References
1 Drews J. Innovation deficit revisited: reflections on the productivity of pharmaceutical R&D Drug Discov Today 1998 3:491-494
2 Oprea TI. Sense and nonsense in drug discovery: a chemical perspective Towards Drugs of the Future IOS Press Amsterdam 2008 29-36
3 Stone M,Jonathan P. Statistical thinking and technique for QSAR and related studies. Part I. General theory J Chemom 1993 7:455-475
4 Weininger D. Combinatorics of small molecular structures Encyclopedia of Computational Chemistry Wiley New York 1998 425-430
5 Hann MM,Oprea TI. Pursuing the leadlikeness concept in pharmaceutical research Curr Opin Chem Biol 2004 8:255-263
6 Blum LC,Reymond J-L. 970 Million druglike small molecules for virtual screening in the chemical universe database GDB-13 J Am Chem Soc 2009 131:8732-8733
7 Pollock SN,Coutsias EA,Wester MJ,Oprea TI. Scaffold topologies. 1. Exhaustive enumeration up to eight rings J Chem Inf Model 2008 48:1311-1324
8 Wester MJ,Pollock SN,Coutsias EA,Allu TK,Muresan S,Oprea TI. Scaffold topologies. 2. Analysis of chemical databases J Chem Inf Model 2008 48:1311-1324
9 Rosén J,Gottfries J,Muresan S,Backlund A,Oprea TI. Novel chemical space exploration via natural products J Med Chem 2009 52:1953-1962
10 Oprea TI,Allu TK,Fara DC,Rad RF,Ostopovici L,Bologa CG. Lead-like, drug-like or pub-like: how different are they J Comput Aided Mol Des 2007 21:113-119
11 Leo A. Estimating LogPoct from structures Chem Rev 1993 5:1281-1306
12 Lipinski CA,Lombardo F,Dominy BW,Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv Drug Deliv Rev 1997 23:3-25
13 Thomson Reuters, World Drug Index. Available at:
http://thomsonreuters.com/products_services/science/science_products/a-z/world_drug_index. (Accessed March 31,
2010).14 Olah MM,Bologa CG,Oprea TI. Strategies for compound selection Curr Drug Discov Technol 2004 1:211-220
15 Oprea TI. Property distribution of drug-related chemical databases J Comput Aided Mol Des 2000 14:251-264
16 Frimurer TM,Bywater R,Naerum L,Lauritsen LN,Brunak S. Improving the odds in discriminating Drug-like from Non Drug-like compounds J Chem Inf Comput Sci 2000 40:1315-1324
17 Rayan A,Marcus D,Goldblum A. Predicting oral druglikeness by iterative stochastic elimination J Chem Inf Model 2010 50:437-445
18 Teague SJ,Davis AM,Leeson PD,Oprea TI. The design of leadlike combinatorial libraries Angew Chem Int Ed Engl 1999 38:3743-3748
19 Hann MM,Leach AR,Harper G. Molecular complexity and its impact on the probability of finding leads for drug discovery J Chem Inf Comput Sci 2001 41:856-864
20 Sneader W. Drug Prototypes and their Exploitation Wiley Chichester 1996
21 Andrews PR,Craik DJ,Martin JL. Functional group contributions to drug-receptor interactions J Med Chem 1984 27:1648-1657
22 Oprea TI,Davis AM,Teague SJ,Leeson PD. Is there a difference between leads and drugs? A historical perspective J Chem Inf Comput Sci 2001 41:1308-1315
23 Proudfoot JR. Drugs, leads, and drug-likeness: an analysis of some recently launched drugs Bioorg Med Chem Lett 2002 12:1647-1650
24 Allu TK,Oprea TI. Rapid evaluation of synthetic and molecular complexity for
in silico chemistry J Chem Inf Model 2005 45:1237-1243
25 Perola E. An analysis of the binding efficiencies of drugs and their leads in successful drug discovery programs J Med Chem 2010 53:2986-2997
26 Leeson PD,Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry Nat Rev Drug Discov 2007 6:881-890
27 DeStevens G. Serendipity and structured research in drug discovery Progress in Drug Research Basel Birkhauser 1985 189-203
28 Horrobin DF. Innovation in the pharmaceutical industry J R Soc Med 2000 93:341-345
29 Cuatrecasas P. Drug discovery in jeopardy J Clin Invest 2006 116:2837-2842
