Abstract
Partial Least Squares Discriminant Analysis (PLS-DA) is employed to obtain novel combinations of energetic terms present in classical scoring functions, which exceed and compensates the “traditional” consensus scheme. These novel scoring functions were involved to rank the database of indirubin inhibitors of glycogen synthase kinase-3β and cyclin dependent kinase-2 decoys from Directory of Useful Decoys. The ability of docking-scoring algorithm to prioritize the actives is assessed by means of several metrics. The best classification function includes donor component of Chemgauss2, steric contribution from Chemgauss3 and rotatable bond term of ScreenScore and provide significant improvement of enrichment factor at 5% of database. 
[1] L. Meijer, N. Guyard, L.A. Skaltsounis, G. Eisenbrand (Eds.), Indirubin, the Red Shade of Indigo (Life in Progress), (Station Biologique, Roscoff, 2006) Search in Google Scholar
[2] A.R. Katritzky, L.M. Pacureanu, D.A. Dobchev, D.C. Fara, P.R. Duchowicz, M. Karelson, Bioorg. Med. Chem. 14, 4987 (2006) http://dx.doi.org/10.1016/j.bmc.2006.03.00910.1016/j.bmc.2006.03.009Search in Google Scholar
[3] A.M.F. Oliveira-Campos, A.M. Salaheldin, F.A. Almeida Paz, L.M. Rodrigues, Arkivoc xi, 121 (2011) http://dx.doi.org/10.3998/ark.5550190.0012.b1110.3998/ark.5550190.0012.b11Search in Google Scholar
[4] G.Y. Wu, F.D. Fang, Acta Acad. Med. Sinica 2, 83 (1980) Search in Google Scholar
[5] K. Suzuki, R. Adachi, A. Hirayama, H. Watanabe, S. Otani, Y. Watanabe, T. Kasahara, Br. J. Haematol. 130, 681 (2005) http://dx.doi.org/10.1111/j.1365-2141.2005.05655.x10.1111/j.1365-2141.2005.05655.xSearch in Google Scholar
[6] G. Sethi, K.S. Ahn, S.K. Sandur, X. Lin, M.M. Chaturvedi, B.B. Aggarwal, J. Biol. Chem. 281, 23425 (2006) http://dx.doi.org/10.1074/jbc.M60262720010.1074/jbc.M602627200Search in Google Scholar
[7] T. Kunikata, T. Tatefuji, H. Aga, K. Iwaki, M. Ikeda, M. Kurimoto, Eur. J. Pharmacol. 410, 93 (2000) http://dx.doi.org/10.1016/S0014-2999(00)00879-710.1016/S0014-2999(00)00879-7Search in Google Scholar
[8] K. Suzuki, R. Adachi, A. Hirayama, H. Watanabe, S. Otani, Y. Watanabe, S. Leclerc, M. Garnier, R. Hoessel, D. Marko, J.A. Bibb, G.L. Snyder, P. Greengard, J. Biernat, Y.Z. Wu, E.M. Mandelkow, G. Eisenbrand, J. Biol. Chem. 276, 251 (2001) 10.1074/jbc.M002466200Search in Google Scholar PubMed
[9] M.N. Kosmopoulou, D.D. Leonidas, E.D. Chrysina, N. Bischler, G. Eisenbrand, C.E. Sakarellos, R. Pauptit, N.G. Oikonomakos, N. G. Eur. J. Biochem. 271, 2280 (2004) http://dx.doi.org/10.1111/j.1432-1033.2004.04173.x10.1111/j.1432-1033.2004.04173.xSearch in Google Scholar PubMed
[10] J. Adachi, Y. Mori, S. Matsui, H. Takigami, J. Fujino, H. Kitagawa, C.A. Miller III, T. Kato, K. Saeki, T. Matsuda, J. Biol. Chem. 276, 31475 (2001) http://dx.doi.org/10.1074/jbc.C10023820010.1074/jbc.C100238200Search in Google Scholar PubMed
