Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method

Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes

The role of water in host-ligand binding was investigated using a combination of molecular dynamics simulation and three-dimensional reference interaction site model theory. Three different hosts were selected (CB6, CB7, and CB8). Six organic molecules were used as representative ligands: dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF), acetone, 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO), cyclopentanone (CPN), and pyrrole. From the binding free energy and its components, we divided the ligands into two groups: those with relatively small molecular size (DMSO, DMF, acetone, and pyrrole) and those with relatively large molecular size (DBO and CPN). We established that the solvent water in the CB6 cavity can be completely displaced by small ligands, resulting in a greater binding affinity compared with larger CBs, except in the case of the small pyrrole ligand, due to outstanding intrinsic properties such as the relatively high hydrophobicity and low dipole moment. In the case of the large ligands, the solvent water can be displaced by DBO and CPN in both CB6 and CB7; there were similar tendencies in their binding affinities, with the greatest affinity in the CB7 complexes. However, the tendencies of the binding affinity components are completely different due to the difference between the complex structure and the solvation structure when a ligand binds with a CB structure. The binding affinities suggest that the size fit between the ligand and CB cannot guarantee the greatest binding affinity gain because the binding structure and intrinsic properties of CB and ligand equally play a crucial role.

Differential mode of cholesterol inclusion with 2-hydroxypropyl-cyclodextrins increases safety margin in treatment of Niemann-Pick disease type C

BACKGROUND AND PURPOSE

Niemann-Pick disease type C (NPC) is a lysosomal storage disorder with disrupted intracellular cholesterol trafficking. A cyclic heptasaccharide, 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), is a cholesterol solubilizer that is being developed to treat NPC, but its ototoxicity and pulmonary toxicity remain important issues. We have characterized 2-hydroxypropyl-γ-cyclodextrin (HP-γ-CD), a cyclic octasaccharide with a larger cavity than HP-β-CD, as a candidate drug to treat NPC. However, the molecular target of HP-γ-CD with respect to NPC and its potential for clinical application are still unclear.

EXPERIMENTAL APPROACH

We investigated the mode of interaction between HP-γ-CD and cholesterol by phase-solubility analysis, proton NMR spectroscopy and molecular dynamics simulations. We then evaluated the therapeutic effects of HP-γ-CD compared with HP-β-CD using cellular and murine NPC models. Mouse auditory and pulmonary function tests were also conducted.

KEY RESULTS

HP-γ-CD solely formed a 1:1 inclusion complex with cholesterol with an affinity similar to that of HP-β-CD. In vitro, HP-γ-CD and HP-β-CD amelioration of NPC-related manifestations was almost equivalent at lower concentrations. However, at higher concentrations, the cholesterol inclusion mode of HP-β-CD shifted to the highly soluble 2:1 complex whereas that of HP-γ-CD maintained solely the 1:1 complex. The constant lower cholesterol solubilizing ability of HP-γ-CD conferred it with significantly reduced toxicity compared with HP-β-CD, but equal efficacy in treating a mouse model of NPC.

CONCLUSIONS AND IMPLICATIONS

HP-γ-CD can serve as a fine-tuned cholesterol solubilizer for the treatment of NPC with a wider safety margin than HP-β-CD in terms of ototoxicity and pulmonary toxicity.

Computational Screening of a Functional Cyclodextrin Derivative for Suppressing a Side Effect of Doxorubicin

The binding affinity of the beta-cyclodextrin (β-CyD) derivatives with Doxorubicin (Dox) is evaluated by means of the 3D-RISM/KH theory combined with the molecular dynamics simulation in order to screen the compounds for suppressing a side-effect of the cancer drug. A protocol revised for the external and conformational entropies of the host-guest system is employed to calculate the binding free energy. It is found that the direct interactions of CyD with Dox and the desolvation free-energies of the both compounds largely cancel out to leave moderate contributions to the affinity, which are comparable to those from the entropies. The results shed light on the entropy terms for determining the binding affinity, although the external-entropy terms are essentially constant over all the compounds examined and do not affect the screening. The theoretical result is compared with the experimental data of the association constant for a CyD derivative which was predicted to be the best compound by the preliminary calculation without the entropy terms.

Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory

There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

3D matters! 3D-RISM and 3D convolutional neural network for accurate bioaccumulation prediction

In this work, we present a new method for predicting complex physical-chemical properties of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) that uses solvent spatial distributions around solutes as input. These spatial distributions are obtained by a molecular theory called three-dimensional reference interaction site model. We have shown that the method allows one to achieve a good accuracy of prediction of bioconcentration factor which is difficult to predict by direct application of methods of molecular theory or simulations. Our research demonstrates that combination of molecular theories with modern machine learning approaches can be effectively used for predicting properties that are otherwise inaccessible to purely theory-based models.

Perspective: Structural fluctuation of protein and Anfinsen's thermodynamic hypothesis

The thermodynamics hypothesis, casually referred to as "Anfinsen's dogma," is described theoretically in terms of a concept of the structural fluctuation of protein or the first moment (average structure) and the second moment (variance and covariance) of the structural distribution. The new theoretical concept views the unfolding and refolding processes of protein as a shift of the structural distribution induced by a thermodynamic perturbation, with the variance-covariance matrix varying. Based on the theoretical concept, a method to characterize the mechanism of folding (or unfolding) is proposed. The transition state, if any, between two stable states is interpreted as a gap in the distribution, which is created due to an extensive reorganization of hydrogen bonds among back-bone atoms of protein and with water molecules in the course of conformational change. Further perspective to applying the theory to the computer-aided drug design, and to the material science, is briefly discussed.

Predicting the Binding Mode of 2-Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH Theory

It has been found that a cyclodextrin derivative, 2-hydroxypropyl-β-cyclodextrin (HPβCD), has reasonable therapeutic effect on Niemann-Pick disease type C, which is caused by abnormal accumulation of unesterified cholesterol and glycolipids in the lysosomes and shortage of esterified cholesterol in other cellular compartments. We study the binding affinity and mode of HPβCD with cholesterol to elucidate the possible mechanism of HPβCD for removing cholesterol from the lysosomes. The dominant binding mode of HPβCD with cholesterol is found based on the molecular dynamics simulation and a statistical mechanics theory of liquids, or the three-dimensional reference interaction site model theory with Kovalenko-Hirata closure relation. We examine the two types of complexes between HPβCD and cholesterol, namely, one-to-one (1:1) and two-to-one (2:1). It is predicted that the 1:1 complex makes two or three types of stable binding mode in solution, in which the βCD ring tends to be located at the edge of the steroid skeleton. For the 2:1 complex, there are four different types of the complex conceivable, depending on the orientation between the two HPβCDs: head-to-head (HH), head-to-tail (HT), tail-to-head (TH), and tail-to-tail (TT). The HT and HH cyclodextrin dimers show higher affinity to cholesterol compared to the other dimers and to all the binding modes of 1:1 complexes. The physical reason why the HT and HH dimers have higher affinity compared to the other complexes is discussed based on the consistency with the 1:1 complex. On the one hand, in case of the HT and HH dimers, the position of each CD in the dimer along the cholesterol chain comes right on or close to one of the positions where a single CD makes a stable complex. On the other hand, one of the CD molecules is located on unstable region along the cholesterol chain, for the case of TH and TT dimers.

A Systematic Analysis of the Binding Affinity between the Pim-1 Kinase and Its Inhibitors Based on the MM/3D-RISM/KH Method

A systematic study of the binding affinities of 16 lead compounds targeting the Pim-1 kinase based on the 3D-RISM/KH theory and MD simulations is reported. The results show a correlation coefficient R = 0.69 between the theoretical and experimental values of the binding free energy. This demonstrates that the method is applicable to the problem of compound screening and lead optimization, for which relative values of the free energy among the compounds have significance. We elucidate the contribution of the ligand fragments to the binding free energy. Our results indicate that the interactions between the residues and the triazolo[4,3-b]pyridazine scaffold as well as the phenyl ring of the ligand molecule make significant contributions to stabilization of the complex. Using the 3D-RISM/KH theory, we further analyze the probability distribution of a ligand fragment around the protein-ligand complex in which the substituent around the phenyl ring is removed from the ligand. The results demonstrate that the 3D-RISM/KH theory is capable of predicting the position of substitution on a ligand that has a higher affinity to a target protein.