Proteins interact with small molecules to modulate several important cellular functions. Many acute diseases were cured by small molecule binding in the active site of protein either by inhibition or activation. Currently, there are several docking programs to estimate the binding position and the binding orientation of protein–ligand complex. Many scoring functions were developed to estimate the binding strength and predict the effective protein–ligand binding. While the accuracy of current scoring function is limited by several aspects, the solvent effect, entropy effect, and multibody effect are largely ignored in traditional machine learning methods. In this paper, we proposed a new deep neural network-based model named DeepBindRG to predict the binding affinity of protein–ligand complex, which learns all the effects, binding mode, and specificity implicitly by learning protein–ligand interface contact information from a large protein–ligand dataset. During the initial data processing step, the critical interface information was preserved to make sure the input is suitable for the proposed deep learning model. While validating our model on three independent datasets, DeepBindRG achieves root mean squared error (RMSE) value of pKa (−logKd or −logKi) about 1.6–1.8 and R value around 0.5–0.6, which is better than the autodock vina whose RMSE value is about 2.2–2.4 and R value is 0.42–0.57. We also explored the detailed reasons for the performance of DeepBindRG, especially for several failed cases by vina. Furthermore, DeepBindRG performed better for four challenging datasets from DUD.E database with no experimental protein–ligand complexes. The better performance of DeepBindRG than autodock vina in predicting protein–ligand binding affinity indicates that deep learning approach can greatly help with the drug discovery process. We also compare the performance of DeepBindRG with a 4D based deep learning method “pafnucy”, the advantage and limitation of both methods have provided clues for improving the deep learning based protein–ligand prediction model in the future.

We showed an association between the ACYP2 polymorphism and cisplatin-induced ototoxicity, but not with the TPMT and COMT. A meta-analysis was statistically significant for both the COMT rs4646316 and the ACYP2 rs1872328 SNPs. Grading the hearing of children with asymmetric hearing loss requires additional clarification.

SummaryBackgroundA serious adverse effect of corticosteroid therapy is adrenal suppression. Our aim was to identify genetic variants affecting susceptibility to corticosteroid-induced adrenal suppression.MethodsWe enrolled children with asthma who used inhaled corticosteroids as part of their treatment from 25 sites across the UK (discovery cohort), as part of the Pharmacogenetics of Adrenal Suppression with Inhaled Steroids (PASS) study. We included two validation cohorts, one comprising children with asthma (PASS study) and the other consisting of adults with chronic obstructive pulmonary disorder (COPD) who were recruited from two UK centres for the Pharmacogenomics of Adrenal Suppression in COPD (PASIC) study. Participants underwent a low-dose short synacthen test. Adrenal suppression was defined as peak cortisol less than 350 nmol/L (in children) and less than 500 nmol/L (in adults). A case-control genome-wide association study was done with the control subset augmented by Wellcome Trust Case Control Consortium 2 (WTCCC2) participants. Single nucleotide polymorphisms (SNPs) that fulfilled criteria to be advanced to replication were tested by a random-effects inverse variance meta-analysis. This report presents the primary analysis. The PASS study is registered in the European Genome-phenome Archive (EGA). The PASS study is complete whereas the PASIC study is ongoing.FindingsBetween November, 2008, and September, 2011, 499 children were enrolled to the discovery cohort. Between October, 2011, and December, 2012, 81 children were enrolled to the paediatric validation cohort, and from February, 2010, to June, 2015, 78 adults were enrolled to the adult validation cohort. Adrenal suppression was present in 35 (7%) children in the discovery cohort and six (7%) children and 17 (22%) adults in the validation cohorts. In the discovery cohort, 40 SNPs were found to be associated with adrenal suppression (genome-wide significance p<1 × 10−6), including an intronic SNP within the PDGFD gene locus (rs591118; odds ratio [OR] 7·32, 95% CI 3·15–16·99; p=5·8 × 10−8). This finding for rs591118 was validated successfully in both the paediatric asthma (OR 3·86, 95% CI 1·19–12·50; p=0·02) and adult COPD (2·41, 1·10–5·28; p=0·03) cohorts. The proportions of patients with adrenal suppression by rs591118 genotype were six (3%) of 214 patients with the GG genotype, 15 (6%) of 244 with the AG genotype, and 22 (25%) of 87 with the AA genotype. Meta-analysis of the paediatric cohorts (discovery and validation) and all three cohorts showed genome-wide significance of rs591118 (respectively, OR 5·89, 95% CI 2·97–11·68; p=4·3 × 10−9; and 4·05, 2·00–8·21; p=3·5 × 10−10).InterpretationOur findings suggest that genetic variation in the PDGFD gene locus increases the risk of adrenal suppression in children and adults who use corticosteroids to treat asthma and COPD, respectively.FundingDepartment of Health Chair in Pharmacogenetics.

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These preliminary results are encouraging, but further randomised studies are required before leflunomide can be recommended for the treatment of IgA nephropathy.

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Novel (nua) kinase family 1 (NUAK1) is a member of the human adenosine monophosphate-activated protein kinases family, which is overexpressed in multiple human malignancies and thought to be involved in tumor invasion and metastasis ability. Our study is to investigate the association of NUAK1 expression with clinicopathological parameters and prognostic significance of patients with gastric cancer. The expression patterns of the NUAK1 protein in 117 primary archival gastric cancer specimens and 46 adjacent normal epithelial tissues from patients were detected by immunohistochemistry assay. Staining evaluation results were analyzed statistically in relation to various clinicopathological characters, recurrence-free survival and overall survival. High level of NUAK1 expression was detected in gastric cancer, significantly more than in adjacent normal epithelial cells. In gastric cancer, NUAK1 was positively correlated with depth of invasion, lymph node metastasis, pathological stage, surgical resection and histological differentiation. However, no correlations between NUAK1 expression and patients' age, sex, tumor size, location, CA19-9 or CEA were detected. The recurrence-free survival and overall survival were significantly shorter for patients with NUAK1 higher scores than those with NUAK1 lower scores. Multivariate analysis identified NUAK1 was an independent prognostic factor for both recurrence-free survival and overall survival. Our findings provided convincing evidence for NUAK1 overexpression, which was tightly associated with more aggressive tumor behavior and a poor prognosis, indicating that NUAK1 is a valuable molecular biomarker for gastric cancer progression. It might also act as a promising target for both prognostic prediction and therapeutics.

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