Micelle/water partition properties of phenols determined by liquid chromatographic method. Proposal for versatile measure of hydrophobicity

Dapsone is not a Pharmacodynamic Lead Compound for its Aryl Derivatives

BACKGROUND

The relatedness between the linear equations of thermodynamics and QSAR was studied thanks to the recently elucidated crystal structure complexes between sulfonamide pterin conjugates and dihydropteroate synthase (DHPS) together with a published set of thirty- six synthetic dapsone derivatives with their reported entropy-driven activity data. Only a few congeners were slightly better than dapsone.

OBJECTIVE

Our study aimed at demonstrating the applicability of thermodynamic QSAR and to shed light on the mechanistic aspects of sulfone binding to DHPS.

METHODS

To this end ligand docking to DHPS, quantum mechanical properties, 2D- and 3D-QSAR as well as Principle Component Analysis (PCA) were carried out.

RESULTS

The short aryl substituents of the docked pterin-sulfa conjugates were outward oriented into the solvent space without interacting with target residues which explains why binding enthalpy (ΔH) did not correlate with potency. PCA revealed how chemically informative descriptors are evenly loaded on the first three PCs (interpreted as ΔG, ΔH and ΔS), while chemically cryptic ones reflected higher dimensional (complex) loadings.

CONCLUSION

It is safe to utter that synthesis efforts to introduce short side chains for aryl derivatization of the dapsone scaffold have failed in the past. On theoretical grounds we provide computed evidence why dapsone is not a pharmacodynamic lead for drug profiling because enthalpic terms do not change significantly at the moment of ligand binding to target.

Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies

It is frequently mentioned that QSARs have not generally lived up to expectations, especially in cases where high predictability is expected yet failed to deliver satisfactory results. Even though outliers can provide an increased opportunity in drug discovery research, outliers in SAR and QSAR can contort predictions and affect the accuracy if proper attention is not given. The percentages of outliers in QSARs have not changed appreciably over the last decade. In our previous studies, we suggested two possible sources of outliers in SAR and QSAR. In this paper, we suggest an additional possible source of outliers in QSAR. We presented several literature examples that show one or more water molecules that play a critical role in protein-ligand binding interactions as observed in their crystal structures. These examples illustrate that failing to account for the effects of water molecules in protein-ligand interactions could mislead interpretation and possibly yield outliers in SAR and QSAR. Examples include cases where QSAR, considering the role of water molecules in protein-ligand crystal structures, provided deeper insight into the understanding and interpretation of the developed QSAR.

Resolution of small molecules by passage through an open capillary

When a solute passes through an open capillary, in which a laminar flow is established, different peak profiles can be obtained according to its diffusion property under a working condition, i.e., the radius and length of the capillary and the flow rate of the carrier solution. If a solute diffuses over the entire cross section of the capillary before it is eluted, a Gaussian-shaped diffusion peak appears, which has an apex at the travel time of the average flow. Insufficient solute diffusion, which is realized, e.g., by increasing flow rates or capillary radius, produces a new peak having an apex at the travel time of the maximum flow. This implies that two solutes can be resolved simply by passing through a capillary. However, our previous study indicated that the diffusion coefficients of two solutes should be at least one order different for their resolution based on this principle, suggesting that its applicability is highly restricted. In the present paper, this concept has been extended to the resolution between dissolved solutes that have similar intrinsic diffusion properties. The incorporation of molecular aggregates in the carrier makes a solute less diffusive according to the extent of their interaction and allows the resolution of a dissolved molecule from other ones differing in the affinity to the molecular aggregates. Several examples of peak resolution for phenols, aromatic hydrocarbons, and inorganic anions are shown and discussed on the basis of the modification of the diffusion natures due to their interactions with micelles or vesicles.

Thermodynamic aspects of hydrophobicity and biological QSAR

A protein contains a large amount of water molecules, and the nature of the interactions of the water molecules with a protein play an important role in the thermodynamics of the ligand binding process. In this paper, thermodynamic aspects of drug-receptor interactions, enthalpy-entropy compensation or reinforcement, hydrophobicity, and biological 2D- and 3D-QSAR are discussed. Comparisons of the thermodynamic QSAR of phenyl esters of N-benzoyl L-alanine in phosphate buffer and pentanol provide useful insight for the ligand-enzyme interactions.

Thermodynamic quantitative structure-activity relationship analysis for enzyme-ligand interactions in aqueous phosphate buffer and organic solvent

Thermodynamic quantitative structure-activity relationships (QSAR) for chymotrypsin-ligand binding is developed, and the results are compared for the effects of organic solvent on the substrate specificity of the enzymes to those in aqueous phosphate buffer. This is the first of such analysis utilizing thermodynamic QSAR. A possible explanation for the difference describing the effects of organic solvent for the binding of substituted phenyl esters of N-benzoyl L-alanine analogues [PhCONHCH(Me)COOC(6)H(4)-p-X, I] observed in both the classical and the thermodynamic QSAR is presented.

Determination of lipophilicity of some non-steroidal anti-inflammatory agents and their relationships by using principal component analysis based on thin-layer chromatographic retention data

The relative lipophilicity of ten non-steroidal anti-inflammatory agents have been determined by reversed-phase thin layer chromatography using different reversed-phase high-performance thin-layer chromatography plates and water-methanol mixtures as eluents. The compounds studied showed regular retention behavior, their RM values decreasing linearly with increasing concentration of methanol in the eluent. Principal component analysis allowed a more rational and objective estimation and comparison of lipophilicity determined by reversed-phase thin-layer chromatography. It also affords a useful graphical tool, since scatterplots of the scores onto the plane described by the first two components will have the effect of separating compounds from each other most effectively, thus obtaining "congeneric lipophilicity chart".

Thermodynamic aspects of hydrophobicity and the blood-brain barrier permeability studied with a gel filtration chromatography

It has been said that the selective permeability across the blood--brain barrier depends on several physicochemical properties of drugs such as hydrophobicity, molecular weight, and hydrogen-bonding potential. In order to investigate quantitatively the relationship between the blood--brain barrier permeability and the hydrophobicity of drugs, we have measured the micelle/water partition properties (Pmic) by the MLC (micellar liquid chromatography) method using a gel filtration version and compared with the blood--brain barrier permeability. The thermodynamic aspects of partition were derived by separating the micelle/water partition coefficient (log Pmic) into the enthalpy term PH and the entropy term PS. It was found that the PH shows a good correlation to the permeability, although log Pmic fails to do so. The result means that PH, which is easily obtained from the in vitro experiment, can be used as an excellent standard in discussing the transport phenomena through the blood--brain barrier.