Analysis of vitamin D receptor binding affinities of enzymatically synthesized triterpenes including ambrein and unnatural onoceroids

Onoceroids are a rare family of triterpenes. One representative onoceroid is ambrein, which is the main component of ambergris used as a traditional medicine. We have previously identified the onoceroid synthase, BmeTC, in Bacillus megaterium and succeeded in creating ambrein synthase by introducing mutations into BmeTC. Owing to the structural similarity of ambrein to vitamin D, a molecule with diverse biological activities, we hypothesized that some of the activities of ambergris may be induced by the binding of ambrein to the vitamin D receptor (VDR). We demonstrated the VDR binding ability of ambrein. By comparing the structure-activity relationships of triterpenes with both the VDR affinity and osteoclastic differentiation-promoting activity, we observed that the activity of ambrein was not induced via the VDR. Therefore, some of the activities of ambergris, but not all, can be attributed to its VDR interaction. Additionally, six unnatural onoceroids were synthesized using the BmeTC reactions, and these compounds exhibited higher VDR affinity than that of ambrein. Enzymatic syntheses of onoceroid libraries will be valuable in creating a variety of bioactive compounds beyond ambergris.

Evaluation of ambrein and epicoprostanol for their antioxidant properties: Protection against adriamycin-induced free radical toxicity

Ambrein and epicoprostanol were evaluated for their antioxidant potential in vitro by chemiluminescence (CL), as well as in vivo using lipid peroxides and glutathione levels as indicators in liver tissue of rats treated with adriamycin (doxorubicin) a well known free radicals producing drug. In the in vitro test, the inhibition in CL by ambrein was dose dependent. Both the high concentrations of ambrein (20-40 microg/ml) inhibited CL response significantly (P<0.05 and P<0.01, respectively) when compared to control. Similarly two low concentrations (5-20 microg/ml) of epicoprostanol inhibited CL significantly (P<0.001 and P<0.01, respectively) in comparison of DMSO control. The high concentration (40 microg/ml) of epicoprostanol behaved exceptionally and caused an increase in CL response that was more than control and significantly (P<0.001) higher than both the low concentrations. In the in vivo studies adriamycin treatment significantly (P<0.05) increased malondialdehyde (MDA) and decreased non-protein sulfhydryl (NP-SH) contents in the liver tissue of mice after 5 days treatment. Ambrein (25 and 50 mg/kg) treatment as a solo therapy at both the dose levels significantly (P<0.001) decreased MDA contents in the liver tissue. On the other hand, in the combined treatment the high dose effectively prevented any rise in MDA contents and it remained around the levels of ambrein alone. In the same experiment, adriamycin declined NP-SH contents significantly (P<0.001). Ambrein alone at both the dose levels caused a decline (P<0.01) in NP-SH contents when compared to adriamycin group. But in the combined treatment this decline in NP-SH was significantly (P<0.05) different from adriamycin alone. In the experiments dealing with epicoprostanol, adriamycin treatment increased MDA contents significantly (P<0.05) that declined significantly (P<0.001) with epicoprostanol (10- or 20mg/kg) treatment. In the same experiment co-treatment with adriamycin prevented any rise in MDA contents significantly (P<0.001) as it was observed in adriamycin alone group. Although, this treatment failed to prevent any decline in NP-SH contents either alone or in combination with adriamycin. Epicoprostanol itself had the comparative declining effect on the contents of NP-SH as seen in adriamycin group. From the results of our experiments it seems that ambrein at all concentrations behaves like antioxidant in in vitro studies but the same time it decreased NP-SH contents in vivo accompanied by a decline in MDA contents. Whereas, epicoprostanol at two low concentrations had a decline in CL indicating a possible antioxidant potential but the high concentration increased CL showing a tendency towards oxidant prospective. However, in animal studies it has shown a clear protection against adriamycin induced free radical damage.

Chemical transformation and biological activities of ambrein, a major product of ambergris from Physeter macrocephalus (sperm whale)

Ten new derivatives (2-11) of ambrein (1), isolated from ambergris, were prepared by chemical transformation. Oxidation and/or cyclization were effected by reactions with selenium oxide or p-toluenesulfonyl chloride or with the use of shortwave UV light. The structures of 2-12 were elucidated by spectroscopic analysis, with the structure and relative configuration of 9 confirmed by single-crystal X-ray crystallography. The cytotoxic activities of 1-12 were investigated against human liver carcinoma (Hepa59T/VGH), colon adenocarcinoma (WiDr), lung carcinoma (A-549), and human breast adenocarcinoma (MCF-7) cell lines. The anti-inflammatory activities of 1-11, in terms of the inhibition of human neutrophil function, were also evaluated.

