work presents several novel scaffolds as potential candidates for experimental validation against SARS-CoV-2 M^pro.

Identification and Validation of Carbonic Anhydrase II as the First Target of the Anti-Inflammatory Drug Actarit

Background and purpose: Identifying the macromolecular targets of drug molecules is a fundamental aspect of drug discovery and pharmacology. Several drugs remain without known targets (orphan) despite large-scale in silico and in vitro target prediction efforts. Ligand-centric chemical-similarity-based methods for in silico target prediction have been found to be particularly powerful, but the question remains of whether they are able to discover targets for target-orphan drugs. Experimental Approach: We used one of these in silico methods to carry out a target prediction analysis for two orphan drugs: actarit and malotilate. The top target predicted for each drug was carbonic anhydrase II (CAII). Each drug was therefore quantitatively evaluated for CAII inhibition to validate these two prospective predictions. Key Results: Actarit showed in vitro concentration-dependent inhibition of CAII activity with submicromolar potency (IC₅₀ = 422 nM) whilst no consistent inhibition was observed for malotilate. Among the other 25 targets predicted for actarit, RORγ (RAR-related orphan receptor-gamma) is promising in that it is strongly related to actarit’s indication, rheumatoid arthritis (RA). Conclusion and Implications: This study is a proof-of-concept of the utility of MolTarPred for the fast and cost-effective identification of targets of orphan drugs. Furthermore, the mechanism of action of actarit as an anti-RA agent can now be re-examined from a CAII-inhibitor perspective, given existing relationships between this target and RA. Moreover, the confirmed CAII-actarit association supports investigating the repositioning of actarit on other CAII-linked indications (e.g., hypertension, epilepsy, migraine, anemia and bone, eye and cardiac disorders).

Global reprogramming of virulence and antibiotic resistance in Pseudomonas aeruginosa by a single nucleotide polymorphism in elongation factor, fusA1

Clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa from patients with cystic fibrosis (CF) frequently contain mutations in the gene encoding an elongation factor, FusA1. Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the efflux pump, MexXY. However, we wondered whether these mutants might also be affected in other virulence-associated phenotypes. Here, we isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1^P443L) in which mexXY expression was increased. Proteomic and transcriptomic analyses revealed that the fusA1 mutant also exhibited discrete changes in the expression of key pathogenicity-associated genes. Most notably, the fusA1 mutant displayed greatly increased expression of the Type III secretion system (T3SS), widely considered to be the most potent virulence factor in the P. aeruginosa arsenal, and also elevated expression of the Type VI (T6) secretion machinery. This was unexpected because expression of the T3SS is usually reciprocally coordinated with T6 secretion system expression. The fusA1 mutant also displayed elevated exopolysaccharide production, dysregulated siderophore production, elevated ribosome synthesis, and transcriptomic signatures indicative of translational stress. Each of these phenotypes (and almost all of the transcriptomic and proteomic changes associated with the fusA1 mutation) were restored to levels comparable with that in the progenitor strain by expression of the WT fusA1 gene in trans, indicating that the mutant gene is recessive. Our data show that in addition to elevating antibiotic resistance through mexXY expression (and also additional contributory resistance mechanisms), mutations in fusA1 can lead to highly selective dysregulation of virulence gene expression.

Abstract P098: Statins Relax Systemic Mesenteric Arteries Via The Inhibition Of Phosphodiesterases

Purpose: Statins are the world’s most prescribed drugs with a range of vascular effects. Conventional view is that the vascular effects of statins are lipid-lowering-dependent and/or -independent, and both require long-term treatment. However, studies to examine direct vascular effects of statins are lacking as previous studies used supratherapeutic (≥1000-fold) concentrations of statins on non-resistance or cultured arteries that do not simulate physiology.

Methods: Pressurized arterial myography, in-vitro phosphodiesterase (PDE) inhibition assay (colorimetric assay) and cGMP measurement using ELISA.

