Preclinical Drug Development Planning

Productivity in drug development has been disappointing over the last decade, due to lack of efficacy and/or unexpected adverse reactions. This high attrition rate can be dramatically reduced by improving the preclinical testing process, by taking account of multidisciplinary approaches and by improving the design of preclinical projects to facilitate the collection and interpretation of relevant information from such studies, and its extrapolation to the clinical setting. This article provides an overview of the early drug discovery and development processes, including in vitro and in silico methods. Keywords: productivity; drug development; preclinical testing process; in vitro assays; systems biology

[1]  B. van Ravenzwaay,et al.  The significance of in vitro rat skin absorption studies to human risk assessment. , 2004, Toxicology in vitro : an international journal published in association with BIBRA.

[2]  Didier Rognan,et al.  sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank , 2006, J. Chem. Inf. Model..

[3]  J. Fix,et al.  Use of everted intestinal rings for in vitro examination of oral absorption potential. , 1994, Journal of pharmaceutical sciences.

[4]  T. Soukka,et al.  Enzyme Inhibitor Screening Using a Homogeneous Proximity-Based Immunoassay for Estradiol , 2005, Journal of biomolecular screening.

[5]  S Coecke,et al.  The use of Long-term Hepatocyte Cultures for Detecting Induction of Drug Metabolising Enzymes: The Current Status , 1999, Alternatives to laboratory animals : ATLA.

[6]  Ulrich Rester,et al.  Dock around the Clock – Current Status of Small Molecule Docking and Scoring , 2006 .

[7]  L. Abdullah,et al.  Mucociliary differentiation of serially passaged normal human tracheobronchial epithelial cells. , 1996, American journal of respiratory cell and molecular biology.

[8]  Candace Black-Schaefer,et al.  Automatic mass spectrometry method development for drug discovery: application in metabolic stability assays. , 2004, Rapid communications in mass spectrometry : RCM.

[9]  A. Cavalli,et al.  QT prolongation through hERG K+ channel blockade: Current knowledge and strategies for the early prediction during drug development , 2005, Medicinal research reviews.

[10]  Walter Huber,et al.  A new strategy for improved secondary screening and lead optimization using high‐resolution SPR characterization of compound–target interactions , 2005, Journal of molecular recognition : JMR.

[11]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[12]  Mina J Bissell,et al.  Modeling tissue-specific signaling and organ function in three dimensions , 2003, Journal of Cell Science.

[13]  S. Batalov,et al.  A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT , 2005, Science.

[14]  J. Thevelein,et al.  Sex and sugar in yeast: two distinct GPCR systems , 2001, EMBO reports.

[15]  Robert Combes,et al.  TGN1412: Time to Change the Paradigm for the Testing of New Pharmaceuticals , 2006, Alternatives to laboratory animals : ATLA.

[16]  J. Contrera,et al.  A new highly specific method for predicting the carcinogenic potential of pharmaceuticals in rodents using enhanced MCASE QSAR-ES software. , 1998, Regulatory toxicology and pharmacology : RTP.

[17]  T R Sutter,et al.  Molecular and cellular approaches to extrapolation for risk assessment. , 1995, Environmental health perspectives.

[18]  R. Levy,et al.  Arterial uptake of biodegradable nanoparticles: effect of surface modifications. , 1998, Journal of pharmaceutical sciences.

[19]  T. Xia,et al.  Toxic Potential of Materials at the Nanolevel , 2006, Science.

[20]  J. Tolan,et al.  MDCK (Madin-Darby canine kidney) cells: A tool for membrane permeability screening. , 1999, Journal of pharmaceutical sciences.

[21]  I. Poggesi,et al.  Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs. , 2006, European journal of medicinal chemistry.

[22]  J. Valentin,et al.  Nonclinical proarrhythmia models: predicting Torsades de Pointes. , 2005, Journal of pharmacological and toxicological methods.

[23]  A. Merlo,et al.  Design, construction, and characterization of a large synthetic human antibody phage display library , 2005, Proteomics.

