Global Pharma R&D Informatics and AI Congress

Oct 29 – 30, 2018 · London, UK booth - #12

We are gold sponsors of 2nd Medicinal Chemistry Summit and 2nd Global Pharma R&D Informatics and AI Congress. Stop by at our booth #12 to chat about our solutions. Our posters have been accepted for presentation in positions #3 and #4, stay tuned for more details.

Sprouting out new ideas from knowledge ground

We present a platform supporting the design of novel compounds by collecting the right amount of data into a unified design space. Our platform, Marvin Live, provides an integrated solution, and combines raw data sources, predictive models and digested information into a single application. Besides, it efficiently supports streamlined design and triage of the hypothetical compounds. Without this list being exhaustive, the integrated knowledge includes physicochemical descriptors, combined metrics like the CNS MPO score, basic modeling capabilities and matched molecular pair (MMP) analysis. Visualizing data pre-processed by matched molecular pair analysis in straightforward, and conveniently transformed form has high impact on rational design. In this study we present a solution how MMP analysis can be applied to extend chemical intuition with computer-aided approach. This hypothetic study shows the potential evolution of a compound idea from the reference compound to a synthesis candidate through an example discovery project on hERG dataset. Data was extracted from ChEMBL [1] to mine chemical and related data and to generate matched molecular pairs. Fragmentation and matched pair generation were performed using MMPDB [2], whereas post-processing and visualization were implemented within the framework of Marvin Live. The “smart assistant” capability presented here is nourished by available knowledge and is designed to improve decision-making on what kind of compounds to design or synthesize next.

[1] https://www.ebi.ac.uk/chembl/ [2] https://github.com/rdkit/mmpdb

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Chemical Intelligence That Makes Hidden Knowledge Effortlessly Reachable

The knowledge, that is being produced and stored in the forms of reports, patents and scientific journal articles is expanding exponentially. Although, the unstructured nature of such contents impose constraints for seamless information access and scientific decision support. Chemistry is a unique field in this regard, for two reasons. First, the nomenclature is verbose in a sense that a chemical structure can be represented with various synonyms, for example traditional name, IUPAC name or a wide range of brand names or chemical formats (SMILES). Second, the navigation in the knowledge base, with queries related to the encapsulated chemical space, calls for peculiar search methods like similarity-based or substructure searches.

Our study highlights computational approaches to turn chemistry related knowledge stored in all the open access articles easily accessible (Fig. 1.). We present our results obtained on this large corpus through the following workflow: i) large-scale conversion of text content to chemical objects, ii) automated preparation of databases to store and organize relevant data, and iii) analysis of the collected chemistry space. Extraction of chemical objects was done from nearly 1.9M articles that stretches the chemical space of open access scientific literature with ChemLocator application. Chemical space was analysed with calculation of fingerprint-based chemical similarity matrix and clustering by MadFast Similarity Search. In order to explore the scaffold diversity of this exclusive chemical space, the obtained set was fragmented to yield rings and ring systems. Hidden relationships were explored by combining text and chemical information in graph data model and related visualization. In summary, our use-case highlights the potential of novel technologies to pre-process, search and explore the information network enfolded in large document sets on the field of chemistry.

Schematic workflow

Download the poster: Chemical Intelligence That Makes Hidden Knowledge Effortlessly Reachable

About the conference

Global Engage is pleased to announce as part of their Drug Discovery Series of events, the 2nd Medicinal Chemistry Summit: Europe– a key senior level R&D event that was hugely successful last year, confirmed to be held on 29th-30th October 2018 in London, U.K. This conference will be co-located with the 2nd Global Pharma R&D Informatics and AI Congress

Designed to attract experts working in all areas of medicinal chemistry, the Summit has three tracks focusing on key topics such as hit-to-lead optimization, protein degradation, DNA encoded libraries, SBDD, small molecule targeting of RNAs, immuno-oncology research, and the use of Artificial Intelligence in the drug discovery process. The Summit will provide a forum to network, learn, and engage with senior representatives of leading pharmaceutical and biotech companies worldwide.

Visit conference website.