A computational study of chiral separation of tryptophan by using cyclodextrin

A COMPUTATIONAL STUDY OF CHIRAL SEPARATION OF TRYPTOPHAN BY USING CYCLODEXTRIN LIANG JIANCHAO NATIONAL UNIVERSITY OF SINGAPORE 2009 A COMPUTATIONAL STUDY OF CHIRAL SEPARATION OF TRYPTOPHAN BY USING CYCLODEXTRIN LIANG JIANCHAO (B Eng (Hons.), NUS) A THESIS SUBMITTED FOR THE DEGREE OF MASTER OF ENGINEERING DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2009 ACKNOWLEDGEMENTS First of all, I would like to thank my main supervisor, Prof Raj Rajagopalan, for his enthusiasm, constant encouragement, insight and invaluable suggestions, patience and understanding during my research at the National University of Singapore His recommendations and ideas have helped me very much in completing this research project successfully I also want to thank my co-supervisor, Dr Jiang Jianwen, for his patient guidance and relentless encouragement He provides me with excellent training in molecular simulation, from which I benefited a lot during my Master research and will continue to benefit in my future career Next, I am grateful for the guidance and help in different ways from my group members, Hu Zhongqiao, Dr Fan Yanping, Li Jianguo, Sivashangari Gnanasambandam, Dhawal Shah, Ramakrishnan Vigneshwar, Babarao Ravichandar, Babarao Ravichandar, and Chen Yifei Last but not least, I want to thank my family and friends for their unconditional love and support throughout the years i TABLE OF CONTENTS Page Acknowledgements ⅰ Table of Contents ⅱ Summary ⅳ List of Tables ⅵ List of Figures ⅶ Chapter Introduction 1.1 General Background on Chirality 1.2 Implication of Chirality and Need for Producing Single Enantiomer Drugs 1.3 1.4 Motivations and Objectives 16 1.5 Chapter Methods for Chiral Separation 1.3.1 Direct Chiral Separation 1.3.2 Indirect Chiral Separation Structure of Thesis 17 Literature Reviews 2.1 19 2.2 Experimental Studies 21 2.3 Computational Studies 23 2.4 Chapter Fundamentals of Cyclodextrins What Remains Unsolved 26 Simulation Methodology 3.1 Molecular Models for β-Cyclodextrin and Tryptophan 27 ii 3.2 Chapter Simulation Methodology 3.2.1 Monte Carlo Simulations 3.2.2 Molecular Dynamics Simulations 28 Interaction Energy Calculations for the Inclusion Complexes 4.1 31 4.2 Binding Energy Calculations 4.2.1 Evolution of the Inclusion Complex 4.2.2 Interaction Energy of the Inclusion Complex 4.2.3 Formation of Hydrogen-Bonded Network 4.2.4 Radial Distribution Function Analysis 33 4.3 Chapter Complexation of β-Cyclodextrin and Tryptophan Summary 41 Membrane-Based Separation 5.1 43 5.2 Results and Discussion 46 5.3 Chapter Experiment Using Cyclodextrin-Functionalized Membranes Summary 49 Enhanced Chiral Separation Using Modified Cyclodextrin 6.1 6.2 References Enhanced Selectivity by Modified Cyclodextrin 52 6.2.1 Complexation of Modified Cyclodextrin and Tryptophan 6.2.2 Interaction Energy Calculation of the Inclusion Complex 6.3 Chapter Modification of Cyclodextrin Summary Concluding Remarks 50 57 59 61 iii SUMMARY Chirality is ubiquitous in living organisms, as nature has evolved to favor one “handedness” over the other The role of chirality has become firmly established in the pharmaceutical industry because of the fact that around 56% of the drugs currently in use are chiral compounds and about 88% of these chiral synthetic drugs are racemic mixtures The two enantiomers of a chiral drug may possess different pharmacological activity, potency, and mode of action In addition, a therapeutically inactive enantiomer may sometimes show unwanted effects and have antagonistic functions and even toxic effects Therefore, development of pure enantiomer drugs is of immense importance, and kinetic resolution of enantiomers from racemic mixtures is a critical element in the commercial production of enantiomerically pure chiral compounds It has been found in the literature that cyclodextrins have the ability to recognize and discriminate two enantiomers by forming transient inclusion diastereomeric complexes Hence, our objective here is to investigate the mechanisms of the complexation and