Abstract
With the wealth of experimental physicochemical data available to chemoinformaticians from the literature, commercial, and company databases an increasing challenge is the interpretation of such datasets. Subtle differences in experimental methodology used to generate these datasets can give rise to variations in physicochemical property values. Such methodology nuances will be apparent to an expert experimentalist but not necessarily to the data analyst and modeller. This paper describes the differences between common methodologies for measuring the four most important physicochemical properties namely aqueous solubility, octan-1-ol/water distribution coefficient, pK a and plasma protein binding highlighting key factors that can lead to systematic differences. Insight is given into how to identify datasets suitable for combining.
Similar content being viewed by others
References
Stouch TR, Kenyon JR, Johnson SR, Chen X, Doweyko A, Li Y (2003) In silico ADME/Tox: why models fail. J Comput-Aided Mol Des 17:83–92
Bard B, Martel S, Carrupt PA (2008) High throughput UV method for the estimation of thermodynamic solubility and the determination of the solubility in biorelevant media. Eur J Pharm Sci 33:230–240
Colclough N, Hunter A, Kenny PW, Kittlety RS, Lobedan L, Tam KY, Timms MA (2008) High throughput solubility determination with application to selection of compounds for fragment screening. Bioorgan Med Chem 16:6611–6616
Chen T, Shen H, Zhu C (2002) Evaluation of a method for high throughput solubility determination using a multi-wavelength UV plate reader. Comb Chem High Throughput Screen 5:575–581
Avdeef A (2001) High throughput measurements of solubility profiles. In: Testa B, van de Waterbeemd H, Folkers G, Guy R (eds) Pharmacokinetic optimization in drug research: biological, physicochemical, and computational strategies. Verlag Helvetica Chimica Acta, Zürich
Wenlock MC, Austin RP, Potter T, Barton P (2011) A highly automated assay for determining the aqueous equilibrium solubility of drug discovery compounds. J Lab Autom 16:276–284
Alelyunas YW, Liu R, Pelosi-Kilby L, Shen C (2009) Application of a dried-DMSO rapid throughput 24-h equilibrium solubility in advancing discovery candidates. Eur J Pharm Sci 37:172–182
Zhou L, Yang L, Tilton S, Wang J (2007) Development of a high throughput equilibrium solubility assay using miniaturized shake-flask method in early drug discovery. J Pharm Sci 96:3052–3071
Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 23:4–25
Bevan C, Lloyd RS (2000) A high-throughput screening method for the determination of aqueous drug solubility using laser nephelometry in micro-titer plates. Anal Chem 72:1781–1787
Fligge TA, Schuler A (2006) Integration of a rapid automated solubility classification into early validation of hits obtained by high throughput screening. J Pharm Biomed Anal 42:449–454
Avdeef A, Berger CM, Brownell C (2000) pH-metric solubility. 2: correlation between the acid–base titration and the saturation shake-flask solubility-pH methods. Pharm Res 17:85–89
Stuart M, Box K (2005) Chasing equilibrium: measuring the intrinsic solubility of weak acids and bases. Anal Chem 77:983–990
Pudipeddi M, Serajuddin AT (2005) Trends in solubility of polymorphs. J Pharm Sci 94:929–939
Buckton G (2002) Particle science and powder technology-Solid state properties. In: Aulton ME (ed) Pharmaceutics the science of dosage form design, 2nd edn. Churchill Livingstone, London
Colclough N, Ruston L, Tam K (2009) Aqueous solubility in drug discovery chemistry, DMPK, and biological assays. In: van de Waterbeemd H, Testa B (eds) Drug bioavailability: estimation of solubility, permeability, absorption and bioavailability, 2nd edn. Wiley-VCH, Weinheim
Hancock B, Parks M (2000) What is the true solubility advantage for amorphous pharmaceuticals. Pharm Res 17:397–404
Sugano K, Kato T, Suzuki K, Keiko K, Sujaku T, Mano T (2006) High throughput solubility measurement with automated polarized light microscopy analysis. J Pharm Sci 95:2115–2122
Di L, Fish PV, Mano T (2012) Bridging solubility between drug discovery and development. Drug Discov Today 17:486–495
Leo AJ (1991) Hydrophobic parameter: measurement and calculation. Method Enzymol 202:544–591