30 Keseru GM,Makara GM. The influence of lead discovery strategies on the properties of drug candidates Nat Rev Drug Discov 2009 8:203-212
31 Vaz RJ,Klabunde T. Antitargets: Prediction and Prevention of Drug Side Effects Wiley-VCH Weinheim 2008
32 Oprea TI. Current trends in lead discovery: are we looking for the appropriate properties J Comput Aided Mol Des 2002 16:325-334
33 Muegge I. Selection criteria for drug-like compounds Med Res Rev 2003 23:302-321
34 Gillet VJ,Willett P,Bradshaw J. Identification of biological activity profiles using substructural analysis and genetic algorithms J Chem Inf Comput Sci 1998 38:165-179
35 Ajay A,Walters WP,Murcko MA. Can we learn to distinguish between drug-like and nondrug-like molecules J Med Chem 1998 41:3314-3324
36 Sadowski J,Kubinyi H. A scoring scheme for discriminating between drugs and nondrugs J Med Chem 1998 41:3325-3329
37 Symyx, MDL Drug Data Report. Thomson Reuters, World Drug Index, Available at:
http://www.symyx.com/products/databases/bioactivity/mddr/index.jsp. (Accessed March 31,
2010).38 Symyx, Available Chemicals Directory. Available at:
http://www.symyx.com/products/databases/sourcing/acd/index.jsp. (Accessed March 31,
2010).39 Walters WP,Stahl MT,Murcko MA. Virtual screeningan overview Drug Discov Today 1998 3:160-178
40 Oprea TI,Matter H. Integrating virtual screening in lead discovery Curr Opin Chem Biol 2004 8:349-358
41 Tetko IV,Livingstone DJ,Luik AI. Neural network studies. 1. Comparison of overfitting and overtraining J Chem Inf Comput Sci 1995 35:826-833
42 Hawkins DM. The problem of overfitting J Chem Inf Comput Sci 2003 44:1-12
43 Burges CJC. A Tutorial on support vector machines for pattern recognition Data Min Knowl Discov 1998 2:121-167
44 Ursu O,Oprea TI. Model-Free Drug-likeness from fragments J Chem Inf Model 2010 50:1387-1394
45 Wang J,Ramnarayan K. Toward designing drug-like libraries: a novel computational approach for prediction of drug feasibility of compounds J Comb Chem 1999 1:524-533
46 Wagener M,van Geerestein VJ. Potential drugs and nondrugs: prediction and identification of important structural features J Chem Inf Comput Sci 2000 40:280-292
47 Xu J,Stevenson J. Drug-like index: a new approach to measure drug-like compounds and their diversity J Chem Inf Comput Sci 2000 40:1177-1187
48 Oprea TI,Gottfries J,Sherbukhin V,Svensson P,Kühler TC. Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces J Mol Graph Model 2000 18:512-524
49 Anzali S,Barnickel G,Cezanne B,Krug M,Filimonov D,Poroikov V. Discriminating between drugs and nondrugs by prediction of activity spectra for substances (PASS) J Med Chem 2001 44:2432-2437
50 Muegge I,Heald SL,Brittelli D. Simple selection criteria for drug-like chemical matter J Med Chem 2001 44:1841-1846
51 Brustle M,Beck B,Schindler T,King W,Mitchell T,Clark T. Descriptors, physical properties, and drug-likeness J Med Chem 2002 45:3345-3355
52 Takaoka Y,Endo Y,Yamanobe S,Kakinuma H,Okubo T,Shimazaki Y,Ota T,Sumiya S,Yoshikawa K, Development of a method for evaluating drug-likeness and ease of synthesis using a data set in which compounds are assigned scores based on chemists` intuition. J Chem Inf Comput Sci 2003 43:1269
53 Zernov VV,Balakin KV,Ivaschenko AA,Savchuk NP,Pletnev IV. Drug discovery using support vector machines. The case studies of drug-likeness, agrochemical-likeness, and enzyme inhibition predictions J Chem Inf Comput Sci 2003 43:2048-2056
54 Zheng S,Luo X,Chen G,Zhu W,Shen J,Chen K,Jiang H, A new rapid and effective chemistry space filter in recognizing a druglike database J Chem Inf Model 2005 45:856-862
55 Muller KR,Ratsch G,Sonnenburg S,Mika S,Grimm M,Heinrich N. Classifying drug-likeness with kernel-based learning methods J Chem Inf Model 2005 45:249-253
