MedChem Studio™

Advanced data mining and molecule design

Design Module

What is the Design Module?

The Design Module in MedChem Studio provides:

  • Functionality to encode and explode combinatorial chemistry reactions:
    • Powerful, customizable engine allows specification of complex reactions and transformations in SMIRKS and ISIS/Draw™ formats
  • Generate structural analogs of a lead molecule to help guide lead evolution
  • Perform R-group explosion to created missing compounds in an R-Table matrix


Structural Analog Generation

MedChem Studio provides functionality to perform de novo generation of new structures by applying rule-based transforms:

  • Generate analogs by applying structural transformation rules to an existing lead molecule. By default, MedChem Studio uses a set of 120 rules designed in collaboration with medicinal chemists, but the rules can be customized by you
  • Use common bioisoteric rules to generate products
  • Rules can be applied multiple times
  • Easily apply structural filters to eliminate unwanted products
  • Generate analogs of a lead molecule by replacing its scaffold with one or more drug-like fragments from a database (“scaffold hopping”). Each new molecule preserves the original groups, along with the bond distances between R-group attachment points

R Table Explosion

MedChem Studio can combine every R group with all other R groups to create a large number of virtual products:

  • Empty cells in an R table represent new molecules – the R table Exploder can generate them automatically
  • Because all new molecules use only groups that have already been synthesized at each R position, the new molecules are likely to be synthetically feasible
  • Potencies/properties of new molecules can be easily predicted and filtered to prioritize chemical synthesis

Regardless of which approach you use to design your molecules, when combining the Design Module with the powerful ADMET Risk™ scoring function in ADMET Predictor™ (independently judged the most accurate property prediction software in the industry), MedChem Studio lets you ‘see’ in many-dimensional space to optimize molecules not only for activity, but also to ensure that physicochemical, biopharmaceutical, metabolism, and toxicity properties are also acceptable.