Development of molecular hydrogen-bonding potentials (MHBPs) and their application to structure-permeation relations

J Mol Graph Model. 2001;19(6):521-35, 594-7. doi: 10.1016/s1093-3263(00)00105-4.


Hydrogen bonds are major forces of recognition in biochemistry and molecular pharmacology; they are an essential component of intermolecular interactions and determine to a significant extent the 3D-structure of bio-macromolecules. To explore three-dimensional H-bonding properties, a new tool called Molecular Hydrogen-Bonding Potentials (MHBPs) was created. The development of this tool is based on a stepwise procedure similar to the one used successfully to generate the Molecular Lipophilicity Potential (MLP). First, a H-bonding fragmental system was developed starting from published solvatochromic parameters. An atomic H-bonding donor fragmental value (alpha) is associated to each hydrogen atom in a polar moiety. Similarly, an atomic H-bonding acceptor fragmental value (beta) is associated to each polar atom. A distance function and an angle function were defined to take into account variations of the MHBPs in space. The fragmental system and the geometric functions were then combined to generate the MHBPs. These are calculated at each point of an adequate molecular surface or on a three-dimensional grid. The MHBPs were compared with GRID interactions energies and correlated with success to oral drug absorption data. Available examples demonstrate that the MHBPs are a promising computational tool in drug design. Their combination with CoMFA and VolSurf is being studied.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Energy Transfer
  • Hydrogen Bonding*
  • Hydrogen-Ion Concentration
  • Mathematical Computing
  • Molecular Structure
  • Software
  • Structure-Activity Relationship