56 Li QL,Bender A,Pei JF,Lai LH. A large descriptor set and a probabilistic kernel-based classifier significantly improve druglikeness classification J Chem Inf Model 2007 47:1776-1786
57 Schneider N,Jackels C,Andres C,Hutter MC. Gradual in silico filtering for druglike substances J Chem Inf Model 2008 48:613-628
58 Schierz A,King R. Drugs and drug-like compounds: discriminating approved pharmaceuticals from screening-library compounds Pattern Recognition in Bioinformatics Springer Berlin/Heidelberg 2009 331-343
59 Ohno K,Nagahara Y,Tsunoyama K,Orita M. Are there differences between launched drugs, clinical candidates, and commercially available compounds J Chem Inf Model 2010 50:815-821
60 Wager TT,Hou X,Verhoest PR,Villalobos A. Moving beyond rules: the development of a central nervous system multiparameter optimization (CNS MPO) approach to enable alignment of druglike properties ACS Chem Neurosci 2010 1:435-449
61 Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability J Pharmacol Toxicol Methods 2000 44:235-249
62 Oprea TI. Chemical space navigation in lead discovery Curr Opin Chem Biol 2002 6:384-389
63 Lovering F,Bikker J,Humblet C. Escape from flatland: increasing saturation as an approach to improving clinical success J Med Chem 2009 52:6752-6756
64 Ritchie TJ,Macdonald SJF. The impact of aromatic ring count on compound developabilityare too many aromatic rings a liability in drug design Drug Discovery Today 2009 14:1011-1020
65 Vistoli G,Pedretti A,Testa B. Assessing drug-likenesswhat are we missing Drug Discov Today 2008 13:285-294
66 Kulkarni A,Han Y,Hopfinger AJ. Predicting caco-2 cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis J Chem Inf Comput Sci 2002 42:331-342
67 Palm K,Luthman K,Ungell A-L,Strandlund G,Beigi F,Lundahl P,Artursson P, Evaluation of dynamic polar molecular surface area as predictor of drug absorption: comparison with other computational and experimental predictors J Med Chem 1998 41:5382-5392
68 Clark DE. Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of bloodbrain barrier penetration J Pharm Sci 1999 88:815-821
69 Veber DF,Johnson SR,Cheng HY,Smith BR,Ward KW,Kopple KD. Molecular properties that influence the oral bioavailability of drug candidates J Med Chem 2002 45:2615-2623
70 Hitchcock SA. Bloodbrain barrier permeability considerations for CNS-targeted compound library design Curr Opin Chem Biol 2008 12:318-323
71 Broccatelli F,Carosati E,Cruciani G,Oprea TI. Transporter-mediated efflux influences CNS side effects: ABCB1, from antitarget to target Mol Inf 2010 29:16-26
72 Vieth M,Siegel MG,Higgs RE,Watson IA,Robertson DH,Savin KA,Durst GL,Hipskind PA, Characteristic physical properties and structural fragments of marketed oral drugs J Med Chem 2004 47:224-232
73 Bender A,Mussa HY,Glen RC,Reiling S. Molecular similarity searching using atom environments, information-based feature selection, and a Naive Bayesian classifier J Chem Inf Comput Sci 2003 44:170-178
74 Bender A,Mussa HY,Glen RC,Reiling S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance J Chem Inf Comput Sci 2004 44:1708-1718
75 Hert J,Willett P,Wilton DJ,Acklin P,Azzaoui K,Jacoby E,Schuffenhauer A, Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures Org Biomol Chem 2004 2:3256-3266
76 Faulon J-L,Visco DP,Pophale RS. The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies J Chem Inf Comput Sci 2003 43:707-720
77 Faulon J-L,Churchwell CJ,Visco DP. The signature molecular descriptor. 2. Enumerating molecules from their extended valence sequences J Chem Inf Comput Sci 2003 43:721-734
78 Faulon J-L,Collins MJ,Carr RD. The Signature molecular descriptor. 4. Canonizing molecules using extended valence sequences J Chem Inf Comput Sci 2004 44:427-436
79 ChemAxon: JChem Base version 5.3.1. Budapest,
