Molecular dynamics of substrate complexes with hamster cytochrome P450c17 (CYP17): mechanistic approach to understanding substrate binding and activities

The cytochrome P450c17 isoforms from various animal species have different substrate selectivity, especially for 17,20-lyase activity. In particular, the human P450c17 selectively produces dehydroepiandrosterone with little androstenedione (AD). Hamster P450c17, on the other hand, produces both of these steroids at comparable rates. We thus investigated if computational analysis could explain the difference in activity profiles. Therefore, we inserted the four P450c17 substrates-pregnenolone, progesterone, and their 17alpha-hydroxylated forms-inside our hamster P450c17 model, which we derived from our human P450c17 model based on the crystal structure of P450BMP. We performed molecular dynamics (MD) simulations on the complexes and analyzed the resultant trajectories to identify amino acids that interact with substrates. Starting with substrates in two different orientations, we obtained two sets of binding trajectories in each case. The first set of trajectories reveal structural rearrangements that occur during binding, whereas the second set of trajectories reflects substrate orientations during catalysis. Our modeling suggests that three distinct steps are required for substrate selectivity and binding to the hamster P450c17: (1) recognition of the substrate at the putative substrate entrance, characterized by a pocket at the surface of the hamster P450c17 containing charged residues R96 and D116; (2) entry of the substrate into the active site, in an intermediate position directed by possible hydrogen bonding of the substrates with the heme D-ring propionate group, R96, R440, and T306; followed by (3) 90 degrees counterclockwise rotation of the substrates, positioning them in optimal position for reactivity, a process that may be directed by hydrogen bonding to the 110-112 region of the hamster P450c17. With some substrates, we obtained trajectories which suggest that major distortions in the I-helix and opening of the H-I loop occur during substrate binding. In conclusion, these modeling exercises provide insight to possible structural reorganizations that occur during substrate binding and suggest that amino acids that participate in three distinct steps of this process may all contribute to substrate binding and activity.     

3D-structure of human estrogenic 17beta-HSD1: binding with various steroids.

Human estrogenic dehydrogenase (17β-HSD1) catalyses the last step in the biosynthesis of the active estrogens that stimulate the proliferation of breast cancer cells. While the primary substrate for the enzyme is estrone, the enzyme has some activity for the non-estrogenic substrates. To better understand the structure–function relationships of 17β-HSD1 and to provide a better ground for the design of inhibitors, we have determined the crystal structures of 17β-HSD1 in complex with different steroids.

The structure of the complex of estradiol with the enzyme determined previously (Azzi et al., Nature Structural Biology 3, 665–668) showed that the narrow active site was highly complementary to the substrate. The substrate specificity is due to a combination of hydrogen bonding and hydrophobic interactions between the steroid and the enzyme binding pocket. We have now determined structures of 17β-HSD1 in complex with dihydrotestosterone and 20-OH-progesterone. In the case of the C19 androgen, several residues within the enzyme active site make some small adjustments to accommodate the increased bulk of the substrate. In addition, the C19 steroids bind in a slightly different position from estradiol with shifts in positions of up to 1.4 Å. The altered binding position avoids unfavorable steric interactions between Leu 149 and the C19 methyl group (Han et al., unpublished). The known kinetic parameters for these substrates can be rationalized in light of the structures presented. These results give evidence for the structural basis of steroid recognition by 17β-HSD1 and throw light on the design of new inhibitors for this pivotal steroid enzyme.     

17 beta-Hydroxysteroid dehydrogenase of the sheep ovary : purification, properties and substrate binding site.

Sheep ovarian 17 beta HSDH has been purified about 1000 fold to a specific activity of 0.5 IU/mg protein, using DEAE cellulose chromatography, affinity chromatography on estrone-amino caproate-Sepharose and a second DEAE cellulose chromatography. The molecular weight is 70,000 ; the pH optimum for activity is 9.2 and the energy of activation is 16.5 Kcal/mole. The kinetics of the oxidation of estradiol and many analogues have been studied at various concentrations and in the presence of different amounts of coenzyme. The data are in agreement with a compulsory order mechanism with the binding of NAD+ as the first substrate. Sheep ovarian 17 beta HSDH accepts subtituents in position C3, C11, C13 ; the substrate binding site is open in this region. On the contrary, the binding requirements are strict for the region of C10 since the presence of a C19 methyl group impairs binding and (or) oxidation of the steroid. Sheep ovarian and human placental 17 beta HSDH have close analogies : molecular weight, pH optimum, substrate binding site requirements. Their reaction mechanisms are different : random for the placental 17 beta HSDH, compulsory order for the ovarian 17 beta HSDH : this can be explained by the effect of the coenzyme upon the binding of the substrate : without effect on placental enzyme, the coenzyme fixation enhances the affinity of the ovarian 17 beta HSDH for any substrate.     

