The influence of lipophilicity in drug discovery and design

Bibliography

• DiMasi JA, Hansen RW, Grabowski HG. The price of innovation: new estimates of drug development costs. J Health Econ 2003;22:151-85
   PubMed Web of Science ®Google Scholar
• Paul SM, Mytelka DS, Dunwiddie CT, How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov 2010;9:203-14
   PubMed Web of Science ®Google Scholar
• Liu X, Testa B, Fahr A. Lipophilicity and its relationship with passive drug permeation. Pharm Res 2011;28:962-77
   PubMed Web of Science ®Google Scholar
• Lipinski CA, Lombardo F, Dominy BW, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001;46:3-26
   PubMed Web of Science ®Google Scholar
• Veber DF, Johnson SR, Cheng HY, Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 2002;45:2615-23
   PubMed Web of Science ®Google Scholar
• Tian S, Li Y, Wang J, ADME evaluation in drug discovery. 9. Prediction of oral bioavailability in humans based on molecular properties and structural fingerprints. Mol Pharm 2011;8:841-51
   PubMed Web of Science ®Google Scholar
• Leeson PD, Davis AM. Time-related differences in the physical property profiles of oral drugs. J Med Chem 2004;47:6338-48
   PubMed Web of Science ®Google Scholar
• Leeson PD, Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 2007;6:881-90
   PubMed Web of Science ®Google Scholar
• Testa B, Crivori P, Reist M, The influence of lipophilicity on the parmacokinetic behavior of drugs: concepts and examples. Perspect Drug Discov Des 2000;19:179-210
   Google Scholar
• Waring MJ. Defining optimum lipophilicity and molecular weight ranges for drug candidates-molecular weight dependent lower logD limits based on permeability. Bioorg Med Chem Lett 2009;19:2844-51
   PubMed Web of Science ®Google Scholar
• Gleeson MP, Hersey A, Montanari D, Probing the links between in vitro potency, ADMET and physicochemical parameters. Nat Rev Drug Discov 2011;10:197-208
   PubMed Web of Science ®Google Scholar
• Gleeson MP. Generation of a set of simple, interpretable ADMET rules of thumb. J Med Chem 2008;51:817-34
   PubMed Web of Science ®Google Scholar
• Hughes JD, Blagg J, Price DA, Physiochemical drug properties associated with in vivo toxicological outcomes. Bioorg Med Chem Lett 2008;18:4872-5
   PubMed Web of Science ®Google Scholar
• van De Waterbeemd H, Smith DA, Beaumont K, Property-based design: optimization of drug absorption and pharmacokinetics. J Med Chem 2001;44:1313-33
   PubMed Web of Science ®Google Scholar
• Azzaoui K, Hamon J, Faller B, Modeling promiscuity based on in vitro safety pharmacology profiling data. ChemMedChem 2007;2:874-80
   PubMed Web of Science ®Google Scholar
• Bender A, Scheiber J, Glick M, Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. ChemMedChem 2007;2:861-73
   PubMed Web of Science ®Google Scholar
• Peters JU, Schnider P, Mattei P, Pharmacological promiscuity: dependence on compound properties and target specificity in a set of recent roche compounds. ChemMedChem 2009;4:680-6
   PubMed Web of Science ®Google Scholar
• Greene N, Aleo MD, Louise-May S, Using an in vitro cytotoxicity assay to aid in compound selection for in vivo safety studies. Bioorg Med Chem Lett 2010;20:5308-12
   PubMed Web of Science ®Google Scholar
• Price DA, Blagg J, Jones L, Physicochemical drug properties associated with in vivo toxicological outcomes: a review. Expert Opin Drug Metab Toxicol 2009;5:921-31
   PubMed Web of Science ®Google Scholar
• Leeson PD, St-Gallay SA. The influence of the 'organizational factor' on compound quality in drug discovery. Nat Rev Drug Discov 2011;10:749-65
   PubMed Web of Science ®Google Scholar
• Walters WP, Green J, Weiss JR, What do medicinal chemists actually make? A 50-year retrospective. J Med Chem 2011;54:6405-16
   PubMed Web of Science ®Google Scholar
• Waring MJ. Liphophilicity in drug discovery. Expert Opin Drug Discov 2010;5:235-8
   PubMed Web of Science ®Google Scholar
• Meanwell NA. Improving drug candidates by design: a focus on physicochemical properties as a means of improving compound disposition and safety. Chem Res Toxicol 2011;24:1420-56