2010.80 Cramer RD,Redl G,Berkoff CE. Substructural analysis. Novel approach to the problem of drug design J Med Chem 1974 17:533-535
81 Hodes L,Hazard GF,Geran RI,Richman S. A statistical-heuristic method for automated selection of drugs for screening J Med Chem 1977 20:469-475
82 Oprea TI. Property distribution of drug-related chemical databases J Comput Aided Mol Des 2000 14:251-264
83 Clark DE. Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 1. Prediction of intestinal absorption J Pharm Sci 1999 88:807-814
84 Gavaghan C,Arnby C,Blomberg N,Strandlund G,Boyer S. Development, interpretation and temporal evaluation of a global QSAR of hERG electrophysiology screening data J Comput Aided Mol Des 2007 21:189-206
85 Abad-Zapatero C. A Sorcerer`s apprentice and the rule of five: from rule-of-thumb to commandment and beyond Drug Discov Today 2007 12:995-997
86 Kubinyi H. Drug research: myths, hype and reality Nat Rev Drug Discov 2003 2:665-668
87 van de Waterbeemd H,Gifford E. ADMET in silico modelling: towards prediction paradise Nat Rev Drug Discov 2003 2:192-204
88 Bai JPF,Utis A,Crippen G,He HD,Fischer V,Tullman R,Yin HQ,Hsu CP,Jiang L,Hwang KK, Use of classification regression tree in predicting oral absorption in humans J Chem Inf Comput Sci 2004 44:2061-2069
89 Bergstrom CAS,Strafford M,Lazorova L,Avdeef A,Luthman K,Artursson P. Absorption classification of oral drugs based on molecular surface properties J Med Chem 2003 46:558-570
90 Martin YC. A bioavailability score J Med Chem 2005 48:3164-3170
91 Wenlock MC,Austin RP,Barton P,Davis AM,Leeson PD. A comparison of physiochemical property profiles of development and marketed oral drugs J Med Chem 2003 46:1250-1256
92 Yoshida F,Topliss JG. QSAR model for drug human oral bioavailability J Med Chem 2000 43:2575-2585
93 Hou TJ,Wang JM,Zhang W,Xu XJ. ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules J Chem Inf Model 2007 47:460-463
94 Glick M,Rayan A,Goldblum A. A stochastic algorithm for global optimization and for best populations: a test case of side chains in proteins Proc Natl Acad Sci USA 2002 99:703-708
95 Rayan A,Barasch D,Brinker G,Cycowitz A,Geva-Dotan I,Scaiewicz A,Goldblum A, New stochastic algorithm to determine drug-likeness Abstr Pap Am Chem Soc 2003 226:U297-U297
96 Rayan A,Senderowitz H,Goldblum A. Exploring the conformational space of cyclic peptides by a stochastic search method J Mol Graph Model 2004 22:319-33
97 Zuccotto F. Pharmacophore features distributions in different classes of compounds J Chem Inf Comput Sci 2003 43:1542-1552
98 Kubinyi H. From narcosis to hyperspace: the history of QSAR Quant Struct-Act Relat 2002 21:348-356
99 Pospisil P,Ballmer P,Scapozza L,Folkers G. Tautomerism in computer-aided drug design J Recept Signal Transduct Res 2003 23:361-371
100 Tetko IV,Bruneau P. Application of ALOGPS to predict 1-octanol/water distribution coefficients, logP, and logD, of AstraZeneca in-house database J Pharm Sci 2004 93:3103-3110
101 Vilar S,Cozza G,Moro S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery Curr Top Med Chem 2008 8:1555-1572
0 Balakin KV. Pharmaceutical Data Mining: Approaches and Applications for Drug Discovery John Wiley & Sons Hoboken, NJ 2010
0 Bultinck P. Computational Medicinal Chemistry for Drug Discovery Marcel Dekker New York 2004
0 Chorghade MS. Drug Discovery and Development Wiley-Interscience New York 2006
0 Fischer J,Ganellin CR. Analogue-Based Drug Discovery Wiley-VCH Weinheim 2006
0 Gad SC. Drug Discovery Handbook Wiley-Interscience New York 2005
0 Samuelsson G. Drugs of Natural Origin: A Textbook of Pharmacognosy Swedish Pharmaceutical Press Stockholm 2004
0 Wermuth CG. The Practice of Medicinal Chemistry Academic Press San Diego, CA 2003