The Calculation of Physicochemical Descriptors and their Application in Predicting Properties of Drugs and Other Compounds A Thesis Presented to the University of London for the Degree of Doctor of Philosophy in the Faculty of Science By JOELLE LE Sir Christopher Ingold Laboratories Chemistry Department University College London January 2001 ProQuest Number: 10010399 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest 10010399 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 To my mother Abstract The work presented may be divided into two main sections: The first section focuses on the important aspect of compound descriptor determination. The method by which descriptors are obtained indirectly through compound solubility in organic solvents and direct water-solvent partition measurements is illustrated by example for drug compounds. This approach is extended through the derivation of gas-water and water-solvent partition equations for the n-alcohols which in the future will be available for use in descriptor determination. Importantly, the equation coefficients are also interpreted to deduce various physicochemical properties of the homologous series of alcohols. An alternative method to assign descriptors is probed through reversed-phase HPLC. Measurements are recorded for a series of solutes on several bonded phases and multivariate analysis is used to investigate the interrelationship between columns in an effort to isolate the most suitable phases. The second section is concerned with application of the Abraham General Solvation Equation to examine processes of special interest in drug design; aqueous solubility and intestinal absorption. An algorithm to predict water solubility is obtained containing an additional Eocz^x Ep 2^ cross-term which is found to compensate at least partly for a melting point correction term. The amended equation is shown to be comparable in accuracy to commercially available packages for a test set of 268 structurally diverse compounds. Of further importance in drug delivery is the process of intestinal absorption. An extensive literature search provides evaluated absorption data for a large set of drug compounds and forms a strong basis for subsequent QSAR analysis. Intestinal absorption is found to be comparable in humans and rat, and predominantly dependent on the hydrogen-bonding capability of the drug. The mechanism of absorption is considered through transformation of the percent absorption data to an overall rate constant. Table of Contents Page no. Abstract 1 Table of Contents 2 List of Tables 6 Acknowledgements 10 Chapter 1 Introduction to the Abraham General Solvation Equation 1.1 History of QSAR and LFERs 11 1.2 Physicochemical Descriptors 13 1.3 Linear Solvation Energy Relationships 20 1.4 The Abraham General Solvation Equations 22 1.4.1 The Excess Molar Refraction, R 2 24 1.4.2 Solute Hydrogen-bond acidity, (% 2^ 25 1.4.3 Solute Hydrogen-bond acidity, p 2^ 26 1.4.4 Effective solute scales of S a 2^, Sp 2^, 7t2^ 27 1.4.5 McGowan’s Characteristic Volume, Vx 30 1.4.6 Estimation of Descriptors using Group Contribution Approach 31 1.5 Multiple Linear Regression Analysis (MLRA) 33 1.5.1 Difficulties with MLRA 37 1.6 References 38 Chapter 2 Aims of the Present Work 2.0 Aims of the Present Work 42 Chapter 3 The Determination of Solute Descriptors 3.1 Method for Descriptor Determination 45 3.2 Example : Descriptors for Vinclozin 49 3.3 Descriptors for Diazepam Analogues 51 3.4 Descriptors for P-blockers 65 3.5 Conclusion 71 3.6 References 72 Chapter 4 The Solvation Properties of the Aliphatic Alcohols 4.1 The Solubility of Gases and Vapours in Alkan-l-ols 73 4.2 Water-alcohol Partitions 86 4.3 References 92 4.4 Data tables 100 Chapter 5 Characterization of HPLC phases and use of HPLC in descriptor determination 5.1 Introduction to HPLC 117 5.2 Concepts of HPLC 118 5.2.1 Fundamental Relationships of Chromatography 120 123 5.2.2 Retention Mechanisms 126 5.2.3 Stationary Phases 129 5.2.4 Solvents 5.2.5 Instrumental Aspects 130 5.3 Experimental Section 132 5.4 Comparison of Stationary Phases 140 5.5 Use of Water-solvent Partition Measurements (WSPM) to obtain 147 Abraham Descriptors and Comparison with HPLC Systems 5.5.1 WSPM in Descriptor Determination 147 5.5.2 Characterization of HPLC Systems 149 5.5.2a Vector Analysis 151 5.5.2b Principal Component Analysis (PCA) 153 5.5.3 Comparison of HPLC and Water-solvent Partition Systems 154 5.5.4 Application of HPLC in Descriptor Determination 156 5.5.5 Conclusion 