IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2–3 billion to deliver one new drug. This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic. In silico methodologies need to be improved both to select better lead compounds, so as to improve the efficiency of later stages in the drug discovery protocol, and to identify those lead compounds more quickly. No known methodological approach can deliver this combination of higher quality and speed. Here, we describe an Integrated Modeling PipEline for COVID Cure by Assessing Better LEads (IMPECCABLE) that employs multiple methodological innovations to overcome this fundamental limitation. We also describe the computational framework that we have developed to support these innovations at scale, and characterize the performance of this framework in terms of throughput, peak performance, and scientific results. We show that individual workflow components deliver 100 × to 1000 × improvement over traditional methods, and that the integration of methods, supported by scalable infrastructure, speeds up drug discovery by orders of magnitudes. IMPECCABLE has screened ∼ 1011 ligands and has been used to discover a promising drug candidate. These capabilities have been used by the US DOE National Virtual Biotechnology Laboratory and the EU Centre of Excellence in Computational Biomedicine

Introduction of a web portal for an Individual Health Management and observational health data sciences

Dieter Melchart,1,2 Axel Eustachi,1 Stephan Gronwald,3 Erich Wühr,3 Kristina Wifling,1 Beatrice E Bachmeier1,4 1Competence Centre for Complementary Medicine and Naturopathy, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany; 2Institute for Complementary and Integrative Medicine, University Hospital Zurich and University of Zurich, Zurich, Switzerland; 3Applied Health Care Science, Deggendorf Institute of Technology, Deggendorf, Germany; 4Institute of Laboratory Medicine, Ludwig-Maximilians-University, Munich, Germany Background: There is a global trend to a stronger active involvement of persons in the maintenance and restoring of health. The Competence Centre for Complementary Medicine and Naturopathy (CoCoNat) of the Technical University of Munich (TUM) has developed a lifestyle concept to enable each individual to manage his or her health – Individual Health Management (IHM) – and a web-based health portal named Virtual Tool for Education, Reporting, Information and Outcomes (VITERIO®), which addresses these needs for practice and research. Objectives: The objectives of this study were to establish a core set of questionnaires for a self-assessment program on certain risk indications and comprehensive protection factors of health and to develop and enhance 1) tools for individual feedback, longitudinal self-monitoring, self-assessment, and (self-)care-planning; 2) training packages; 3) open notes and records for provider and patient; and 4) tools for monitoring groups and single participants in various indicators for individual coaching and scientific evaluation. Methods: The CoCoNat of TUM, Faculty for Applied Health Science of Technische Hochschule Deggendorf, VITERIO® company, IHM campus network, and Erich Rothenfußer Foundation, Munich, provide a consortium responsible for content, research strategy, technical production and implication, postgraduate education for IHM coaches, implementation of IHM in various settings, and funding resources. Results: A data set of indicators for health screening and self-monitoring of findings, symptoms, health behavior, and attitudes are integrated into a web-based health portal named VITERIO®. The article introduces some implemented graphical solutions of developed tools and gives examples for daily use. Conclusion: Behavioral change and adaptation in attitudes and personal values are difficult issues of health education and lifestyle medicine. To address this problem best, the implementation of a patient-centric, performance measures-based program including open records and a blended learning concept were elaborated. The combination of an individual web-based health portal with personal coaching allows the implementation of IHM in everyday practice. Keywords: lifestyle program, Individual Health Management, IHM, blended learning, performance measures, web-based health portal, adherenc

Mimicking of arginine by functionalized Nω-carbamoylated arginine as a new broadly applicable approach to labeled bioactive peptides: high affinity angiotensin, neuropeptide Y, neuropeptide FF and neurotensin receptor ligands as examples

Derivatization of biologically active peptides by conjugation with fluorophores or radionuclide-bearing moieties is an effective and commonly used approach to prepare molecular tools and diagnostic agents. Whereas lysine, cysteine, and N-terminal amino acids have been mostly used for peptide conjugation, we describe a new, widely applicable approach to peptide conjugation based on the nonclassical bioisosteric replacement of the guanidine group in arginine by a functionalized carbamoylguanidine moiety. Four arginine-containing peptide receptor ligands (angiotensin II, neurotensin(8-13), an analogue of the C-terminal pentapeptide of neuropeptide Y, and a neuropeptide FF analogue) were subject of this proof-of-concept study. The N-omega-carbamoylated arginines, bearing spacers with a terminal amino group, were incorporated into the peptides by standard Fmoc solid phase peptide synthesis. The synthesized chemically stable peptide derivatives showed high receptor affinities with K-i values in the low nanomolar range, even when bulky fluorophores had been attached. Two new tritiated tracers for angiotensin and neurotensin receptors are described

Catabolite Repression of the Citrate Fermentation Genes in Klebsiella pneumoniae: Evidence for Involvement of the Cyclic AMP Receptor Protein

Klebsiella pneumoniae is able to grow anaerobically with citrate as a sole carbon and energy source by a fermentative pathway involving the Na(+)-dependent citrate carrier CitS, citrate lyase, and oxaloacetate decarboxylase. The corresponding genes are organized in the divergent citC and citS operons, whose expression is strictly dependent on the citrate-sensing CitA-CitB two-component system. Evidence is provided here that the citrate fermentation genes are subject to catabolite repression, since anaerobic cultivation with a mixture of citrate and glucose or citrate and gluconate resulted in diauxic growth. Glucose, gluconate, and also glycerol decreased the expression of a chromosomal citS-lacZ fusion by 60 to 75%, whereas a direct inhibition of the citrate fermentation enzymes was not observed. The purified cyclic AMP (cAMP) receptor protein (CRP) of K. pneumoniae bound to two sites in the citC-citS intergenic region, which were centered at position −41.5 upstream of the citC and citS transcriptional start sites. Binding was apparently stimulated by the response regulator CitB. These data indicate that catabolite repression of the citrate fermentation genes is exerted by CRP and that in the absence of repressing carbon sources the cAMP-CRP complex serves to enhance the basal, CitB-dependent transcription level