Results: We found that, within 2-3 minutes of application, statins at 1nM produced mesenteric artery vasodilation that was reversed upon drug washout. Rosuvastatin and simvastatin produced vasodilation of ≥30μm while others dilated arteries by ≤20μm. Endothelium removal, or co-application of L-NAME, an inhibitor of endothelial nitric oxide (NO) synthase (eNOS), or ODQ, an inhibitor of smooth muscle cell guanylyl cyclase (sGC), or APC5, an inhibitor of protein kinase G (PKG), each inhibited statin-evoked vasodilation, suggesting the involvement of NO-sGC-PKG signaling axis. In contrast, mevalonate supplementation did not alter statin-induced vasodilation, precluding the role of lipid synthesis inhibition. To investigate potential involvement of phosphodiesterases (PDEs) that hydrolyze cGMP, we co-applied statins with a cGMP-specific PDE5 inhibitor sildenafil and found that statins indeed potentiated sildenafil-induced vasodilation. Our in-vitro PDE inhibition assay also showed that the vasodilatory statins have significant inhibitory actions on cGMP-dependent PDEs.

Conclusion: Our study unveils a novel mechanism of systemic mesenteric artery vasodilation by statins. Future studies will examine if statins can be re-purposed for treating hypertension and/or erectile dysfunction.

Proposed model of the Dictyostelium cAMP receptors bound to cAMP

3',5'-cyclic adenosine monophosphate (cAMP) is well known as a ubiquitous intracellular messenger regulating a diverse array of cellular processes. However, for a group of social amoebae or Dictyostelia undergoing starvation, intracellular cAMP is secreted in a pulsatile manner to their exterior. This then uniquely acts as a first messenger, triggering aggregation of the starving amoebae followed by their developmental progression towards multicellular fruiting bodies formation. Such developmental signalling for extracellularly-acting cAMP is well studied in the popular dictyostelid, Dictyostelium discoideum, and is mediated by a distinct family ('class E') of G protein-coupled receptors (GPCRs) collectively designated as the cAMP receptors (cARs). Whilst the biochemical aspects of these receptors are well characterised, little is known about their overall 3D architecture and structural basis for cAMP recognition and subtype-dependent changes in binding affinity. Using a ligand docking-guided homology modelling approach, we hereby present for the first time, plausible models of active forms of the cARs from D. discoideum. Our models highlight some structural features that may underlie the differential affinities of cAR isoforms for cAMP binding and also suggest few residues that may play important roles for the activation mechanism of this GPCR family.

Ethaninidothioic acid (R5421) is not a selective inhibitor of platelet phospholipid scramblase activity

Background and Purpose

Ethaninidothioic acid (R5421) has been used as a scramblase inhibitor to determine the role of phospholipid scrambling across a range of systems including platelet procoagulant activity. The selectivity of R5421 has not been thoroughly studied. Here, we characterised the effects of R5421 on platelet function and its suitability for use as a scramblase inhibitor.

Experimental Approach

Human platelet activation was measured following pretreatment with R5421 and stimulation with a range of agonists. Phosphatidylserine exposure was measured using annexin V binding. Integrin α_IIbβ₃ activation and α‐granule release were measured by flow cytometry. Cytosolic Ca²⁺ signals were measured using Cal520 fluorescence. An in silico ligand‐based screen identified 16 compounds which were tested in these assays.

Key Results

R5421 inhibited A23187‐induced phosphatidylserine exposure in a time‐ and temperature‐dependent manner. R5421 inhibited Ca²⁺ signalling from the PAR1, PAR4 and glycoprotein VI receptors as well as platelet α_IIbβ₃ integrin activation and α‐granule release. R5421 is therefore not a selective inhibitor of platelet scramblase activity. An in silico screen identified the pesticide thiodicarb as similar to R5421. It also inhibited platelet phosphatidylserine exposure, Ca²⁺ signalling from the PAR1 and glycoprotein VI, α_IIbβ₃ activation and α‐granule release. Thiodicarb additionally disrupted Ca²⁺ homeostasis in unstimulated platelets.

Conclusion and Implications

R5421 is not a selective inhibitor of platelet scramblase activity. We have identified the pesticide thiodicarb, which had similar effects on platelet function to R5421 as well as additional disruption of Ca²⁺ signalling which may underlie some of thiodicarb's toxicity.