[24]  J A Landro,et al.  HTS in the new millennium: the role of pharmacology and flexibility. , 2000, Journal of pharmacological and toxicological methods.

[25]  H. Farghali,et al.  Evaluation of a Flat Membrane Hepatocyte Bioreactor for Pharmacotoxicological Applications: Evidence that Inhibition of Spontaneously Produced Nitric Oxide Improves Cell Functionality , 2004, Alternatives to laboratory animals : ATLA.

[26]  D. Morton Importance of species selection in drug toxicity testing. , 1998, Toxicology letters.

[27]  M Gumbleton,et al.  Progress and limitations in the use of in vitro cell cultures to serve as a permeability screen for the blood-brain barrier. , 2001, Journal of pharmaceutical sciences.

[28]  James A Thomson,et al.  Human Embryonic Stem Cells Develop Into Multiple Types of Cardiac Myocytes: Action Potential Characterization , 2003, Circulation research.

[29]  J A Eisen,et al.  Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? , 2001, Science.

[30]  D Bergsma,et al.  Orphan G-protein coupled receptors: novel drug targets for the pharmaceutical industry. , 2000, Drug design and discovery.

[31]  K. Clarke,et al.  A study of metabolic compartmentation in the rat heart and cardiac mitochondria using high‐resolution magic angle spinning 1H NMR spectroscopy , 2003, FEBS letters.

[32]  R. Sheridan,et al.  A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules. , 2003, Journal of medicinal chemistry.

[33]  P. Karp,et al.  Computational prediction of human metabolic pathways from the complete human genome , 2004, Genome Biology.

[34]  R Harkov,et al.  Health effects. , 1980, Journal of the Air Pollution Control Association.

[35]  Alan G. E. Wilson,et al.  Role of predictive metabolism and toxicity modeling in drug discovery--a summary of some recent advancements. , 2003, Current opinion in drug discovery & development.

[36]  K Enslein,et al.  International Commission for Protection Against Environmental Mutagens and Carcinogens. Use of SAR in computer-assisted prediction of carcinogenicity and mutagenicity of chemicals by the TOPKAT program. , 1994, Mutation research.

[37]  I. Roninson,et al.  Human (MDR1) and mouse (mdr1, mdr3) P-glycoproteins can be distinguished by their respective drug resistance profiles and sensitivity to modulators. , 1995, Biochemistry.

[38]  A. Plückthun,et al.  In vitro selection and evolution of functional proteins by using ribosome display. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[39]  J. Lindon,et al.  NMR‐based metabonomic approaches for evaluating physiological influences on biofluid composition , 2005, NMR in biomedicine.

[40]  R. Clothier,et al.  The Development of a Standardised Protocol to Measure Squamous Differentiation in Stratified Epithelia, by using the Fluorescein Cadaverine Incorporation Technique , 2004, Alternatives to laboratory animals : ATLA.

[41]  E. Kunkel Systems biology in drug discovery , 2004, Nature Biotechnology.

[42]  Tim Morris,et al.  The international symposium on regulatory testing and animal welfare: recommendations on best scientific practices for animal care in regulatory toxicology. , 2002, ILAR journal.

[43]  Ronald W. Davis,et al.  Systematic screen for human disease genes in yeast , 2002, Nature Genetics.

[44]  L. Kleiman,et al.  A human immunodeficiency virus type 1 protease biosensor assay using bioluminescence resonance energy transfer , 2005, Journal of Virological Methods.

[45]  Hugo O Villar,et al.  Using NMR for ligand discovery and optimization. , 2004, Current opinion in chemical biology.

[46]  J. Hoehner,et al.  Neuroblastoma survival and death: an in vitro model of hypoxia and metabolic stress. , 2004, The Journal of surgical research.

[47]  R. Tompkins,et al.  Long‐Term in Vitro Function of Adult Hepatocytes in a Collagen Sandwich Configuration , 1991, Biotechnology progress.