[11] S.E. Nikoulina, T.P. Ciaraldi, S. Mudaliar, L. Carter, K. Johnson, R.R. Henry, Diabetes 51, 2190 (2002) http://dx.doi.org/10.2337/diabetes.51.7.219010.2337/diabetes.51.7.2190Search in Google Scholar PubMed
[12] I. Muegge, M. Rarey, Small molecule docking and scoring (Wiley-VCH, New-York, 2001) Vol. 17, pp.1–60 10.1002/0471224413.ch1Search in Google Scholar
[13] R.D. Taylor, P.J. Jewsbury, J.W. Essex, J. Comput. Aided Mol. Des. 16, 151 (2002) http://dx.doi.org/10.1023/A:102015551071810.1023/A:1020155510718Search in Google Scholar
[14] I. Halperin, B. Ma, H. Wolfson, R. Nussinov, Proteins: Struct., Funct., Genet. 47, 409 (2002) http://dx.doi.org/10.1002/prot.1011510.1002/prot.10115Search in Google Scholar PubMed
[15] FRED, version 2.2.5 OpenEye (Scientific Software, Inc., Santa Fe, NM, 2009) Search in Google Scholar
[16] M. McGann, J. Comp. Aid. Mol. Design. 26, 897 (2012) http://dx.doi.org/10.1007/s10822-012-9584-810.1007/s10822-012-9584-8Search in Google Scholar PubMed
[17] M. McGann, J. Chem. Inf. Model. 51, 578 (2011) http://dx.doi.org/10.1021/ci100436p10.1021/ci100436pSearch in Google Scholar PubMed
[18] S.L. Swann, S.P. Brown, S.W. Muchmore, H. Patel, P. Merta, J. Locklear, P.J.. Hajduk, J. Med. Chem. 54, 1223 (2011) http://dx.doi.org/10.1021/jm101367710.1021/jm1013677Search in Google Scholar PubMed
[19] A.J.S. Knox, T. Price, M. Pawlak, G. Golfis, C.T. Flood, D. Fayne, D.C. Williams, M.J. Meegan, D.G. Lloyd, J. Med. Chem. 52, 2177 (2009) http://dx.doi.org/10.1021/jm801569z10.1021/jm801569zSearch in Google Scholar PubMed
[20] G.B. McGaughey, R.P. Sheridan, C.I. Bayly, J.C. Culberson, C. Kreatsolas, S. Lindsley, V. Maiorov, J.F. Truchon, W.D. Cornell, J. Chem. Inf. Model. 47, 1504 (2007) http://dx.doi.org/10.1021/ci700052x10.1021/ci700052xSearch in Google Scholar PubMed
[21] M.R. McGann, H.R. Almond, A. Nicholls, J.A. Grant, F.K. Brown, Biopolymers 68, 76 (2003) http://dx.doi.org/10.1002/bip.1020710.1002/bip.10207Search in Google Scholar PubMed
[22] S. Avram, L.M. Pacureanu, E. Seclaman, A. Bora, L. Kurunczi, J. Chem. Inf. Model. 51, 3169 (2011) http://dx.doi.org/10.1021/ci200226810.1021/ci2002268Search in Google Scholar PubMed
[23] S. Leclerc, M. Garnier, R Hoessel, D. Marko, J.A. Bibb, G.L. Snyder, P. Greengard, J. Biernat, Y.Z. Wu, E.M. Mandelkow, G. Eisenbrand, L. Meijer, J. Biol. Chem. 276, 251 (2001) http://dx.doi.org/10.1074/jbc.M00246620010.1074/jbc.M002466200Search in Google Scholar PubMed
[24] P. Polychronopoulos, P. Magiatis, A.L. Skaltsounis, V. Myrianthopoulos, E. Mikros, A. Tarricone, A. Musacchio, S.M. Roe, L. Pearl, M. Leost, P. Greengard, L. Meijer, J. Med. Chem. 47, 935 (2004) http://dx.doi.org/10.1021/jm031016d10.1021/jm031016dSearch in Google Scholar PubMed
