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Novel Ways of Understanding Chemical Space Applied to Screening Library Design

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1st Year PhD Talk

Identifying novel compounds for medicinal use is difficult due to the vast size of chemically accessible space (approximately 10^60). Therefore, the analysis of previous biological screens can be useful to understand how to empirically inform library design in exploring and identifying relevant areas of chemical space. The main objective of the study is to perform a time-course-analysis of the relationship between chemical structures and biological activities. The present work summarises the outcome of analysing ChEMBL-20, by extracting the compound (activities of <=100nM)-target annotations and calculating their physicochemical properties, Murkco Scaffolds and labelling their target classes for comparison over their published years. This was completed for the purpose of identify trends in physicochemical properties (including molecular weight (MW)). Additionally, the number of compounds and scaffolds associated with a particular target class (enzyme, GPC Rs, kinases, transporters, ion channels, nuclear hormone receptors and other) has been investigated. This analysis shows that the physicochemical properties of compounds analysed have become tighter around the median value. The number of molecules that are associated with GPC Rs and kinases increased over time and became the target classes with the greatest number of associations since 2004 and 2013 respectively. Several scaffolds are particularly popular from 2000, such as simple ones like benzene or more complex such as that of Staurosporine frequently used in 2009 which potentially reduces the scaffold diversity in those years (for instance, in 2000 where only 9% of scaffolds associated with ion channels were unique). Despite the large compound variation, there has been a greater understanding of what makes a compound drug-like, leading to properties becoming tighter around their median values. Target class popularity has changed from 2000 onwards and scaffold uniqueness varies throughout the years.

This talk is part of the Theoretical Chemistry Informal Seminars series.

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