Wan H, Holmén AG (2009) High throughput screening of physicochemical properties and in vitro ADME profiling in drug discovery. Comb Chem High Throughput Screen 12:315–329
Wilson DM, Wang X, Walsh E, Rourick RA (2001) High throughput log D determination using liquid chromatography–mass spectrometry. Comb Chem High Throughput Screen 4:511–519
Alelyunas YW, Pelosi-Kilby L, Turcotte PL, Kary M, Spreen RC (2010) A high throughput dried DMSO log D lipophilicity measurement based on 96-well shake-flask and atmospheric pressure photoionization mass spectrometry detection. J Chromatogr A 1217:1950–1955
Wenlock MC, Potter T, Barton P, Austin RP (2011) A method for measuring the lipophilicity of compounds in mixtures of 10. J Biomol Screen 16:348–355
Dohta Y, Yamashita T, Horiike S, Nakamura T, Fukami T (2007) A system for logD screening of 96-well plates using a water-plug aspiration/injection method combined with high-performance liquid chromatography-mass spectrometry. Anal Chem 79:8312–8315
Valkó K (2004) Application of high-performance liquid chromatography based measurements of lipophilicity to model biological distribution. J Chromatogr A 1037:299–310
Slater B, McCormack A, Avdeef A, Comer JE (1994) pH-metric log P. 4. Comparison of partition coefficients determined by HPLC and potentiometric methods to literature values. J Pharm Sci 83:1280–1283
Alimuddin M, Grant D, Bulloch D, Lee N, Peacock M, Dahl R (2008) Determination of log D via automated microfluidic liquid–liquid extraction. J Med Chem 51:5140–5142
Vrakas D, Giaginis C, Tsantili-Kakoulidou A (2006) Different retention behavior of structurally diverse basic and neutral drugs in immobilized artificial membrane and reversed-phase high performance liquid chromatography: comparison with octanol-water partitioning. J Chromatogr A 1116:158–164
Wong K, Kenseth J, Strasburg R (2004) Validation and long-term assessment of an approach for the high throughput determination of lipophilicity (log Pow) values using multiplexed, absorbance-based capillary electrophoresis. J Pharm Sci 93:916–931
Lombardo F, Shalaeva MY, Tupper KA, Gao F (2001) ElogDoct: a tool for lipophilicity determination in drug discovery. 2. Basic and neutral compounds. J Med Chem 44:2490–2497
Leo A, Hansch C, Elklns D (1971) Partition coefficients and their uses. Chem Rev 71:525–616
Schumacher GE, Nagwekar JB (1974) Kinetic and thermodynamic aspects of in vitro interphase transfer of sulfonamides I: influence of methyl group substitution on transfer of unionized sulfonamides. J Pharm Sci 63:240–244
Austin RP, Barton P, Davis AM, Manners CN, Stansfield MC (1998) The effect of ionic strength on liposome-buffer and 1-octanol-buffer distribution coefficients. J Pharm Sci 87:599–607
Wenlock MC, Barton P, Luker T (2011) Lipophilicity of acidic compounds: impact of ion pair partitioning on drug design. Bioorg Med Chem Lett 21:3550–3556
Li A, Yalkowsky SH (1998) Predicting cosolvency. 2. Correlation with solvent physicochemical properties. Ind Eng Chem Res 37:4476–4480
DeWitte RS (2006) Avoiding physicochemical artefacts in early ADME-Tox experiments. Drug Discov Today 11:855–859
Analiza Inc (2000) Technical note ADW-01, Cleveland,http://disruptechno2.free.fr/Analiza/ADW%20Tech%20Note%201%20-%20Buffer%20Effects.pdf. Accessed 26 Jan 2015
Alvarado YJ, Ballestas-Barrientos A, Cubillán N, Morales-Toyo M, Restrepo J, Ferrer-Amado G (2013) Preferential solvation of thiophene and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures. Spectrochim Acta A Mol Biomol Spectrosc 103:361–367
Leeson PD, Springthorpe B (2007) The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 6:881–890
Hughes JD, Blagg J, Price DA, Bailey S, DeCrescenzo GA, Devraj RV, Ellsworth E, Fobian YM, Gibbs ME, Gilles RW, Greene N, Huang E, Krieger-Burke T, Loesel J, Wager T, Whiteley L, Zhang Y (2008) Physiochemical drug properties associated with in vivo toxicological outcomes. Bioorg Med Chem Lett 18:4872–4875
Völgyi G, Ruiz R, Box K, Comer J, Bosch E, Takács-Novák K (2007) Potentiometric and spectrophotometric pK a determination of water-insoluble compounds: validation study in a new cosolvent system. Anal Chim Acta 583:418–428
Ishihama Y, Oda Y, Asakawa N (1994) Microscale determination of dissociation constants of multivalent pharmaceuticals by capillary electrophoresis. J Pharm Sci 83:1500–1507