[25] A. Beauchard, Y. Ferandin, S. Frère, O. Lozach, M. Blairvacq, L. Meijer, V. Thiéry, T. Besson, Bioorg. Med. Chem. 14, 6434 (2006) http://dx.doi.org/10.1016/j.bmc.2006.05.03610.1016/j.bmc.2006.05.036Search in Google Scholar PubMed
[26] Y. Ferandin, K. Bettayeb, M. Kritsanida, O. Lozach, P. Polychronopoulos, P. Magiatis, A.L. Skaltsounis, L. Meijer, J. Med. Chem. 49, 4638 (2006) http://dx.doi.org/10.1021/jm060314i10.1021/jm060314iSearch in Google Scholar PubMed
[27] K. Vougogiannopoulou, Y. Ferandin, K. Bettayeb, V. Myrianthopoulos, O. Lozach, Y. Fan, C.H. Johnson, P. Magiatis, A.L. Skaltsounis, E. Mikros, L. Meijer, J. Med. Chem. 51, 6421 (2008) http://dx.doi.org/10.1021/jm800648y10.1021/jm800648ySearch in Google Scholar PubMed PubMed Central
[28] N. Huang, B.K. Shoichet, J.J. Irwin, J. Med. Chem. 49, 6789 (2006) http://dx.doi.org/10.1021/jm060835610.1021/jm0608356Search in Google Scholar PubMed PubMed Central
[29] A. Jahn, G. Hinselmann, N. Fechner, A. Zell, J. Cheminf. 1, 14 (2009) http://dx.doi.org/10.1186/1758-2946-1-1410.1186/1758-2946-1-14Search in Google Scholar PubMed PubMed Central
[30] Schrodinger Suite 2010, LigPrep, version 2.4 (Schrödinger, LLC, New York, NY, 2010) Search in Google Scholar
[31] H. Eldar-Finkelman, A. Martinez, Front. Mol. Neurosci. 4, 32 (2011) http://dx.doi.org/10.3389/fnmol.2011.0003210.3389/fnmol.2011.00032Search in Google Scholar PubMed PubMed Central
[32] OpenEye Scientific Software (OpenEye Scientific Software, Inc., USA, 2009) http://www.eyesopen.com/ Search in Google Scholar
[33] P.C.D. Hawkins, A. Nicholls, J. Chem. Inf. Model. 52, 2919 (2012) http://dx.doi.org/10.1021/ci300314k10.1021/ci300314kSearch in Google Scholar PubMed
[34] P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson, M.T Stahl, J. Chem. Inf. Model. 50, 572 (2010) http://dx.doi.org/10.1021/ci100031x10.1021/ci100031xSearch in Google Scholar PubMed PubMed Central
[35] E. Perola, P.S. Charifson, J. Med. Chem. 47, 2499 (2004) http://dx.doi.org/10.1021/jm030563w10.1021/jm030563wSearch in Google Scholar PubMed
[36] J. Bostrom, J.R. Greenwood, J. Gottfries, J. Mol. Graphics Model. 21, 449 (2003) http://dx.doi.org/10.1016/S1093-3263(02)00204-810.1016/S1093-3263(02)00204-8Search in Google Scholar
[37] L. Crisan, L. Pacureanu, A. Bora, S. Avram, L. Kurunczi, Z. Simon, Cent. Eur. J. Chem. 11, 63 (2013) http://dx.doi.org/10.2478/s11532-012-0133-z10.2478/s11532-012-0133-zSearch in Google Scholar
[38] D.K. Gehlhaar, G.M. Verkhivker, P.A. Rejto, C.J. Sherman, D.B. Fogel, L.J. Fogel, S. T. Freer, Chem. Biol. 2, 317 (1995) http://dx.doi.org/10.1016/1074-5521(95)90050-010.1016/1074-5521(95)90050-0Search in Google Scholar
[39] M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini, R.P. Mee, J. Comput.-Aided Mol. Des. 11, 425 (1997) http://dx.doi.org/10.1023/A:100799612454510.1023/A:1007996124545Search in Google Scholar