Efficacy of Intra-peritoneal Tramadol Instillation for Postoperative Pain Management after Laparoscopic Cholecystectomy

Gall stone disease is one of the most common conditions encountered in general surgical practices in adult population. The gold standard treatment for symptomatic gall stone disease is laparoscopic cholecystectomy. It results in less post-operative pain as compared to open cholecystectomy but post-operative pain may be mild, moderate or even severe in some patients. This Randomized control trail was conducted to In-patient department of Surgery, Mymensingh Medical College & Hospital (MMCH), Mymensingh, Bangladesh from April 2018 to September 2018. It was undertaken to evaluate the analgesic effect of intra-peritoneal tramadol instillation in patients undergoing laparoscopic cholecystectomy. Total 70 patients with symptomatic gallstone disease undergoing laparoscopic cholecystectomy were randomized equally in two groups. Then patients were selected in according to the inclusion and exclusion criteria. In first group (Group A), patients were received intra-peritoneal tramadol 100mg (diluted in 20.0ml distilled water). Sprayed 10.0ml diluted tramadol into the sub diaphragmatic area, 5.0ml into the area of gall bladder bed and 5.0ml into the space between the liver and kidney under direct vision just before removal of trocars. In second group (Group B) the conventional operative procedure was followed. Postoperatively, patient was extubated and shifted to recovery room. Data recorded and analyzed, such as post-operative pain score at 1, 4, 8, and 24 hour; cumulative 1, 8 and 24 hour analgesic consumption. In addition that postoperative hospital period monitoring of heart rate, blood pressure, respiratory rate, temperature at 0, 4, 8, 24 hours was also analyzed. Intensity of pain was assessed by Visual Analogue Scale (VAS) scoring system. Patients showed a VAS ≥3 or patients who requested for analgesia was administrated a supplemental dose of analgesic. In the present study the mean pain scores in Group A were found to be low at1hourpost-operative was 0.60±0.56 and there was a gradual increase in score in respect of time interval with peak of 2.07±0.91 at 24 hours. Whereas, in Group B the mean pain scores immediate post-operative period were at its peak was, 2.50±0.82 which decreased to 1.30±0.84 at 1 hour and further there was rise at 4 hours (2.10±0.71) and 24 hours (2.33±0.0.71). But at any point of time the mean VAS remained significantly low (p<0.050) in patients with Group A compared to Group B except at 1st 24 hours (p=0.210). Intra-peritoneal instillation of tramadol for postoperative pain control in laparoscopic cholecystectomy has beneficial effect in terms of postoperative pain relief following laparoscopic cholecystectomy.

Structure-Based Design of Novel Biphenyl Amide Antagonists of Human Transient Receptor Potential Cation Channel Subfamily M Member 8 Channels with Potential Implications in the Treatment of Sensory Neuropathies

Structure-activity relationship studies of a reported menthol-based transient receptor potential cation channel subfamily M member 8 channel (TRPM8) antagonist, guided by computational simulations and structure-based design, uncovers a novel series of TRPM8 antagonists with >10-fold selectivity versus related TRP subtypes. Spiro[4.5]decan-8-yl analogue 14 inhibits icilin-evoked Ca²⁺ entry in HEK-293 cells stably expressing human TRPM8 (hTRPM8) with an IC₅₀ of 2.4 ± 1.0 nM, while in whole-cell patch-clamp recordings this analogue inhibits menthol-evoked currents with a hTRPM8 IC₅₀ of 64 ± 2 nM. Molecular dynamics (MD) simulations of compound 14 in our homology model of hTRPM8 suggest that this antagonist forms extensive hydrophobic contacts within the orthosteric site. In the wet dog shakes (WDS) assay, compound 14 dose-dependently blocks icilin-triggered shaking behaviors in mice. Upon local administration, compound 14 dose dependently inhibits cold allodynia evoked by the chemotherapy oxaliplatin in a murine model of peripheral neuropathy at microgram doses. Our findings suggest that 14 and other biphenyl amide analogues within our series can find utility as potent antagonist chemical probes derived from (-)-menthol as well as small molecule therapeutic scaffolds for chemotherapy-induced peripheral neuropathy (CIPN) and other sensory neuropathies.

