Investigation Of Cyclodextrin-Based Supramolecular Recognition By Molecular Dynamics Simulation

As a second generation of supramolecular targets after crown ether, cyclodextrins (CDs) have attracted considerable attention from scientific and technological workers since CDs were discovered. The particular property of CDs with a somewhat hydrophobic cavity and a hydrophilic surface allows accommodating guest molecules of suitable size in CD cavities and hence leads to a wide range of interesting applications, like in the food chemistry, Pharmaceuticals, environmental protection, and chemical industry. In the chromatography, they have been extensively used as a ligand coupled to stationary phases or mobile phase additives for efficient separation and purification of the target analyte. Further investigation on the mechanism behind such chromatography experiments helps explore a more economical purification process. Based on the separation of Radix puerariae isoflavones by CD-coupled media, here we have carried out molecular dynamics simulations, together with chromatography determination, to unveil the mechanism of molecular recognition between CDs and R. puerariae isoflavones and to give a structural explanation for the chromatography retention. This thesis also provides valuable insights into the CD-based supramolecular complexation and assembly in aqueous and nonaqueous phases. The systematic studies were given below:1. Formation process of inclusion complexes of puerarin and daidzin with β-CD in water and effects of solvent molecules (water and acetic acid) and media on the stability of the inclusion complexes. Computational results reveal that there are two types of inclusion complexes for β-CD/puerarin and β-CD/daidzin, in agreement with the docking results. The inclusion complex where the isoflavone skeleton of puerarin locates inside the cavity of β-CD with the glucose unit closing to the secondary rim appears more favorable, which agrees with the NMR observation. Guest-host induced structural changes, hydrogen bonding, and shuttle motions of puerarin and daidzin inside β-CD cavity in aqueous acetic acid were then analyzed to explore the mechanism of using P-CD-coupled media for separation of puerarin from daidzin. Both puerarin and daidzin can induce the conformational change of β-CD, which is compressed in one direction and stretched in the other. The induced effect of puerarin on β-CD is stronger than that of daidzin. After linkage to agarose monomers, the conformation of β-CD can be maintained well and guest-induced effects are weakened somewhat. With the concentration of HAc increasing, host-guest interaction energies decrease, and the guest molecule can get out of the cavity of β-CD at higher concentrations of HAc, indicating the elution effect of acetic acid on the separation process. Puerarin is eluted more easily in HAc/water than daidzin because of its stronger interaction with the solvent and weaker interaction with the host.2. Effects of short-chain alcohols (methanol, ethanol,2-propanol and 1-propanol) as cosolvents on the separation of puerarin from daidzin using P-CD-coupled media. Structural changes of isolated β-CD molecule and [β-CD:guest] complexes in these alcohol solutions, the alcohol residence time within the (3-CD cavity, solvent distribution around β-CD, and guest-induced structural changes were analyzed. The retention behavior of puerarin and daidzin on a P-CD-coupled medium was determined via chromatographic experiments and simulation results provided a structural explanation for such interactions. Compared to water, higher concentrations of alcohol endow free P-CD with a more rigid structure, while lower concentrations of methanol and ethanol give a more flexible one. Interaction with puerarin endowed β-CD with a more rigid structure than with daidzin and a weaker ternary complex β-CD/puerarin/alcohol was formed with a local participation of water molecules. In higher concentration the β-CD cavity is almost completely occupied by alcohol and thus guest molecules have low probability to be incorporated into the cavity. In lower concentration the β-CD cavity is partly occupied by alcohol and guests have more of a chance to enter the cavity, producing a hydrophobic interaction for the chromatography retention. As the alcohol concentration decreases, retentions of puerarin and daidzin both increase and are more sensitive to alcohol concentrations. Big differences between puerarin and daidzin occur in 50% MeOH,29% EtOH,20% i-PrOH and 15% n-PrOH.3. Effects of organic solvents with different polarity on hydrogen bond (HB) orientations of β-CD and the stability of head-to-head β-CD dimer. An intra-molecular inter-glucopyranose HB in the secondary rim of β-CD can be oriented in two types; type A looks like (2)OH�'O(3’)H and type B is H(2)O←HO(3’). Orientational preferences of β-CD HBs in ten solvents (MeOH, EtOH, DMSO, DMA, DMF, ACO, THF, ACN, and CHC13) are discussed. HB exchanges between these two types at the secondary rim of β-CD are observed with a fast rate in water and with a low rate or even no exchange in other solvents. Polar solvents with stronger HB accepting abilities can interrupt intra-and intermolecular HBs more easily, resulting in a less stable dimer. In the solvents with higher polarity (such as water), the channel-type dimer is not stable and tends to form layer-or cage-type structures. Guest molecules included in the channel-type cavity strengthen the binding affinity between two monomers to some extent, particularly in polar solvents. Formation of the head-to-head dimer is therefore solvent-dependent and guest-modulated. There is only limited correlation between the dimer binding energies and solvent properties like the dielectric constant. This implies that implicit solvent models will not be capable of predicting important properties like binding energy.4. Solvent contribution to the stability of CD-based supramolecular complexes. Potential of mean force and entropy calculations were carried out to investigate all possible binding modes between P-CD (host) and four drug molecules puerarin, daidzin, daidzein, and nabumetone (guest) in explicit water. We then introduce an indirect approach to estimate the solvation contributions to the thermodynamics of non-covalent complex formation. The total enthalpy (△H) and entropy (△S) change are evaluated and further decomposed into individual items in order to quantify the energetics of binding (△G) in detail. Binding reactions between β-CD and the guests studied are predominantly enthalpy-driven and in some cases an entropy loss weakens the binding. Configurational fit between host and guest molecules leads to fluctuations in atomic positions. The bonded term (angle and dihedral torsions) of binding partners tends to disfavor the complexation, while the nonbonded ones (electrostatic and van der Waals) favor the binding. By association, △H for interactions between host and guest molecules increases, and the binding partners are desolvated. The desolvation releases the water molecules that participate in host and guest solvation and leads to enthalpy gains of solvent molecules, thus favoring the binding reactions. Configurational fit results in an entropy loss for guest and host molecules, while the solvent entropy increases and tends to favor the binding. Most of entropy changes take place when flexible moieties of the guest are included inside the CD cavity or interact with the CD surface. This approach presented here can be readily adopted for obtaining a deeper understanding of the mechanisms governing noncovalent associations in solution.5. Cooperative binding of cyclodextrin dimers to isoflavone analogues. Compared to the monomer, cooperative drug binding to two CD cavities gives an increase in the binding free energy (△G0) by-30% for daidzin and by-60% for daidzein, whereas for puerarin no obvious enhancement is observed. For such isoflavone binding, head-to-head (HH) dimer outperforms the other two orientations of head-to-tail (HT) and tail-to-tail (TT). HH packing therefore appears as a better model for building blocks of CD-based nanostructured materials. For selection of the templates, stick-like molecules (such as daidzin and daidzein) are preferred over branch-like ones (such as puerarin). Hydroxyl groups of adjacent CDs face each other in the center-of-mass of the dimer, yielding a somewhat hydrophilic environment, as indicated by the local favorable minima in the free energy profiles. Thus, a hydrophobic stick-like template with a central hydrophilic moiety is expected to give enhanced binding to CD dimers.