Integrating computational and mixture-based screening of combinatorial libraries

Journal of Molecular Modeling

Volumn 17, Issue 6, 2011, Pages 1473-1482

  Yongye, Austin B ^a   Pinilla, Clemencia ^a   Medina Franco, Jose L ^a   Giulianotti, Marc A ^a   Dooley, Colette T ^a   Appel, Jon R ^a   Nefzi, Adel ^a   Scior, Thomas ^b   Houghten, Richard A ^a   Martínez Mayorga, Karina ^a  

^a TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

^b BENEMÉRITA UNIVERSIDAD AUTÓNOMA DE PUEBLA   (Mexico)

Author keywords

Biometric analysis; Combinatorial chemistry; Mixture based screening; Molecular similarity; Virtual screening

Indexed keywords

GUANIDINE; KAPPA OPIATE RECEPTOR;

ARTICLE; BIOMETRY; CHEMICAL ANALYSIS; COMBINATORIAL LIBRARY; CONTROLLED STUDY; PRIORITY JOURNAL; SCREENING; SYNTHESIS;

BICYCLO COMPOUNDS; COMPUTER SIMULATION; DATABASES, FACTUAL; GUANIDINES; HIGH-THROUGHPUT SCREENING ASSAYS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTORS, OPIOID, KAPPA; SMALL MOLECULE LIBRARIES;

EID: 79958175893     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0850-1     Document Type: Article

References (37)

