Assessing drug-likeness--what are we missing?

The concept of drug-likeness helps to optimise pharmacokinetic and pharmaceutical properties, for example, solubility, chemical stability, bioavailability and distribution profile. A number of molecular descriptors have emerged as reasonably informative and predictive, for example, the Rule-of-Five. Here, we review some current approaches, then discuss their major shortcoming, namely the static nature of the structural features and physicochemical properties they encode. As we demonstrate, molecules are not 'frozen statues' but 'dancing ballerinas', and several of their computable physicochemical properties are conformation-dependent and lead to the concept of property spaces. Molecular sensitivity (namely, how much a given computable physicochemical property varies as a function of flexibility) appears as a promising descriptor to encode some of the information contained in molecular property spaces.

[1]  Tudor I. Oprea,et al.  Pursuing the leadlikeness concept in pharmaceutical research. , 2004, Current opinion in chemical biology.

[2]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[3]  Bernard Testa,et al.  Quantitative Structure-Permeation Relationships (QSPeRs) to Predict Skin Permeation: A Critical Evaluation , 2004, Pharmaceutical Research.

[4]  N el Tayar,et al.  Morphine 6-glucuronide and morphine 3-glucuronide as molecular chameleons with unexpected lipophilicity. , 1991, Journal of medicinal chemistry.

[5]  Michael C. Hutter Separating Drugs from Nondrugs: A Statistical Approach Using Atom Pair Distributions , 2007, J. Chem. Inf. Model..

[6]  Miklos Feher,et al.  Property Distributions: Differences Between Drugs, Natural Products, and Molecules from Combinatorial Chemistry. , 2003 .

[7]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[8]  Berith F. Jensen,et al.  In silico prediction of membrane permeability from calculated molecular parameters. , 2005, Journal of medicinal chemistry.

[9]  Alexander Hillisch,et al.  In Silico ADMET Traffic Lights as a Tool for the Prioritization of HTS Hits , 2006, ChemMedChem.

[10]  B. Testa,et al.  Muscarinic Receptors: A Comparative Analysis of Structural Features and Binding Modes through Homology Modelling and Molecular Docking , 2006, Chemistry & biodiversity.

[11]  Tudor I. Oprea,et al.  Is There a Difference between Leads and Drugs? A Historical Perspective , 2001, J. Chem. Inf. Comput. Sci..

[12]  Michael S Lajiness,et al.  Molecular properties that influence oral drug-like behavior. , 2004, Current opinion in drug discovery & development.

[13]  Ian A. Watson,et al.  Characteristic physical properties and structural fragments of marketed oral drugs. , 2004, Journal of medicinal chemistry.

[14]  Tudor I. Oprea Current trends in lead discovery: Are we looking for the appropriate properties? , 2002, J. Comput. Aided Mol. Des..

[15]  Michael S Roberts,et al.  Molecular size as the main determinant of solute maximum flux across the skin. , 2004, The Journal of investigative dermatology.

[16]  Alessandro Pedretti,et al.  VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. , 2002, Journal of molecular graphics & modelling.

[17]  Paul D Leeson,et al.  Time-related differences in the physical property profiles of oral drugs. , 2004, Journal of medicinal chemistry.

[18]  Michal Vieth,et al.  Dependence of molecular properties on proteomic family for marketed oral drugs. , 2006, Journal of medicinal chemistry.

[19]  Alessandro Pedretti,et al.  Musings on ADME Predictions and Structure–Activity Relations , 2005, Chemistry & biodiversity.

[20]  P. Leeson,et al.  The influence of drug-like concepts on decision-making in medicinal chemistry , 2007, Nature Reviews Drug Discovery.

[21]  Stephen R. Johnson,et al.  Molecular properties that influence the oral bioavailability of drug candidates. , 2002, Journal of medicinal chemistry.

[22]  B. Testa,et al.  Lessons learned from marketed and investigational prodrugs. , 2004, Journal of medicinal chemistry.

[23]  H. Kubinyi Drug research: myths, hype and reality , 2003, Nature Reviews Drug Discovery.

[24]  Alex Avdeef,et al.  Absorption and drug development , 2003 .

[25]  Andrew R. Leach,et al.  Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery , 2001, J. Chem. Inf. Comput. Sci..

[26]  P. Carrupt,et al.  Development of molecular hydrogen-bonding potentials (MHBPs) and their application to structure-permeation relations. , 2001, Journal of molecular graphics & modelling.

[27]  Ajay,et al.  Can we learn to distinguish between "drug-like" and "nondrug-like" molecules? , 1998, Journal of medicinal chemistry.

[28]  Bernard Testa,et al.  Computational Approaches to Lipophilicity: Methods and Applications , 2007 .

[29]  A. Hopkins,et al.  Navigating chemical space for biology and medicine , 2004, Nature.

[30]  Alex Avdeef,et al.  Absorption and Drug Development: Solubility, Permeability, and Charge State , 2003 .

[31]  B. Testa Prodrug research: futile or fertile? , 2004, Biochemical pharmacology.

[32]  H. Kubinyi,et al.  A scoring scheme for discriminating between drugs and nondrugs. , 1998, Journal of medicinal chemistry.

[33]  Patrick Gaillard,et al.  Molecular Lipophilicity Potential, a tool in 3D QSAR: Method and applications , 1994, J. Comput. Aided Mol. Des..

[34]  T. Keller,et al.  A practical view of 'druggability'. , 2006, Current opinion in chemical biology.

[35]  Daniel R. Caffrey,et al.  Structure-based maximal affinity model predicts small-molecule druggability , 2007, Nature Biotechnology.

[36]  B. Testa,et al.  The conformational and property space of acetylcholine bound to muscarinic receptors: an entropy component accounts for the subtype selectivity of acetylcholine. , 2007, Archives of biochemistry and biophysics.

[37]  Y. Martin,et al.  A bioavailability score. , 2005, Journal of medicinal chemistry.

[38]  Andrew C. Good,et al.  Measuring CAMD Technique Performance, 2. How "Druglike" Are Drugs? Implications of Random Test Set Selection Exemplified Using Druglikeness Classification Models , 2007, J. Chem. Inf. Model..

[39]  B. Testa Prodrug Objectives and Design , 2007 .

[40]  Leslie Z. Benet,et al.  Predicting Drug Disposition via Application of BCS: Transport/Absorption/ Elimination Interplay and Development of a Biopharmaceutics Drug Disposition Classification System , 2004, Pharmaceutical Research.

[41]  Richard Morphy,et al.  The influence of target family and functional activity on the physicochemical properties of pre-clinical compounds. , 2006, Journal of medicinal chemistry.