Molecular Diversity

, Volume 10, Issue 3, pp 341–347 | Cite as

Scoring of KDR Kinase Inhibitors: Using Interaction Energy as a Guide for Ranking

  • Georgia B. McGaughey
  • J. Chris Culberson
  • Bradley P. Feuston
  • Constantine Kreatsoulas
  • Vladimir Maiorov
  • Joseph Shpungin
Full–length Paper


Within a congeneric series of ATP-competitive KDR kinase inhibitors, we determined that the IC50 values, which span four orders of magnitude, correlated best with the calculated ligand-protein interaction energy using the Merck Molecular Force Field (MMFFs(94)). Using the ligand-protein interaction energy as a guide, we outline a workflow to rank order virtual KDR kinase inhibitors prior to synthesis. When structural information of the target is available, the ability to score molecules a priori can be used to rationally select reagents. Our implementation allows one to select thousands of readily available reagents, enumerate compounds in multiple poses and score molecules in the active site of a protein within a few hours. In our experience, virtual library enumeration is best used when a correlation between computed descriptors/properties and IC50 or K i values has been established.

Key words

KDR kinase scoring virtual library enumeration Merck Molecular Force Field 


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Georgia B. McGaughey
    • 1
  • J. Chris Culberson
    • 1
  • Bradley P. Feuston
    • 1
  • Constantine Kreatsoulas
    • 1
  • Vladimir Maiorov
    • 2
  • Joseph Shpungin
    • 2
  1. 1.Molecular SystemsWest PointUSA
  2. 2.RahwayUSA

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