[48]  Eva Schlede,et al.  Evaluation of a Rule Base for Identifying Contact Allergens by using a Regulatory Database: Comparison of Data on Chemicals Notified in the European Union with “Structural Alerts” Used in the DEREK Expert System , 2002, Alternatives to laboratory animals : ATLA.

[49]  Patrick J. Sinko,et al.  Estimating Human Oral Fraction Dose Absorbed: A Correlation Using Rat Intestinal Membrane Permeability for Passive and Carrier-Mediated Compounds , 2004, Pharmaceutical Research.

[50]  Sean Ekins,et al.  Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity. , 2005, Trends in pharmacological sciences.

[51]  Luke P. Lee,et al.  Continuous perfusion microfluidic cell culture array for high-throughput cell-based assays. , 2005, Biotechnology and bioengineering.

[52]  K. Enslein,et al.  Use of SAR in computer-assited prediction of carcinogenicity and mutagenicity of chemicals by the TOPKAT program , 1994 .

[53]  Peter Greaves,et al.  First dose of potential new medicines to humans: how animals help , 2004, Nature Reviews Drug Discovery.

[54]  I. Wainer,et al.  On-line drug metabolism in capillary electrophoresis. 1. Glucuronidation using rat liver microsomes. , 2006, Analytical chemistry.

[55]  M Cortina Borja,et al.  The Design of Animal Experiments: Reducing the use of animals in research through better experimental design. (Revised and updated edition) , 2002 .

[56]  John P. Overington,et al.  How many drug targets are there? , 2006, Nature Reviews Drug Discovery.

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

[58]  C. Pidgeon,et al.  IAM chromatography: an in vitro screen for predicting drug membrane permeability. , 1995, Journal of medicinal chemistry.

[59]  A. Ray,et al.  In silico strategies for modeling membrane transporter function. , 2005, Drug discovery today.

[60]  H. Horvitz,et al.  Genetics of programmed cell death in C. elegans: past, present and future. , 1998, Trends in genetics : TIG.

[61]  Janet E. Paulsen,et al.  Functional expression of human and mouse P2Y12 receptors in Saccharomyces cerevisiae. , 2004, Biochemical and biophysical research communications.

[62]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[63]  D. Sabatini,et al.  Microarrays of cells expressing defined cDNAs , 2001, Nature.

[64]  B. Hirst,et al.  Predicting oral drug absorption and hepatobiliary clearance: Human intestinal and hepatic in vitro cell models. , 2006, Environmental toxicology and pharmacology.

[65]  R. Tyndale,et al.  Ethnic variability in the allelic distribution of human aryl hydrocarbon receptor codon 554 and assessment of variant receptor function in vitro. , 2001, Pharmacogenetics.

[66]  Rachel D. Vanderlaan,et al.  Electrophysiological profiling of cardiomyocytes in embryonic bodies derived from human embryonic stem cells: therapeutic implications. , 2003, Circulation research.

[67]  William S Hancock,et al.  National Cancer Institute shows the way. , 2003, Journal of proteome research.

[68]  M. Prato,et al.  Functionalized carbon nanotubes as emerging nanovectors for the delivery of therapeutics. , 2006, Biochimica et biophysica acta.

[69]  M. Gerstein,et al.  Subcellular localization of the yeast proteome. , 2002, Genes & development.

[70]  R. Lerner,et al.  Encoded combinatorial chemistry. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[71]  N. Benvenisty,et al.  Differentiation and genetic manipulation of human embryonic stem cells and the analysis of the cardiovascular system. , 2003, Trends in cardiovascular medicine.

[72]  M. Ingelman-Sundberg,et al.  Nomenclature for human CYP2D6 alleles. , 1996, Pharmacogenetics.

[73]  R. E. White,et al.  High-throughput screening in drug metabolism and pharmacokinetic support of drug discovery. , 2000, Annual review of pharmacology and toxicology.

[74]  F W Schildberg,et al.  Protein binding capacity in vitro changes metabolism of substrates and influences the predictability of metabolic pathways in vivo. , 2004, Toxicology in vitro : an international journal published in association with BIBRA.