enantiorecognition of cyclodextrin using computational methods and, further, to provide a framework for designing cyclodextrin chiral selectors with enhanced binding affinity and chiral selectivity In the present work, we study the energetic and conformational preferences involved in the chiral discrimination of tryptophan enantiomers by β-cyclodextrin using solventexplicit molecular simulations to elucidate chiral recognition mechanisms The behavior of the inclusion compounds formed by β-cyclodextrin and the guest molecule is examined through energy minimization and molecular dynamics (MD) simulations The iv trajectories from the MD simulations are used to obtain the relative weights of the different interaction energy components responsible for the discrimination In addition, we also formulate a computational model to simulate a macroscopic separation process involving flow of racemic mixture passing through a cyclodextrin-coated membrane The separation occurs because of the differences in the interactions of the two enantiomers with the β-cyclodextrin molecules, resulting in different effective mobility Our analysis based on MD simulations highlight the differences in the interactions between β-cyclodextrin and tryptophan enantiomers The simulations show that βcyclodextrin tends to perform induced-fit structural changes in order to accommodate the guest molecules more tightly The interaction energy calculations for the two diastereomeric complexes show that L-tryptophan forms a more stable complex with βcyclodextrin The results from the computational rendition of the membrane separation experiment are also consistent with the actual experimental results, which show that βcyclodextrin can be used to discriminate and separate the enantiomers of tryptophan However, the energy difference between the pair of diastereomeric complexes is quite small and the separation efficiency is not large enough for industrial application Therefore, in addition to native cyclodextrin, we have examined the possibility of using a cyclodextrin derivative, heptakis (2-O-Acetylated)-β-cyclodextrin, in place of native βcyclodextrin We find that the enantioselectivity of acetylated cyclodextrin is enhanced compared to native cyclodextrin However, the binding affinity is reversed, i.e the native cyclodextrin prefers binding with L-enantiomer, whereas acetylated cyclodextrin favors D-enantiomer v LIST OF TABLES Chapter Table 4.1 Binding energies between L-/D-tryptophan and β-cyclodextrin from the long-range (LR) and short-range (SR) Lennard-Jones (LJ) interactions as well as the Coulomb interactions .38 Table 4.2 The number of hydrogen bonds formed between β-cyclodextrin and the tryptophan enantiomer during the equilibrium simulation 39 Chapter Table 5.1 Self-diffusion coefficients for tryptophan enantiomers and water molecules 48 Chapter Table 6.1 Overall binding energies calculated and their individual components for the complexes…………………………………………………………….55 Table 6.2 The number of hydrogen bonds formed between Heptakis (2-OAcetylated)-β-cyclodextrin and tryptophan enantiomer at equilibrium …56 vi LIST OF FIGURES Chapter Figure 1.1 Schematic structures of S- and R-citalopram………………………… Figure 1.2 Conglomerate crystals of sodium ammonium ……………………………5 Figure 1.3 Simple three-point interaction model for stereochemical resolution…… Figure 1.4 Example of enantio-separation of adrenergic drugs (metoprolol or bisoprolol) by amide CSP …… Figure 1.5 Simple three-point interaction model for stereochemical resolution…… Figure 1.6 Model of metal complexation mechanism …… 10 Figure 1.7 The chemical structure of 18-crown-6-tetra-carboxylic acid …… 11 Figure 1.8 Structures of α-, β- and γ-cyclodextrins…… 13 Chapter Figure 2.1 The schematic representation of glucopyranoside unit and the cyclic structure of cyclodextrin ……………………………………………… 20 Chapter Figure 3.1 Graphical representations of β-cyclodextrin and D/L-tryptophan zwitterion molecules ……………………………………………… 28 Chapter Figure 4.1 Complex structures of D-tryptophan and β-cyclodextrin from MC simulation……………………………………………………………… 32 Figure 4.2 Complex