QSAR4U

Chemoinformatics tools

Institute of Molecular and Translational Medicine, Palacky University

Publications

(only written in English)

Book chapters

  1. Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N.; Ognichenko, L. N.; Hromov, A. I.; Liahovskij, A. V.; Polischuk, P. G., The Hierarchic Informational Technology for QSAR Investigations. Molecular Design of Antiviral Compounds In National Institute of Allergy and Infectious Diseases, National Institutes of Health: Frontiers in Research, Georgiev, V. S.; Western, K. A.; McGowan, J. J., Eds. Humana Press: Totowa, 2008; Vol. 1, pp 163-177.

  2. Kuz’min, V. E.; Artemenko, A. G.; Muratov, E. N.; Polischuk, P. G.; Ognichenko, L. N.; Liahovsky, A. V.; Hromov, A. I.; Varlamova, E. V., Virtual screening and molecular design based on hierarchical QSAR technology. In Recent Advances in QSAR Studies, T. Puzyn, J. L., M. Cronin, Ed. Springer: London, 2010; pp 127-176.

  3. Ognichenko, L. N.; Kuz'min, V. E.; Gorb, L.; Muratov, E. N.; Artemenko, А. G.; Kovdienko, N. A.; Polishchuk, P. G.; Hill, F. C.; Leszczynski, J., New Advances in QSPR/QSAR Analysis of Nitrocompounds: Solubility, Lipophilicity and Toxicity. In Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends, Leszczynski, J.; Shukla, M. K., Eds. Springer: 2012; pp 279-334.

  4. Golovenko, N. Y.; Borisyuk, I. Y.; Kulinskiy, М. А.; Polishchuk, P. G.; Мuratov, E. N.; Кuzmin, V. Е., Quantitative structure-pharmacokinetic relationships of drugs within the framework of biopharmaceutics classification system by using simplex representation of molecular structure. In Applications of Computational Techniques in Pharmacy and Medicine, Gorb, L.; Kuz’min, V.; Muratov, E., Eds. Springer: 2014; pp 461-500.

  5. Polishchuk, P.; Mokshyna, E.; Kosinskaya, A.; Muats, A.; Kulinsky, M.; Tinkov, O.; Ognichenko, L.; Khristova, T.; Artemenko, A.; Kuz’min, V., Structural, Physicochemical and Stereochemical Interpretation of QSAR Models Based on Simplex Representation of Molecular Structure. In Advances in QSAR Modeling: Applications in Pharmaceutical, Chemical, Food, Agricultural and Environmental Sciences, Roy, K., Ed. Springer International Publishing: Cham, 2017; pp 107-147.

Articles:

  1. Kuz’min, V. E.; Artemenko, A. G.; Polischuk, P. G.; Muratov, E. N.; Khromov, A. I.; Liahovskiy, A. V.; Andronati, S. A.; Makan, S. Y., Hierarchic System of QSAR Models (1D-4D) on the Base of Simplex Representation of Molecular Structure Journal of Molecular Modelling 2005, 11, 457-467. (http://dx.doi.org/10.1007/s00894-005-0237-x)

  2. Kuz’min, V. E.; Polischuk, P. G.; Artemenko, A. G.; Makan, S. Y.; Andronati, S. A., Quantitative structure-affinity relationship of 5-HT1A receptor ligands by the classification tree method SAR & QSAR in Environmental Research 2008, 19, 213-244. (http://www.tandfonline.com/doi/abs/10.1080/10629360802085090#)

  3. Polischuk, P. G.; Muratov, E. N.; Artemenko, A. G.; Kolumbin, O. G.; Muratov, N. N.; Kuz'min, V. E., Application of Random Forest method to QSAR prediction of aquatic toxicity. Journal of Chemical Information and Modeling 2009, 49, 2481-2488. (http://dx.doi.org/10.1021/ci900203n)

  4. Kovdienko, N. A.; Polishchuk, P. G.; Muratov, E. N.; Artemenko, A. G.; Kuz’min, V. E.; Gorb, L.; Hill, F.; Leszczynski, J., Application of Random Forest and Multiple Linear Regression Techniques to QSPR Prediction of an Aqueous Solubility for Military Compounds. Molecular Informatics 2010, 29, 394-406. (http://dx.doi.org/10.1002/minf.201000001)

