Physicochemical analysis of chiral pharmaceutical molecular behavior in solution and solid state

Chiral molecules are widely used in the multiple fields including food science, agriculture and medicinal drug as highly functionalized molecules. Chirality in medicinal drug, especially, is of great importance because it enhances the binding affinity of drug with its receptor and yields higher drug efficacy. We are focusing on thalidomide and its derivatives which recently attract worldwide attentions again.

Thalidomide was developed at a German pharmaceutical company in 1957 as a safe sedative hypnotic. In those days many pregnant women took thalidomide to prevent morning sickness, but their baby suffered from severe birth defects (phocomelia). In 1962 a German pediatrician Widukind Lenz first pointed out the relationship between thalidomide and teratogenesis [1]. The “thalidomide syndrome” exerted a big impact on the world and then thalidomide was withdrawn soon from the worldwide market.

In subsequent work, the relationship between teratogenicity and chirality in thalidomide was reported. The study using animal examination revealed that only (S)-isomer of thalidomide was a potent teratogen whereas opposite (R)-isomer did not perform as a teratogen [2]. At the time when thalidomide was sold, all medicinal drugs involving thalidomide were used as racemate because the technique of chiral chromatography and asymmetric synthesis was poorly developed and the importance of drug chirality was not well recognized. The drug disaster caused by thalidomide opened our eyes to the significance of chiral discrimination in drug development.

Figure 1. Our strategies for addressing thalidomide mechanism
Recent studies on thalidomide and the related molecules demonstrate effectiveness of thalidomide on various intractable diseases [5]. In the United States thalidomide is used as a treatment for Hansen’s disease [6], and under aggressive examination for other diseases such as Behcet disease, Crohn disease and AIDS [7-9]. To enhance drug efficacy, the derivatives and the analogues of thalidomide have been synthesized in these days. Our collaborator has synthesized a non-racemizable thalidomide analogue 3’-fluorothalidomide which stereogenic center of thalidomide is substituted with a stable fluorine atom [10]. The amino derivative of thalidomide, pomalidomide, is also used as one of immunomodulatory drugs (iMiDs) in the United States [11]. Most recently, cereblon protein was identified as a principle receptor of thalidomide, and the binding mechanism of thalidomide with cereblon was solved employing X-lay crystal structure analysis of their co-crystal [12,13]. We conceive that thalidomide and the related molecules should be studied not only as a historical lesson but also for future possibility.

In our group, the molecular state of thalidomide in crystalline state was analyzed using X-lay crystal structure analysis and quantum chemical calculation [14]. Our results clarified the homo- and hetero-chiral dimeric structures in enantiomeric and racemic thalidomide crystals (figure 2). Moreover, we reported that the difference in physicochemical properties such as melting point between enantiomer and racemate of thalidomide was originated from the difference in the energy of intermolecular hydrogen bonds that forms the homo- and hetero-chiral dimers with theoretical computations.

Right: Figure 2. Homo-chiral dimeric structure of thalidomide crystal (from ref.14)

The metabolism of thalidomide is consist of verious chemical reactions, especially spontaneous hydrolysis, enzymatic oxidation, and non-enzymatic chiral inversion. These simultaneous biological transformations result in the formation and degradation of multiple chiral metabolites of thalidomide. We reconstructed this complex metabolic systems of thalidomide in vitro and measured the chiral metabolites generated from enantiomeric thalidomide employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) and chiroptical spectroscopic assay [17]. Based on the quantification of each metabolite by LC-MS/MS, we drew a “metabolic map” for each step of metabolism that illustrates the amount of metabolites at each time point with different reaction times of hydrolysis and hydroxylation. We estimated a possible preferential pathway for once hydrolyzed and hydroxylated metabolites. We also found that chirality in the hydrolyzed and hydroxylated metabolites was mostly maintained as the same chirality in the non-metabolized thalidomide. Our achievements will contribute for the rational design of bioactive molecule based on the structure of metabolites of thalidomide and its derivatives, and also the development of new analytical methods for metabolism on chiral drugs.

Figure 3. Quantification of thalidomide metabolites suffering from once hydrolysis and hydroxylation, and the metabolism map (from ref.17)

We also developed a model describing biotransformation of thalidomide based on chemical kinetics, and estimated temporal change of enantiomeric excess during metabolic systems with several experimental kinetic parameters [17]. Our numerical study demonstrated that approximately 40% of enantiomeric excess remained at the end of metabolic process and this unbalance of chirality can induce stereoselective drug efficacy of thalidomide. We furthermore proposed a novel definition of racemization rate constant that are preferable in the complex chemical reactions.

Right: Figure 4. Chemical reaction graph describing chiral inversion and metabolism (from ref.17)

Our group are also addressing the unique and interesting characteristics of thalidomide and other chiral molecules using experimental and theoretical approaches such as chiroptical spectroscopy, analytical chemistry, crystal optics, thermal analysis, quantum chemistry and mathematical modeling, like the following topics:

1) Experimental observation of simultaneous chiral inversion and biotransformation of thalidomide and its derivatives
2) Physicochemical properties of the metabolites of thalidomide and its derivatives
3) Dynamic multimer formation in thalidomide and its derivatives
4) Chemical reaction of thalidomide and its derivatives in solid state


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