Combining machine learning and structure-based approaches to develop oncogene PIM kinase inhibitors.

Introduction: PIM kinases are targets for therapeutic intervention since they are associated with a number of malignancies by boosting cell survival and proliferation. Over the past years, the rate of new PIM inhibitors discovery has increased significantly, however, new generation of potent molecules with the right pharmacologic profiles were in demand that can probably lead to the development of Pim kinase inhibitors that are effective against human cancer. Method: In the current study, a machine learning and structure based approaches were used to generate novel and effective chemical therapeutics for PIM-1 kinase. Four different machine learning methods, namely, support vector machine, random forest, k-nearest neighbour and XGBoost have been used for the development of models. Total, 54 Descriptors have been selected using the Boruta method. Results: SVM, Random Forest and XGBoost shows better performance as compared to k-NN. An ensemble approach was implemented and, finally, four potential molecules (CHEMBL303779, CHEMBL690270, MHC07198, and CHEMBL748285) were found to be effective for the modulation of PIM-1 activity. Molecular docking and molecular dynamic simulation corroborated the potentiality of the selected molecules. The molecular dynamics (MD) simulation study indicated the stability between protein and ligands. Discussion: Our findings suggest that the selected models are robust and can be potentially useful for facilitating the discovery against PIM kinase.

Structural characterization and conformational dynamics of alpha-1 antitrypsin pathogenic variants causing alpha-1-antitrypsin deficiency.

Background: Alpha-1 antitrypsin deficiency (A1ATD) is a progressive lung disease caused by inherited pathogenic variants in the SERPINA1 gene. However, their actual role in maintenance of structural and functional characteristics of the corresponding α-1 anti-trypsin (A1AT) protein is not well characterized. Methods: The A1ATD causative SERPINA1 missense variants were initially collected from variant databases, and they were filtered based on their pathogenicity potential. Then, the tertiary protein models were constructed and the impact of individual variants on secondary structure, stability, protein-protein interactions, and molecular dynamic (MD) features of the A1AT protein was studied using diverse computational methods. Results: We identified that A1ATD linked SERPINA1 missense variants like F76S, S77F, L278P, E288V, G216C, and H358R are highly deleterious as per the consensual prediction scores of SIFT, PolyPhen, FATHMM, M-CAP and REVEL computational methods. All these variants were predicted to alter free energy dynamics and destabilize the A1AT protein. These variants were seen to cause minor structural drifts at residue level (RMSD = <2Å) of the protein. Interestingly, S77F and L278P variants subtly alter the size of secondary structural elements like beta pleated sheets and loops. The residue level fluctuations at 100 ns simulation confirm the highly damaging structural consequences of all the six missense variants on the conformation dynamics of the A1AT protein. Moreover, these variants were also predicted to cause functional deformities by negatively impacting the binding energy of A1AT protein with NE ligand molecule. Conclusion: This study adds a new computational biology dimension to interpret the genotype-protein phenotype relationship between SERPINA1 pathogenic variants with its structural plasticity and functional behavior with NE ligand molecule contributing to the Alpha-1-antitrypsin deficiency. Our results support that A1ATD complications correlates with the conformational flexibility and its propensity of A1AT protein polymerization when misfolded.

Relationship Between Vitamin D Status and Brain Perfusion in Neuropsychiatric Lupus.

Purpose: Neuropsychiatric manifestation of lupus (NPSLE) is related with vitamin D (vit-D) deficiency which is possibly amenable to supplementation. This study was done to explore link of serum vit-D level and clinical mini-mental state examination (MMSE) with brain perfusion SPECT (BS) in patients with NPSLE. Methods: Patients who underwent BS with the diagnosis of NPSLE and had serum levels of vit-D and MMSE within a span of 1 month were retrospectively included. The BS DICOM data were used to generate 3D surface images of brain for visual identification of regional hypoperfusion, and the z-scores from eZIS software and then to perform voxel-based regression analysis in order to explore association between serum vit-D level and cerebral perfusion deficit using SPM8. Distribution of serum vit-D level was checked across MMSE and BS z-score using R. Results: A total 19 patients with means ± SD age of 28.4 ± 9.2 years, having mean levels of serum vit-D of 18.7 ± 9.8 ng/ml and mean MMSE scores 24.2 ± 1.6, had undergone BS. The eZIS-derived z-score fall in the category of normal in six (31.6%), mild perfusion deficit (PD) in 10 (52.6%) and moderate PD in three (15.8%) with the means ± SD of z-score being 0.52 ± 0.2, 1.72 ± 0.2, and 2.33 ± 0.2. Voxel-based analysis revealed significant positive correlation between vit-D level and hypoperfusion in brain regions related to cognitive function (p<0.05). Serum vit-D levels were significantly lower in NPSLE patients with lower MMSE scores as well as in higher eZIS z-score (p < 0.01). Conclusions: Our results may support the utility of vit-D supplementation in NPSLE and applicability of BS as a clinical adjunct for monitoring response to vit-D supplementation.

Calcium Influx and Release Cooperatively Regulate AChR Patterning and Motor Axon Outgrowth during Neuromuscular Junction Formation.

