Chemistry of Heterocyclic Compounds

, Volume 50, Issue 3, pp 444–457 | Cite as

Prediction of the Biological Activity Spectra of Organic Compounds Using the Pass Online Web Resource

  • D. A. Filimonov
  • A. A. Lagunin
  • T. A. Gloriozova
  • A. V. Rudik
  • D. S. Druzhilovskii
  • P. V. Pogodin
  • V. V. Poroikov
Article

The freely accessible web resource PASS Online is presented. This resource is designed for the prediction of the biological activity spectra of organic compounds based on their structural formulas for more than 4000 types of biological activity with average accuracy above 95% (http://www.way2drug.com/passonline). The prediction is based on an analysis of the structure-activity relationships in the training set containing information on the structure and biological activity of more than 300000 organic compounds. The possibilities and limitations of this approach are described. Recommendations are given for interpreting the prediction results. Examples are given for the practical use of the PASS Online web resource in order to establish priorities for chemical synthesis and biological testing of substances on the basis of prediction results. The further trends are considered for the using PASS Online as an Internet platform for joint projects of academic researchers for the search and development of new pharmaceutical agents.

Keywords

PASS Online biological activity computer prediction organic compounds pharmacologically active compounds web resource 

Supplementary material

10593_2014_1496_MOESM1_ESM.pdf (864 kb)
ESM 1(PDF 864 kb)

