The cellular uptake of pharmaceutical drugs is mainly carrier-mediated and is thus an issue not so much of biophysics but of systems biology

It is widely believed that most drug molecules are transported across the phospholipid bilayer portion of biological membranes via passive diffusion at a rate related to their lipophilicity (expressed as log P, a calculated c log P or as log D, the octanol:water partition coefficient). However, studies of this using purely phospholipid bilayer membranes have been very misleading since transfer across these typically occurs via the solvent reservoirs or via aqueous pore defects, neither of which are prevalent in biological cells. Since the types of biophysical forces involved in the interaction of drugs with lipid membrances are no different from those involved in their interaction with proteins, arguments based on lipophilicity also apply to drug uptake by membrane transporters or carriers. A similar story attaches to the history of mechanistic explanations of the mode of action of general anaesthetics (narcotics). Carrier-mediated and active uptake of drugs is far more common than is usually assumed. This has considerable implications for the design of libraries for drug discovery and development, as well as for chemical genetics/genomics and systems chemistry.

[1]  E. Overton Studien über die Narkose : zugleich ein Beitrag zur allgemeinen Pharmakologie , 1901 .

[2]  Bertrand Russell Am I an atheist or an agnostic , 1950 .

[3]  D. O. Rudin,et al.  Reconstitution of Cell Membrane Structure in vitro and its Transformation into an Excitable System , 1962, Nature.

[4]  I. Ueda Effects of Diethyl Ether and Halothane on Firefly Luciferin Bioluminescence , 1965, Anesthesiology.

[5]  W. R. Lieb,et al.  Biological Membranes behave as Non-porous Polymeric Sheets with Respect to the Diffusion of Non-electrolytes , 1969, Nature.

[6]  A. Parsegian,et al.  Energy of an Ion crossing a Low Dielectric Membrane: Solutions to Four Relevant Electrostatic Problems , 1969, Nature.

[7]  P. Seeman,et al.  The membrane actions of anesthetics and tranquilizers. , 1972, Pharmacological reviews.

[8]  S. Singer,et al.  The fluid mosaic model of the structure of cell membranes. , 1972, Science.

[9]  F. Johnson The Bimolecular Lipid Membrane: A System , 1973 .

[10]  H. Ti Tien,et al.  Bilayer lipid membranes (BLM) : theory and practice , 1974 .

[11]  P. Barts,et al.  Uptake of the lipophilic cation dibenzyldimethylammonium into Saccharomyces cerevisiae. Interaction with the thiamine transport system. , 1980, Biochimica et biophysica acta.

[12]  N. P. Franks,et al.  Do general anaesthetics act by competitive binding to specific receptors? , 1984, Nature.

[13]  R. Dickinson,et al.  Can the stereoselective effects of the anesthetic isoflurane be accounted for by lipid solubility? , 1994, Biophysical journal.

[14]  D B Kell,et al.  Solvent selection for whole cell biotransformations in organic media. , 1995, Critical reviews in biotechnology.

[15]  A. Blume,et al.  A comparative study of diffusive and osmotic water permeation across bilayers composed of phospholipids with different head groups and fatty acyl chains. , 1995, Biophysical journal.

[16]  P. Hajduk,et al.  Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.

[17]  J. Weaver,et al.  Theory of electroporation: A review , 1996 .

[18]  Zbigniew Michalewicz,et al.  Handbook of Evolutionary Computation , 1997 .

[19]  R. Harris,et al.  Sites of alcohol and volatile anaesthetic action on GABAA and glycine receptors , 1997, Nature.

[20]  John M. Barnard,et al.  Chemical Similarity Searching , 1998, J. Chem. Inf. Comput. Sci..

[21]  Douglas B. Kell,et al.  Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation , 1998, Bioinform..

[22]  P. Brick,et al.  Structural basis for the inhibition of firefly luciferase by a general anesthetic. , 1998, Biophysical journal.

[23]  N R Smalheiser,et al.  Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. , 1998, Computer methods and programs in biomedicine.

