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

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.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. 1.

    http://www.chemnavigator.com/cnc/products/iRL.asp.

  2. 2.

    L. Ruddigkeit, L. C. Blum, and J.-L. Reymond, J. Chem. Inf. Model., 53, 56 (2013).

    CAS  Article  Google Scholar 

  3. 3.

    Thomson Reuters Integrity SM, http://integrity.thomson-pharma.com.

  4. 4.

    A. L. Hopkins, Nat. Chem. Biol., 4, 682 (2008).

    CAS  Article  Google Scholar 

  5. 5.

    R. Morphy and Z. Rankovic, J. Med. Chem., 49, 4961 (2006).

    CAS  Article  Google Scholar 

  6. 6.

    I. M. Kapetanovic, Chem.-Biol. Interact., 171, 165 (2008).

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    CAS  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).

    CAS  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).

    CAS  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).

    CAS  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).

    CAS  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).

    CAS  Article  Google 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).

  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).

  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).

    CAS  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).

    CAS  Google Scholar 

  31. 31.

    A. V. Stepanchikova, A. A. Lagunin, D. A. Filimonov, and V. V. Poroikov, Curr. Med. Chem., 10, 225 (2003).

    CAS  Article  Google Scholar 

  32. 32.

    D. A. Filimonov and V. V. Poroikov, Ros. Khim. Zh., L, No. 2, 66 (2006).

  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.

    Google 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.

  35. 35.

    D. Filimonov, V. Poroikov, Yu. Borodina, and T. Gloriozova, J. Chem. Inf. Comput. Sci., 39, 666 (1999).

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    CAS  Article  Google 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)].

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    CAS  Article  Google Scholar 

  44. 44.

    V. Poroikov, D. Akimov, E. Shabelnikova, and D. Filimonov, SAR QSAR Environ. Res., 12, 327 (2001).

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    Article  Google 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).

    CAS  Article  Google Scholar 

  49. 49.

    A. Lagunin, A. Stepanchikova, D. Filimonov, and V. Poroikov, Bioinformatics, 16, 747 (2000).

    CAS  Article  Google 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).

    CAS  Article  Google Scholar 

  52. 52.

    A. Geronikaki, D. Druzhilovsky, A. Zakharov, and V. Poroikov, SAR QSAR Environ. Res., 19, 27 (2008).

    CAS  Article  Google Scholar 

  53. 53.

    PASS Online, http://www.way2drug.com/passonline.

  54. 54.

    D. Weininger, J. Chem. Inf. Comput. Sci., 28, 31 (1988).

    CAS  Article  Google Scholar 

  55. 55.

    http://www.chemaxon.com.

  56. 56.

    http://www.chemspider.com/.

  57. 57.

    http://bioinformatics.charite.de/superpred/.

  58. 58.

    http://cpi.bio-x.cn/drar/.

  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.

  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).

    CAS  Article  Google 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).

    CAS  Article  Google 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).

    CAS  Article  Google Scholar 

  63. 63.

    I. Shcherbakova, Khim. Geterotsikl. Soedin., 6 (2013). [Chem. Heterocycl. Compd., 49, 2 (2013)].

    CAS  Article  Google Scholar 

  64. 64.

    http://www.cerep.fr.

  65. 65.

    http://www.kinomescan.com.

  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).

    CAS  Article  Google Scholar 

  67. 67.

    A. Lagunin, D. A. Filimonov, and V. V. Poroikov, Curr. Pharm. Des., 16, 1703 (2010).

    CAS  Article  Google Scholar 

  68. 68.

    J. Frearson and P. Wyatt, Expert Opin. Drug Discovery, 5, 909 (2010).

    Article  Google Scholar 

  69. 69.

    W. Rhodes, J. Transl. Med., 10 (Suppl. 2), A42 (2012).

    Article  Google Scholar 

  70. 70.

    D. M. Huryn, L. O. Resnick, and P. Wipf, J. Med. Chem., 56, 7161 (2013).

    CAS  Article  Google 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 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to V. V. Poroikov.

Additional information

This work was supported by the Russian Foundation for Basic Research (grant 12-07-00597-a).

Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 483-499, March, 2014.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 864 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Filimonov, D.A., Lagunin, A.A., Gloriozova, T.A. et al. Prediction of the Biological Activity Spectra of Organic Compounds Using the Pass Online Web Resource . Chem Heterocycl Comp 50, 444–457 (2014). https://doi.org/10.1007/s10593-014-1496-1

Download citation

Keywords

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