[75]  Y T Woo,et al.  Development of structure-activity relationship rules for predicting carcinogenic potential of chemicals. , 1995, Toxicology letters.

[76]  M. Brewster,et al.  The use of human nasal in vitro cell systems during drug discovery and development. , 2005, Toxicology in vitro : an international journal published in association with BIBRA.

[77]  D. Burgess,et al.  DNA-based therapeutics and DNA delivery systems: A comprehensive review , 2005, The AAPS Journal.

[78]  B J Blaauboer,et al.  The integration of data on physico-chemical properties, in vitro-derived toxicity data and physiologically based kinetic and dynamic as modelling a tool in hazard and risk assessment. A commentary. , 2003, Toxicology letters.

[79]  S. Schreiber,et al.  Target-oriented and diversity-oriented organic synthesis in drug discovery. , 2000, Science.

[80]  M. Mascini,et al.  Electrochemical biosensor evaluation of the interaction between DNA and metallo-drugs , 2006, Biometals.

[81]  Yi Wang,et al.  In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction. , 2006, Toxicology letters.

[82]  U. Schwarz,et al.  Clinical relevance of genetic polymorphisms in the human CYP2C9 gene , 2003, European journal of clinical investigation.

[83]  S. Loefas,et al.  Optimizing the hit-to-lead process using SPR analysis. , 2004, Assay and drug development technologies.

[84]  O. H. Chan,et al.  Comparison of Intestinal Permeabilities Determined in Multiple in Vitro and inSitu Models: Relationship to Absorption in Humans , 1995, Pharmaceutical Research.

[85]  D. Lewis,et al.  Human carcinogens: an evaluation study via the COMPACT and HazardExpert procedures , 2002, Human & experimental toxicology.

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

[87]  T. Gilliam,et al.  Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[88]  J. Boonstra,et al.  Molecular events associated with reactive oxygen species and cell cycle progression in mammalian cells. , 2004, Gene.

[89]  C. Nichols,et al.  Drosophila melanogaster neurobiology, neuropharmacology, and how the fly can inform central nervous system drug discovery. , 2006, Pharmacology & therapeutics.

[90]  Aaron Sin,et al.  Development of a Microscale Cell Culture Analog To Probe Naphthalene Toxicity , 2008, Biotechnology progress.

[91]  W. Purcell,et al.  BRAIN SPHEROID AND OTHER ORGANOTYPIC CULTURE SYSTEMS IN IN VITRO NEUROTOXICOLOGY. , 1996 .

[92]  H. Keun,et al.  Metabonomic modeling of drug toxicity. , 2006, Pharmacology & therapeutics.

[93]  J. Winderickx,et al.  A yeast-based model of α-synucleinopathy identifies compounds with therapeutic potential , 2006 .

[94]  Eric T. Boder,et al.  Yeast surface display for screening combinatorial polypeptide libraries , 1997, Nature Biotechnology.

[95]  M. Ott,et al.  Rapid assessment of p-glycoprotein-drug interactions at the blood-brain barrier. , 2006, Analytical biochemistry.

[96]  Per B. Brockhoff,et al.  In silico prediction of cytochrome P450 inhibitors , 2006 .

[97]  M. Alonso Nanomedicines for overcoming biological barriers. , 2004, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[98]  William Thomsen,et al.  Functional assays for screening GPCR targets. , 2005, Current opinion in biotechnology.

[99]  G. W. Price,et al.  Differences in the central nervous system distribution and pharmacology of the mouse 5-hydroxytryptamine-6 receptor compared with rat and human receptors investigated by radioligand binding, site-directed mutagenesis, and molecular modeling. , 2003, Molecular pharmacology.

[100]  F. Pontén,et al.  Towards a human proteome atlas: High‐throughput generation of mono‐specific antibodies for tissue profiling , 2005, Proteomics.

[101]  R. Griffey,et al.  SAR by MS: a ligand based technique for drug lead discovery against structured RNA targets. , 2002, Journal of medicinal chemistry.

