Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers

Journal of Computer-Aided Molecular Design

Volumn 28, Issue 6, 2014, Pages 631-646

  Sprague, Brienne ^a   Shi, Qian ^b   Kim, Marlene T ^a,c   Zhang, Liying ^d   Sedykh, Alexander ^e   Ichiishi, Eiichiro ^f   Tokuda, Harukuni ^g   Lee, Kuo Hsiung ^b,h   Zhu, Hao ^a,c  

^a RUTGERS UNIVERSITY   (United States)

^b UNC Hamner Institute for Drug Safety Sciences   (United States)

^c USA   (United States)

^d PFIZER INC   (United States)

^e MULTICASE Inc   (United States)

^f International University of Health and Welfare   (Japan)

^g KANAZAWA UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCE   (Japan)

^h CHINA MEDICAL UNIVERSITY   (Taiwan)

Author keywords

Cheminformatics; Chemoprevention; Natural products; QSAR; Virtual screening

Indexed keywords

CLASSIFICATION (OF INFORMATION); COMPUTATIONAL CHEMISTRY; DECISION TREES; DISEASES; LEAD COMPOUNDS; ORGANIC COMPOUNDS; PRODUCT DESIGN;

BINARY CLASSIFIERS; CHEMINFORMATICS; CHEMOPREVENTION; CHEMOPREVENTIVE AGENTS; EXPERIMENTAL VALIDATIONS; NATURAL PRODUCTS; QSAR; RANDOM FORESTS; SUPPORT VECTORS MACHINE; VIRTUAL SCREENING;

SUPPORT VECTOR MACHINES;

2 (2,3 DIHYDROXYPHENYL) 6 METHOXYCHROMAN 4 ONE; 2 (3,4 DIHYDROXYPHENYL) 6 HYDROXY 4H CHROMEN 4 ONE; 2 (3,4 DIHYDROXYPHENYL) 6 METHOXY 4H CHROMEN 4 ONE; 2 (3,4 DIMETHOXYPHENYL) 6 METHOXY 4H CHROMEN 4 ONE; 2 (4 HYDROXY 3 METHOXYPHENYL) 6 METHOXY 4H CHROMEN 4 ONE; 2 (NAPHTHALEN 1 YLOXY)ACETIC ACID; 3 (2,3 DIHYDROXYPHENYL) 1 (2,5 DIHYDROXYPHENYL)PROP 2 EN 1 ONE; 3 (2,3 DIMETHOXYPHENYL) 1 (2 HYDROXY 5 METHOXYPHENYL)PROP 2 EN 1 ONE; 3 (3 HYDROXYPHENYL)N(3 METHOXYBENZYL)N METHYLACRYLAMIDE; 3 (BENZO[D][1,3]DIOXOL 5 YL)N(3 PHENYLPROPYL)ACRYLAMIDE; 3 (BENZO[D][1,3]DIOXOL 5 YL)N(3,4 DIMETHOXYPHENETHYL)ACRYLAMIDE; 3 (BENZO[D][1,3]DIOXOL 5 YL)N(4 CHLOROPHENETHYL)ACRYLAMIDE; 3 (BENZO[D][1,3]DIOXOL 5 YL)N[3 (DIMETHYLAMINO)PROPYL]ACRYLAMIDE; ANTINEOPLASTIC AGENT; METHYL 2 (NAPHTHALEN 1 YLOXY)ACETATE; N(3 HYDROXYBENZYL) 3 (3 HYDROXYPHENYL)ACRYLAMIDE; N(3 HYDROXYBENZYL) 3 (3 HYDROXYPHENYL)N METHYLACRYLAMIDE; N(3 METHOXYBENZYL) 3 (3 METHOXYPHENYL)ACRYLAMIDE; UNCLASSIFIED DRUG; BIOLOGICAL PRODUCT;

ARTICLE; CHEMOPROPHYLAXIS; CONTROLLED STUDY; DRUG DESIGN; DRUG SYNTHESIS; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RANDOM FOREST; SUPPORT VECTOR MACHINE; VIRTUAL REALITY; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DATABASE; HUMAN; NEOPLASMS; SYNTHESIS;

ANTICARCINOGENIC AGENTS; BIOLOGICAL PRODUCTS; COMPUTER-AIDED DESIGN; DATABASES, PHARMACEUTICAL; DRUG DESIGN; HUMANS; MODELS, BIOLOGICAL; NEOPLASMS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SUPPORT VECTOR MACHINES;

EID: 84902785117     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9748-9     Document Type: Article

References (67)

