ZINC Biogenic Libraries

Biogenic and Biogenic-like libraries in ZINC.

We have created screening libraries based on molecules of biological origin. To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of biogenic molecules. These libraries are inspired by the argument in |Hert et al NCB 2008, we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries. We are also inspired by the Dortmund and Broad/Harvard groups working in the areas of natural products and nature-inspired compounds.

Assembly

• 1. All biogenic compounds from public sources. The purchasable version of this is subset 98. Zbc - ZINC Biogenic compounds.
• 2. Tanimoto 80% similarity or better to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits.
• 3. We fragment Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration. type 2 and 3 fragmentation). We retain only ring systems of 10 or more atoms and then accept compounds having Tanimoto 80% similarity or better (rdkit 2048 pathbased) to any Biogenic 10+ atom fragment thus calculated.

Results

• Subsets are organized into lead-like, fragment-like, drug-like, all, and shard-like subsets as usual, for both biogenic and biogenic like. These are called Zbc - ZINC Biogenic compounds and Zni - ZINC Nature Inspired. We made these names deliberately different for clarity. Zbc compounds are produced by nature, and nature has been seeing them for evolutionary time. Zni - nature inspired - include both natural and compounds that look natural, when you have your Tanimoto 80% glasses on.

Inspiration

Hert, Dortmund Group, Broad/Harvard Group.