Formation of synapses between motor neurons and muscles is initiated by clustering of acetylcholine receptors (AChRs) in the center of muscle fibers prior to nerve arrival. This AChR patterning is considered to be critically dependent on calcium influx through L-type channels (CaV1.1). Using a genetic approach in mice, we demonstrate here that either the L-type calcium currents (LTCCs) or sarcoplasmic reticulum (SR) calcium release is necessary and sufficient to regulate AChR clustering at the onset of neuromuscular junction (NMJ) development. The combined lack of both calcium signals results in loss of AChR patterning and excessive nerve branching. In the absence of SR calcium release, the severity of synapse formation defects inversely correlates with the magnitude of LTCCs. These findings highlight the importance of activity-dependent calcium signaling in early neuromuscular junction formation and indicate that both LTCC and SR calcium release individually support proper innervation of muscle by regulating AChR patterning and motor axon outgrowth.

Chikungunya-dengue co-infection during pregnancy requiring preterm Caesarean section: first case report from Bangladesh.

We report the first case of chikungunya-dengue co-infection during pregnancy requiring emergency Caesarean section (CS) because of fetal distress in a Bangladeshi primigravida. Though previously unreported, this situation may become increasingly common.

Restricting calcium currents is required for correct fiber type specification in skeletal muscle.

Skeletal muscle excitation-contraction (EC) coupling is independent of calcium influx. In fact, alternative splicing of the voltage-gated calcium channel CaV1.1 actively suppresses calcium currents in mature muscle. Whether this is necessary for normal development and function of muscle is not known. However, splicing defects that cause aberrant expression of the calcium-conducting developmental CaV1.1e splice variant correlate with muscle weakness in myotonic dystrophy. Here, we deleted CaV1.1 (Cacna1s) exon 29 in mice. These mice displayed normal overall motor performance, although grip force and voluntary running were reduced. Continued expression of the developmental CaV1.1e splice variant in adult mice caused increased calcium influx during EC coupling, altered calcium homeostasis, and spontaneous calcium sparklets in isolated muscle fibers. Contractile force was reduced and endurance enhanced. Key regulators of fiber type specification were dysregulated and the fiber type composition was shifted toward slower fibers. However, oxidative enzyme activity and mitochondrial content declined. These findings indicate that limiting calcium influx during skeletal muscle EC coupling is important for the secondary function of the calcium signal in the activity-dependent regulation of fiber type composition and to prevent muscle disease.

Cardiac troponin I does not independently predict mortality in critically ill patients with severe sepsis.

OBJECTIVE: Patients with sepsis often have elevated cardiac troponin I even in the absence of coronary artery disease. The prognostic value of cardiac troponins in critically ill patients with sepsis remains debatable. Our objective was to evaluate the prognostic value of cardiac troponin I in critically ill patients with severe sepsis. METHODS: In this retrospective study, we included patients with severe sepsis who had troponin assayed within 12 h of admission to intensive care over a 6 year period. Patients who had myocardial infarction at intensive care admission in the setting of sepsis were excluded. Included patients were classified into two groups based on their serum troponin I levels: low troponin group (troponin ≤ 0.1 µg/L) and elevated troponin group (troponin > 0.1 µg/L). The primary outcome of interest was hospital mortality. The secondary outcome measures included intensive care mortality, intensive care and hospital length of stay. RESULTS: A total of 382 patients were admitted to intensive care with sepsis. Of these, 293 patients were included in analyses. There was a statistically significant difference in hospital (15% vs 36.1%; P < 0.01) and intensive care (11% vs 25%; P < 0.01) mortality, but not in intensive care and hospital duration of stay. Logistic regression analysis revealed temperature, simplified acute physiology score II and serum lactate to be independent predictors of hospital mortality. Cardiac troponin I was not an independent predictor of hospital mortality. CONCLUSION: Critically ill patients with severe sepsis who had elevated troponin had increased hospital and intensive care mortality. However, cardiac troponin I did not independently predict hospital mortality.

Analysis of immune responses and serological cross reactivities among Vibrio cholerae O1, Shigella flexneri 2a and Haemophilus influenzae b.

Antigenic determinants expressed on the bacterial cell surface are of importance in the serological characterization and microbiological diagnosis. The bacterial strains carrying these identical or similar antigenic epitopes might react with antibodies produced against other strains. In this study, strong immunogenicity and antigenic cross reactivity were demonstrated among V. cholerae O1, S. flexnerii 2a and H. influenzae b surface components. The enzyme linked immunosorbent assay (ELISA) results were supported by Western blot analysis, where at least 20 antigenic bands, were obtained in each of the reactions, when the surface components were reacted with the homologous antisera. The indirect ELISA results also demonstrated high degree of antigenic relatedness between the surface components of these species, where each surface component was reacted with the heterologous antisera. Western blot analysis also revealed cross reactions between the surface components suggesting common distribution of antigens/epitopes in these bacterial species. This study, thus, gave a clear idea of the level of antigenic sharing and variations among the pathogenic V. cholerae O1, S. flexneri 2a and H. influenzae b strains, which in future, may help in selecting a proper candidate for vaccines and immunodiagnostics development.

Protein film electrochemistry of microsomes genetically enriched in human cytochrome p450 monooxygenases.

This communication demonstrates direct electron delivery from electrodes to cyt P450 reductases in stable films ( approximately 100 nm thick) of genetically enriched CYP1A2 and CYP3A4 microsomes made by layer-by-layer assembly with polyions. Reversible voltammetry of films containing genetically enriched cyt P450 monooxygenase microsomes was shown to involve cyt P450 reductase by comparison with the pure rabbit reductase and by lack of characteristic reactions of iron heme enzymes, such as reaction of the FeII form with CO and catalytic electrochemical reduction of oxygen and hydrogen peroxide. The microsome films were activated electrochemically to catalyze styrene epoxidation, consistent with the pathway utilized in the human liver, although further work is required to establish this definitively.