Probing the active site of aromatase with 2-methyl-substituted androstenedione analogs

Molecular docking and QSAR studies of aromatase inhibitor androstenedione derivatives

Objectives

Aromatase (CYP19) inhibitors have emerged as promising candidates for the treatment of estrogen-dependent breast cancer. In this study, a series of androstenedione derivatives with CYP19 inhibitory activity was subjected to a molecular docking study followed by quantitative structure–activity relationship (QSAR) analyses in search of ideal physicochemical characteristics of potential aromatase inhibitors.

Methods

The QSAR studies were carried out using both two-dimensional (topological, and structural) and three-dimesional (spatial) descriptors. We also used thermodynamic parameters along with 2D and 3D descriptors. Genetic function approximation (GFA) and genetic partial least squares (G/PLS) were used as chemometric tools for QSAR modelling.

Key findings

The docking study indicated that the important interacting amino acids in the active site were Met374, Arg115, Ile133, Ala306, Thr310, Asp309, Val370, Leu477 and Ser478. The 17-keto oxygen of the ligands is responsible for the formation of a hydrogen bond with Met374 and the remaining parts of the molecules are stabilized by the hydrophobic interactions with the non-polar amino acids. The C2 and C19 positions in the ligands are important for maintaining the appropriate orientation of the molecules in the active site. The results of docking experiments and QSAR studies supported each other.

Conclusions

The developed QSAR models indicated the importance of some Jurs parameters, structural parameters, topological branching index and E-state indices of different fragments. All the developed QSAR models were statistically significant according to the internal and external validation parameters.

Biochemical aromatization of 2-methyleneandrostenedione: stereochemistry of hydrogen removal at the C-1 position

To explore a stereochemistry of hydrogen removal at C-1 of the powerful aromatase inhibitor 2-methyleneandrostenedione (1), of which the A-ring conformation is markedly different from that of the natural substrate androstenedione (AD), in the course of the aromatase-catalyzed A-ring aromatization producing 2-methylestrone (2), we synthesized [1alpha-2H]labeled steroid 1 and its [1beta-2H]stereoisomer, and the metabolic fate of the C-1 deuterium in aromatization was analyzed by gas chromatography-mass spectrometry (GC-MS) in each. Parallel experiments with the natural substrates [1alpha-2H] and [1beta-2H]ADs were also carried out. The GC-MS analysis indicated that 2-methyl estrogen 2 produced from [1alpha-2H]labeled substrate 1 retained completely the 1alpha-deuterium (1beta-H elimination), while product 2 obtained from [1beta-2H]isomer 1 lost completely the 1beta-deuterium. Stereospecific 1beta-hydrogen elimination was also observed in the parallel experiments with the labeled ADs as established previously. The results indicate that biochemical aromatization of the 2-methylene steroid 1 proceeds through the 1beta-hydrogen removal concomitant with cleavage of the C(10)-C(19) bond, yielding 1(10),4-dienone 9, in a similar manner to that involved in AD aromatization. This would give additional evidence for the stereomechanisms for the last step of aromatization of AD, requiring the stereospecific 1beta-hydrogen abstraction and cleavage of the C(10)-C(19) bond, and for the enolization of a carbonyl group at C-3 in the A-ring aromatization.

Gas chromatography-mass spectrometric study of 19-oxygenation of the aromatase inhibitor 19-methylandrostenedione with human placental microsomes

To gain insight into the catalytic function of aromatase, we studied 19-oxygenation of 19-methyl-substituted derivative of the natural substrate androstenedione (AD), compound 1, with human placental aromatase by use of gas chromatography-mass spectrometry (GC-MS). Incubation of the 19-methyl derivative 1 with human placental microsomes in the presence of NADPH under an aerobic condition did not yield a detectable amount of [19S]19-hydroxy product 2 or its [19R]-isomer 3 when the product was analyzed as the bis-methoxime-trimethylsilyl (TMS) derivative by GC-MS; moreover, the production of estrogen was not detected as the bis-TMS derivative of estradiol (detection limit: about 3 ng and 10 pg per injection for the 19-ol and estradiol, respectively). The results reveal that the 19-methyl steroid 1 does not serve as a substrate of aromatase, although it does serve as a powerful inhibitor of the enzyme.