   PubMed Web of Science ®Google Scholar
• Wyatt PG, Woodhead AJ, Berdini V, Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxamide (AT7519), a novel cyclin dependent kinase inhibitor using fragment-based X-ray crystallography and structure based drug design. J Med Chem 2008;51:4986-99
   PubMed Web of Science ®Google Scholar
• Squires MS, Feltell RE, Wallis NG, Biological characterization of AT7519, a small-molecule inhibitor of cyclin-dependent kinases, in human tumor cell lines. Mol Cancer Ther 2009;8:324-32
   PubMed Web of Science ®Google Scholar
• Saxty G, Woodhead SJ, Berdini V, Identification of inhibitors of protein kinase B using fragment-based lead discovery. J Med Chem 2007;50:2293-6
   PubMed Web of Science ®Google Scholar
• Imig JD, Hammock BD. Soluble epoxide hydrolase as a therapeutic target for cardiovascular diseases. Nat Rev Drug Discov 2009;8:794-805
   PubMed Web of Science ®Google Scholar
• Ryckmans T, Edwards MP, Horne VA, Rapid assessment of a novel series of selective CB(2) agonists using parallel synthesis protocols: a Lipophilic Efficiency (LipE) analysis. Bioorg Med Chem Lett 2009;19:4406-9
   PubMed Web of Science ®Google Scholar
• Lange JH, van der Neut MA, Wals HC, Synthesis and SAR of novel imidazoles as potent and selective cannabinoid CB2 receptor antagonists with high binding efficiencies. Bioorg Med Chem Lett 2010;20:1084-9
   PubMed Web of Science ®Google Scholar
• Freeman-Cook KD, Autry C, Borzillo G, Design of selective, ATP-competitive inhibitors of Akt. J Med Chem 2010;53:4615-22
   PubMed Web of Science ®Google Scholar
• Liu KK, Bagrodia S, Bailey S, 4-methylpteridinones as orally active and selective PI3K/mTOR dual inhibitors. Bioorg Med Chem Lett 2010;20:6096-9
   PubMed Web of Science ®Google Scholar
• Mowbray CE, Burt C, Corbau R, Pyrazole NNRTIs 4: selection of UK-453,061 (lersivirine) as a development candidate. Bioorg Med Chem Lett 2009;19(20):5857-60
   PubMed Web of Science ®Google Scholar
• Keseru GM, Makara GM. The influence of lead discovery strategies on the properties of drug candidates. Nat Rev Drug Discov 2009;8:203-12
   PubMed Web of Science ®Google Scholar
• Tarcsay A, Nyiri K, Keseru GM. Impact of lipophilic efficiency on compound quality. J Med Chem 2012;55:1252-60
   PubMed Web of Science ®Google Scholar
• Mannhold R, Poda GI, Ostermann C, Calculation of molecular lipophilicity: state-of-the-art and comparison of log P methods on more than 96,000 compounds. J Pharm Sci 2009;98:861-93
   PubMed Web of Science ®Google Scholar
• Sangster J. editor. Octanol-water partition coefficients: fundamentals and physical chemistry. John Wiley & Sons Ltd; Chichester: 1997
   Google Scholar
• Avdeef A. pH-metric log P. II: refinement of partition coefficients and ionization constants of multiprotic substances. J Pharm Sci 1993;82:183-90
   PubMed Web of Science ®Google Scholar
• Scherrer RA, Donovan SF. Automated potentiometric titrations in KCl/water-saturated octanol: method for quantifying factors influencing ion-pair partitioning. Anal Chem 2009;81:2768-78
   PubMed Web of Science ®Google Scholar
• Gocan S, Cimpan G, Comer J. Lipophilicity measurements by liquid chromatography. Adv Chromatogr 2006;44:170-6
   Google Scholar
• Hitzel L, Watt AP, Locker KL. An increased throughput method for the determination of partition coefficients. Pharm Res 2000;17:1389-95
   PubMed Web of Science ®Google Scholar
• Giaginis C, Theocharis S, Tsantili-Kakoulidou A. Structural basis for the design of PPAR-gamma ligands: a survey on quantitative structure- activity relationships. Mini Rev Med Chem 2009;9:1075-83
   PubMed Web of Science ®Google Scholar
• Pallicer JM, Sales J, Roses M, Lipophilicity assessment of basic drugs (log P(o/w) determination) by a chromatographic method. J Chromatogr A 2011;1218:6356-68
   PubMed Web of Science ®Google Scholar
• Lombardo F, Faller B, Shalaeva MY, The good, the bad and the ugly of distribution coefficients: current status, views and outlook. In: Mannhold R, editor. Molecular drug properties. Measurement and prediction. Wiley-VCH; Denmark 2008. p. 407-37