In silico screening of GMQ-like compounds reveals guanabenz and sephin1 as new allosteric modulators of acid-sensing ion channel 3

Acid-sensing ion channels (ASICs) are voltage-independent cation channels that detect decreases in extracellular pH. Dysregulation of ASICs underpins a number of pathologies. Of particular interest is ASIC3, which is recognised as a key sensor of acid-induced pain and is important in the establishment of pain arising from inflammatory conditions, such as rheumatoid arthritis. Thus, the identification of new ASIC3 modulators and the mechanistic understanding of how these compounds modulate ASIC3 could be important for the development of new strategies to counteract the detrimental effects of dysregulated ASIC3 activity in inflammation. Here, we report the identification of novel ASIC3 modulators based on the ASIC3 agonist, 2-guanidine-4-methylquinazoline (GMQ). Through a GMQ-guided in silico screening of Food and Drug administration (FDA)-approved drugs, 5 compounds were selected and tested for their modulation of rat ASIC3 (rASIC3) using whole-cell patch-clamp electrophysiology. Of the chosen drugs, guanabenz (GBZ), an α₂-adrenoceptor agonist, produced similar effects to GMQ on rASIC3, activating the channel at physiological pH (pH 7.4) and potentiating its response to mild acidic (pH 7) stimuli. Sephin1, a GBZ derivative that lacks α₂-adrenoceptor activity, has been proposed to act as a selective inhibitor of a regulatory subunit of the stress-induced protein phosphatase 1 (PPP1R15A) with promising therapeutic potential for the treatment of multiple sclerosis. However, we found that like GBZ, sephin1 activates rASIC3 at pH 7.4 and potentiates its response to acidic stimulation (pH 7), i.e. sephin1 is a novel modulator of rASIC3. Furthermore, docking experiments showed that, like GMQ, GBZ and sephin1 likely interact with the nonproton ligand sensor domain of rASIC3. Overall, these data demonstrate the utility of computational analysis for identifying novel ASIC3 modulators, which can be validated with electrophysiological analysis and may lead to the development of better compounds for targeting ASIC3 in the treatment of inflammatory conditions.

Elevated intracellular cAMP concentration mediates growth suppression in glioma cells

Supressed levels of intracellular cAMP have been associated with malignancy. Thus, elevating cAMP through activation of adenylyl cyclase (AC) or by inhibition of phosphodiesterase (PDE) may be therapeutically beneficial. Here, we demonstrate that elevated cAMP levels suppress growth in C6 cells (a model of glioma) through treatment with forskolin, an AC activator, or a range of small molecule PDE inhibitors with differing selectivity profiles. Forskolin suppressed cell growth in a PKA-dependent manner by inducing a G₂/M phase cell cycle arrest. In contrast, trequinsin (a non-selective PDE2/3/7 inhibitor), not only inhibited cell growth via PKA, but also stimulated (independent of PKA) caspase-3/-7 and induced an aneuploidy phenotype. Interestingly, a cocktail of individual PDE 2,3,7 inhibitors suppressed cell growth in a manner analogous to forskolin but not trequinsin. Finally, we demonstrate that concomitant targeting of both AC and PDEs synergistically elevated intracellular cAMP levels thereby potentiating their antiproliferative actions.

Evolutionary plasticity in the allosteric regulator-binding site of pyruvate kinase isoform PykA from Pseudomonas aeruginosa

Unlike many other well-characterized bacteria, the opportunistic human pathogen Pseudomonas aeruginosa relies exclusively on the Entner-Doudoroff pathway (EDP) for glycolysis. Pyruvate kinase (PK) is the main "pacemaker" of the EDP, and its activity is also relevant for P. aeruginosa virulence. Two distinct isozymes of bacterial PK have been recognized, PykA and PykF. Here, using growth and expression analyses of relevant PK mutants, we show that PykA is the dominant isoform in P. aeruginosa Enzyme kinetics assays revealed that PykA displays potent K-type allosteric activation by glucose 6-phosphate and by intermediates from the pentose phosphate pathway. Unexpectedly, the X-ray structure of PykA at 2.4 Å resolution revealed that glucose 6-phosphate binds in a pocket that is distinct from the binding site reported for this metabolite in the PK from Mycobacterium tuberculosis (the only other available bacterial PK structure containing bound glucose 6-phosphate). We propose a mechanism by which glucose 6-phosphate binding at the allosteric site communicates with the PykA active site. Taken together, our findings indicate remarkable evolutionary plasticity in the mechanism(s) by which PK senses and responds to allosteric signals.