References

  1. 1.
  2. 2.
    L. Ruddigkeit, L. C. Blum, and J.-L. Reymond, J. Chem. Inf. Model., 53, 56 (2013).CrossRefGoogle Scholar
  3. 3.
    Thomson Reuters Integrity SM, http://integrity.thomson-pharma.com.
  4. 4.
    A. L. Hopkins, Nat. Chem. Biol., 4, 682 (2008).CrossRefGoogle Scholar
  5. 5.
    R. Morphy and Z. Rankovic, J. Med. Chem., 49, 4961 (2006).CrossRefGoogle Scholar
  6. 6.
    I. M. Kapetanovic, Chem.-Biol. Interact., 171, 165 (2008).CrossRefGoogle Scholar
  7. 7.
    C. G. Wermuth (editor), The Practice of Medicinal Chemistry, Third Edition, Academic Press, San Diego (2008).Google Scholar
  8. 8.
    C. Hansch, Acc. Chem. Res., 26, 147 (1993).CrossRefGoogle Scholar
  9. 9.
    R. Franke, Theoretical Drug Design Methods, Akademie-Verlag, Berlin (1984), p. 382.Google Scholar
  10. 10.
    V. V. Avidon, Khim.-Farm. Zh., 8, 22 (1974).Google Scholar
  11. 11.
    V. V. Avidon and V. S. Arolovich, Nauchno-Tekhnicheskaya Informatsiya, Ser. 2, No. 5, 26 (1975).Google Scholar
  12. 12.
    V. V. Avidon, V. S. Arolovich, V. G. Blinova, S. P. Kozlova, and A. M. Freidina, Khim.-Farm. Zh., 17, 321 (1983).Google Scholar
  13. 13.
    V. V. Avidon, V. S. Arolovich, S. P. Kozlova, and L. A. Piruzyan, Khim.-Farm. Zh., 12, No. 5, 88 (1978).Google Scholar
  14. 14.
    V. V. Avidon, V. S. Arolovich, S. P. Kozlova, and L. A. Piruzyan, Khim.-Farm. Zh., 12, No. 6, 99 (1978).Google Scholar
  15. 15.
    V. E. Golender and A. B. Rozenblit, Avtomatika i Telemekhanika, 11, 99 (1974).Google Scholar
  16. 16.
    V. E. Golender and A. B. Rozenblit, Computer Methods for Drug Design [in Russian], Zinatne, Riga (1978).Google Scholar
  17. 17.
    V. E. Golender and A. B. Rozenblit, Zh. Vses. Khim. Obshch. Im. D. I. Mendeleeva, 25, No. 1, 28 (1980).Google Scholar
  18. 18.
    A. B. Rozenblit and V. E. Golender, Logic-combinatorial Methods in Drug Design [in Russian], Zinatne, Riga (1984).Google Scholar
  19. 19.
    L. A. Piruzyan, V. V. Avidon, A. B. Rozenblit, V. S. Arolovich, V. E. Golender, S. P. Kozlova, E. M. Mikhailovskii, and E. G. Gavrishchuk, Khim.-Farm. Zh., 11, 35 (1977).Google Scholar
  20. 20.
    V. V. Avidon, I. A. Pomerantsev, V. E. Golender, and A. B. Rozenblit, J. Chem. Inf. Comput. Sci., 22, 207 (1982).CrossRefGoogle Scholar
  21. 21.
    V. V. Avidon and L. A. Leksina, Nauchno-Tekhnicheskaya Informatsiya, Ser. 2, No. 3, 22 (1975).Google Scholar
  22. 22.
    N. Veretennikova, A. Skorova, V. Kudryashova, A. Rozenblit, A. Barkans, Ya. Betinsh, V. Drboglav, L. Gitlina, Ya. Grinfelds, P. Mellis, D. Petersone, and V. Shatokhin, in: F. Chen and G. Schüürmann (editors), Quantitative Structure-Activity Relationships in Environmental Sciences, SETAC, Pensacola (1997), p. 115.Google Scholar
  23. 23.
    G. M. Barenboim, L. A. Piruzyan, and A. G. Malenkov, Vestn. Akad. Nauk SSSR, No. 2, 50 (1977).Google Scholar
  24. 24.
    L. A. Piruzyan, A. G. Malenkov, and G. M. Barenboim, Chemical Aspects of Human Activities and Nature Conservation [in Russian], Preprint, Otdel. Inst. Khim. Fiz. Akad. Nauk SSSR, Chernogolovka (1979).Google Scholar
  25. 25.
    G. M. Barenboim and A. G. Malenkov, Biologically Active Compounds. New Search Principles [in Russian], Nauka, Moscow (1986).Google Scholar
  26. 26.
    Yu. V. Burov, L. V. Korol'chenko, and V. V. Poroikov, Byull. Vses. Nauchn. Tsentra po Bezopasnosti Biologicheski Aktivnykh Veshchestv, No. 1, 4 (1990).Google Scholar
  27. 27.
    V. V. Poroikov, D. A. Filimonov, and A. P. Budunova, Nauchno-tekhnicheskaya Informatsiya, Ser. 2, No. 6, 11 (1993).Google Scholar