[24]  Riccardo Poli,et al.  New ideas in optimization , 1999 .

[25]  Michael D. Gordon,et al.  Literature-based discovery by lexical statistics , 1999 .

[26]  F. Bordi Ion transport in lipid bilayer membranes through aqueous pores , 1999 .

[27]  C. Lipinski Drug-like properties and the causes of poor solubility and poor permeability. , 2000, Journal of pharmacological and toxicological methods.

[28]  R. Dickinson,et al.  Stereoselective loss of righting reflex in rats by isoflurane. , 2000, Anesthesiology.

[29]  A century of thinking about cell membranes. , 2000, Annual review of physiology.

[30]  Petra Schneider,et al.  De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks , 2000, J. Comput. Aided Mol. Des..

[31]  P. De Weer,et al.  A Century of Thinking About Cell Membranes , 2000 .

[32]  S. Thompson,et al.  Mechanism of action of general anaesthetics--new information from molecular pharmacology. , 2001, Current opinion in pharmacology.

[33]  D B Kell,et al.  Genomic computing. Explanatory analysis of plant expression profiling data using machine learning. , 2001, Plant physiology.

[34]  Han van de Waterbeemd,et al.  Property-Based Design: Optimization of Drug Absorption and Pharmacokinetics , 2001 .

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

[36]  RONALD N. KOSTOFF Overcoming Specialization , 2002 .

[37]  K. Miller,et al.  The nature of sites of general anaesthetic action. , 2002, British journal of anaesthesia.

[38]  H. Jhoti,et al.  Structure-based screening of low-affinity compounds. , 2002, Drug discovery today.

[39]  T. Buzan How to Mind Map , 2002 .

[40]  Ajay Predicting drug-likeness: why and how? , 2002, Current topics in medicinal chemistry.

[41]  B. Urban Current assessment of targets and theories of anaesthesia. , 2002, British journal of anaesthesia.

[42]  B. Antkowiak,et al.  General anesthetic actions in vivo strongly attenuated by a point mutation in the GABAA receptor β3 subunit , 2003, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[43]  M. Congreve,et al.  A 'rule of three' for fragment-based lead discovery? , 2003, Drug discovery today.

[44]  R. Guidelli Planar Lipid Bilayers (BLMs) and Their Applications: H.T. Tien, A. Ottova-Leitmannova (Eds.), Elsevier, Amsterdam, 2003 , 2003 .

[45]  K. Miller,et al.  Mechanisms of actions of inhaled anesthetics. , 2003, The New England journal of medicine.

[46]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[47]  Carmen G. Moles,et al.  Parameter estimation in biochemical pathways: a comparison of global optimization methods. , 2003, Genome research.

[48]  Joanna Owens,et al.  Chris Lipinski discusses life and chemistry after the Rule of Five. , 2003 .

[49]  W. Sadee,et al.  Intestinal membrane transport of drugs and nutrients: genomics of membrane transporters using expression microarrays. , 2004, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[50]  Nigel W. Hardy,et al.  A proposed framework for the description of plant metabolomics experiments and their results , 2004, Nature Biotechnology.

[51]  B. Antkowiak,et al.  Molecular and neuronal substrates for general anaesthetics , 2004, Nature Reviews Neuroscience.

[52]  N. Franks,et al.  The TREK K2P channels and their role in general anaesthesia and neuroprotection. , 2004, Trends in pharmacological sciences.

[53]  M. Congreve,et al.  Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.

[54]  Akira Tsuji,et al.  Transporter-mediated drug delivery: recent progress and experimental approaches. , 2004, Drug discovery today.

[55]  Siewert J Marrink,et al.  Molecular dynamics simulations of hydrophilic pores in lipid bilayers. , 2004, Biophysical journal.

[56]  Erik M. van Mulligen,et al.  Constructing an associative concept space for literature-based discovery , 2004, J. Assoc. Inf. Sci. Technol..

