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

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

Sex-Related Differences in Gene Expression by Porcine Aortic Valvular Interstitial Cells

<div><p>While many large-scale risk factors for calcific aortic valve disease (CAVD) have been identified, the molecular etiology and subsequent pathogenesis of CAVD have yet to be fully understood. Specifically, it is unclear what biological phenomena underlie the significantly higher occurrence of CAVD in the male population. We hypothesized the existence of intrinsic, cellular-scale differences between male and female valvular interstitial cells (VICs) that contribute to male sex being a risk factor for CAVD. Differences in gene expression profiles between healthy male and female porcine VICs were investigated via microarray analysis. Mean expression values of each probe set in the male samples were compared to the female samples, and biological processes were analyzed for overrepresentation using Gene Ontology term enrichment analysis. There were 183 genes identified as significantly (fold change>2; P<0.05) different in male versus female aortic valve leaflets. Within this significant gene list there were 298 overrepresented biological processes, several of which are relevant to pathways identified in CAVD pathogenesis. In particular, pathway analysis indicated that cellular proliferation, apoptosis, migration, ossification, angiogenesis, inflammation, and extracellular matrix reorganization were all significantly represented in the data set. These gene expression findings also translated into functional differences in VIC behavior in the <em>in vitro</em> environment, as sex-related differences in proliferation and apoptosis were confirmed in VIC populations cultured <em>in vitro</em>. These data suggest that a sex-related propensity for CAVD exists on the cellular level in healthy subjects, a phenomenon that could have significant clinical implications. These findings also strongly support discontinuing the use of mixed-sex VIC cultures, thereby changing the current standard in the field.</p> </div

Functional categorization analysis of most significant pathways and diseases represented by microarray data.

<p>A functional categorization analysis of the most significant pathways and diseases represented in the microarray-generated list of significantly different genes was generated using Ingenuity software. The p-value was calculated using the right-tailed Fisher’s exact test. Each bar represents the highest level of function for each category, each of which includes many sub-level functions and is represented by the number of genes in the male and female samples (denoted in parentheses, respectively). The bar was determined by the lowest p-value among sub-level functions for each category. Threshold indicates p-value cutoff of 0.05.</p

IPA-generated molecular networks assembled from differentially expressed genes (bold) in males versus females in the significant genes list.

‡<p>The score is a numerical rank of the degree of relevance of the network to the molecules in the significant genes list and is based on the hypergeometric distribution calculated as –log(Fisher’s exact test result).</p>*<p>indicates multiple identifiers in the significant genes dataset map to a single gene in the IPA Global Molecular Network.</p

Translation of findings to <i>in vitro</i> VIC function.

<p>Male and female VICs were cultured for 5 days in serum-free media and evaluated for (A) proliferation, using the Click-iT EdU Alexa Fluor 488 Imaging Assay, and (B) apoptosis, using the Promega Caspase-Glo 3/7 Assay System. Values are means plus standard deviation, n = 4 per condition. *P<0.05 compared to male VICs.</p

Ingenuity pathway analysis Network #1.

<p>Ingenuity pathway analysis was used to assemble a network based upon 22 differentially expressed focus genes that were upregulated in male VICs compared to female VICs. Genes are represented as nodes, with node shape representing the functional class of the gene product (seen in legend). Node color depicts degree of overrepresentation in male samples; uncolored nodes are depicted based upon evidence in the IPA Knowledge Base indicating a strong biological relevance to the network. *indicates multiple identifiers in the dataset file map to a single gene in the IPA Global Molecular Network. Corresponding fold change values are listed beneath each gene label. Focus gene names are defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039980#pone.0039980.s005" target="_blank">Table S1</a>.</p

Significant biological processes determined by GO enrichment analysis and categorized according to disease-related pathway grouping (expanded table available in Table S4).

<p>Significant biological processes determined by GO enrichment analysis and categorized according to disease-related pathway grouping (expanded table available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039980#pone.0039980.s008" target="_blank">Table S4</a>).</p

Ingenuity pathway analysis Network #2.

<p>Ingenuity pathway analysis was used to assemble a network based upon 20 differentially expressed focus genes that were upregulated in male VICs compared to female VICs. * indicates multiple identifiers in the dataset file map to a single gene in the IPA Global Molecular Network. Corresponding fold change values are listed beneath each gene label. Focus gene names are defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039980#pone.0039980.s005" target="_blank">Table S1</a>.</p

qRT-PCR validation of microarray data.

<p>Data are displayed as mean log2(fold-change) in gene expression in male versus female samples. Gene abbreviations: aggrecan (<i>ACAN</i>), dipeptidyl-peptidase 4 (<i>DPP4</i>), stanniocalcin 1 precursor (<i>STC1</i>), natriuretic peptide precursor C (<i>NPPC</i>), kinase insert domain receptor (<i>KDR</i>), angiopoietin-like 4 (<i>ANGPTL4</i>), apolipoprotein E (<i>APOE</i>), calcitonin receptor-like (<i>CALCRL</i>), and insulin-like growth factor binding protein 5 (<i>IGFBP5</i>). *P<0.05 compared to female VIC RT-PCR results, ^#P<0.05 compared to female VIC microarray results.</p