  28. 28.
    D. A. Filimonov, V. V. Poroikov, E. I. Karaicheva, R. K. Kazaryan, A. P. Budunova, E. M. Mikhailovskii, A. V. Rudnitskikh, L. V. Goncharenko, and Yu. V. Burov, Eksperimental'naya i Klinicheskaya Farmakologiya, 58, No. 2, 56 (1995).Google Scholar
  29. 29.
    D. A. Filimonov and V. V. Poroikov, in: M. G. Ford, R. Greenwood, G. T. Brooks, and R. Franke (editors), Bioactive Compound Design: Possibilities for Industrial Use, BIOS Scientific Publishers, Oxford (1996), p. 47.Google Scholar
  30. 30.
    T. A. Gloriozova, D. A. Filimonov, A. A. Lagunin, and V. V. Poroikov, Khim.-farm. Zh., 32, No. 12, 33 (1998).Google Scholar
  31. 31.
    A. V. Stepanchikova, A. A. Lagunin, D. A. Filimonov, and V. V. Poroikov, Curr. Med. Chem., 10, 225 (2003).CrossRefGoogle Scholar
  32. 32.
    D. A. Filimonov and V. V. Poroikov, Ros. Khim. Zh., L, No. 2, 66 (2006).Google Scholar
  33. 33.
    D. A. Filimonov and V. V. Poroikov, in: A. Varnek and A. Tropsha (editors), Chemoinformatics Approaches to Virtual Screening, RSC Publishing, Cambridge (2008), p. 182.CrossRefGoogle Scholar
  34. 34.
    D. A. Filimonov, V. V. Poroikov, T. A. Gloriozova, and A. A. Lagunin, Certificate for the Official Registration of the PASS Computer Program No. 2006613275, September 15, 2006 [in Russian], Federal Service for Intellectual Property, Patents, and Trademarks, Moscow.Google Scholar
  35. 35.
    D. Filimonov, V. Poroikov, Yu. Borodina, and T. Gloriozova, J. Chem. Inf. Comput. Sci., 39, 666 (1999).CrossRefGoogle Scholar
  36. 36.
    V. V. Poroikov, D. A. Filimonov, Yu. V. Borodina, A. A. Lagunin, and A. Kos, J. Chem. Inf. Comput. Sci., 40, 1349 (2000).CrossRefGoogle Scholar
  37. 37.
    V. A. Trapkov, A. P. Budunova, O. A. Burova, D. A. Filimonov, and V. V. Poroikov, Voprosy Med. Khim., 43, 39 (1997).Google Scholar
  38. 38.
    A. Geronikaki, V. Poroikov, D. Hadjipavlou-Litina, D. Filimonov, A. Lagunin, and R. Mgonzo, Quant. Struct.-Act. Relat., 18, 16 (1999).CrossRefGoogle Scholar
  39. 39.
    V. V. Poroikov, D. A. Filimonov, W.-D. Ihlenfeldt, T. A. Gloriozova, A. A. Lagunin, Yu. V. Borodina, A.V. Stepanchikova, and M. C. Nicklaus, J. Chem. Inf. Comput. Sci., 43, 228 (2003).CrossRefGoogle Scholar
  40. 40.
    A. Geronikaki, J. Dearden, D. Filimonov, I. Galaeva, T. Garibova, T. Gloriozova, V. Krajneva, A. Lagunin, F. Macaev, G. Molodavkin, V. Poroikov, S. Pogrebnoi, F. Shepeli, T. Voronina, M. Tsitlakidou, and L. Vlad, J. Med. Chem., 47, 2870 (2004).CrossRefGoogle Scholar
  41. 41.
    A. Geronikaki, S. Vasilevsky, D. Hadjipavlou-Litina, A. Lagunin, and V. Poroikov, Khim. Geterotsikl. Soedin., 769 (2006). [Chem. Heterocycl. Compd., 42, 675 (2006)].CrossRefGoogle Scholar
  42. 42.
    A. A. Lagunin, O. A. Gomazkov, D. A. Filimonov, T. A. Gureeva, E. A. Dilakyan, E. V. Kugaevskaya, Yu. E. Elisseeva, N. I. Solovyeva, and V. V. Poroikov, J. Med. Chem., 46, 3326 (2003).CrossRefGoogle Scholar
  43. 43.
    A. A. Geronikaki, A. A. Lagunin, D. I. Hadjipavlou-Litina, P. T. Elefteriou, D. A. Filimonov, V. V. Poroikov, I. Alam, and A. K. Saxena, J. Med. Chem., 51, 1601 (2008).CrossRefGoogle Scholar
  44. 44.
    V. Poroikov, D. Akimov, E. Shabelnikova, and D. Filimonov, SAR QSAR Environ. Res., 12, 327 (2001).CrossRefGoogle Scholar
  45. 45.
    S. A. Kryzhanovskii, R. M. Salimov, A. A. Lagunin, D. A. Filimonov, T. A. Gloriozova, and V. V. Poroikov, Khim.-farm. Zh., 45, No. 10, 25 (2011).Google Scholar
  46. 46.