  5. Muratov, E. N.; Artemenko, A. G.; Varlamova, E. V.; Polischuk, P. G.; Lozitsky, V. P.; Fedtchuk, A. S.; Lozitska, R. L.; Gridina, T. L.; Koroleva, L. S.; Sil'nikov, V. N.; Galabov, A. S.; Makarov, V. A.; Riabova, O. B.; Wutzler, P.; Schmidtke, M.; Kuz’min, V. E., Per aspera ad astra: application of Simplex QSAR approach in antiviral research. Future Medicinal Chemistry 2010, 2, 1205-1226. (http://dx.doi.org/10.4155/fmc.10.194)

  6. Sushko, I.; Novotarskyi, S.; Korner, R.; Pandey, A. K.; Cherkasov, A.; Li, J.; Gramatica, P.; Hansen, K.; Schroeter, T.; Muller, K.; Xi, L.; Liu, H.; Yao, X.; Oberg, T.; Hormozdiari, F.; Dao, P.; Sahinalp, C.; Todeschini, R.; Polishchuk, P.; Artemenko, A.; Kuz’min, V.; Martin, T. M.; Young, D. M.; Fourches, D.; Muratov, E.; Tropsha, A.; Baskin, I.; Horvath, D.; Marcou, G.; Muller, C.; Varnek, A.; Prokopenko, V. V.; Tetko, I. V., Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. Journal of Chemical Information and Modeling 2010, 50, 2094–2111. (http://dx.doi.org/10.1021/ci100253r)

  7. Krysko, A. A.; Samoylenko, G. V.; Polishchuk, P. G.; Andronati, S. A.; Kabanova, T. A.; Khristova, T. M.; Kuz'min, V. E.; Kabanov, V. M.; Krysko, O. L.; Varnek, A. A.; Grygorash, R. Y., RGD mimetics containing phthalimidine fragment, novel ligands of fibrinogen receptor. Bioorganic & Medicinal Chemistry Letters 2011, 21, 5971–5974. (http://dx.doi.org/10.1016/j.bmcl.2011.07.063)

  8. Kuz’min, V. E.; Polishchuk, P. G.; Artemenko, A. G.; Andronati, S. A., Interpretation of QSAR models based on Random Forest method. Molecular Informatics 2011, 30, 593-603. (http://dx.doi.org/10.1002/minf.201000173)

  9. Muratov, E. N.; Varlamova, E. V.; Artemenko, A. G.; Polishchuk, P. G.; Kuz’min, V. E., Existing and Developing Approaches for QSAR Analysis of Mixtures. Molecular Informatics 2012, 31, 202-221. (http://dx.doi.org/10.1002/minf.201100129)

  10. Ognichenko, L. N.; Kuz’min, V. E.; Gorb, L.; Hill, F. C.; Artemenko, A. G.; Polischuk, P. G.; Leszczynski, J., QSPR Prediction of Lipophilicity for Organic Compounds Using Random Forest Technique on the Basis of Simplex Representation of Molecular Structure. Molecular Informatics 2012, 31, 273-280. (http://dx.doi.org/10.1002/minf.201100102)

  11. Oprisiu, I.; Varlamova, E.; Muratov, E.; Artemenko, A.; Marcou, G.; Polishchuk, P.; Kuz'min, V.; Varnek, A., QSPR Approach to Predict Nonadditive Properties of Mixtures. Application to Bubble Point Temperatures of Binary Mixtures of Liquids. Molecular Informatics 2012, 31, 491-502. (http://dx.doi.org/10.1002/minf.201200006)

  12. Kolumbin, O. G.; Ognichenko, L. N.; Artemenko, A. G.; Polischuk, P. G.; Kulinsky, М. A.; Мuratov, Е. N.; Kuz’min, V. E.; Bobeica, V. A., Nonexperimental screening of the water solubility, lipophilicity, bioavailability, mutagenicity and toxicity of various pesticides with QSAR models aid. Chemistry Journal of Moldova. General, Industrial and Ecological Chemistry. 2013, 8, 95-100. (http://www.cjm.asm.md/node/237)

