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    QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?
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    Computational & Structural Chemistry, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom, and Department of Chemistry, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
    * Corresponding author phone: +44 (0)1438 768682; fax: +44 (0) 1438 763352; e-mail: [email protected]
    †GlaxoSmithKline Medicines Research Centre.
    ‡King Mongkut’s Institute of Technology Ladkrabang.
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    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2009, 49, 3, 670–677
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    https://doi.org/10.1021/ci800419j
    Published February 13, 2009
    Copyright © 2009 American Chemical Society
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    Abstract

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    Herein we investigate whether QM/MM could prove useful as a tool to study the often subtle binding phenomena found within pharmaceutical drug discovery programs. The goal of this investigation is to determine whether it is possible to employ high level QM/MM calculations to answer specific questions around a binding event in a cycle time that is aligned with medicinal chemistry synthesis. To this end QM/MM calculations have been performed on four protein kinase-ligand complexes using five different levels of theory, using standard hardware, in an effort to assess their utility. We conclude that the accuracy and turnaround time of such calculations mean they could prove valuable to (1) probe the subtle nature of the interactions within protein active sites, (2) facilitate the interpretation of poorly resolved electron density, and (3) study the impact of substituent changes on the binding conformation or in the assessment of alternate scaffolds. In practice, the successful application of such methods will be limited by the size of the system under investigation, the level of theory used, and whether there is a need for conformational sampling.

    Copyright © 2009 American Chemical Society

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    Cite this: J. Chem. Inf. Model. 2009, 49, 3, 670–677
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ci800419j
    Published February 13, 2009
    Copyright © 2009 American Chemical Society
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