Nielsen JE (2008) Analysing protein NMR pH-titration curves. In: Wheeler R, Spellmeyer D (eds) Annual reports in computational chemistry, 1st edn. Elsevier, Amsterdam
Valkó K (2014) Physicochemical and biomimetic properties in drug discovery: chromatographic techniques for lead optimization. Wiley, New Jersey
Avdeef A (2007) Solubility of sparingly-soluble ionizable drugs. Adv Drug Deliv Rev 59:568–590
Wenlock MC, Barton P (2013) In silico physicochemical parameter predictions. Mol Pharm 10:1224–1235
ACD/pK a DB (2012) Advanced Chemistry Development Inc. Toronto, Canada. http://www.acdlabs.com/products/percepta/predictors/pka/
Avdeef A (1983) Weighting scheme for regression analysis using pH data from acid–base titrations. Anal Chim Acta 148:237–244
Avdeef A (1993) pH-metric log P. II: refinement of partition coefficients and ionization constants of multiprotic substances. J Pharm Sci 82:183–190
Tam KY, Takács-Novák K (2001) Multi-wavelength spectrophotometric determination of acid dissociation constants: a validation study. Anal Chim Acta 434:157–167
Allen RI, Box KJ, Comer JEA, Peake C, Tam KY (1998) Multi-wavelength spectrophotometric determination of acid dissociation constants of ionizable drugs. J Pharm Biomed Anal 17:699–712
Wan H, Holmén AG, Wang Y, Lindberg W, Englund M, Någård M, Thompson RA (2003) High-throughput screening of pK a values of pharmaceuticals by pressure-assisted capillary electrophoresis and mass spectrometry. Rapid Commun Mass Spectrom 17:2639–2648
Miller JM, Blackburn AC, Shi Y, Melzak AJ, Ando HY (2002) Semi-empirical relationships between effective mobility, charge, and molecular weight of pharmaceuticals by pressure-assisted capillary electrophoresis: application in drug discovery. Electrophoresis 23:2833–2841
Avdeef A, Comer JE, Thomson SJ (1993) pH-metric log P. 3. Glass electrode calibration in methanol-water, applied to pK a determination of water-insoluble substances. Anal Chem 65:42–49
Trainor GL (2007) Plasma protein binding and the free drug principle: Recent developments and applications. In: Macor JE (ed) Annual reports in medicinal chemistry. Elsevier, Amsterdam
Tozer TN, Rowland M (2006) Introduction to pharmacokinetics and pharmacodynamics: the quantitative basis of drug therapy. Lippincott Williams & Wilkins, Baltimore
Wan H, Rehngren M (2006) High-throughput screening of protein binding by equilibrium dialysis combined with liquid chromatography and mass spectrometry. J Chromatogr A 1102:125–134
Weder HG, Schildknecht J, Kesselring P (1971) A new equilibrium dialyzing system. Am Lab 10:15–21
Kariv I, Cao H, Oldenburg KR (2001) Development of a high throughput equilibrium dialysis method. J Pharm Sci 90:580–587
Klotz IM, Walker FM, Pivan RB (1946) The binding of organic ions by proteins. J Am Chem Soc 68:1486–1490
Liu Z, Li F, Huang Y (1999) Determination of unbound drug concentration and protein-drug binding fraction in plasma. Biomed Chromatogr 13:262–266
Lin JH, Cocchetto DM, Duggan DE (1987) Protein binding as a primary determinant of the clinical pharmacokinetic properties of non-steroidal anti-inflammatory drugs. Clin Pharmacokinet 12:402–432
Colowick SP, Womack FC (1969) Binding of diffusible molecules by macromolecules: rapid measurement by rate of dialysis. J Biol Chem 244:774–777
Zhang J, Musson DG (2006) Investigation of high-throughput ultrafiltration for the determination of an unbound compound in human plasma using liquid chromatography and tandem mass spectrometry with electrospray ionization. J Chromatogr B Anal Technol Biomed Life Sci 843:47–56
Hall S, Rowland M (1983) Relationship between renal clearance, protein binding and urine flow for digitoxin, a compound of low clearance in isolated perfused rat kidney. J Pharmacol Exp Ther 228:174–180
Aarons L, Grennan DM, Siddiqui M (1983) The binding of ibuprofen to plasma proteins. Eur J Clin Pharmacol 25:815–818
Yuan J, Yang DC, Birkmeier J, Stolzenbac J (1995) Determination of protein binding by in vitro charcoal adsorption. J Pharmacokinet Biopharm 23:41–55
Wenlock MC, Barton P, Austin RP (2011) A kinetic method for the determination of plasma protein binding of compounds unstable in plasma: specific application to enalapril. J Pharm Biomed Anal 55:385–390