  13. Krysko, A. A.; Samoylenko, G. V.; Polishchuk, P. G.; Fonari, M. S.; Kravtsov, V. C.; Andronati, S. A.; Kabanova, T. A.; Lipkowski, J.; Khristova, T. M.; Kuz’min, V. E.; Kabanov, V. M.; Krysko, O. L.; Varnek, A. A., Synthesis, biological evaluation, X-ray molecular structure and molecular docking studies of RGD mimetics containing 6-amino-2,3-dihydroisoindolin-1-one fragment as ligands of integrin αIIbβ3. Bioorganic & Medicinal Chemistry 2013, 21, 4646-4661. (http://dx.doi.org/10.1016/j.bmc.2013.05.019)

  14. Muratov, E. N.; Varlamova, E. V.; Artemenko, A. G.; Polishchuk, P. G.; Nikolaeva-Glomb, L.; Galabov, A. S.; Kuz’min, V. E., QSAR analysis of poliovirus inhibition by dual combinations of antivirals. Structural Chemistry 2013, 24, 1665-1679. (http://dx.doi.org/10.1007/s11224-012-0195-8)

  15. Polishchuk, P. G.; Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N., Universal Approach for Structural Interpretation of QSAR/QSPR Models. Molecular Informatics 2013, 32, 843-853. (http://dx.doi.org/10.1002/minf.201300029)

  16. Polishchuk, P. G.; Madzhidov, T. I.; Varnek, A., Estimation of the size of drug-like chemical space based on GDB-17 data. Journal of Computer-Aided Molecular Design 2013, 27, 675-679. (http://dx.doi.org/10.1007/s10822-013-9672-4)

  17. Madzhidov, T. I.; Polishchuk, P. G.; Nugmanov, R. I.; Bodrov, A. V.; Lin, A. I.; Baskin, I. I.; Varnek, A. A.; Antipin, I. S., Structure-Reactivity Relationships in Terms of the Condensed Graphs of Reactions Russian Journal of Organic Chemistry 2014, 50, 459-463. (http://dx.doi.org/10.1134/S1070428014040010)

  18. Mokshyna, E.; Nedostup, V. I.; Polischuk, P. G.; Kuzmin, V. E., ‘Quasi-Mixture’ Descriptors for QSPR Analysis of Molecular Macroscopic Properties. The Critical Properties of Organic Compounds. Molecular Informatics 2014, 33, 647-654. (http://dx.doi.org/10.1002/minf.201400036)

  19. Mokshyna, E.; Polishchuk, P. G.; Nedostup, V. I.; Kuzmin, V. E., Predictive QSPR Modelling for the Second Virial Coefficient of the Pure Organic Compounds. Molecular Informatics 2015, 34, 53-59. (http://dx.doi.org/10.1002/minf.201400081)

  20. Polishchuk, P. G.; Samoylenko, G. V.; Khristova, T. M.; Krysko, O. L.; Kabanova, T. A.; Kabanov, V. M.; Kornylov, A. Y.; Klimchuk, O.; Langer, T.; Andronati, S. A.; Kuz’min, V. E.; Krysko, A. A.; Varnek, A., Design, Virtual Screening, and Synthesis of Antagonists of αIIbβ3 as Antiplatelet Agents. Journal of Medicinal Chemistry 2015, 58, 7681-7694. (http://dx.doi.org/10.1021/acs.jmedchem.5b00865)

  21. Tin’kov, O. V.; Polishchuk, P. G.; Artemenko, A. G.; Kuz’min, V. E., QSAR Investigation of Acute Toxicity of Organic Acids and their Derivatives Upon Intraperitoneal Injection in Mice. Pharmaceutical Chemistry Journal 2015, 49, 104-110. (http://dx.doi.org/10.1007/s11094-015-1231-y)

  22. Klimenko, K.; Kuz'min, V.; Ognichenko, L.; Gorb, L.; Shukla, M.; Vinas, N.; Perkins, E.; Polishchuk, P.; Artemenko, A.; Leszczynski, J., Novel enhanced applications of QSPR models: Temperature dependence of aqueous solubility. Journal of Computational Chemistry 2016, 37, 2045-2051. (http://dx.doi.org/10.1002/jcc.24424)