[57]  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.

[58]  Daniel A Erlanson,et al.  Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly. , 2004, Current opinion in chemical biology.

[59]  D. Kell,et al.  Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[60]  J. Crison,et al.  A Theoretical Basis for a Biopharmaceutic Drug Classification: The Correlation of in Vitro Drug Product Dissolution and in Vivo Bioavailability , 1995, Pharmaceutical Research.

[61]  Daniel A. Erlanson,et al.  Fragment‐Based Drug Discovery. , 2004 .

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

[63]  Anthony G Lee,et al.  How lipids affect the activities of integral membrane proteins. , 2004, Biochimica et biophysica acta.

[64]  Jürgen Bajorath,et al.  Chemoinformatics : concepts, methods, and tools for drug discovery , 2004 .

[65]  M. Lazdunski,et al.  TREK‐1, a K+ channel involved in neuroprotection and general anesthesia , 2004, The EMBO journal.

[66]  I. Kola,et al.  Can the pharmaceutical industry reduce attrition rates? , 2004, Nature Reviews Drug Discovery.

[67]  Christopher W Murray,et al.  Fragment-based lead discovery using X-ray crystallography. , 2005, Journal of medicinal chemistry.

[68]  Hans Lennernäs,et al.  The use of biopharmaceutic classification of drugs in drug discovery and development: current status and future extension , 2005, The Journal of pharmacy and pharmacology.

[69]  Y. Sai,et al.  Biochemical and molecular pharmacological aspects of transporters as determinants of drug disposition. , 2005, Drug metabolism and pharmacokinetics.

[70]  Christian Blaschke,et al.  Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks , 2005, Science's STKE.

[71]  B. Orser,et al.  Emerging molecular mechanisms of general anesthetic action. , 2005, Trends in pharmacological sciences.

[72]  Nigel W. Hardy,et al.  MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics , 2006, BMC Bioinformatics.

[73]  Barend Mons,et al.  Online tools to support literature-based discovery in the life sciences , 2005, Briefings Bioinform..

[74]  Hugh D. Spence,et al.  Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.

[75]  S. Ananiadou,et al.  Introduction to Text Mining for Biology and Biomedicine , 2006 .

[76]  P. Mura,et al.  Development and evaluation of an in vitro method for prediction of human drug absorption II. Demonstration of the method suitability. , 2006, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[77]  Bradley D Anderson,et al.  Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. , 2006, Advanced drug delivery reviews.

[78]  J. Sear,et al.  Determinants of Volatile General Anesthetic Potency: A Preliminary Three-Dimensional Pharmacophore for Halogenated Anesthetics , 2006, Anesthesia and analgesia.

[79]  P. Bork,et al.  Literature mining for the biologist: from information retrieval to biological discovery , 2006, Nature Reviews Genetics.

[80]  R. Olsen,et al.  Low-dose alcohol actions on alpha4beta3delta GABAA receptors are reversed by the behavioral alcohol antagonist Ro15-4513. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[81]  N. Franks,et al.  Molecular targets underlying general anaesthesia , 2006, British journal of pharmacology.

[82]  Sophia Ananiadou,et al.  Text mining and its potential applications in systems biology. , 2006, Trends in biotechnology.

[83]  P. Hajduk Fragment-based drug design: how big is too big? , 2006, Journal of medicinal chemistry.

[84]  D Peter Tieleman,et al.  Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop. , 2006, Journal of the American Chemical Society.

[85]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[86]  D. Kell Systems biology, metabolic modelling and metabolomics in drug discovery and development. , 2006, Drug discovery today.

[87]  B. Antkowiak,et al.  Anaesthetic drugs: linking molecular actions to clinical effects. , 2006, Current pharmaceutical design.

[88]  Sophia Hober,et al.  A human protein atlas based on antibody proteomics. , 2006, Current opinion in molecular therapeutics.

[89]  Maria Rodriguez-Fernandez,et al.  A hybrid approach for efficient and robust parameter estimation in biochemical pathways. , 2006, Bio Systems.