163 5.6 References 167 Chapter 6 The Solubility of Compounds in Water 6.1 Introduction 169 6.2 Prediction Methods 170 6.2.1 Comparison of Literature Models 175 6.3 Application of the Abraham General Solvation Equation in Prediction 178 6.3.1 Test set results : Comparison with Other Prediction Methods 184 6.3.2 Final Equations (for total dataset) 187 6.3.3 Influence of Very High and Very Low Soluble Compounds 189 6.3.4 The Factors that Influence Aqueous Solubility 191 6.4 The Solubility of Bronsted Acids and Bases 193 6.5 References 198 6.6 Data tables 202 Chapter 7 Gastrointestinal (GI) Absorption of Drug Compounds 7.1 Introduction 225 7.1.1 General Mechanisms for Transport of Substances Across 226 Biological Membranes 7.1.2 Factors Influencing Intestinal Absorption 229 7.1.2a Physicochemical Properties 230 7.1.2b Physiological Properties 235 7.1.3 Hepatic Drug Metabolism 238 7.1.4 The Prediction of Human GI Absorption 240 7.2 Human GI Absorption 244 7.2.1 Evaluation of Human Absorption Data 244 7.2.2 Relationship Between Human GI Absorption and Abraham 269 Descriptors 7.3 Rat GI Absorption 283 7.3.1 Evaluation of Rat GI Absorption Data 284 7.3.2 Relationship Between Rat GI absorption and Abraham 290 Descriptors 7.4 Comparison Between Human and Rat GI absorption 299 7.5 The Mechanism of Human GI Absorption 302 7.5.1 Bronsted Acids and Bases 309 7.5.2 Characterization of the Absorption System 313 7.5.3 Conclusion 317 7.6 Partitioning of Drug Compounds onto a C]g Disk 319 7.6.1 Experimental 319 7.6.2 Calculations 320 7.6.3 Results 321 7.7 References 328 Chapter 8 Visualisation of the Abraham General Solvation Equation 8.0 Visualisation of the Abraham General Solvation Equation 354 Chapter 9 Conclusions and Suggestions for Future Work 9.0 Conclusions and Suggestions for Future Work 357 List of Tables Chapter 1 Introduction to the Abraham General Solvation Equation Page no. Table 1.1 Multivariate statistical techniques 20 Table 1.2 Comparison of effective solute descriptors and those based on 28 1:1 equilibrium constants Table 1.3 Characteristic atomic volumes, Vx in cm^ mol'^ 31 Table 1.4 Results of regression using 81 modified parameters to estimate 32 Abraham descriptors Table 1.5 Results of training and test set regressions using Group 32 Contribution approach Chapter 3 The Determination of Solute Descriptors Table 3.1 Eqn coefficients for partition between water and solvents 47 Table 3.2 Eqn coefficients for partition between the gas phase and 48 solvents Table 3.3 Solvent solubilities of vinclozolin (S in mol dm'^), and derived 49 partition coefficients Table 3.4 Observed and calculated values of log P and log for 50 vinclozolin Table 3.5 Descriptors for Diazepam analogues and (3-blockers 71 Chapter 4 The Solvation Properties of the Aliphatic Alcohols Table 4.01 Calculation of log L in dry octan-l-ol at 298K 75 Table 4.02 Descriptor space for the octan-l-ol regression (eqn 14) 79 Table 4.03 Coefficients in the log L equations for gas-solvent partitions at 80 298K Table 4.04 Some properties of bulk solvents 82 Table 4.05 A term-by-term analysis of solvation of gaseous solutes at 84 298K Table 4.06 Values of the Kamlet-Taft solvatochromie parameters for 85 water and some alcohol solvents Table 4.07 Coefficients in the log? equation for water-solvent partitions 88 6 Table 4.08 Solute Abraham descriptors and log values used in alkan-1- 100 ol regressions PrOH Table 4.09 Values of log L"^"calc, log L'^, log and log 104 cale for solutes at 298K Table 4.10 Values of log log L'^, log and log 106 calc for solutes at 298K Table 4.11 Values of log log L'^, log and log 108 calc for solutes at 298K Table 4.12 Values of log log L'^, log P " " ° " ^ and log 110 calc for solutes at 298K Table 4.13 Values of log log L’^, log and log 111 pHeptOHAv 298K Table 4.14 Values of log log L", log p°'='°H™' and log P°"°"™ 112 calc for solutes at 298K Table 4.15 Values of log log L*, log pD“ °H^ and log pD“=°H™' 115 calc for solutes at 298K Chapter 5 Characterization of HPLC phases and use of HPLC in Descrijptor Determination Table 5.01 Solvent properties 130 Table 5.02 Abraham descriptors for training set solutes 134 Table 5.03 HPLC columns used 136 Table 5.04 Log k’ values for compounds obtained from each stationary ^37 phase and mobile phase composition (MeCN/H 2 0 ) Table 5.05 LFERs obtained for each of the HPLC systems 139 Table 5.06 Coefficients of 60/40 (MeCN/HzO) mobile phase composition for the different stationary phases Table 5.07 Ratios of LEER coefficients