1. Amercian Cancer Society. Lifetime risk of developing or dying from cancer. http://www.cancer.org/research/cancerfactsfigures/cancerfactsfigures/ cancer-facts-figures-2013. 11-14-2013. 2-1-0014
2. Maduro JH, Pras E, Willemse PH, de Vries EG (2003) Acute and long-term toxicity following radiotherapy alone or in combination with chemotherapy for locally advanced cervical cancer. Cancer Treat Rev 29:471-488 (Pubitemid 37428320)
3. Kelloff GJ, Sigman CC, Greenwald P (1999) Cancer chemoprevention: progress and promise. Eur J Cancer 35:2031-2038
4. Sharma D, Sukumar S (2013) Big punches come in nanosizes for chemoprevention. Cancer Prev Res 6:1007-1010
5. Tsao AS, Kim ES, Hong WK (2004) Chemoprevention of cancer. Ca-A Cancer J Clin 54:150-180 (Pubitemid 38812180)
6. Takemura H, Sakakibara H, Yamazaki S, Shimoi K (2013) Breast cancer and flavonoids - a role in prevention. Curr Pharm Des 19:6125-6132
7. Steward WP, Brown K (2013) Cancer chemoprevention: a rapidly evolving field. Br J Cancer 109:1-7
8. Patterson SL, Maresso KC, Hawk E (2013) Cancer chemoprevention: successes and failures. Clin Chem 59:94-101
9. Malik M, Magnuson BA (2004) Rapid method for identification of chemopreventive compounds using multiplex RT-PCR for cyclooxygenase mRNA expression. Cancer Detect Prev 28:277-282 (Pubitemid 40125378)
10. Heijink DM, Fehrmann RS, de Vries EG, Koornstra JJ, Oosterhuis D, van der Zee AG, Kleibeuker JH, de Jong S (2011) A bioinformatical and functional approach to identify novel strategies for chemoprevention of colorectal cancer. Oncogene 30:2026-2036
11. Gerhauser C, Klimo K, Heiss E, Neumann I, Gamal-Eldeen A, Knauft J, Liu GY, Sitthimonchai S, Frank N (2003) Mechanismbased in vitro screening of potential cancer chemopreventive agents. Mutat Res 523-524:163-172 (Pubitemid 36293243)
12. Tokuda H, Arai T, Suzuki R, Strong JM, Schneider A, Suzuzki N (2012) Efficient evaluation of healthy tea, Gromwell seed against tumor promoting stage. Planta Medica 78:1177
13. Perestelo NR, Jimenez IA, Tokuda H, Hayashi H, Bazzocchi IL (2010) Sesquiterpenes from Maytenus jelskii as potential cancer chemopreventive agents. J Nat Prod 73:127-132
14. Terazawa R, Garud DR, Hamada N, Fujita Y, Itoh T, Nozawa Y, Nakane K, Deguchi T, Koketsu M, Ito M (2010) Identification of organoselenium compounds that possess chemopreventive properties in human prostate cancer LNCaP cells. Bioorg Med Chem 18:7001-7008
15. Stan SD, Singh SV (2009) Transcriptional repression and inhibition of nuclear translocation of androgen receptor by diallyl trisulfide in human prostate cancer cells. Clin Cancer Res 15:4895-4903
16. Kim Y, Kim J, Lee SM, Lee HA, Park S, Kim Y, Kim JH (2012) Chemopreventive effects of Rubus coreanus Miquel on prostate cancer. Biosci Biotechnol Biochem 76:737-744
17. Johnson JJ, Syed DN, Suh Y, Heren CR, Saleem M, Siddiqui IA, Mukhtar H (2010) Disruption of androgen and estrogen receptor activity in prostate cancer by a novel dietary diterpene carnosol: implications for chemoprevention. Cancer Prev Res (Phila) 3:1112-1123
18. Steele VE, Sharma S, Mehta R, Elmore E, Redpath L, Rudd C, Bagheri D, Sigman CC, Kelloff GJ (1996) Use of in vitro assays to predict the efficacy of chemopreventive agents in whole animals. J Cell Biochem Suppl 26:29-53 (Pubitemid 27203751)
19. Ito Y, Kawanishi M, Harayama T, Takabayashi S (1981) Combined effect of the extracts from Croton tiglium, Euphorbia lathyris or Euphorbia tirucalli and n-butyrate on Epstein-Barr virus expression in human lymphoblastoid P3HR-1 and Raji cells. Cancer Lett 12:175-180 (Pubitemid 11111737)
