AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Genetic, physical and functional interactions between the double-stranded RNA-dependent protein kinase PKR and the tumor suppressor p53

The tumor suppressor p53 is a multifunctional protein that plays a critical role in modulating cellular responses such as cell cycle arrest and apoptosis upon DNA damage or other stresses. These functions of p53 can be regulated by protein-protein interactions and by phosphorylation. The interferon (IFN)-inducible, double-stranded RNA activated protein kinase PKR is a serine/threonine kinase that mediates the antiviral and antigrowth effects of IFNs by inhibiting protein synthesis through the phosphorylation of the translation initiation factor eIF-2alpha. Both PKR and p53 have the capacity to inhibit cell growth and to modulate gene expression at both the transcriptional and translational level. However, the exact molecular mechanism(s) behind the regulation of cell growth by PKR are not-well understood. Based on previous reports demonstrating a cross talk between other IFN-inducible proteins and p53, it was of interest to examine whether and how PKR might modulate p53 function to explain the ability of PKR to regulate cell growth. This study demonstrates that PKR can physically, functionally and genetically interact with p53. PKR and p53 physically interact both in vivo and in vitro, and the interaction of PKR with p53 is a functional one since PKR can directly phosphorylate p53 on serine392 in vitro. Furthermore, studies using PKR+/+ and PKR-/- cells treated with adriamycin or expressing a temperature sensitive mutant of p53, showed that p53-mediated gene expression and G0/G 1 arrest was inhibited in PKR-/- cells. The phosphorylation levels of serine18 of p53, which plays a role in p53 function in vivo, was inhibited in PKR+/+ cells expressing temperature sensitive p53 compared to PKR-/- cells. Induction of serine18 phosphorylation was inhibited in PKR-/- cells in response to gamma-radiation and adriamycin but not ultraviolet radiation. While PKR does not directly phosphorylate serine18 of p53 in vitro, the specific phosphatidylinositol-3 (PI-3) kinase inhibi

Self-rated preparedness of Australian prevocational hospital doctors for emergencies

Objective: To determine perceived preparedness of Australian hospital-based prevocational doctors for resuscitation skills and management of emergencies, and to identify differences between doctors who perceive themselves well prepared and those who perceive themselves poorly prepared for emergencies, in demographics and exposure to desired learning methods.Methods: Questionnaire consisting of a mix of graded Likert scales and free-text answers distributed to 36 Australian hospitals for secondary distribution to hospital medical officers.Results: From 2607 questionnaires posted, 470 (18.1%) were returned. Thirty-one per cent (95% confidence interval [CI] 26&ndash;35%) felt well prepared for resuscitation and management of emergencies, 41% (CI 37&ndash;45%) felt adequately prepared and 28% (CI 24&ndash;32%) felt they were not well prepared. Those who felt well prepared reported that they had experienced more exposure to a range of educational methods, including consultant contact, supervisor feedback, clinical skills, high fidelity simulator sessions and unit meetings. Well-prepared and poorly prepared doctors had similar opinions of the usefulness of various learning methods, but the poorly prepared group more frequently expressed a desire for increased exposure to contact with registrars and consultants, clinical skills sessions and hospital and unit meetings. There were no differences in gender, age or country of origin (Australia vs international medical graduates) between those who felt well or poorly prepared.Conclusions: Many prevocational hospital doctors feel inadequately prepared for the management of emergencies. Perceived preparedness is associated with more exposure to particular educational activities. Increasing exposure to learning of emergencies in undergraduate and prevocational years could reduce the number of junior doctors who feel poorly prepared for emergencies.<br /

Coordination of DNA Damage Responses via the Smc5/Smc6 Complex

The detection of DNA damage activates DNA repair pathways and checkpoints to allow time for repair. Ultimately, these responses must be coordinated to ensure that cell cycle progression is halted until repair is completed. Several multiprotein complexes containing members of the structural maintenance of chromosomes family of proteins have been described, including the condensin and cohesin complexes, that are critical for chromosomal organization. Here we show that the Smc5/Smc6 (Smc5/6) complex is required for a coordinated response to DNA damage and normal chromosome integrity. Fission yeast cells lacking functional Smc6 initiate a normal checkpoint response to DNA damage, culminating in the phosphorylation and activation of the Chk1 protein kinase. Despite this, cells enter a lethal mitosis, presumably without completion of DNA repair. Another subunit of the complex, Nse1, is a conserved member of this complex and is also required for this response. We propose that the failure to maintain a checkpoint response stems from the lack of ongoing DNA repair or from defective chromosomal organization, which is the signal to maintain a checkpoint arrest. The Smc5/6 complex is fundamental to genome integrity and may function with the condensin and cohesin complexes in a coordinated manner

Novel combination therapy targeting rDNA transcription and Histone Deacetylation Provides Effective Treatment for Multiple Myeloma, and Synergises in Bortezomib-Resistant MM

Background: Multiple myeloma (MM) requires combination drug therapies to delay acquired drug resistance and clinical relapse. We co-developed CX-5461, a highly-selective inhibitor of RNA polymerase I-mediated rDNA transcription(1), currently in phase I trials for relapsed haematological malignancies (Peter Mac). CX-5461 produces a targeted nucleolar DNA damage response (DDR), triggering both a p53-dependent and -independent nucleolar stress response and killing malignant cells while sparing normal cells(2,3). Single-agent CX-5461 provides an impressive survival benefit in mouse models of B-cell lymphoma, acute myeloid leukaemia and now MM(2,4,5). However, drug resistance eventually occurs, confirming the need for combination therapies. Aim: To test the efficacy of CX-5461 in combination with the histone deacetylase inhibitor panobinostat, (prioritised from a boutique high-throughput screen of anti-myeloma agents), with a focus on the setting of resistance to proteasome-inhibitors (PIs). Methods: We assessed the impact of CX-5461 and panobinostat on overall survival in mouse models of MM, then surveyed the effects on cellular response and molecular markers of DDR. We developed bortezomib-resistant cell lines and an in vivo model of bortezomib-resistance to test this combination in the setting of PI-resistance. Results: CX-5461 in combination with panobinostat provides a significant survival advantage in both the transplanted Vk*MYC and the 5T33/KaLwRij models, with minimal bone marrow toxicity