[90]  B. Fan,et al.  Molecular similarity and diversity in chemoinformatics: From theory to applications , 2006, Molecular Diversity.

[91]  Andrew R Leach,et al.  Fragment screening: an introduction. , 2006, Molecular bioSystems.

[92]  B. Palsson Systems Biology: Properties of Reconstructed Networks , 2006 .

[93]  M. Bleckwenn,et al.  Interactions of anesthetics with their targets: non-specific, specific or both? , 2006, Pharmacology & therapeutics.

[94]  Wanda Pratt,et al.  Using statistical and knowledge-based approaches for literature-based discovery , 2006, J. Biomed. Informatics.

[95]  D. Kell Metabolomics, modelling and machine learning in systems biology – towards an understanding of the languages of cells , 2006, The FEBS journal.

[96]  Neil R. Smalheiser,et al.  Ranking indirect connections in literature-based discovery: The role of medical subject headings , 2006, J. Assoc. Inf. Sci. Technol..

[97]  Roderick E Hubbard,et al.  Informatics and modeling challenges in fragment-based drug discovery. , 2007, Current opinion in drug discovery & development.

[98]  Chris Abell,et al.  Fragment-based approaches to enzyme inhibition. , 2007, Current opinion in biotechnology.

[99]  Douglas B Kell,et al.  Metabolomic biomarkers: search, discovery and validation , 2007, Expert review of molecular diagnostics.

[100]  Jan Schultz,et al.  Integration of fragment screening and library design. , 2007, Drug discovery today.

[101]  Li Di,et al.  PAMPA--critical factors for better predictions of absorption. , 2007, Journal of pharmaceutical sciences.

[102]  I. Vattulainen,et al.  Molecular mechanism for lipid flip-flops. , 2007, The journal of physical chemistry. B.

[103]  Roderick E Hubbard,et al.  The SeeDs approach: integrating fragments into drug discovery. , 2007, Current topics in medicinal chemistry.

[104]  P. Hajduk,et al.  A decade of fragment-based drug design: strategic advances and lessons learned , 2007, Nature Reviews Drug Discovery.

[105]  E. Bertaccini,et al.  The Common Chemical Motifs Within Anesthetic Binding Sites , 2007, Anesthesia and analgesia.

[106]  A. A. Gurtovenko,et al.  Ion transport through chemically induced pores in protein-free phospholipid membranes. , 2007, The journal of physical chemistry. B.

[107]  Jürgen Bajorath,et al.  Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. , 2007, Drug discovery today.

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

[109]  H. Jhoti,et al.  Fragment-based drug discovery using rational design. , 2007, Ernst Schering Foundation symposium proceedings.

[110]  Leann Nguyen,et al.  Is PAMPA a useful tool for discovery? , 2007, Journal of pharmaceutical sciences.

[111]  P Chiba,et al.  Future directions for drug transporter modelling , 2007, Xenobiotica; the fate of foreign compounds in biological systems.

[112]  Ronald N. Kostoff,et al.  Literature-Related Discovery (LRD) , 2007 .

[113]  O. Demin,et al.  The Edinburgh human metabolic network reconstruction and its functional analysis , 2007, Molecular systems biology.

[114]  K. Kremer,et al.  Aggregation and vesiculation of membrane proteins by curvature-mediated interactions , 2007, Nature.

[115]  Ken Solt,et al.  Correlating the clinical actions and molecular mechanisms of general anesthetics , 2007, Current opinion in anaesthesiology.

[116]  Douglas B Kell,et al.  The virtual human: Towards a global systems biology of multiscale, distributed biochemical network models , 2007, IUBMB life.

[117]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[118]  Neil R. Smalheiser,et al.  A Quantitative Model for Linking Two Disparate Sets of Articles in Medline , 2022 .

[119]  D. Broomhead,et al.  Something from nothing − bridging the gap between constraint‐based and kinetic modelling , 2007, The FEBS journal.