Mining of Ebola virus entry inhibitors identifies approved drugs as two-pore channel pore blockers

Two-pore channels (TPCs) are Ca2+-permeable ion channels localised to the endo-lysosomal system where they regulate trafficking of various cargoes including viruses. As a result, TPCs are emerging as important drug targets. However, their pharmacology is ill-defined. There are no approved drugs to target them. And their mechanism of ligand activation is largely unknown. Here, we identify a number of FDA-approved drugs as TPC pore blockers. Using a model of the pore of human TPC2 based on recent structures of mammalian TPCs, we virtually screened a database of ~1500 approved drugs. Because TPCs have recently emerged as novel host factors for Ebola virus entry, we reasoned that Ebola virus entry inhibitors may exert their effects through inhibition of TPCs. Cross-referencing hits from the TPC virtual screen with two recent high throughput anti-Ebola screens yielded approved drugs targeting dopamine and estrogen receptors as common hits. These compounds inhibited endogenous NAADP-evoked Ca2+ release from sea urchin egg homogenates, NAADP-mediated channel activity of TPC2 re-routed to the plasma membrane, and PI(3,5)P2-mediated channel activity of TPC2 expressed in enlarged lysosomes. Mechanistically, single channel analyses showed that the drugs reduced mean open time consistent with a direct action on the pore. Functionally, drug potency in blocking TPC2 activity correlated with inhibition of Ebola virus-like particle entry. Our results expand TPC pharmacology through the identification of approved drugs as novel blockers, support a role for TPCs in Ebola virus entry, and provide insight into the mechanisms underlying channel regulation. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.

Exploration of inositol 1,4,5-trisphosphate (IP3) regulated dynamics of N-terminal domain of IP3 receptor reveals early phase molecular events during receptor activation

Inositol 1, 4, 5-trisphosphate (IP₃) binding at the N-terminus (NT) of IP₃ receptor (IP₃R) allosterically triggers the opening of a Ca²⁺-conducting pore located ~100 Å away from the IP₃-binding core (IBC). However, the precise mechanism of IP₃ binding and correlated domain dynamics in the NT that are central to the IP₃R activation, remains unknown. Our all-atom molecular dynamics (MD) simulations recapitulate the characteristic twist motion of the suppressor domain (SD) and reveal correlated ‘clam closure’ dynamics of IBC with IP₃-binding, complementing existing suggestions on IP₃R activation mechanism. Our study further reveals the existence of inter-domain dynamic correlation in the NT and establishes the SD to be critical for the conformational dynamics of IBC. Also, a tripartite interaction involving Glu283-Arg54-Asp444 at the SD – IBC interface seemed critical for IP₃R activation. Intriguingly, during the sub-microsecond long simulation, we observed Arg269 undergoing an SD-dependent flipping of hydrogen bonding between the first and fifth phosphate groups of IP₃. This seems to play a major role in determining the IP₃ binding affinity of IBC in the presence/absence of the SD. Our study thus provides atomistic details of early molecular events occurring within the NT during and following IP₃ binding that lead to channel gating.

Knowledge, Attitude and Practice of Bangladeshi Women towards Breast Cancer: A Cross Sectional Study