structures of L-tryptophan and β-cyclodextrin from MC simulation 33 vii As shown in Figure 6.1, the β-cyclodextrin molecule consists of numerous hydroxyl groups, which are located in the C2, C3 and C6 positions It has been reported that the C6-OH groups at the primary rim are the most basic and nucleophilic; the C2-OH groups at the secondary rim are the most acidic; the C3-OH groups are the most inaccessible [69] The derivatives that are used in experiments are usually randomly substituted They are not homogenous; instead, they consist of a large number of isomers which differ in the degree of substitution as well as the position of substitution Almost every isomer has different chiral recognition abilities The degree of substitution is important in complexing capability of β-cyclodextrin derivatives with the guest molecules For example, in the case of (2-hydroxyl)propyl-β-cyclodextrin, the higher the degree of hydroxypropyl substitution, the poorer was the observed drug binding [70] Hence, the degree of chiral selectivity may also be affected by the degree of substitution For instance, it has been reported that the retention order of enantiomers could be reversed by using different degrees of substitution of sulfated β-cyclodextrin [58] Moreover, randomly substituted derivatives are difficult to reproduce and are unsuitable for mechanistic studies and method validation However, the synthesis of single-isomeric substituted derivatives is quite difficult Figure 6.1 Atom-labeling scheme for β- cyclodextrin 51 6.2 Enhanced Selectivity by Modified Cyclodextrin In order to enhance chiral selectivity, we study the cyclodextrin derivative, Heptakis (2O-Acetylated)-β-cyclodextrin, which is a single-isomeric derivative with a degree of substitution of seven, as shown in Figure 6.2 Figure 6.2 Atomic structures of Heptakis (2-O-Acetylated)-β-cyclodextrin 6.2.1 Complexation of Modified Cyclodextrin and Tryptophan We use Monte Carlo Simulations (details discussed in Chapter 4.1) to identify the possible binding site about the complexation occurred between (L- or D-) tryptophan and Heptakis (2-O-Acetylated)-β-cyclodextrin In contrast to the native β-cyclodextrin, where only one binding configuration occurs, two different binding modes are found for the Heptakis (2-O-Acetylated)-β-cyclodextrin and tryptophan, named as L1-complex and L2complex for L-tryptophan with the chiral selector and the name of D1-complex and D252 complex for D-tryptophan with the chiral selector As shown in Figure 6.3, for L1complex and D1-complex, the aromatic ring of tryptophan faces the primary rim; whereas it faces the secondary rim in the L2-complex and D2-complex (a) (b) (c) (d) Figure 6.3 The structures of complexes of tryptophan and Heptakis (2-O-Acetylated)-βcyclodextrin from MC simulations (a) L1-complex, (b) D1-complex, (c) L2complex, (d) D2-complex 53 6.2.2 6.2.2.1 Interaction Energy Calculations of the Inclusion Complex Comparison between the L-complex and D-complex As we have stated, the interaction energy of complexation is one measurement of the stability of the inclusion complexes formed by enantiomers and Heptakis (2-OAcetylated)-β-cyclodextrin The overall interaction energy of the complex and the different components of the energy are shown in Table 6.1 The first column shows the center of mass distance (COM) between the tryptophan and the chiral selector, which gives indication of how closely the two molecules are packed together It is found that for both inclusion modes, the COM distances for the D-complex are smaller than that for the L-complex (0.244 nm for the D1-complex and 0.306 nm for the L1-complex, 0.132 nm for the D2-complex and 0.132 for the L2-complex); correspondingly, the interaction energies for the D-complex are lower than those for the L-complex (−162.1 kJ/mol for the D1-complex and −137.9 kJ/mol for the L1-complex, −205.4 kJ/mol for the D2complex and −193.6 kJ/mol for the L2-complex) Hence, we conclude that D-tryptophan binds more strongly with the chiral selector than L-tryptophan for both the inclusion modes From the analysis of the individual components of