Rich RL, Day YS, Morton TA, Myszka DG (2001) High-resolution and high-throughput protocols for measuring drug/human serum albumin interactions using BIACORE. Anal Biochem 296:197–207
Lázaro E, Lowe PJ, Briand X, Faller B (2008) New approach to measure protein binding based on a parallel artificial membrane assay and human serum albumin. J Med Chem 51:2009–2017
Yasgar A, Furdas SD, Maloney DJ, Jadhav A, Jung M, Simeonov A (2012) High-throughput 1,536-well fluorescence polarization assays for a1-acid glycoprotein and human serum albumin binding. PLoS One. doi:10.1371/journal.pone.0045594
Valkó K, Nunhuck S, Bevan C, Abraham MH, Reynolds DP (2003) Fast gradient HPLC method to determine compounds binding to human serum albumin. Relationships with octanol/water and immobilized artificial membrane lipophilicity. J Pharm Sci 92:2236–2248
Hage DS, Austin J (2000) High-performance affinity chromatography and immobilized serum albumin as probes for drug- and hormone-protein binding. J Chromatogr B Biomed Sci Appl 739:39–54
Betucci C, Salvadori P, Domenici E (1997) Circular dichroism in the study of stereoselective binding of drugs to serum proteins. In: Aboul-Ebnein HY, Wainer IW (eds) The impact of stereochemistry on drug development and use. Wiley, New York
Di L, Umland JP, Trapa PE, Maurer TS (2012) Impact of recovery on fraction unbound using equilibrium dialysis. J Pharm Sci 101:1327–1335
Fura A, Harper TW, Zhang H, Fung L, Shyu WC (2003) Shift in pH of biological fluids during storage and processing: effect on bioanalysis. J Pharm Biomed Anal 32:513–522
Ha CE, Petersen CE, Park DS, Harohalli K, Bhagavan NV (2000) Investigations of the effects of ethanol on warfarin binding to human serum albumin. J Biomed Sci 7:114–121
Banker MJ, Clark TH, Williams JA (2003) Development and validation of a 96-well equilibrium dialysis apparatus for measuring plasma protein binding. J Pharm Sci 92:967–974
Malik N, Glazier AP, Chadwick AP, Adjin-Tetty G, Lankester DJ (2008) Measurement of plasma protein binding: a comparison of conventional 96 well plate and rapid equilibrium dialysis (RED) methodologies. Drug Metab Rev 40(S1):112
Huang JD (1983) Errors in estimating the unbound fraction of drugs due to the volume shift in equilibrium dialysis. J Pharm Sci 72:1368–1369
Lee KJ, Mower R, Hollenbeck T, Castelo J, Johnson N, Gordon P, Sinko PJ, Holme K, Lee YH (2003) Modulation of nonspecific binding in ultrafiltration protein binding studies. Pharm Res 20:1015–1021
Israili ZH, Dayton PG (2001) Human alpha-1-glycoprotein and its interactions with drugs. Drug Metab Rev 33:161–235
Buttar D, Colclough N, Gerhardt S, MacFaul PA, Phillips SD, Plowright A, Whittamore P, Tam K, Maskos K, Steinbacher S, Steuber H (2010) A combined spectroscopic and crystallographic approach to probing drug–human serum albumin interactions. Bioorg Med Chem 18:7486–7496
Bhattacharya AA, Grüne T, Curry S (2000) Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin. J Mol Biol 303:721–732
Wenlock MC, Carlsson LA (2015) How experimental errors influence drug metabolism and pharmacokinetic QSAR/QSPR models. J Chem Inf Model 55:125–134
Steinmetz FP, Enoch SJ, Madden JC, Nelms MD, Rodriguez-Sanchez N, Rowe PH, Wen Y, Cronin MTD (2014) Methods for assigning confidence to toxicity data with multiple values—identifying experimental outliers. Sci Total Environ 482–483:358–365
Acknowledgments
The authors would like to thank the AstraZeneca scientists who have worked in the physical chemistry field across the company (Alderley Park, Charnwood, Reims, Wilmington, Lund, Södertälje, Mölndal, Montreal, Boston) over the last 25 years who have generated much of the data discussed in this paper. Also thanks to our colleagues at Pharmaron who have generated the more recent physical property results. In particular the authors would like to thank our Alderley Park and Charnwood physical chemistry colleagues past and present for the many discussions which have contributed to the learning presented in this paper.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Colclough, N., Wenlock, M.C. Interpreting physicochemical experimental data sets. J Comput Aided Mol Des 29, 779–794 (2015). https://doi.org/10.1007/s10822-015-9850-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10822-015-9850-7