Molecular Networks GmbH Computerchemie

Erlangen, Germany

Molecular Networks GmbH Computerchemie

Erlangen, Germany

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Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2010.4.2-9-4 | Award Amount: 6.80M | Year: 2011

The COSMOS project will address the assessment needs of the cosmetics industry by delivering an integrated suite of computational tools to predict the effects of long-term exposure to cosmetic ingredients in humans, thus reducing the need for repeated dose toxicity testing in animals. To achieve this, individual modules comprising: (new) databases, thresholds of toxicological concern (TTC), in silico toxicology (grouping, read-across and QSAR), in vitro data and physiologically-based pharmacokinetic (PBPK) modelling, will be used to construct flexible workflows for assessing toxicity. The COSMOS project will be informed by the needs of industry through active stakeholder engagement, and will utilise innovative technologies from outside the cosmetics area. New databases for TTC and modelling studies will be created by harvesting US FDA legacy data for cosmetics. New and current databases will be combined to advance the state-of-the-art providing a transparent, freely-available public resource. Grouping and read-across will be achieved mechanistically and on the basis of structural similarity. The effective dose-response at the target organ will be estimated from in vitro effects and PBPK models, establishing an alternative (non-animal) basis for risk assessment. All models and Workflows developed will be transparent, fully documented and open access. The partners include world leaders committed to donating software and algorithms to support the open architecture. Data and models will be integratable with existing systems. Workflows will be automated through the KNIME software.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE-2007-3-2-07;KBBE-2007-3-2-08 | Award Amount: 7.53M | Year: 2009

The exponential increase in microbial genome and metagenome sequencing throughput has widened the gap between sequence and functional understanding. A clear picture of metabolic processes across the spectrum of bacterial species is essential to enable the exploitation of microbial genomics for the purposes of environmental biotechnology. The Microme project endeavors to extend the scope of microbial genome annotation from functional assignment at the gene level to the systematic generation of pathway assemblies and genome-scale metabolic models. A few key ideas and design principles will enable the Microme reconstruction pipeline to achieve this ambitious goal.A clear definition of a metabolic pathway as a collection of reaction sets, each of which convert the same defined inputs into the same outputs, will allow species-specific pathway variants to be identified, assembled into networks, compared across species, and used for downstream computations. A unique pathways projection, curation and assembly cycle, feeding directly into the flow of newly sequenced genomes, will allow a qualitative increase in the speed and reliability of the pathway generation process. Pathways and models produced the pipeline will be accessible to the scientific community as an integrated resource via the Microme portal. Finally, taking advantage of the availability of pathway assemblies from a large sample of genomes, methods for comparative and phylogenetic analyses and novel metabolic engineering strategies for environmental biotechnology goals will be developed, applied to proof-of-concept studies, and integrated to the resource as an analytical tool layer. Microme will be supported by a robust bioinformatics infrastructure, developed by integrating a set of established European databases and tools, integrated with reference protein annotation, metabolites and reactions databases, and interfaced with the annotation pipelines of the two main European sequencing centers.


El-Sayed W.A.,National Research Center of Egypt | Abbas H.-A.S.,National Research Center of Egypt | Abbas H.-A.S.,King Khalid University | Abdel Mageid R.E.,National Research Center of Egypt | Magdziarz T.,Molecular Networks GmbH Computerchemie
Medicinal Chemistry Research | Year: 2016

We report here, the synthesis of 1-(1-ethyl-1H-indol-3-yl)-3-pyridin-4-yl-prop-2-en-1-one (2) which was used as a base to the synthesis of new 3-(pyrimidin-4-yl)-1H-indole derivatives; their thioglycoside and N-glycoside derivatives 3-10a, b; pyrane derivatives and pyranopyrimidine derivative 11-13; and tricyclic pyranotriazolo[1, 5-a]pyrimidine 14. Moreover, reaction of N-ethyl-3-acetylindole 2 with phenylhydrazine and hydroxylamine hydrochloride gave pyrazolyl-indole and oxazolyl-indole derivatives 15 and 16, respectively. The structures of the products obtained were confirmed by elemental analysis, IR, 1HNMR and 13C NMR. The newly synthesized compounds were investigated for their antimicrobial activity, and some of them showed high growth inhibition activities. Anti-bacterial activity of the synthesized compounds was further analyzed by the molecular docking approach, a method of simulation of fitting ligands into binding site(s) of macromolecular targets. AutoDock Vina results showed that compounds 5a and 6a, b were located in a pocket in the active site. © 2015 Springer Science+Business Media New York.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: KBBE.2011.3.6-04 | Award Amount: 3.89M | Year: 2011

The concept of METACODE is to preform genetic code engineering in microbial strains with parallel recruitment of novel bio-orthogonal chemistries for mass production of desired protein/peptide based products. In combination with computational and classical chemical synthetic approaches as well as chemo-informatics, enzyme guided evolution, synthetic metabolism, and directed evolution of microbial strains, artificial industrial microbial strains will be designed. This will enable the access to genetically robust and safe strains with added/novel functionalities and topologies from renewable resources. These strains will be characterized with alternative reading of the genetic code (genetic firewall) and with predetermined chemistries (metathesis), as well as necessary robustness for efficient industrial use.

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