Design of chemical libraries with potentially bioactive molecules applying a maximum common substructure concept

Villar HO, Koehler RT (2000) Comments on the design of chemical libraries for screening. Mol Divers 5: 13–24. doi: 10.1023/A:1011326914800

Miller JL (2006) Recent developments in focused library design: targeting gene-families. Curr Top Med Chem 6: 19–29

Irwin JJ (2006) How good is your screening library. Curr Opin Chem Biol 10: 352–356. doi: 10.1016/j.cbpa.2006.06.003

Xue L, Bajorath J (2000) Molecular descriptors for effective classification of biologically active compounds based on principal component analysis identified by a genetic algorithm. J Chem Inf Comput Sci 40: 801–809. doi: 10.1021/ci000322m

Brenk R, Schipani A, James D, Krasowski A, Gilbert IH, Frearson J, Wyatt PG (2008) Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. ChemMedChem 3: 435–444. doi: 10.1002/cmdc.200700139

Zartler ER, Shapiro MJ (2005) Fragonomics: fragment-based drug discovery. Curr Opin Chem Biol 9: 366–370. doi: 10.1016/j.cbpa.2005.05.002

Hartshorn MJ, Murray CW, Cleasby A, Frederickson M, Tickle IJ, Jhoti H (2005) Fragment-based lead discovery using X-ray crystallography. J Med Chem 48: 403–413. doi: 10.1021/jm0495778

Jacoby E, Davies J, Blommers MJ (2003) Design of small molecule libraries for NMR screening and other applications in drug discovery. Curr Top Med Chem 3: 11–23. doi: 10.2174/1568026033392606

Schmidt MF, Isidro-Llobet A, Lisurek M, El-Dahshan A, Tan J, Hilgenfeld R, Rademann J (2008) Sensitized detection of inhibitory fragments and iterative development of non-peptidic protease inhibitors by dynamic ligation screening. Angew Chem Int Ed Engl 47: 3275–3278. doi: 10.1002/anie.200704594

Bemis GW, Murcko MA (1996) The properties of known drugs. 1. Molecular frameworks. J Med Chem 39: 2887–2893. doi: 10.1021/jm9602928

Xu YJ, Johnson M (2002) Using molecular equivalence numbers to visually explore structural features that distinguish chemical libraries. J Chem Inf Comput Sci 42: 912–926. doi: 10.1021/ci025535l

Martin YC (1990) Computer design of potentially bioactive molecules by geometric searching with ALADDIN. Tetrahedron Comput Methodol 3: 15–25. doi: 10.1016/0898-5529(90)90117-Q

Martin YC (1992) 3D database searching in drug design. J Med Chem 35: 2145–2154. doi: 10.1021/jm00090a001

Abel U, Koch C, Speitling M, Hansske FG (2002) Modern methods to produce natural-product libraries. Curr Opin Chem Biol 6: 453–458. doi: 10.1016/S1367-5931(02)00338-1

Koch MA, Schuffenhauer A, Scheck M, Wetzel S, Casaulta M, Odermatt A, Ertl P, Waldmann H (2005) Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc Natl Acad Sci USA 102: 17272–17277. doi: 10.1073/pnas.0503647102

Wagener M, Gasteiger J (1994) The determination of maximum common substructures by a genetic algorithm: application in synthesis design and for the structural analysis of biological activity. Angew Chem Int Ed Engl 33: 1189–1192. doi: 10.1002/anie.199411891

Evans BE, Rittle KE, Bock MG, DiPardo RM, Freidinger RM, Whiter WL, Lundell GF, Veber DF, Anderson PS, Chang RSL, Lotti VJ, Cerino DJ, Chen TB, Kling PJ, Kunkel KA, Springer JP, Hirshfield J (1988) Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists. J Med Chem 31: 2235–2246. doi: 10.1021/jm00120a002

Patchett AA, Nargund RP (2000) Privileged structures—an update. Annu Rep Med Chem 35: 289–298. doi: 10.1016/S0065-7743(00)35027-8

Schnur DM, Hermsmeier MA, Tebben AJ (2006) Are target- family-privileged substructures truly privileged. J Med Chem 49: 2000–2009. doi: 10.1021/jm0502900

WDI, Derwent World Drug Index, Release 2005, Derwent Information Ltd., London

ChemDiv Inc., ChemDiv Chemical Database, http://www.chemdiv.com , 6605 Nancy Ridge Drive, San Diego, CA, 92121, USA

MOE Molecular Operating Environment, version 2005.06, Chemical Computing Group Inc., Montreal, Quebec, Canada

Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 23: 3–25. doi: 10.1016/S0169-409X(96)00423-1

Labute P (2000) A widely applicable set of descriptors. J Mol Graph Model 18: 464–477. doi: 10.1016/S1093-3263(00)00068-1

ChemACX, CambridgeSoft, http://www.chemacx.com , 100 CambridgePark Drive, Cambridge, MA, 02140, USA

Dictionary of Natural Products, version 14.1 (2005). Chapman & Hall/CRC Informa, London