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Continuous indicator fields: a novel universal type of molecular fields

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Abstract

A novel type of molecular fields, Continuous Indicator Fields (CIFs), is suggested to provide 3D structural description of molecules. The values of CIFs are calculated as the degree to which a point with given 3D coordinates belongs to an atom of a certain type. They can be used similarly to standard physicochemical fields for building 3D structure–activity models. One can build CIF-based 3D structure–activity models in the framework of the continuous molecular fields approach described earlier (J Comput-Aided Mol Des 27 (5):427–442, 2013) for the case of physicochemical molecular fields. CIFs are thought to complement and further extend traditional physicochemical fields. The models built with CIFs can be interpreted in terms of preferable and undesirable positions of certain types of atoms in space. This helps to understand which changes in chemical structure should be made in order to design a compound possessing desirable properties. We have demonstrated that CIFs can be considered as 3D analogues of 2D topological molecular fragments. The performance of this approach is demonstrated in structure–activity studies of thrombin inhibitors, multidentate N-heterocyclic ligands for Am3+/Eu3+ separation, and coloring dyes.

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Acknowledgments

This work was supported by Russian Foundation for Basic Research (Grant 13-07-00511).The work is performed according to the Russian Government Program of Competitive Growth of Kazan Federal University.

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Authors and Affiliations

  1. A.N.Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991, Moscow, Russia

    Gleb V. Sitnikov

  2. Faculty of Physics, M.V.Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russia

    Nelly I. Zhokhova & Igor I. Baskin

  3. Department of Chemistry, M.V.Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russia

    Yury A. Ustynyuk

  4. Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, 1 rue Blaise Pascal, 67000, Strasbourg, France

    Gleb V. Sitnikov & Alexandre Varnek

  5. Kazan (Volga River) Federal University, ul. Kremlevskaya 18, 420008, Kazan, Tatarstan, Russia

    Igor I. Baskin

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  1. Gleb V. Sitnikov
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  2. Nelly I. Zhokhova
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Correspondence to Igor I. Baskin.

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Sitnikov, G.V., Zhokhova, N.I., Ustynyuk, Y.A. et al. Continuous indicator fields: a novel universal type of molecular fields. J Comput Aided Mol Des 29, 233–247 (2015). https://doi.org/10.1007/s10822-014-9818-z

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