1. Fox S, Farr-Jones S, Sopchak L, Boggs A, Comley J (2004) High-throughput screening: searching for higher productivity. J Biomol Screen 9:354-358. doi: 10.1177/1087057104265290
2. DR Goode RK Totten JT Heeres PJ Hergenrothert 2008 Identification of promiscuous small molecule activators in high-throughput enzyme activation screens J Med Chem 51 2346 2349 10.1021/jm701583b 10.1021/jm701583b 1:CAS:528:DC%2BD1cXjvFejt7s%3D (Pubitemid 351628495)
3. RP Hertzberg AJ Pope 2000 High-throughput screening: new technology for the 21st century Curr Opin Chem Biol 4 445 451 10.1016/S1367-5931(00)00110-1 1:CAS:528:DC%2BD3cXlvVCisbk%3D (Pubitemid 30621048)
4. RE Dolle 2001 Comprehensive survey of combinatorial library synthesis: 2000 J Comb Chem 3 477 517 10.1021/cc010049g 10.1021/cc010049g 1:CAS:528:DC%2BD3MXnt12qurk%3D
5. RA Houghten C Pinilla JR Appel SE Blondelle CT Dooley J Eichler A Nefzi JM Ostresh 1999 Mixture-based synthetic combinatorial libraries J Med Chem 42 3743 3778 10.1021/jm990174v 1:CAS:528:DyaK1MXmtVCjuro%3D (Pubitemid 29453457)
6. Houghten RA, Pinilla C, Giulianotti MA, Appel JR, Dooley CT, Nefzi A, Ostresh JM, Yu YP, Maggiora GM, Medina-Franco JL, Brunner D, Schneider J (2008) Strategies for the use of mixture-based synthetic combinatorial libraries: scaffold ranking, direct testing, in vivo, and enhanced deconvolution by computational methods. J Comb Chem 10:3-19. doi: 10.1021/cc7001205
7. C Pinilla JR Appel E Borras RA Houghten 2003 Advances in the use of synthetic combinatorial chemistry: mixture-based libraries Nat Med 9 118 122 10.1038/70946 10.1038/nm0103-118 1:CAS:528:DC%2BD3sXivFKk (Pubitemid 36098272)
8. CJ Armishaw N Singh JL Medina-Franco RJ Clark KC Scott RA Houghten AA Jensen 2010 A synthetic combinatorial strategy for developing alpha-conotoxin analogs as potent alpha7 nicotinic acetylcholine receptor antagonists J Biol Chem 285 1809 1821 10.1074/jbc.M109.071183 1:CAS:528:DC%2BC3cXjsVSltw%3D%3D
9. KJ Reilley M Giulianotti CT Dooley A Nefzi JP McLaughlin RA Houghten 2010 Identification of two novel, potent, low-liability antinociceptive compounds from the direct in vivo screening of a large mixture-based combinatorial library AAPS J 12 318 329 10.1208/s12248-010-9191-3 10.1208/s12248-010-9191-3 1:CAS:528:DC%2BC3cXovVKnsrc%3D
10. Yongye AB, Appel JR, Giulianotti MA, Dooley CT, Medina-Franco JL, Nefzi A, Houghten RA, Martinez-Mayorga K (2009) Identification, structure-activity relationships and molecular modeling of potent triamine and piperazine opioid ligands. Biorg Med Chem 17:5583-5597. doi: 10.1016/j.bmc.2009.06.026
11. B Hemmer B Gran YD Zhao A Marques J Pascal A Tzou T Kondo I Cortese B Bielekova SE Straus HF McFarland R Houghten R Simon C Pinilla R Martin 1999 Identification of candidate T-cell epitopes and molecular mimics in chronic Lyme disease Nat Med 5 1375 1382 10.1002/0471142735.im0905s45 10.1038/70946 1:CAS:528:DyaK1MXnvFCqt7s%3D
12. Y Zhao B Gran C Pinilla S Markovic-Plese B Hemmer A Tzuo LW Whitney WE Biddison R Martin R Simon 2001 Combinatorial peptide libraries and biometric score matrices permit the quantitative analysis of specific and degenerate interactions between clonotypic TCR and MHC peptide ligands J Immunol 167 2130 2141 1:CAS:528:DC%2BD3MXlvFequrc%3D (Pubitemid 32747522)
13. Dooley CT, Chung NN, Wilkes BC, Schiller PW, Bidlack JM, Pasternak GW, Houghten RA (1994) An all D-amino-acid opioid peptide with central analgesic activity from a combinatorial library. Science 266:2019-2022. doi: 10.1126/science.7801131
14. RA Houghten CT Dooley JR Appel 2006 In vitro and direct in vivo testing of mixture-based combinatorial libraries for the identification of highly active and specific opiate ligands AAPS J 8 E371 E382
15. J Venhorst AM ter Laak JN Commandeur Y Funae T Hiroi NP Vermeulen 2003 Homology modeling of rat and human cytochrome P450 2D (CYP2D) isoforms and computational rationalization of experimental ligand-binding specificities J Med Chem 46 74 86 10.1021/jm0209578 10.1021/jm0209578 1:CAS:528: DC%2BD38Xpt1anurs%3D (Pubitemid 36043787)