20. Ito Y, Yanase S, Fujita J, Harayama T, Takashima M, Imanaka H (1981) A short-term in vitro assay for promoter substances using human lymphoblastoid cells latently infected with Epstein-Barr virus. Cancer Lett 13:29-37 (Pubitemid 11071018)
21. Bertosa B, Aleksic M, Karminiski-Zamola G, Tomic S (2010) QSAR analysis of antitumor active amides and quinolones from thiophene series. Int J Pharm 394:106-114
22. Saeed BA, Saour KY, Elias RS, Al-Masoudi NA, La Cola P (2010) Antitumor and quantitative structure activity relationship study for dihydropyridones derived from curcumin. Am J Immun 6:7-10
23. Aleksic M, Bertosa B, Nhili R, Uzelac L, Jarak I, Depauw S, vid-Cordonnier MH, Kralj M, Tomic S, Karminski-Zamola G (2012) Novel substituted benzothiophene and thienothiophene carboxanilides and quinolones: synthesis, photochemical synthesis, DNA-binding properties, antitumor evaluation and 3D-derived QSAR analysis. J Med Chem 55:5044-5060
24. Girija CR, Karunakar P, Poojari CS, Begun NS, Syed AA (2013) Molecular docking studies of curcumin derivatives with multiple protein targets for procarcinogen activating enzyme inhibition. J Proteom Bioinfor 3:200-203
25. Akihisa T, Tokuda H, Yasukawa K, Ukiya M, Kiyota A, Sakamoto N, Suzuki T, Tanabe N, Nishino H (2005) Azaphilones, furanoisophthalides, and amino acids from the extracts of Monascus pilosus-fermented rice (red-mold rice) and their chemopreventive effects. J Agric Food Chem 53:562-565 (Pubitemid 40194373)
26. Nakagawa-Goto K, Yamada K, Taniguchi M, Tokuda H, Lee KH (2009) Cancer preventive agents 9. Betulinic acid derivatives as potent cancer chemopreventive agents. Bioorg Med Chem Lett 19:3378-3381
27. Akihisa T, Tokuda H, Hasegawa D, Ukiya M, Kimura Y, Enjo F, Suzuki T, Nishino H (2006) Chalcones and other compounds from the exudates of Angelica keiskei and their cancer chemopreventive effects. J Nat Prod 69:38-42 (Pubitemid 43241751)
28. Akihisa T, Tokuda H, Ukiya M, Iizuka M, Schneider S, Ogasawara K, Mukainaka T, Iwatsuki K, Suzuki T, Nishino H (2003) Chalcones, coumarins, and flavanones from the exudate of Angelica keiskei and their chemopreventive effects. Cancer Lett 201:133-137 (Pubitemid 37357162)
29. Sakurai N, Kozuka M, Tokuda H, Mukainaka T, Enjo F, Nishino H, Nagai M, Sakurai Y, Lee KH (2005) Cancer preventive agents. Part 1: chemopreventive potential of cimigenol, cimigenol-3,15- dione, and related compounds. Bioorg Med Chem 13:1403-1408 (Pubitemid 40164623)
30. Ito C, Itoigawa M, Mishina Y, Filho VC, Enjo F, Tokuda H, Nishino H, Furukawa H (2003) Chemical constituents of Calophyllum brasiliense. 2. Structure of three new coumarins and cancer chemopreventive activity of 4-substituted coumarins. J Nat Prod 66:368-371 (Pubitemid 36384013)
31. Suzuki M, Nakagawa-Goto K, Nakamura S, Tokuda H, Morris-Natschke SL, Kozuka M, Nishino H, Lee KH (2006) Cancer preventive agents. Part 5. Anti-tumor-promoting effects of coumarins and related compounds on Epstein-Barr virus activation and two-stage mouse skin carcinogenesis. Pharm Biol 44:178-182
32. Akihisa T, Higo N, Tokuda H, Ukiya M, Akazawa H, Tochigi Y, Kimura Y, Suzuki T, Nishino H (2007) Cucurbitane-type triterpenoids from the fruits of Momordica charantia and their cancer chemopreventive effects. J Nat Prod 70:1233-1239 (Pubitemid 47401558)
33. Kikuchi T, Akihisa T, Tokuda H, Ukiya M, Watanabe K, Nishino H (2007) Cancer chemopreventive effects of cycloartane-type and related triterpenoids in in vitro and in vivo models. J Nat Prod 70:918-922 (Pubitemid 47056102)
34. Ito C, Itoigawa M, Mishina Y, Tomiyasu H, Litaudon M, Cosson JP, Mukainaka T, Tokuda H, Nishino H, Furukawa H (2001) Cancer chemopreventive agents. New depsidones from Garcinia plants. J Nat Prod 64:147-150 (Pubitemid 32198335)