  23. Krysko, A. A.; Kornylov, A. Y.; Polishchuk, P. G.; Samoylenko, G. V.; Krysko, O. L.; Kabanova, T. A.; Kravtsov, V. C.; Kabanov, V. M.; Wicher, B.; Andronati, S. A., Synthesis, biological evaluation and molecular docking studies of 2-piperazin-1-yl-quinazolines as platelet aggregation inhibitors and ligands of integrin αIIbβ3. Bioorganic & Medicinal Chemistry Letters 2016, 26, 1839-1843. (http://dx.doi.org/10.1016/j.bmcl.2016.02.011)

  24. Mokshyna, E.; Polishchuk, P.; Nedostup, V.; Kuz'min, V., QSPR-Modeling for the Second Virial Cross-Coefficients of Binary Organic Mixtures. International Journal of Quantitative Structure-Property Relationships (IJQSPR) 2016, 1, 72-84. (http://dx.doi.org/10.4018/ijqspr.2016070104)

  25. Polishchuk, P.; Tinkov, O.; Khristova, T.; Ognichenko, L.; Kosinskaya, A.; Varnek, A.; Kuz’min, V., Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis. Journal of Chemical Information and Modeling 2016, 56, 1455-1469. (http://dx.doi.org/10.1021/acs.jcim.6b00371)

  26. Klimenko, K.; Lyakhov, S.; Shibinskaya, M.; Karpenko, A.; Marcou, G.; Horvath, D.; Zenkova, M.; Goncharova, E.; Amirkhanov, R.; Krysko, A.; Andronati, S.; Levandovskiy, I.; Polishchuk, P.; Kuz'min, V.; Varnek, A., Virtual screening, synthesis and biological evaluation of DNA intercalating antiviral agents. Bioorganic & Medicinal Chemistry Letters 2017, 27, 3915-3919. (https://doi.org/10.1016/j.bmcl.2017.06.035)

  27. Polishchuk, P., Interpretation of Quantitative Structure–Activity Relationship Models: Past, Present, and Future. Journal of Chemical Information and Modeling 2017, 57, 2618-2639. (http://dx.doi.org/10.1021/acs.jcim.7b00274)

  28. Polishchuk, P.; Madzhidov, T.; Gimadiev, T.; Bodrov, A.; Nugmanov, R.; Varnek, A., Structure–reactivity modeling using mixture-based representation of chemical reactions. Journal of Computer-Aided Molecular Design 2017, 31, 829-839. (http://dx.doi.org/10.1007/s10822-017-0044-3)

  29. Polishchuk, P. G.; Kosinskaya, A. P.; Larionov, V. B.; Ognichenko, L. N.; Kuz’min, V. E.; Golovenko, N. Y., A Ranged Series of Drug Molecule Fragments Defining Their Neuroavailability. Pharmaceutical Chemistry Journal 2017, 51, 35-38. (10.1007/s11094-017-1553-z)

  30. Kutlushina, A.; Khakimova, A.; Madzhidov, T.; Polishchuk, P., Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures. Molecules 2018, 23, 3094. (https://doi.org/10.3390/molecules23123094)

  31. Matveieva, M.; Cronin, M. T. D.; Polishchuk, P., Interpretation of QSAR Models: Mining Structural Patterns Taking into Account Molecular Context. Molecular Informatics 2018, 38, 1800084. (https://doi.org/10.1002/minf.201800084)

  32. Gimadiev, T.; Madzhidov, T.; Tetko, I.; Nugmanov, R.; Casciuc, I.; Klimchuk, O.; Bodrov, A.; Polishchuk, P.; Antipin, I.; Varnek, A., Bimolecular Nucleophilic Substitution Reactions: Predictive Models for Rate Constants and Molecular Reaction Pairs Analysis. Molecular Informatics 2019, 38, 115032. (http://dx.doi.org/10.1002/minf.201800104)

