A Telescope for Chemical Space: SpaceProp2 is out

Chemical fragment spaces implement make-on-demand catalogs like Enamine REAL, eXplore by eMolecules, or the most recent AMBrosia by Ambinter in a highly efficient way. But what do we know about these super-large collections encoded? In contrast to enumerated libraries, already the calculation of property histograms gets quite tricky. We just published our next generation SpaceProp2 analysis tool in JCIM which is able to give some answers. Besides histograms for molecular weight, clogP, H-bond acceptor and donor counts, we were able to extend the list of properties by the number of rotatable bonds and topological polar surface area. For the first time, we show a comparison to one of the largest pharma inhouse spaces, BICLAIM. Furthermore, SpaceProp2 can calculate distributions of SMARTS patterns (no recursions, sorry) in spaces. We exemplify this feature by showing numbers for a collection of 141 potential electrophilic warheads. Applause goes to Justin Lübbers who implemented SpaceProp2 and has done the experiments together with Uta Lessel. Big thanks to 勃林格殷格翰 for collaboration and enabling this research. SpaceProp2 is part of our NAOMI software library available for free for academic research purposes.