the interaction energy, it is found that short-range Lennard-Jones interactions are mainly responsible for the complex formation since they are the main constituents for the overall interaction energy; however, Coulombic interactions take the primary responsibility for the enantiodiscrimination 54 because the difference for the Coulomb interaction for the L-complex and D-complex dominates in the overall interaction energy difference Table 6.1 Overall binding energies calculated and their individual components for the complexes COM stands for Center of Mass Distance (nm) (kJ/mol) L1-Complex COM (nm) 0.306 LJ-(SR) LJ-(LR) Coulomb – 113.8 – 0.3 – 23.8 Interaction Energy – 137.9 D1-Complex 0.244 – 109.6 – 0.3 – 52.2 – 162.1 Difference L2-complex 0.062 0.132 – 4.2 – 121.4 0.0 – 0.2 28.4 – 72.0 24.2 – 193.6 D2-complex 0.093 – 123.8 – 0.2 – 81.5 – 205.4 Difference 0.039 2.4 0.0 9.5 11.8 The same conclusion, namely, that D-tryptophan binds to Heptakis (2-O-Acetylated)β-cyclodextrin more strongly than L-tryptophan, can also be drawn from the hydrogen bond formation analysis as shown in Table 6.2 The average number of hydrogen bond formed during the simulation is larger for the D-complex compared to the number for the L-complex (1.81 for the D1-complex and 0.80 for the L1-complex, 2.34 for the D2complex and 2.29 for the L2-complex) Moreover, the number of time–frames over which several hydrogen bonds exist simultaneously between tryptophan and cyclodextrin molecules is larger for the D-complex than the L-complex This means that D-tryptophan seems to form network of multiple hydrogen bonds with the chiral selector so that the formation of the inclusion complex by D-tryptophan and cyclodextrin is more energetically favorable 55 Table 6.2 The number of hydrogen bonds (HB) between Heptakis (2-O-Acetylated)-βcyclodextrin and tryptophan enantiomer at equilibrium “Single HB” represents the number of time frames over which only one hydrogen-bond is formed “Two HB”, “Three HB” and “Four HB” represent the number of time frames over which there are two, three and four hydrogen bonds formed simultaneously No of Hbond Average Single HB Two HB Three HB Four HB L1-Complex D1-Complex 0.80 1.81 4558 2536 1264 4614 52 76 0 L2-complex 2.29 1775 3614 2636 783 D2-complex 2.34 1293 3997 2727 781 6.2.2.2 Comparison between the Two Inclusion Modes As already stated, there are two possible binding modes for the formation of the inclusion complex One is the aromatic ring of tryptophan facing the primary rim (L1-complex and D1-complex); the other is the aromatic ring facing the secondary rim (L2-complex and D2-complex) The second inclusion mode is more stable than the first one because of the smaller COM distance (0.132 nm for the L2-complex and 0.306 nm for the L1-complex, 0.093 nm for the D2-complex and 0.244 nm for the D1-complex), the lower overall interaction energy and the more average number of hydrogen bonds for the second inclusion mode Although the second inclusion mode is more favorable, the first inclusion mode provides larger possibility for enantiodiscrimination since there exits a large difference in the overall interaction energy and average number of hydrogen bonds between the L-complex and the D-complex 56 6.2.2.3 Comparison between the Native and Derivatized Cyclodextrin As we have discussed, the purpose of derivatizing native cyclodextrins is to enhance the binding affinity and chiral discrimination of the chiral selector for analyte enantiomers For the acetylated cyclodextrin, we found that the enantioselectivity towards tryptophan has been enhanced compared to native cyclodextrin (∆∆E ~ 18 kJ/mol for acetylated cyclodextrin and ∆∆E ~ kJ/mol for native cyclodextrin) In the case of the native cyclodextrin, short-range Lennard-Jones interactions are responsible for both the complex formation and chiral discrimination; however, for the acetylated cyclodextrin, it is the coulomb interactions that take the responsibility for enantiodiscrimination although the short-range Lennard-Jones interactions still play an important role in complex formation Moreover, the binding