35. Nakagawa-Goto K, Bastow KF, Wu JH, Tokuda H, Lee KH (2005) Total synthesis and bioactivity of unique flavone desmosdumotinB and its analogs. Bioorg Med Chem Lett 15:3016-3019 (Pubitemid 40755188)
36. Lin AS, Shibano M, Nakagawa-Goto K, Tokuda H, Itokawa H, Morris-Natschke SL, Lee KH (2007) Cancer preventive agents. 7. Antitumor-promoting effects of seven active flavonolignans from milk thistle (Silybum marianum) on Epstein-Barr virus activation. Pharm Biol 45:735-738 (Pubitemid 350208828)
37. Wang XH, Nakagawa-Goto K, Kozuka M, Tokuda H, Nishino H, Lee KH (2006) Cancer preventive agents. Part 6: chemopreventive potential of furanocoumarins and related compounds. Pharm Biol 44:116-120
38. Cui W, Iwasa K, Tokuda H, Kashihara A, Mitani Y, Hasegawa T, Nishiyama Y, Moriyasu M, Nishino H, Hanaoka M, Mukai C, Takeda K (2006) Potential cancer chemopreventive activity of simple isoquinolines, 1-benzylisoquinolines, and protoberberines. Phytochemistry 67:70-79 (Pubitemid 41811250)
39. Akihisa T, Takahashi A, Kikuchi T, Takagi M, Watanabe K, Fukatsu M, Fujita Y, Banno N, Tokuda H, Yasukawa K (2011) The melanogenesis-inhibitory, anti-inflammatory, and chemopreventive effects of limonoids in n-hexane extract of Azadirachta indica A. Juss. (neem) seeds. J Oleo Sci 60:53-59
40. Kapadia GJ, Azuine MA, Takayasu J, Konoshima T, Takasaki M, Nishino H, Tokuda H (2000) Inhibition of Epstein-Barr virus early antigen activation promoted by 12-O-tetradecanoylphorbol-13-acetate by the non-steroidal anti-inflammatory drugs. Cancer Lett 161:221-229
41. Itoigawa M, Ito C, Tan HT, Kuchide M, Tokuda H, Nishino H, Furukawa H (2001) Cancer chemopreventive agents, 4-phenylcoumarins from Calophyllum inophyllum. Cancer Lett 169:15-19 (Pubitemid 32532091)
42. Itoigawa M, Ito C, Tokuda H, Enjo F, Nishino H, Furukawa H (2004) Cancer chemopreventive activity of phenylpropanoids and phytoquinoids from Illicium plants. Cancer Lett 214:165-169 (Pubitemid 39207977)
43. Ito C, Itoigawa M, Miyamoto Y, Onoda S, Rao KS, Mukainaka T, Tokuda H, Nishino H, Furukawa H (2003) Polyprenylated benzophenones from Garcinia assigu and their potential cancer chemopreventive activities. J Nat Prod 66:206-209 (Pubitemid 36278230)
44. Ito C, Itoigawa M, Otsuka T, Tokuda H, Nishino H, Furukawa H (2000) Constituents of Boronia pinnata. J Nat Prod 63:1344-1348
45. Nakamura S, Kozuka M, Bastow KF, Tokuda H, Nishino H, Suzuki M, Tatsuzaki J, Morris Natschke SL, Kuo SC, Lee KH (2005) Cancer preventive agents, part 2: synthesis and evaluation of 2-phenyl-4-quinolone and 9-oxo-9,10-dihydroacridine derivatives as novel antitumor promoters. Bioorg Med Chem 13:4396-4401 (Pubitemid 40813228)
46. Ito C, Itoigawa M, Kojima N, Tan HT, Takayasu J, Tokuda H, Nishino H, Furukawa H (2004) Cancer chemopreventive activity of rotenoids from Derris trifoliata. Planta Med 70:585-588
47. Iranshahi M, Kalategi F, Rezaee R, Shahverdi AR, Ito C, Furukawa H, Tokuda H, Itoigawa M (2008) Cancer chemopreventive activity of terpenoid coumarins from Ferula species. Planta Med 74:147-150 (Pubitemid 351340617)
48. Akihisa T, Tabata K, Banno N, Tokuda H, Nishimura R, Nakamura Y, Kimura Y, Yasukawa K, Suzuki T (2006) Cancer chemopreventive effects and cytotoxic activities of the triterpene acids from the resin of Boswellia carteri. Biol Pharm Bull 29:1976-1979 (Pubitemid 44338431)
49. Akihisa T, Kojima N, Kikuchi T, Yasukawa K, Tokuda H, Masters T, Manosroi A, Manosroi J (2010) Anti-inflammatory and chemopreventive effects of triterpene cinnamates and acetates from shea fat. J Oleo Sci 59:273-280