[102]  K. Kolaja,et al.  Acute molecular markers of rodent hepatic carcinogenesis identified by transcription profiling. , 2004, Chemical research in toxicology.

[103]  M. Prato,et al.  Carbon nanotubes as nanomedicines: from toxicology to pharmacology. , 2006, Advanced drug delivery reviews.

[104]  J. Lindon,et al.  'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. , 1999, Xenobiotica; the fate of foreign compounds in biological systems.

[105]  W. Schwieterman Regulating biopharmaceuticals under CDER versus CBER: an insider's perspective. , 2006, Drug discovery today.

[106]  David H. Blakey,et al.  The International Symposium on Regulatory Testing and Animal Welfare: Recommendations on Best Scientific Practices for Animal Care in Regulatory Toxicology , 2002 .

[107]  M. Eichelbaum,et al.  V79 Chinese hamster cells genetically engineered for polymorphic cytochrome P450 2D6 and their predictive value for humans. , 2003, ALTEX.

[108]  K Gubernator,et al.  Physicochemical high throughput screening: parallel artificial membrane permeation assay in the description of passive absorption processes. , 1998, Journal of medicinal chemistry.

[109]  Masami Niwa,et al.  Permeability Studies on In Vitro Blood–Brain Barrier Models: Physiology, Pathology, and Pharmacology , 2005, Cellular and Molecular Neurobiology.

[110]  K. Igarashi,et al.  Mechanisms of benzene-induced hematotoxicity and leukemogenicity: cDNA microarray analyses using mouse bone marrow tissue. , 2003, Environmental health perspectives.

[111]  C. W. Hume,et al.  The UFAW handbook on the care and management of laboratory animals , 1972 .

[112]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .

[113]  F. H. Sobels,et al.  Evaluating the mutagenic potential of chemicals the minimal battery and extrapolation problems , 1980, Archives of Toxicology.

[114]  S. Lindquist,et al.  Yeast Cells Provide Insight into Alpha-Synuclein Biology and Pathobiology , 2003, Science.

[115]  R. Jefferis Glycosylation of Recombinant Antibody Therapeutics , 2008, Biotechnology progress.

[116]  S. Butler,et al.  Cell-based and biochemical screening approaches for the discovery of novel HIV-1 inhibitors. , 2005, Antiviral research.

[117]  Julie W. Fitzpatrick,et al.  Principles for characterizing the potential human health effects from exposure to nanomaterials: elements of a screening strategy , 2005, Particle and Fibre Toxicology.

[118]  L. Bernstein,et al.  Interspecies extrapolation in carcinogenesis: prediction between rats and mice. , 1989, Environmental health perspectives.

[119]  Gergely M Makara,et al.  Improving success rates for lead generation using affinity binding technologies , 2005, Current Opinion in Biotechnology.

[120]  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.

[121]  J. Proudfoot Drugs, leads, and drug-likeness: an analysis of some recently launched drugs. , 2002, Bioorganic & medicinal chemistry letters.

[122]  Michael Mayersohn,et al.  ACCURACY OF ALLOMETRICALLY PREDICTED PHARMACOKINETIC PARAMETERS IN HUMANS: ROLE OF SPECIES SELECTION , 2005, Drug Metabolism and Disposition.

[123]  D. Fort,et al.  Enhancing the predictive validity of Frog Embryo Teratogenesis Assay—Xenopus (FETAX) , 2002, Journal of applied toxicology : JAT.

[124]  I. Hidalgo Cultured intestinal epithelial cell models. , 1996, Pharmaceutical biotechnology.

[125]  Elisabetta Poluzzi,et al.  Organising evidence on QT prolongation and occurrence of Torsades de Pointes with non-antiarrhythmic drugs: a call for consensus , 2001, European Journal of Clinical Pharmacology.

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

[127]  A. Gołębiowski,et al.  Lead compounds discovered from libraries: part 2. , 2003, Current opinion in chemical biology.