[120]  Alan E Mark,et al.  Ion transport across transmembrane pores. , 2007, Biophysical journal.

[121]  Hod Lipson,et al.  Automated reverse engineering of nonlinear dynamical systems , 2007, Proceedings of the National Academy of Sciences.

[122]  Richard Morphy,et al.  Fragments, network biology and designing multiple ligands. , 2007, Drug discovery today.

[123]  Pei Tang,et al.  Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses. , 2007, Biophysical journal.

[124]  N. Blomberg,et al.  An integrated approach to fragment-based lead generation: philosophy, strategy and case studies from AstraZeneca's drug discovery programmes. , 2007, Current topics in medicinal chemistry.

[125]  Glyn Williams,et al.  Fragment-based screening using X-ray crystallography and NMR spectroscopy. , 2007, Current opinion in chemical biology.

[126]  Alexander A Alex,et al.  Fragment-based drug discovery: what has it achieved so far? , 2007, Current topics in medicinal chemistry.

[127]  Roderick E. Hubbard,et al.  Diffraction Structural Biology Synchrotron Radiation Fragment Approaches in Structure-based Drug Discovery , 2007 .

[128]  N. Franks General anaesthesia: from molecular targets to neuronal pathways of sleep and arousal , 2008, Nature Reviews Neuroscience.

[129]  Ronald N. Kostoff,et al.  Literature-related discovery (LRD): Methodology , 2008 .

[130]  Douglas B Kell,et al.  Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. , 2008, Molecular bioSystems.

[131]  C. Oppenheim,et al.  The Access/Impact Problem and the Green and Gold Roads to Open Access: An Update , 2008 .

[132]  Markus J. Herrgård,et al.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.

[133]  Ferdinando Palmieri,et al.  Diseases caused by defects of mitochondrial carriers: a review. , 2008, Biochimica et biophysica acta.

[134]  David W. Deamer,et al.  Origins of life: How leaky were primitive cells? , 2008, Nature.

[135]  D. Kell,et al.  Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? , 2008, Nature Reviews Drug Discovery.

[136]  Qing Yan,et al.  Human membrane transporter database: A web-accessible relational database for drug transport studies and pharmacogenomics , 2000, AAPS PharmSci.

[137]  Mark Whittaker,et al.  Fragment-based activity space: smaller is better. , 2008, Current opinion in chemical biology.

[138]  MB Kelz,et al.  From Anesthetic Mechanisms Research to Drug Discovery , 2008, Clinical pharmacology and therapeutics.

[139]  E. Lundberg,et al.  Toward a Confocal Subcellular Atlas of the Human Proteome*S , 2008, Molecular & Cellular Proteomics.

[140]  Magnus Rattray,et al.  Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo , 2008, Bioinform..

[141]  Pedro Mendes,et al.  The markup is the model: reasoning about systems biology models in the Semantic Web era. , 2008, Journal of theoretical biology.

[142]  Douglas B. Kell,et al.  Automated manipulation of systems biology models using libSBML within Taverna workflows , 2008, Bioinform..

[143]  B. Orser,et al.  GABAA receptor subtypes underlying general anesthesia , 2008, Pharmacology Biochemistry and Behavior.

[144]  Yong-Hae Han,et al.  Current industrial practices of assessing permeability and P-glycoprotein interaction , 2006, The AAPS Journal.

[145]  Steve Pettifer,et al.  Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web , 2008, PLoS Comput. Biol..

[146]  D. Noble The music of life : biology beyond genes , 2008 .

[147]  I. Goryanin,et al.  Human metabolic network reconstruction and its impact on drug discovery and development. , 2008, Drug discovery today.

[148]  J. Szostak,et al.  Template-directed synthesis of a genetic polymer in a model protocell , 2008, Nature.

[149]  D. Kell,et al.  'Metabolite-likeness' as a criterion in the design and selection of pharmaceutical drug libraries. , 2009, Drug discovery today.