  33. Nowikow, C.; Fuerst, R.; Kauderer, M.; Dank, C.; Schmid, W.; Hajduch, M.; Rehulka, J.; Gurska, S.; Mokshyna, O.; Polishchuk, P.; Zupkó, I.; Dzubak, P.; Rinner, U., Synthesis and biological evaluation of cis-restrained carbocyclic combretastatin A-4 analogs: Influence of the ring size and saturation on cytotoxic properties. Bioorganic & Medicinal Chemistry 2019, 27, 115032. (https://doi.org/10.1016/j.bmc.2019.07.048)

  34. Polishchuk, P.; Kutlushina, A.; Bashirova, D.; Mokshyna, O.; Madzhidov, T., Virtual Screening Using Pharmacophore Models Retrieved from Molecular Dynamic Simulations. International Journal of Molecular Sciences 2019, 20, 5834. (https://dx.doi.org/10.3390/ijms20235834)

  35. Tinkov, O. V.; Grigorev, V. Y.; Polishchuk, P. G.; Yarkov, A. V.; Raevsky, O. A., QSAR investigation of acute toxicity of organic compounds during oral administration to mice. Biomeditsinskaya Khimiya 2019, 65, 123-132. (http://dx.doi.org/10.18097/PBMC20196502123)

  36. Tinkov, O. V.; Polishchuk, P. G.; Khachatryan, D. S.; Kolotaev, A. V.; Balaev, A. N.; Osipov, V. N.; Grigorev, B. Y., Quantitative analysis of "structure - anticancer activity" and rational molecular design of bi-functional VEGFR-2/HDAC inhibitors. Computer Research and Modeling 2019, 11, 911-930. (https://dx.doi.org/10.20537/2076-7633-2019-11-5-911-930)

  37. Madzhidov, T. I.; Rakhimbekova, A.; Kutlushuna, A.; Polishchuk, P., Probabilistic Approach for Virtual Screening Based on Multiple Pharmacophores. Molecules 2020, 25, 385. (https://doi.org/10.3390/molecules25020385)

  38. Polishchuk, P., CReM: chemically reasonable mutations framework for structure generation. Journal of Cheminformatics 2020, 12, 28. (https://doi.org/10.1186/s13321-020-00431-w)

  39. Polishchuk, P., Control of Synthetic Feasibility of Compounds Generated with CReM. Journal of Chemical Information and Modeling 2020, 60, 6074-6080. (https://dx.doi.org/10.1021/acs.jcim.0c00792)

  40. Schadich, E.; Kryshchyshyn-Dylevych, A.; Holota, S.; Polishchuk, P.; Džubak, P.; Gurska, S.; Hajduch, M.; Lesyk, R., Assessing different thiazolidine and thiazole based compounds as antileishmanial scaffolds. Bioorganic & Medicinal Chemistry Letters 2020, 30, 127616. (https://doi.org/10.1016/j.bmcl.2020.127616)

  41. Tinkov, O.; Polishchuk, P.; Matveieva, M.; Grigorev, V.; Grigoreva, L.; Porozov, Y., The Influence of Structural Patterns on Acute Aquatic Toxicity of Organic Compounds. Molecular Informatics 2020, n/a. (https://dx.doi.org/10.1002/minf.202000209)

  42. Zankov, D. V.; Shevelev, M. D.; Nikonenko, A. V.; Polishchuk, P. G.; Rakhimbekova, A. I.; Madzhidov, T. I., Multi-instance Learning for Structure-Activity Modeling for Molecular Properties. In Analysis of Images, Social Networks and Texts. AIST 2019. Communications in Computer and Information Science, van der Aalst, W. M. P.; Batagelj, V.; Ignatov, D. I.; Khachay, M.; Kuskova, V.; Kutuzov, A.; Kuznetsov, S. O.; Lomazova, I. A.; Loukachevitch, N.; Napoli, A.; Pardalos, P. M.; Pelillo, M.; Savchenko, A. V.; Tutubalina, E., Eds. Springer International Publishing: Cham, 2020; Vol. 1086, pp 62-71. (https://doi.org/10.1007/978-3-030-39575-9_7)

© Pavel Polishchuk 2010-2019