    V. Poroikov, D. Filimonov, A. Lagunin, T. Gloriozova, and A. Zakharov, SAR QSAR Environ. Res., 18, 101 (2007).CrossRefGoogle Scholar
  47. 47.
    S. M. Ivanov, A. A. Lagunin, A. V. Zakharov, D. A. Filimonov, and V. V. Poroikov, Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 7, 40 (2013).CrossRefGoogle Scholar
  48. 48.
    A. Dalby, J. G. Nourse, W. D. Hounshell, A. K. I. Gushurst, D. L. Grier, B. A. Leland, and J. Laufer, J. Chem. Inf. Comput. Sci., 32, 244 (1992).CrossRefGoogle Scholar
  49. 49.
    A. Lagunin, A. Stepanchikova, D. Filimonov, and V. Poroikov, Bioinformatics, 16, 747 (2000).CrossRefGoogle Scholar
  50. 50.
    A. V. Sadym, A. A. Lagunin, D. A. Filimonov, and V. V. Poroikov, Khim.-farm. Zh., 36, No. 10, 21 (2002).Google Scholar
  51. 51.
    A. Sadym, A. Lagunin, D. Filimonov, and V. Poroikov, SAR QSAR Environ. Res., 14, 339 (2003).CrossRefGoogle Scholar
  52. 52.
    A. Geronikaki, D. Druzhilovsky, A. Zakharov, and V. Poroikov, SAR QSAR Environ. Res., 19, 27 (2008).CrossRefGoogle Scholar
  53. 53.
  54. 54.
    D. Weininger, J. Chem. Inf. Comput. Sci., 28, 31 (1988).CrossRefGoogle Scholar
  55. 55.
  56. 56.
  57. 57.
  58. 58.
  59. 59.
    D. Filimonov, A. Lagunin, A. Rudik, D. Druzhilovsky, S. Ivanov, P. Pogodin, and V. Poroikov, in: Abstracts of the 19th European Symposium on Quantitative Structure-Activity Relationships, Vienna, Austria, August 26-30, 2012, p. 60.Google Scholar
  60. 60.
    C. B-Rao, A. Kulkarni-Almeida, K. V. Katkar, S. Khanna, U. Ghosh, A. Keche, P. Shah, A. Srivastava, V. Korde, K. V. S. Nemmani, N. J. Deshmukh, A. Dixit, M. K. Brahma, U. Bahirat, L. Doshi, R. Sharma, and H. Sivaramakrishnan, Bioorg. Med. Chem., 20, 2930 (2012).CrossRefGoogle Scholar
  61. 61.
    D. Verbanac, S. C. Jain, N. Jain, M. Chand, H. Čipčić Paljetak, M. Matijašić, M. Perić, V. Stepanić, and L. Saso, Bioorg. Med. Chem., 20, 3180 (2012).CrossRefGoogle Scholar
  62. 62.
    A. Kumar, P. Lohan, D. K. Aneja, G. K. Gupta, D. Kaushik, and O. Prakash, Eur. J. Med. Chem., 50, 81 (2012).CrossRefGoogle Scholar
  63. 63.
    I. Shcherbakova, Khim. Geterotsikl. Soedin., 6 (2013). [Chem. Heterocycl. Compd., 49, 2 (2013)].CrossRefGoogle Scholar
  64. 64.
  65. 65.
  66. 66.
    P. Eleftheriou, A. Geronikaki, D. Hadjipavlou-Litina, P. Vicini, O. Filz, D. Filimonov, V. Poroikov, S. S. Chaudhaery, K. K. Roy, and A. Saxena, Eur. J. Med. Chem., 47, 111 (2012).CrossRefGoogle Scholar
  67. 67.
    A. Lagunin, D. A. Filimonov, and V. V. Poroikov, Curr. Pharm. Des., 16, 1703 (2010).CrossRefGoogle Scholar
  68. 68.
    J. Frearson and P. Wyatt, Expert Opin. Drug Discovery, 5, 909 (2010).CrossRefGoogle Scholar
  69. 69.
    W. Rhodes, J. Transl. Med., 10 (Suppl. 2), A42 (2012).CrossRefGoogle Scholar
  70. 70.
    D. M. Huryn, L. O. Resnick, and P. Wipf, J. Med. Chem., 56, 7161 (2013).CrossRefGoogle Scholar
  71. 71.
    S. Ekins and B. A. Bunin, in: S. Cortagere (editor), In Silico Models for Drug Discovery, Series: Methods in Molecular Biology, Vol. 993, Humana Press, New York (2013), p. 139.Google Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • D. A. Filimonov
    • 1
  • A. A. Lagunin
    • 1
  • T. A. Gloriozova
    • 1
  • A. V. Rudik
    • 1
  • D. S. Druzhilovskii
    • 1
  • P. V. Pogodin
    • 1
    • 2
  • V. V. Poroikov
    • 1
    • 2
  1. 1.V. N. Orekhovich Institute of Biomedical ChemistryRussian Academy of Medical SciencesMoscowRussia
  2. 2.N. I. Pirogov Russian National Research Medical UniversityMoscowRussia

Personalised recommendations