Ligand linking and joining

Identify linkers, from real chemistry, to join two ligands using bioisostere replacement in Spark

Identify linkers to join your ligands

Many drug targets hold multiple binding areas within their protein active site. In situations where two ligands or fragments have been identified at adjacent binding sites, Spark’s ‘Join Two Ligands’ experiment enables design scientists to find a suitable linker and form a larger molecule that combines the binding interactions of the two starter structures.

  • Upload the two starting ligands, and define the region of each molecule to be replaced by a linker
  • Find suitable fragments, from a large collection of chemical databases, with the right number of connection points and correct geometry to the starter molecules
  • Merge the fragments to form the product structures and score these based on their electrostatic similarity and shape to the starting molecules

Visually meaningful analysis of results

Once the calculation is complete, the diverse collection of novel results produced by Spark will be displayed. These results show the scored fragments alongside additional information and property-based coloring to facilitate results triaging and prioritization. Spark results can be visualized in three different modes, each offering different views and groupings of molecular data.

Results can also be exported into our CADD platform Flare™ to help you prioritize, via a wide portfolio of ideas and methods, the best molecules to make.

View poster: 'Effective methods for fragment growing, joining, and cyclization'

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