Reduction of 1,4-Dien-3-one Steroids with LiAl2H4 or NaB2H4: Stereospecific Deuterium-Labeling at the C-1.ALPHA. Position of a 4-En-3-one Steroid

Reduction of a double bond at C-1 of 1,4-dien-3-one steroids 7 and 8 with LiAl2H4 in THF or NaB2H4 in MeOH and H2O gave stereospecifically [1alpha-2H]-labeled 4-en-3-one steroids 9 and 10, respectively. When the deuterated solvents, MeO2H and 2H2O, were used for the reaction of steroid 8 with NaB2H4, [1alpha,2xi-2H2]-labeled compound 10 was produced. This indicates that the reaction proceeds through the initial hydride attack at the C-1alpha position, followed by ketonization of the 2-en-3-ol intermediate.

Structure-activity relationships of 2alpha-substituted androstenedione analogs as aromatase inhibitors and their aromatization reactions

Aromatase catalyzes the conversion of androstenedione (1a, AD) to estrone through three sequential oxygenations of the 19-methyl group. To gain insight into the spatial nature of the AD binding (active) site of aromatase in relation to the catalytic function of the enzyme, we tested for the ability of 2alpha-substituted (halogeno, alkyl, hydroxy, and alkoxy) ADs (1b-1i) to inhibit aromatase in human placental microsomes as well as their ability to serve as a substrate for the enzyme. All of the steroids inhibited the enzyme in a competitive manner with the apparent K(i)'s ranging from 45 to 1150 nM. 2alpha-Halogeno (F, Cl, and Br) and 2alpha-alkyl (CH3 and CH2CH3) steroids 1b-1f were powerful to good inhibitors (Ki=45-171 nM) whereas steroids 1g-1i, having an oxygen function (hydroxy or alkoxy) at C-2alpha, were poor inhibitors (Ki=670-1150 nM). Aromatization of some of the steroids with placental microsomes was analyzed by gas chromatography-mass spectrometry, indicating that the aromatization rate of the bromide 1d was about two-fold that of the natural substrate AD and that of 2alpha-methoxide 1h was similar to that of AD. Kinetic analysis of the aromatization of androgens revealed that a good substrate was not essentially a good inhibitor for aromatase.

Synthesis and Biochemical Properties of 6-Bromoandrostenedione Derivatives with a 2,2-Dimethyl or 2-Methyl Group as Aromatase Inhibitors

To gain insight into the mechanism for irreversible inactivation of aromatase by 6beta-bromoandrostenedione (1), one of the earliest discovered suicide substrates, in relation to the catalytic function of the enzyme, the 2,2-dimethyl derivative of compound 1, steroid 4, and its 6alpha-isomer 5, as well as 2-methyl-1,4-diene steroid 8 and its 6alpha-bromide 10, were synthesized. All of the steroids inhibited aromatase activity in human placental microsomes with apparent K(i)'s ranging between 10 and 81 nM. The 2,2-dimethyl-6beta- and 6alpha-bromo steroids 4 and 5 were extremely powerful inhibitors (K(i): 14 and 10 nM, respectively), but these two did not cause a time-dependent inactivation of aromatase in the presence of NADPH; in contrast, the 2-methyl-1,4-diene steroids 8 and 10 caused time-dependent inactivation with apparent k(inact) of 0.035 and 0.071 min(-1), respectively, in a suicide manner. These results indicate that the 2,2-dimethyl function of the 6beta-bromide 4 would prevent the inactivation of aromatase caused by inhibitor 1 in a suicide manner, probably through steric activity, whereas the 2-methyl group of steroid 8 did not significantly affect the suicidal inactivation by the parent 1,4-diene steroid, a typical suicide substrate.