   Google Scholar
• Valko K, Bevan C, Reynolds D. Chromatographic hydrophobicity index by fast-gradient RP-HPLC: a high-throughput alternative to log P/log D. Anal Chem 1997;69:2022-9
   PubMed Web of Science ®Google Scholar
• Roses M, Bosch E, Rafols C, Chromatographic hydrophobicity index (CHI). 50. CRC Press; Taylor & Francis Group; Boca Raton: 2012
   Google Scholar
• Pallicer JM, Calvet C, Port A, Extension of the liquid chromatography/quantitative structure-property relationship method to assess the lipophilicity of neutral, acidic, basic and amphotheric drugs. J Chromatogr A 2012;1240:113-22
   PubMed Web of Science ®Google Scholar
• Young RJ, Green DV, Luscombe CN, Getting physical in drug discovery II: the impact of chromatographic hydrophobicity measurements and aromaticity. Drug Discov Today 2011;16:822-30
   PubMed Web of Science ®Google Scholar
• Young RJ. The successful quest for oral factor Xa inhibitors; learnings for all of medicinal chemistry? Bioorg Med Chem Lett 2011;21:6228-35
   PubMed Web of Science ®Google Scholar
• Yalkowsky SH, Valvani SC. Solubility and partitioning I: solubility of nonelectrolytes in water. J Pharm Sci 1980;69:912-22
   PubMed Web of Science ®Google Scholar
• Ran Y, Jain N, Yalkowsky SH. Prediction of aqueous solubility of organic compounds by the general solubility equation (GSE). J Chem Inf Comput Sci 2001;41:1208-17
   PubMedGoogle Scholar
• Hill AP, Young RJ. Getting physical in drug discovery: a contemporary perspective on solubility and hydrophobicity. Drug Discov Today 2010;15:648-55
   PubMed Web of Science ®Google Scholar
• Kearns EH, Di L. Drug-like properties: concepts, structure design and methods. Elsevier; USA 2008
   Google Scholar
• Gleeson MP. Plasma protein binding affinity and its relationship to molecular structure: an in-silico analysis. J Med Chem 2007;50:101-12
   PubMed Web of Science ®Google Scholar
• Kakemi K, Arita T, Hori R, Absorption and excretion of drugs. XXXII. Absorption of barbituric acid derivatives from rat small intestine. Chem Pharm Bull (Tokyo) 1967;15:1883-7
   PubMed Web of Science ®Google Scholar
• Kubinyi H. Quantitative structure-activity relationships. 2. A mixed approach, based on hansch and free-wilson analysis. J Med Chem 1976;19:587-600
   PubMed Web of Science ®Google Scholar
• Camenisch G, Alsenz J, van de Waterbeemd H, Estimation of permeability by passive diffusion through Caco-2 cell monolayers using the drugs' lipophilicity and molecular weight. Eur J Pharm Sci 1998;6:317-24
   PubMed Web of Science ®Google Scholar
• Physical model approach to the design of drugs with improved intestinal absorption. In: Roche EB. (ed), Design of biopharmaceutical properties through prodrugs and analogs. APhA/APS; Washington, DC: 1977; p. 136-227
   Google Scholar
• Advancing quantitative and mechanical approaches in interfacing gastrointestinal drug absorption studies in animals and man. In Crouthamel WG, Sarapu A. (eds), Animal models for aral drug delivery in man: In situ and in vivo approaches. APhA/APS; Washington DC: 1983; p. 27-106
   Google Scholar
• Adson A, Burton PS, Raub TJ, Passive diffusion of weak organic electrolytes across Caco-2 cell monolayers: uncoupling the contributions of hydrodynamic, transcellular, and paracellular barriers. J Pharm Sci 1995;84:1197-204
   PubMed Web of Science ®Google Scholar
• Hansch C. Quantitative approach to biochemical structure-activity relationships. Acc Chem Res 1969;2:232-40
   Web of Science ®Google Scholar
• Lee AJ, King JR, Rogers TG. A multiple-pathway model for the diffusion of drugs in skin. IMA J Math Appl Med Biol 1996;13:127-50
   PubMedGoogle Scholar
• Garringues T, Perez-Varona A, Climent E. Bastric absorption of acidic xenobiotics in the rat: biophysical interpretation of an apparently atypical behaviour. Int J Pharm 1990;64:127-38
   Web of Science ®Google Scholar
• Wagner JG. Quantitation of rate of gastrointestinal and buccal absorption of acidic and basic drugs based on extraction theory. J Parmacokinet Biopharm 1973;1:23-50