affinity is reversed for the derivatized cyclodextrin since the native cyclodextrin prefers binding with the L-enantiomer and the acetylated cyclodextrin binds with the D-enantiomer more strongly 6.3 Summary Because of the numerous hydroxyl groups situated at both the primary and secondary rims of native cyclodextrins, cyclodextrins can be derivatized by other functional groups to introduce new structure and functionality into cyclodextrins that are unavailable in the native form The modification of the native cyclodextrins may enhance the binding affinity and chiral selectivity towards analyte molecules However, the challenges facing modification are that there are so many hydroxyl groups and the production of singleisomeric derivative form is difficult In the present work, we studied one single-isomeric 57 derivative, Heptakis (2-O-Acetylated)-β-cyclodextrin, to investigate the effect of the derivatization on chiral selectivity The results show that this derivatized form of cyclodextrin gives better chiral selectivity than native form with a reverse pattern of binding 58 CHAPTER CONCLUDING REMARKS The main objective of this work is to investigate a few key fundamental issues concerning the mechanism of how cyclodextrins as chiral selectors bind and recognize the two enantiomers of chiral molecule through molecular simulations Here, we choose β-cyclodextrin as the chiral selector and tryptophan as the chiral molecule First, an initial picture of the formation of an inclusion complex by β-cyclodextrin and tryptophan enantiomer is obtained from Monte Carlo simulations Then, molecular dynamics simulations are used to study the dynamics of the complex in a solvent as a function of time Based on the overall interaction energy calculations, formation of the hydrogen-bonded networks and radial distribution functions, we conclude that Ltryptophan interacts with β-cyclodextrin more strongly than D-tryptophan Moreover, short-range Lennard-Jones interactions play a major role in both the complex formation and chiral discrimination It is possible to enhance the enantioselectivity by introducing Coulomb interactions using charged cyclodextrin derivatives In addition, the secondary rim of β-cyclodextrin is more responsible for the enantiorecognition because Dtryptophan interacts with the C2 hydroxyl group on β-cyclodextrin more strongly and Ltryptophan interacts with C3 hydroxyl group on β-cyclodextrin molecule favorably (Figure 2.1) Therefore, derivatizing β-cyclodextrin with functional groups at the C2 or C3 position may allow one to alter the selectivity towards tryptophan enantiomers 59 Secondly, a computational model for separating racemic mixtures is established in order to mimic real experiments based on membrane-based separation systems in which the chiral selector grafted on the membrane surface acts as a chiral film to discriminate enantiomers The β-cyclodextrin molecules bind the two enantiomers with different stability, which, in turn, results in different effective transport of the enantiomers and different displacement with time The enantiomer that binds to β-cyclodextrin more strongly will be transported through the chiral film slower than the other enantiomer Further, because of the low chiral selectivity of β-cyclodextrin, the separation efficiency we predict is also quite small (about 1.1), which is consistent with the experimental value of 1.0 reported recently by Xiao and Chung [41] and with our binding energy 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Zhongqiao, Dr Fan Yanping, Li Jianguo, Sivashangari Gnanasambandam, Dhawal Shah, Ramakrishnan Vigneshwar, Babarao Ravichandar, Babarao Ravichandar, and Chen Yifei Last but not least, I want to thank... found application in the chiral separation of a great variety of drugs 2.3 Computational Studies Along with the dramatical increase in experimental studies of chiral separation by cyclodextrins, a. .. the enantiomers are separated by crystallization or by using chiral separation phases, and the other is the indirect method of separation, where the pair of enantiomers are reacted with another