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ZCCHC14 is a novel host factor that is required for Hepatitis B virus RNA polyadenylation
No full textThe hallmark of chronic hepatitis B virus (CHB) infection is the presence of high levels of circulating non-infectious small lipid vesicles containing HBV surface antigen (HBsAg). Although rare, sustained HBsAg loss is the idealized endpoint of any CHB therapy and is considered a functional cure. A novel, potent and orally bioavailable small molecule RG7834 has been previously reported to inhibit HBsAg expression putatively targeting host non-canonical poly(A) RNA polymerases, PAP-associated domain-containing protein 5 and 7 (PAPD5 and PAPD7). In this study, we describe a forward genetic screen exploiting CRISPR-mediated genome-wide editing to identify novel host factors required for HBsAg expression and to gain further insights into the mechanism of RG7834. Several genes were enriched in a cell population resisting to RG7834-mediating HBsAg inhibition, including PAPD5 and a novel host factor zinc finger CCHC-type containing 14 (ZCCHC14). The role of ZCCHC14, PAPD5 as well as its homolog PAPD7 were further confirmed by the siRNA knockdown studies which phenotypically similarly to RG7834 were associated with the strong reduction in polyA tails of HBV-specific RNAs. In addition, as seen previously with RG7834, inhibition of HBsAg expression by ZCCHC14 and PAPD5/7 complex requires intact SL? in the HBV post-transcriptional regulatory elements. In conclusion, we identify ZCCHC14 as a novel cellular factor, which acts together with the PAPD5 and PAPD7 complex to polyadenylate HBV transcripts and as a new therapeutic target for the HBV cure
Estimating Berg Balance Scale and Mini Balance Evaluation System Test Scores by Using Wearable Shoe Sensors
No full textMeasuring humans’ functional balance is important for clinical estimation of fall risk. Although many clinical assessments, such as Berg Balance Scale and Mini Balance Evaluation System Test, are available to test the functional balance, the results are affected by the skills of different operators. This paper proposes an objective approach to access the functional balance by a wearable sensor system embedded in the shoe and a hip accelerometer. Support Vector Machine regression models are built with numerical features selected by mRMR algorithm to estimate the scores of the clinical assessments. Leave one out cross validation is employed to evaluate the regression models. The approach is validated on a group of 30 seniors (76 10.5 years old), containing fallers and non-fallers. The results show that the wearable sensor system has a capability to estimate the Berg Balance Scale and Mini Balance Evaluation System Test scores with absolute mean errors and standard deviations 6.07 3.76 and 5.45 3.65, respectively, and demonstrates high agreement with falls history based risk assessment
A Green Chemistry Continuum for a Robust and Sustainable API Supply Chain
No full textIn an effort to improve sustainability and reduce the cost of goods for active pharmaceutical ingredients (APIs), pharma companies have partnered on varying portions of their supply chain with contract providers. This approach brings with it numerous cost benefits but also logistical challenges. However, it also offers opportunities to integrate sustainable science via green chemistry and engineering more holistically into the entire sequence. The ACS Green Chemistry Institute Pharmaceutical Roundtable (GCIPR) provides a multicompany industrial view on how to address the challenges and best meet cost goals while enhancing the overall sustainability of the global pharmaceutical industry
Site selective amide reduction of cyclosporine A yields derivatives of an important cyclic peptide
No full textThe development of amide reduction catalysts able to function under mild conditions has enabled the development of novel reactions on a complex structure that has been the subject of extensive synthetic studies for its diverse medical effects. While the origins of the innate site-selectivity is as of yet un-clear, the B2-Cat system targets residues not targeted in other systems. The reduction chemistry herein has doubled the num-ber of known amide reduction CsA derivatives. Reduction of secondary amide (Ala7) reveals a secondary amine prone to diversity generating reactivity. Ala7 exists at a position which may modulate both cyclophilin and calcineurin binding. Fur-thermore, the B2-Cat catalyzed amide reductions can be di-rected with secondary silanes in the described case to select for MeBmT1 reduction over other sites. We also report that the O-silyl hemiaminal intermediate (A) can be intercepted to form new C–C bonds. These studies provide a framework which can be used in combination with other reduction chemistries to gen-erate unique selectivities with applications in late-stage func-tionalization of cyclic peptides
Phase I study of BGT226, a pan-PI3K and mTOR inhibitor, in Japanese patients with advanced solid cancers
No full textThe phosphatidylinositol 3-kinase (PI3K) pathway is a promising therapeutic target for various cancers. BGT226 is a pan-PI3K and mammalian target of rapamycin (mTOR) inhibitor. The tolerability and pharmacokinetics/pharmacodynamics of BGT226 were investigated in a phase I study in Japanese patients with advanced solid cancers. BGT226 was orally administered on days 1, 3, and 5 of each week. The initial dose of 10 mg was subsequently escalated to 20, 40, 80, and 100 mg in a cohort of three patients. Pharmacokinetics and pharmacodynamics were investigated using plasma, normal skin, and tumor samples. A total of 18 patients were enrolled and evaluated. The most frequently reported toxicities were diarrhea, nausea, decreased appetite, vomiting, and fatigue. They were all grade 1 or 2, and no dose-limiting toxicity was observed. However, all six patients treated at 100 mg experienced diarrhea and nausea, while two experienced a dose reduction and/or interruptions during the study. Two of five patients who exhibited stable disease continued the study treatment for ≥ 16 weeks. The absorption of BGT226 was rapid, and systemic exposure increased in a dose-dependent manner. Treatment with BGT226 did not change any of the biomarkers in neither normal skin nor tumor tissues. BGT226 was tolerated up to 100 mg three times a week in Japanese patients with solid cancers, without difference in toxicity profiles and pharmacokinetics compared to Western patients
Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening
No full textRecently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular recognition, as intended, or are instead learning biases inherent in the dataset itself. We find that superior enrichment efficiency in CNN models can be attributed to the analogue and decoy bias hidden in the DUD-E dataset rather than successful generalization of the pattern of protein-ligand interactions. Comparing additional deep learning models trained on PDBbind datasets, we found that their enrichment performances using DUD-E are not superior to the performance of the docking program AutoDock Vina. Together, these results suggest that biases that could be present in constructed datasets should be thoroughly evaluated before applying them to machine learning based methodology development
Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion
No full textLiver cancer susceptibility varies amongst humans and between experimental animal
models due to multiple genetic and epigenetic factors. The molecular characterization of
such susceptibilities has the potential to enhance cancer risk assessment of xenobiotic
exposures and disease prevention strategies. Here, using DNase I hypersensitivity
mapping coupled with transcriptomic profiling, we investigate perturbations in cis-acting
gene regulatory elements associated with the early stages of phenobarbital (PB)-
mediated liver tumor promotion in susceptible versus resistant mouse strains (B6C3F1
versus C57BL/6J). Integrated computational analyses of strain-selective changes in
liver chromatin accessibility underlying PB-response reveal differential epigenetic
regulation of molecular pathways associated with PB-mediated tumor promotion,
including Wnt/-catenin signalling. Complementary transcription factor motif analyses
reveal mouse strain-selective gene regulatory networks and a novel role for Stat, Smad
and Fox transcription factors in the early stages of PB-mediated tumor promotion.
Mapping perturbations in cis-acting gene regulatory elements provides novel insights
into the molecular basis for susceptibility to xenobiotic-induced rodent liver tumor
promotion and has the potential to enhance mechanism-based cancer risk assessments
of xenobiotic exposures
Design of potent and selective covalent inhibitors of Bruton’s Tyrosine Kinase targeting an inactive conformation
No full textBruton’s tyrosine kinase (BTK) is a member of the TEC kinase family and is selectively expressed in a subset of immune cells. It is a key regulator of antigen receptor signaling in B cells and of Fc receptor signaling in mast cells and macrophages. A BTK inhibitor will likely have a positive impact on autoimmune diseases which are caused by autoreactive B cells and immune-complex driven inflammation. We report the design, optimization, and characterization of potent and selective covalent BTK inhibitors. Starting from the selective reversible inhibitor 3 binding to an inactive conformation of BTK, we designed covalent irreversible compounds by attaching an electrophilic warhead to reach Cys481. The first prototype 4 covalently modified BTK and showed an excellent kinase selectivity including several Cys-containing kinases, validating the design concept. In addition, this compound blocked FcγR-mediated hypersensitivity in vivo. Optimization of whole blood potency and metabolic stability resulted in compounds such as 8, which maintained the excellent kinase selectivity and showed improved BTK occupancy in vivo
2019 White Paper on Recent Issues in Bioanalysis: FDA Immunogenicity Guidance, Gene Therapy, Critical Reagents, Biomarkers and Flow Cytometry Validation (Part 3-Recommendations on 2019 FDA Immunogenicity Guidance, Gene Therapy Bioanalytical Challenges, Strategies for Critical Reagent Management, Biomarker Assay Validation, Flow Cytometry Validation & CLSI H62)
No full textThe 2019 13th Workshop on Recent Issues in Bioanalysis (WRIB) took place in New Orleans, LA, USA on April 1-5, 2019 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day, week-long event-a full immersion week of bioanalysis, biomarkers, immunogenicity and gene therapy. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small-and large-molecule bioanalysis involving LCMS, hybrid LBA/LCMS, LBA cell-based/flow cytometry assays and qPCR approaches. This 2019 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2019 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers New Insights in Biomarker Assay Validation, Current & Effective Strategies for Critical Reagent Management, Flow Cytometry Validation in Drug Discovery & Development & CLSI H62, Interpretation of the 2019 FDA Immunogenicity Guidance and Gene Therapy Bioanalytical Challenges. Part 1 (Innovation in Small Molecules and Oligonucleotides & Mass Spectrometry Method Development Strategies for Large Molecule Bioanalysis) and Part 2 (Recommendations on the 2018 FDA BMV Guidance, 2019 ICH M10 BMV Draft Guideline and regulatory agencies' input on bioanalysis, biomarkers, immunogenicity and gene therapy) are published in volume 11 of Bioanalysis, issues 22 and 23 (2019), respectively