16. N Brooijmans ID Kuntz 2003 Molecular recognition and docking algorithms Annu Rev Biophys Biomol Struct 32 335 373 10.1186/1471-2105-10-58 10.1146/annurev.biophys.32.110601.142532 1:CAS:528:DC%2BD3sXntFSgtrg%3D (Pubitemid 37056233)
17. YC Martin 1992 3D database searching in drug desing J Med Chem 35 2145 2154 10.1021/jm00090a001 1:CAS:528:DyaK38Xkt1Gmtb4%3D
18. M Boehm T-Y Wu H Claussen C Lemmen 2008 Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces J Med Chem 51 2468 2480 10.1021/jm0707727 1:CAS:528:DC%2BD1cXktFShtL0%3D (Pubitemid 351628508)
19. JL Medina-Franco GM Maggiora MA Giulianotti C Pinilla RA Houghten 2007 A similarity-based data-fusion approach to the visual characterization and comparison of compound databases Chem Biol Drug Desig 70 393 412 10.1111/j.1747-0285.2007.00579.x 1:CAS:528:DC%2BD2sXhtlart7%2FP (Pubitemid 47609964)
20. Maggiora GM (2006) On outliers and activity cliffs: why QSAR often disappoints. J Chem Inf Model 46:1535-1535. doi: 10.1021/ci060117s (Pubitemid 44185680)
21. J Bajorath 2002 Integration of virtual and high-throughput screening Nat Rev Drug Discov 1 882 10.1038/nrd941 10.1038/nrd941 1:CAS:528: DC%2BD38XotleqtLY%3D (Pubitemid 37361583)
22. Johnson MA, Maggiora GM (1990) Concepts and applications of molecular similarity. Wiley, New York
23. Nikolova N, Jaworska J (2003) Approaches to measure chemical similarity-a review. QSAR Comb Sci 22:1006-1026. doi: 10.1186/1471-2121-8-S1-S6
24. JL Medina-Franco K Martinez-Mayorga A Bender RM Mari'n MA Giulianotti C Pinilla RA Houghten 2009 Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs J Chem Inf Model 49 477 491 10.1021/ci800379q 1:CAS:528:DC%2BD1MXht1agsLk%3D
25. Martinez-Mayorga K, Medina-Franco JL, Giulianotti MA, Pinilla C, Dooley CT, Appel JR, Houghten RA (2008) Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis. Bioorg Med Chem 16:5932-5938. doi: 10.1016/j.bmc.2008.04.061 (Pubitemid 351758844)
26. 3H]U69593. J Neurochem 53:27-36. doi: 10.1111/j.1471-4159.1989. tb07291.x (Pubitemid 19158106)
27. Olah M, Mracec M, Ostopovici L, Rad R, Bora A, Hadaruga N, Olah I, Banda M, Simon Z, Mracec M (2004) WOMBAT: world of molecular bioactivity. In: Oprea TI (ed) Chemoinformatics in drug discovery. Wiley-VCH, New York, pp 223-239
28. OpenEye Scientific Software (2007) ROCS v.2.3.1. OpenEye Scientific Software, Santa Fe (see http://www.eyesopen.com )
29. OpenEye Scientific Software (2007) OMEGA v.2.2.1. OpenEye Scientific Software, Santa Fe ( http://www.eyesopen.com )
30. Ostresh JM, Schoner CC, Hamashin VT, Nefzi A, Meyer JP, Houghten RA (1998) Solid-phase synthesis of trisubstituted bicyclic guanidines via cyclization of reduced N-acylated dipeptides. J Org Chem 63:8622-8623. doi: 10.1208/aapsj080242 (Pubitemid 28557502)
31. Sykes MJ, McKinnon RA, Miners JO (2008) Prediction of metabolism by cytochrome P4502C9: alignment and docking studies of a validated database of substrates. J Med Chem 51:780-791. doi: 10.1021/jm7009793 (Pubitemid 351304687)
32. Lasko TA, Bhagwat JG, Zou KH, Ohno-Machado L (2005) The use of receiver operating characteristic curves in biomedical informatics. J Biomed Inform 38:404-415. doi: 10.1186/1471-2105-8-331 (Pubitemid 41405811)
33. Triballeau N, Acher F, Brabet I, Pin J-P, Bertrand H-O (2005) Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem 48:2534-2547. doi: 10.1021/ci800101j (Pubitemid 40520517)
34. Shanmugasundaram V, Maggiora GM (2001) Characterizing property and activity landscapes using an information-theoretic approach. Abstr Pap Am Chem Soc 222:32-CINF
35. Patterson DE, Cramer RD, Ferguson AM, Clark RD, Weinberger LE (1996) Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors. J Med Chem 39:3049-3059. doi: 10.1021/ci025635r (Pubitemid 26260310)
36. Whittle M, Gillet VJ, Willett P, Loesel J (2006) Analysis of data fusion methods in virtual screening: similarity and group fusion. J Chem Inf Model 46:2206-2219. doi: 10.1016/S1367-5931(00)00110-1 (Pubitemid 46008096)
37. Whittle M, Gillet VJ, Willett P, Loesel J (2006) Analysis of data fusion methods in virtual screening: theoretical model. J Chem Inf Model 46:2193-2205. doi: 10.1016/S1367-5931(00)00110-1 (Pubitemid 46008095)