   Google Scholar
• Wagner JG, Sedman AJ. Quantitation of rate of gastrointestinal and buccal absorption of acidic and basic drugs based on extraction theory. J Parmacokinet Biopharm 1973;1:23-50
   Google Scholar
• Egan WJ, Merz KM Jr, Baldwin JJ. Prediction of drug absorption using multivariate statistics. J Med Chem 2000;43:3867-77
   PubMed Web of Science ®Google Scholar
• Yoshida F, Topliss JG. QSAR model for drug human oral bioavailability. J Med Chem 2000;43:2575-85
   PubMed Web of Science ®Google Scholar
• Thomas VH, Bhattachar S, Hitchingham L, The road map to oral bioavailability: an industrial perspective. Expert Opin Drug Metab Toxicol 2006;2:591-608
   PubMed Web of Science ®Google Scholar
• Comer J. In: van De Waterbeemd H, editor. Methods and principles in medicinal chemistry. Wiley VCH; Weinheim 2003. p. 21-45
   Google Scholar
• Martin YC. A bioavailability score. J Med Chem 2005;48:3164-70
   PubMed Web of Science ®Google Scholar
• Varma MV, Obach RS, Rotter C, Physicochemical space for optimum oral bioavailability: contribution of human intestinal absorption and first-pass elimination. J Med Chem 2010;53:1098-108
   PubMed Web of Science ®Google Scholar
• Oie S, Tozer TN. Effect of altered plasma protein binding on apparent volume of distribution. J Pharm Sci 1979;68:1203-5
   PubMed Web of Science ®Google Scholar
• van de Waterbeemd H, Smith DA, Jones BC. Lipophilicity in PK design: methyl, ethyl, futile. J Comput Aided Mol Des 2001;15:273-86
   PubMed Web of Science ®Google Scholar
• Obach RS, Lombardo F, Waters NJ. Trend analysis of a database of intravenous pharmacokinetic parameters in humans for 670 drug compounds. Drug Metab Dispos 2008;36:1385-405
   PubMed Web of Science ®Google Scholar
• Valko K, Nunhuck S, Bevan C, Fast gradient HPLC method to determine compounds binding to human serum albumin. Relationships with octanol/water and immobilized artificial membrane lipophilicity. J Pharm Sci 2003;92:2236-48
   PubMed Web of Science ®Google Scholar
• Lombardo F, Obach RS, Shalaeva MY, Prediction of volume of distribution values in humans for neutral and basic drugs using physicochemical measurements and plasma protein binding data. J Med Chem 2002;45:2867-76
   PubMed Web of Science ®Google Scholar
• Lombardo F, Obach RS, Shalaeva MY, Prediction of human volume of distribution values for neutral and basic drugs. 2. Extended data set and leave-class-out statistics. J Med Chem 2004;47:1242-50
   PubMed Web of Science ®Google Scholar
• Ghuman J, Zunszain PA, Petitpas I, Structural basis of the drug-binding specificity of human serum albumin. J Mol Biol 2005;353:38-52
   PubMed Web of Science ®Google Scholar
• Kremer JM, Wilting J, Janssen LH. Drug binding to human alpha-1-acid glycoprotein in health and disease. Pharmacol Rev 1988;40:1-47
   PubMed Web of Science ®Google Scholar
• Kramer SD, Wunderli-Allenspach H. Physicochemical properties in pharmacokinetic lead optimization. Farmaco 2001;56:145-8
   PubMedGoogle Scholar
• Hitchcock SA, Pennington LD. Structure-brain exposure relationships. J Med Chem 2006;49:7559-83
   PubMed Web of Science ®Google Scholar
• Abbott NJ, Patabendige AA, Dolman DE, Structure and function of the blood-brain barrier. Neurobiol Dis 2010;37:13-25
   PubMed Web of Science ®Google Scholar
• Bain LJ, LeBlanc GA. Interaction of structurally diverse pesticides with the human MDR1 gene product P-glycoprotein. Toxicol Appl Pharmacol 1996;141:288-98
   PubMed Web of Science ®Google Scholar
• Seelig A. A general pattern for substrate recognition by P-glycoprotein. Eur J Biochem 1998;251:252-61
   PubMedGoogle Scholar
• Cavalli A, Poluzzi E, De Ponti F, Toward a pharmacophore for drugs inducing the long QT syndrome: insights from a CoMFA study of HERG K(+) channel blockers. J Med Chem 2002;45:3844-53
   PubMed Web of Science ®Google Scholar
• Clark DE. Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of blood-brain barrier penetration. J Pharm Sci 1999;88:815-21
   PubMed Web of Science ®Google Scholar