In Bangladesh incidence rate of breast cancer was about 22.5 per 100000 females. Breast cancer has been reported as the highest prevalence rate (19.3 per 100,000) among Bangladeshi women between 15 and 44 years of age. For this prevailing situation a cross-sectional study was designed to assess the knowledge, attitude and practices of community-dwelling women in Bangladesh towards breast cancer at Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from July 2013 to June 2014. All female participants attending at outpatient department of BSMMU having age more than 20 years and education at least JSC, purposively selected until the sample size achieved 500. Only applying simple cost free method like self breast examination (SBE) and clinical breast examination (CBE) one can asses her breast. Thereby awareness develops regarding her breast so any mass newly appear can be assessed by the lady herself. Early diagnosis of the breast cancer will reduce the burden of treatment cost, mortality & morbidity. Research and development strategy of the project is to enhance the awareness of the community people about breast cancer prevention. Mean age of the study population was 36.16 years. Regarding education nearly 30% (n=150) of them studied up to Junior School, 16% (n=80) respondents completed masters and above remaining in between. Regarding occupation, almost 60% (n=300) were house wife, 32% (n=160) were service holder and only 8% (n=40) of them were students. Knowledge about common female cancer 60% (n=300) were aware about the cervical cancer, 24% (n=120) mentioned breast cancer, 4% (n=20) mentioned ovarian cancer, and 12% (n=60) don't know anything regarding common women cancer. Knowledge about early symptoms of breast cancer, majority of the respondents 66% (n=330) were aware that mass in the breast is the main symptom, 2% (n=10) mentioned pain in breast, 32% (n=160) mentioned that they don't know anything regarding the early symptoms. About the cause of breast cancer 60% (n=300) mentioned that, they don't know anything regarding the cause of breast cancer, 36% (n=180) were aware that non lactation is a cause of breast cancer. About 4% (n=20) of the study population mentioned others, like due to some ones bad did cancer occur as punishment. Knowledge about risk factor of breast cancer, 65% (n=325) have no idea about the risk of breast cancer, 32% (n=160) mentioned few risk factors which have relation with breast cancer and 3% (n=15) did not mention anything. Regarding diagnosis of cancer breast 72% (n=360) mentioned they don't know anything, 16% (n=80) by doing ultra sonogram of breast, 6% (n=30) mentioned about Mammography and 6% (n=30) MRI & others. Regarding screening for prevention of breast cancer 60% (n=300) mentioned that they don't know anything regarding screening. Thirty percent (n=150) were aware that there is screening method but they are not aware specifically regarding this method and they also not aware that breast cancer is a preventable disease. 10% (n=50) were fully aware about screening method like CBE & SBE. About the cause of not seeking medical advice for prevention of Breast cancer, majority of the respondents 40% (n=200) mentioned expenditure problems, 32% (n=160) they don't have any knowledge about this type of medical advice, 8% (n=40) mentioned communication problems and 20% (n=100) others. Regarding Practice of CBE & SBE 68% (n=340) never practice CBE & SBE, 30% (n=150) occasionally practiced CBE & SBE. Only 2% (n=10) mentioned that they were regularly practicing CBE & SBE.

Measurement of Typhi Vi antibodies can be used to assess adaptive immunity in patients with immunodeficiency

Vaccine‐specific antibody responses are essential in the diagnosis of antibody deficiencies. Responses to Pneumovax II are used to assess the response to polysaccharide antigens, but interpretation may be complicated. Typhim Vi^®, a polysaccharide vaccine for Salmonella typhoid fever, may be an additional option for assessing humoral responses in patients suspected of having an immunodeficiency. Here we report a UK multi‐centre study describing the analytical and clinical performance of a Typhi Vi immunoglobulin (Ig)G enzyme‐linked immunosorbent assay (ELISA) calibrated to an affinity‐purified Typhi Vi IgG preparation. Intra‐ and interassay imprecision was low and the assay was linear, between 7·4 and 574 U/ml (slope = 0·99–1·00; R² > 0·99); 71% of blood donors had undetectable Typhi Vi IgG antibody concentrations. Of those with antibody concentrations  > 7·4 U/ml, the concentration range was 7·7–167 U/ml. In antibody‐deficient patients receiving antibody replacement therapy the median Typhi Vi IgG antibody concentrations were  < 25 U/ml. In vaccinated normal healthy volunteers, the median concentration post‐vaccination was 107 U/ml (range 31–542 U/ml). Eight of eight patients (100%) had post‐vaccination concentration increases of at least threefold and six of eight (75%) of at least 10‐fold. In an antibody‐deficient population (n = 23), only 30% had post‐vaccination concentration increases of at least threefold and 10% of at least 10‐fold. The antibody responses to Pneumovax II and Typhim Vi^® correlated. We conclude that IgG responses to Typhim Vi^® vaccination can be measured using the VaccZyme Salmonella typhi Vi IgG ELISA, and that measurement of these antibodies maybe a useful additional test to accompany Pneumovax II responses for the assessment of antibody deficiencies.