A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

A machine learning method for the identification and characterization of novel COVID-19 drug targets

In addition to vaccines, the World Health Organization sees novel medications as an urgent matter to fight the ongoing COVID-19 pandemic. One possible strategy is to identify target proteins, for which a perturbation by an existing compound is likely to benefit COVID-19 patients. In order to contribute to this effort, we present GuiltyTargets-COVID-19 ( https://guiltytargets-covid.eu/ ), a machine learning supported web tool to identify novel candidate drug targets. Using six bulk and three single cell RNA-Seq datasets, together with a lung tissue specific protein-protein interaction network, we demonstrate that GuiltyTargets-COVID-19 is capable of (i) prioritizing meaningful target candidates and assessing their druggability, (ii) unraveling their linkage to known disease mechanisms, (iii) mapping ligands from the ChEMBL database to the identified targets, and (iv) pointing out potential side effects in the case that the mapped ligands correspond to approved drugs. Our example analyses identified 4 potential drug targets from the datasets: AKT3 from both the bulk and single cell RNA-Seq data as well as AKT2, MLKL, and MAPK11 in the single cell experiments. Altogether, we believe that our web tool will facilitate future target identification and drug development for COVID-19, notably in a cell type and tissue specific manner.

Repurposing of Chemotherapeutics to Combat COVID-19

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a novel strain of SARS coronavirus. The COVID-19 disease caused by this virus was declared a pandemic by the World Health Organization (WHO). SARS-CoV-2 mainly spreads through droplets sprayed by coughs or sneezes of the infected to a healthy person within the vicinity of 6 feet. It also spreads through asymptomatic carriers and has negative impact on the global economy, security and lives of people since 2019. Numerous lives have been lost to this viral infection; hence there is an emergency to build up a potent measure to combat SARS-CoV-2. In view of the non-availability of any drugs or vaccines at the time of its eruption, the existing antivirals, antibacterials, antimalarials, mucolytic agents and antipyretic paracetamol were used to treat the COVID-19 patients. Still there are no specific small molecule chemotherapeutics available to combat COVID-19 except for a few vaccines approved for emergency use only. Thus, the repurposing of chemotherapeutics with the potential to treat COVID-19 infected people is being used. The antiviral activity for COVID-19 and biochemical mechanisms of the repurposed drugs are being explored by the biological assay screening and structure-based in silico docking simulations. The present study describes the various US-FDA approved chemotherapeutics repositioned to combat COVID-19 along with their screening for biological activity, pharmacokinetic and pharmacodynamic evaluation.

Ethical considerations for precision psychiatry: A roadmap for research and clinical practice

Precision psychiatry is an emerging field with transformative opportunities for mental health. However, the use of clinical prediction models carries unprecedented ethical challenges, which must be addressed before accessing the potential benefits of precision psychiatry. This critical review covers multidisciplinary areas, including psychiatry, ethics, statistics and machine-learning, healthcare and academia, as well as input from people with lived experience of mental disorders, their family, and carers. We aimed to identify core ethical considerations for precision psychiatry and mitigate concerns by designing a roadmap for research and clinical practice. We identified priorities: learning from somatic medicine; identifying precision psychiatry use cases; enhancing transparency and generalizability; fostering implementation; promoting mental health literacy; communicating risk estimates; data protection and privacy; and fostering the equitable distribution of mental health care. We hope this blueprint will advance research and practice and enable people with mental health problems to benefit from precision psychiatry.

A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism

The high number of failed pre-clinical and clinical studies for compounds targeting Alzheimer disease (AD) has demonstrated that there is a need to reassess existing strategies. Here, we pursue a holistic, mechanism-centric drug repurposing approach combining computational analytics and experimental screening data. Based on this integrative workflow, we identified 77 druggable modifiers of tau phosphorylation (pTau). One of the upstream modulators of pTau, HDAC6, was screened with 5,632 drugs in a tau-specific assay, resulting in the identification of 20 repurposing candidates. Four compounds and their known targets were found to have a link to AD-specific genes. Our approach can be applied to a variety of AD-associated pathophysiological mechanisms to identify more repurposing candidates.

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Drug-repurposing approach that combines in silico analyses and in vitro screenings

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A drug- and mechanism-oriented model, the Human Brain Pharmacome (HBP) was created

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The HBP was used to mine data related to drugs and targets to generate a hypothesis

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Experimental evidence validated predicted drug-target combinations

Owing to current setbacks in the discovery and development of novel treatments tackling Alzheimer disease (AD), a re-evaluation of research and development (R&D) strategies is underway. Here, we present a holistic pharmacological approach that combines drug-target information with knowledge graphs that represent essential pathophysiology mechanisms. The resulting Human Brain Pharmacome (HBP) embeds hundreds of relevant drug-target interactions in the context of disease mechanisms governing AD. We demonstrate how such a tool can be used to aid AD research by identifying already-approved drugs that have the potential to treat the disease, thereby bypassing the expensive and time-consuming task of researching and developing a new drug. In our study, we identified new drug-target combinations and provided mechanistic explanations that help to improve our understanding of AD pathology and support future development of effective therapeutic strategies.

Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases

Despite available vaccinations COVID-19 case numbers around the world are still growing, and effective medications against severe cases are lacking. In this work, we developed a machine learning model which predicts mortality for COVID-19 patients using data from the multi-center 'Lean European Open Survey on SARS-CoV-2-infected patients' (LEOSS) observational study (>100 active sites in Europe, primarily in Germany), resulting into an AUC of almost 80%. We showed that molecular mechanisms related to dementia, one of the relevant predictors in our model, intersect with those associated to COVID-19. Most notably, among these molecules was tyrosine kinase 2 (TYK2), a protein that has been patented as drug target in Alzheimer's Disease but also genetically associated with severe COVID-19 outcomes. We experimentally verified that anti-cancer drugs Sorafenib and Regorafenib showed a clear anti-cytopathic effect in Caco2 and VERO-E6 cells and can thus be regarded as potential treatments against COVID-19. Altogether, our work demonstrates that interpretation of machine learning based risk models can point towards drug targets and new treatment options, which are strongly needed for COVID-19.