50. Takasaki M, Konoshima T, Tokuda H, Masuda K, Arai Y, Shiojima K, Ageta H (1999) Anti-carcinogenic activity of Taraxacum plant. II. Biol Pharm Bull 22:606-610 (Pubitemid 29314017)
51. Takasaki M, Konoshima T, Tokuda H, Masuda K, Arai Y, Shiojima K, Ageta H (1999) Anti-carcinogenic activity of Taraxacum plant. I. Biol Pharm Bull 22:602-605 (Pubitemid 29314016)
52. Sedykh A, Zhu H, Tang H, Zhang L, Richard A, Rusyn I, Tropsha A (2011) Use of in vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in vivo toxicity. Environ Health Perspect 119:364-370
53. Iwase Y, Takemura Y, Ju-ichi M, Ito C, Furukawa H, Kawaii S, Yano M, Mou XY, Takayasu J, Tokuda H, Nishino H (2000) Inhibitory effect of flavonoids from citrus plants on Epstein-Barr virus activation and two-stage carcinogenesis of skin tumors. Cancer Lett 154:101-105 (Pubitemid 30229915)
54. Solimeo R, Zhang J, Kim M, Sedykh A, Zhu H (2012) Predicting chemical ocular toxicity using a combinatorial QSAR approach. Chem Res Toxicol 25:2763-2769
55. Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV (2008) Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. J Chem Inf Model 48:766-784 (Pubitemid 351757744)
56. Zhang S, Wei L, Bastow K, Zheng W, Brossi A, Lee KH, Tropsha A (2007) Antitumor agents 252. Application of validated QSAR models to database mining: discovery of novel tylophorine derivatives as potential anticancer agents. J Comput Aided Mol Des 21:97-112 (Pubitemid 46416669)
57. Medina-Franco JL, Golbraikh A, Oloff S, Castillo R, Tropsha A (2005) Quantitative structure-activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining. J Comput Aided Mol Des 19:229-242 (Pubitemid 41403209)
58. Shen M, Beguin C, Golbraikh A, Stables JP, Kohn H, Tropsha A (2004) Application of predictive QSAR models to database mining: identification and experimental validation of novel anticonvulsant compounds. J Med Chem 47:2356-2364 (Pubitemid 38478859)
59. Zhang L, Zhu H, Oprea TI, Golbraikh A, Tropsha A (2008) QSAR modeling of the blood-brain barrier permeability for diverse organic compounds. Pharm Res 25:1902-1914
60. Zhu H, Martin TM, Ye L, Sedykh A, Young DM, Tropsha A (2009) Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure. Chem Res Toxicol 22:1913-1921
61. Greenwood PE, Nikulin MS (1996) A guide to chi squared testing. Wiley, New York
62. Kim M, Sedykh A, Chakravarti S K, Saiakhov R D, Zhu H (2014) Critical evaluation of human oral bioavailability for pharmaceutical drugs by using various cheminformatics approaches. Pharm Res 31:1002-1014
63. Irwin JJ, Shoichet BK (2005) ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model 45:177-182 (Pubitemid 40736970)
64. Gafner S, Lee SK, Cuendet M, Barthelemy S, Vergnes L, Labidalle S, Mehta RG, Boone CW, Pezzuto JM (2004) Biologic evaluation of curcumin and structural derivatives in cancer chemoprevention model systems. Phytochemistry 65:2849-2859 (Pubitemid 40292116)
65. Shehzad A, Wahid F, Lee YS (2010) Curcumin in cancer chemoprevention: molecular targets, pharmacokinetics, bioavailability, and clinical trials. Arch Pharm (Weinheim) 343:489-499
66. Meiyanto E, Hermawan A, Anindyajati A (2012) Natural products for cancer-targeted therapy: citrus flavonoids as potent chemopreventive agents. Asian Pac J Cancer Prev 13:427-436
67. Guiguemde WA, Shelat AA, Bouck D, Duffy S, Crowther GJ, Davis PH, Smithson DC, Connelly M, Clark J, Zhu F, Jimenez-Diaz MB, Martinez MS, Wilson EB, Tripathi AK, Gut J, Sharlow ER, Bathurst I, El MF, Fowble JW, Forquer I, McGinley PL, Castro S, Ngulo-Barturen I, Ferrer S, Rosenthal PJ, Derisi JL, Sullivan DJ, Lazo JS, Roos DS, Riscoe MK, Phillips MA, Rathod PK, Van Voorhis WC, Avery VM, Guy RK (2010) Chemical genetics of Plasmodium falciparum. Nature 465:311-315