[40] M. Stahl, M. Rarey, J. Med. Chem. 44, 1035 (2001) http://dx.doi.org/10.1021/jm000399210.1021/jm0003992Search in Google Scholar
[41] M. Barker, W. Rayens, J. Chemometrics 17, 166 (2003) http://dx.doi.org/10.1002/cem.78510.1002/cem.785Search in Google Scholar
[42] S. Wold, M. Sjöström, L. Eriksson, Chemom. Intell. Lab. Syst. 58, 109 (2001) http://dx.doi.org/10.1016/S0169-7439(01)00155-110.1016/S0169-7439(01)00155-1Search in Google Scholar
[43] M. Sjöström, S. Wold, B. Söderström, PLS Discriminant Plots (Proceedings of PARC in Practice) (Elsevier Science Publishers B.V., Amsterdam, North-Holland, 1985) 10.1016/B978-0-444-87877-9.50042-XSearch in Google Scholar
[44] SIMCA P, version 9.0 (Umetrics AB: Umea, Sweden, 2001) Search in Google Scholar
[45] M. Daszykowski, K. Kaczmarek, Y. Vander Heyden, B. Walczak, Chemom. Intel. Lab. Syst. 85, 203 (2007) http://dx.doi.org/10.1016/j.chemolab.2006.06.01610.1016/j.chemolab.2006.06.016Search in Google Scholar
[46] L. Eriksson, E. Johansson, N. Kettaneh-Wold, S. Woold, Multi and Megavariate Data Analysis. Principles and Applications (Umetrics AB: Umea, Sweden, 2001) 92–97, 489–491 Search in Google Scholar
[47] P.P. Roy, S. Paul, I. Mitra, K. Roy, Molecules, 14, 1660 (2009) http://dx.doi.org/10.3390/molecules1405166010.3390/molecules14051660Search in Google Scholar PubMed PubMed Central
[48] J.A. Hanley, B.J. McNeil, Radiology. 143, 29 (1982) 10.1148/radiology.143.1.7063747Search in Google Scholar
[49] J. Kirchmair, P. Markt, R. Distinto, G. Wolber, T. Langer, J. Comput. Aided. Mol. Des. 22, 213 (2008) http://dx.doi.org/10.1007/s10822-007-9163-610.1007/s10822-007-9163-6Search in Google Scholar
[50] N. Triballeau, F. Acher, I. Brabet, J.P. Pin, H.O. Bertrand, J. Med. Chem. 48, 2534 (2005) http://dx.doi.org/10.1021/jm049092j10.1021/jm049092jSearch in Google Scholar
[51] S. Wold, Chemom. Intell. Lab. Syst. 2, 37 (1987) http://dx.doi.org/10.1016/0169-7439(87)80084-910.1016/0169-7439(87)80084-9Search in Google Scholar
[52] S. Wold, E. Johansson, M. Cocchi, 3D QSAR in Drug Design Theory, Methods, and Applications (ESCOM, Leiden, Holland, 1993) 523–550 Search in Google Scholar
[53] SIMCA P, version 9.0. (Umetrics AB: Umea, Sweden, 2001) http://www.umetrics.com Search in Google Scholar
[54] L. Stahle, S. Wold, J. Chemom. 1, 185 (1987) http://dx.doi.org/10.1002/cem.118001030610.1002/cem.1180010306Search in Google Scholar
[55] S. Wold, M. Sjostrom, L. Eriksson, In: P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H. F., Schaefer, III, P.R. Schreiner, (Eds.) PLS in chemistry: The Encyclopedia of Computational Chemistry (Wiley, Chichester, UK, 1999) 20062–2020 Search in Google Scholar
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