QSAR modeling of datasets with enantioselective compounds using chirality sensitive molecular descriptors

Shape descriptors used in 3D QSAR studies naturally take into account chirality; however, for flexible and structurally diverse molecules such studies require extensive conformational searching and alignment. QSAR modeling studies of two datasets of fragrance compounds with complex stereochemistry using simple alignment-free chirality sensitive descriptors developed in our laboratories are presented. In the first investigation, 44 alpha-campholenic derivatives with sandalwood odor were represented as derivatives of several common structural templates with substituents numbered according to their relative spatial positions in the molecules. Both molecular and substituent descriptors were used as independent variables in MLR calculations, and the best model was characterized by the training set q2 of 0.79 and external test set r2 of 0.95. In the second study, several types of chirality descriptors were employed in combinatorial QSAR modeling of 98 ambergris fragrance compounds. Among 28 possible combinations of seven types of descriptors and four statistical modeling techniques, k nearest neighbor classification with CoMFA descriptors was initially found to generate the best models with the internal and external accuracies of 76 and 89%, respectively. The same dataset was then studied using novel atom pair chirality descriptors (cAP). The cAP are based on a modified definition of the atomic chirality, in which the seniority of the substituents is defined by their relative partial charge values: higher values correspond to higher seniorities. The resulting models were found to have higher predictive power than those developed with CoMFA descriptors; the best model was characterized by the internal and external accuracies of 82 and 94%, respectively. The success of modeling studies using simple alignment free chirality descriptors discussed in this paper suggests that they should be applied broadly to QSAR studies of many datasets when compound stereochemistry plays an important role in defining their activity.

Combinatorial QSAR of Ambergris Fragrance Compounds

A combinatorial quantitative structure-activity relationships (Combi-QSAR) approach has been developed and applied to a data set of 98 ambergris fragrance compounds with complex stereochemistry. The Combi-QSAR approach explores all possible combinations of different independent descriptor collections and various individual correlation methods to obtain statistically significant models with high internal (for the training set) and external (for the test set) accuracy. Seven different descriptor collections were generated with commercially available MOE, CoMFA, CoMMA, Dragon, VolSurf, and MolconnZ programs; we also included chirality topological descriptors recently developed in our laboratory (Golbraikh, A.; Bonchev, D.; Tropsha, A. J. Chem. Inf. Comput. Sci. 2001, 41, 147-158). CoMMA descriptors were used in combination with MOE descriptors. MolconnZ descriptors were used in combination with chirality descriptors. Each descriptor collection was combined individually with four correlation methods, including k-nearest neighbors (kNN) classification, Support Vector Machines (SVM), decision trees, and binary QSAR, giving rise to 28 different types of QSAR models. Multiple diverse and representative training and test sets were generated by the divisions of the original data set in two. Each model with high values of leave-one-out cross-validated correct classification rate for the training set was subjected to extensive internal and external validation to avoid overfitting and achieve reliable predictive power. Two validation techniques were employed, i.e., the randomization of the target property (in this case, odor intensity) also known as the Y-randomization test and the assessment of external prediction accuracy using test sets. We demonstrate that not every combination of the data modeling technique and the descriptor collection yields a validated and predictive QSAR model. kNN classification in combination with CoMFA descriptors was found to be the best QSAR approach overall since predictive models with correct classification rates for both training and test sets of 0.7 and higher were obtained for all divisions of the ambergris data set into the training and test sets. Many predictive QSAR models were also found using a combination of kNN classification method with other collections of descriptors. The combinatorial QSAR affords automation, computational efficiency, and higher probability of identifying significant QSAR models for experimental data sets than the traditional approaches that rely on a single QSAR method.

Enzymatic resolution of (+/-)-gamma-cyclohomogeraniol and conversion of its (S)-isomer to (S)-gamma-coronal, the ambergris odorant

Enzymatic acetylation of (+/-)-gamma-cyclohomogeraniol[2-(2',2'-dimethyl-6'-methylenecyc lohexyl)ethanol] with vinyl acetate in the presence of lipase AK yielded the acetate of its (R)-isomer, leaving its (S)-isomer intact. The (S)-isomer was chemically converted to (S)-gamma-coronal[2-methylene-4-(2',2'-dimethyl-6'-methylenecyclohexy l)butanal], the ambergris odorant.

A new electronic-topological investigation of the relationship between chemical structure and ambergris odour

An electronic-topological approach has been used to define an active ambergris fragment (AAF) which correctly describes the presence (or absence) of the ambergris odour of all 181 compounds investigated. The AAF consists of one oxygen atom and three carbon atoms (alpha, beta, gamma) which are separated by certain key distances and which possess certain atomic charges. The C(alpha) atom must bear at least one hydrogen atom (H(alpha)) which is located at a certain distance from one of the unshared electronic pairs of the oxygen atom.