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Quantifying hydrogen bonding in QSAR and molecular modeling.

O A Raevsky1, V S Skvortsov

  • 1Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds, The Russian Academy of Sciences, Chernogolovka, 142432, Moscow, Russia. raevsky@ipac.ac.ru

SAR and QSAR in Environmental Research
|April 5, 2005
PubMed
Summary

New hydrogen bonding descriptors improve drug modeling accuracy. Incorporating experimental thermodynamics is crucial for quantitative structure-activity relationship (QSAR) and molecular modeling, enhancing predictions of drug absorption.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Pharmacokinetics

Background:

  • Quantitative descriptions of hydrogen bonding are vital for QSAR and molecular modeling.
  • Existing descriptors like polar surface area (PSA) may not fully capture H-bonding capabilities.

Purpose of the Study:

  • To analyze and propose new H-bond descriptors for improved molecular modeling.
  • To verify the utility of new and existing descriptors using human intestinal absorption data.

Main Methods:

  • Development of ten new H-bond surface and enthalpy integral descriptors.
  • Validation of descriptors using a dataset of 154 drugs with known human intestinal absorption.

Main Results:

  • Traditional descriptors (e.g., H-bond acceptor/donor counts, PSA) showed limitations in describing H-bonding ability.

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  • New descriptors directly related to experimental hydrogen bonding thermodynamics proved necessary for successful modeling.

    • Conclusions:

    • Directly incorporating experimental thermodynamic data of hydrogen bonding enhances molecular modeling accuracy.
    • The proposed H-bond descriptors offer a more robust approach for QSAR and drug design.