• Gerebtzoff G, Seelig A. In silico prediction of blood-brain barrier permeation using the calculated molecular cross-sectional area as main parameter. J Chem Inf Model 2006;46:2638-50
   PubMed Web of Science ®Google Scholar
• Summerfield SG, Read K, Begley DJ, Central nervous system drug disposition: the relationship between in situ brain permeability and brain free fraction. J Pharmacol Exp Ther 2007;322:205-13
   PubMed Web of Science ®Google Scholar
• Wager T, Hou T, Verhoest PR, Moving beyond rules: the development of a Central Nervous System Multiparameter Optimization (CNS MPO) approach to enable alignment of druglike properties. ACS Chem Neruosci 2010;1:435-9
   PubMed Web of Science ®Google Scholar
• Nassar AE, Kamel AM, Clarimont C. Improving the decision-making process in structural modification of drug candidates: reducing toxicity. Drug Discov Today 2004;9:1055-64
   PubMed Web of Science ®Google Scholar
• Borchard U. Pharmacokinetics of beta-adrenoceptor blocking agents: clinical significance of hepatic and/or renal clearance. Clin Physiol Biochem 1990;8(Suppl):28-34
   PubMedGoogle Scholar
• Varma MV, Feng B, Obach RS, Physicochemical determinants of human renal clearance. J Med Chem 2009;52:4844-52
   PubMed Web of Science ®Google Scholar
• Johnson TW, Dress KR, Edwards M. Using the golden triangle to optimize clearance and oral absorption. Bioorg Med Chem Lett 2009;19:5560-4
   PubMed Web of Science ®Google Scholar
• Jamieson C, Moir EM, Rankovic Z, Medicinal chemistry of hERG optimizations: highlights and hang-ups. J Med Chem 2006;49:5029-46
   PubMed Web of Science ®Google Scholar
• Waring MJ, Johnstone C. A quantitative assessment of hERG liability as a function of lipophilicity. Bioorg Med Chem Lett 2007;17:1759-64
   PubMed Web of Science ®Google Scholar
• Redfern WS, Carlsson L, Davis AS, Relationships between preclinical cardiac electrophysiology, clinical QT interval prolongation and torsade de pointes for a broad range of drugs: evidence for a provisional safety margin in drug development. Cardiovasc Res 2003;58:32-45
   PubMed Web of Science ®Google Scholar
• Anderson N, Borlak J. Drug-induced phospholipidosis. FEBS Lett 2006;580:5533-40
   PubMed Web of Science ®Google Scholar
• Reasor MJ, Hastings KL, Ulrich RG. Drug-induced phospholipidosis: issues and future directions. Expert Opin Drug Saf 2006;5:567-83
   PubMed Web of Science ®Google Scholar
• Nonoyama T, Fukuda R. Drug induced phospholipidosis pathological aspects and its prediction. J toxicol Pathol 2008;1:9-24
   Google Scholar
• Ploemen JP, Kelder J, Hafmans T, Use of physicochemical calculation of pKa and CLogP to predict phospholipidosis-inducing potential: a case study with structurally related piperazines. Exp Toxicol Pathol 2004;55:347-55
   PubMed Web of Science ®Google Scholar
• Pelletier DJ, Gehlhaar D, Tilloy-Ellul A, Evaluation of a published in silico model and construction of a novel Bayesian model for predicting phospholipidosis inducing potential. J Chem Inf Model 2007;47(3):1196-205
   PubMed Web of Science ®Google Scholar
• Hanumegowda UM, Wenke G, Regueiro-Ren A, Phospholipidosis as a function of basicity, lipophilicity, and volume of distribution of compounds. Chem Res Toxicol 2010;23(4):749-55
   PubMed Web of Science ®Google Scholar
• Tomizawa K, Sugano K, Yamada H, Physicochemical and cell-based approach for early screening of phospholipidosis-inducing potential. J Toxicol Sci 2006;31:315-24
   PubMedGoogle Scholar
• Guengerich FP. Cytochrome p450 and chemical toxicology. Chem Res Toxicol 2008;21:70-83
   PubMed Web of Science ®Google Scholar
• Lewis DF, Dickins M. Substrate SARs in human P450s. Drug Discov Today 2002;7:918-25
   PubMed Web of Science ®Google Scholar
• Lewis DF, Dickins M. Baseline lipophilicity relationships in human cytochromes P450 associated with drug metabolism. Drug Metab Rev 2003;35:1-18
   PubMed Web of Science ®Google Scholar
• Wenlock MC, Austin RP, Barton P, A comparison of physiochemical property profiles of development and marketed oral drugs. J Med Chem 2003;46:1250-6
   PubMed Web of Science ®Google Scholar