A new method for the detection of hydantoinases with respect to their enantioselectivity on acrylamide gels based on enzyme activity stain

A new and highly sensitive method was developed for the identification of hydantoinases on acrylamide gels. For this purpose, cell-lysates from different natural isolates are subjected on PAGE under non-denaturating conditions. The respective localisation of the hydantoinase is obtained by in situ product precipitation during the reverse enzyme reaction: in contrast to the used substrate (N-carbamoyltryptophan), the product (indolylmethylhydantoin) is barely soluble and gives a dense precipitation dot caused by crystallisation of the product inside of the polyacrylamide gel at the position corresponding to the location of the enzyme. This method can also be used for the subsequent differentiation between L- and D-selective hydantoinases, since L- or D-carbamoyltryptophan is used as substrate. © Rapid Science Ltd. 1998     

Base promoted air oxidation of 13beta-ethyl-11-methylenegon-4-en-17-one.

The structure of 13-ethyl-11-methylene-18,19-dinor-17alpha-pregn-4-en-20-yn-16beta,17-diol (3, 16beta-OH desogestrel), a by-product obtained in the last step of the synthesis of desogestrel (1) by reaction of monolithium acetylide-ethylenediamine complex with 13beta-ethyl-11-methylenegon-4-en-17-one (2), is here reported. The structural assignments were supported by NMR 1H-, 13C-, 1H-1H COSY, 1H-13C HSQC, COLOC) and mass spectroscopy, and the configuration at the C-16 and C-17 stereocentres was established by X-ray crystallography. When the same 17-ketoderivative 2 was treated with a non-alkylating base, such as potassium tert-butoxide, instead of the expected 16-hydroxylated ketone, a dimeric product, 13beta-ethyl-16-[2'-(des-D-13"-carboxy-13"beta-ethyl-11"-methylenegon-4"-en-14"-yl)-ethyliden]-11-methylenegon-4-en-17-one (4), was isolated in good yield; it was characterized by NMR, mass, ultraviolet spectroscopy, and chemical transformations. Compounds 3 and 4 originate from the high reactivity of the 16-methylenic position of the 17-keto substrate (2) toward molecular oxygen under basic conditions.     

Evidence of 2-hydroxylation of estradiol-17 beta 17-glucuronide by male rat liver microsomes

When estradiol-17 beta 17-glucuronide was incubated with male rat liver microsomal preparations with a NADPH-generating system, 2-hydroxyestradiol-17 beta 17-glucuronide was obtained. This 2-hydroxylation was shown to occur without cleavage of the conjugate group. The result clearly indicates that estradiol-17 beta 17-glucuronide could act as substrate for rat liver microsomal 2-hydroxylase.     

5Alpha-androstane-3beta,7alpha,17beta-triol and 5alpha-androstane-3beta,7beta,17beta-triol as substrates for the human 11beta-hydroxysteroid dehydrogenase type 1

Several studies have shown that the native 7alpha-hydroxy-dehydroepiandrosterone (7alpha-hydroxy-DHEA) is a substrate for the human 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1) which converts the 7alpha- into the 7beta-epimer through an oxido-reduction process. Research on the 11beta-HSD1 has investigated its function and structure through using native glucocorticoid substrates and known inhibitors. Other steroid substrates are also of interest. Among testosterone metabolites, 5alpha-androstane-3beta,17beta-diol (Adiol) is a substrate for the cytochrome P450 7B1 which produces 5alpha-androstane-3beta,7alpha,17beta-triol (7alpha-Adiol). This steroid may be a substrate for the 11beta-HSD1. We used recombinant yeast-expressed 11beta-HSD1 with NADP(H)-regenerating systems for examining the products obtained after incubation with 7alpha-Adiol, 7beta-Adiol or 7-oxo-Adiol. Oxidative conditions for the 11beta-HSD1 provided no trace of 7-oxo-Adiol but the inter-conversion of 7alpha- and 7beta-hydroxy-Adiol with V(max)/K(M) (pmol min(-1) microg(-1)/microM) values of 2 and 0.5, respectively. This state was maintained under reductive conditions. The use of a 7-oxo-Adiol substrate under reductive conditions led to the production of both 7alpha- and 7beta-hydroxy-Adiol with V(max)/K(M) values of 3.43 and 0.22, respectively. These findings support the hypothesis that the oxido-reductase and epimerase activities of 11beta-HSD1 depend on the positioning of the steroid substrates within the active site and may provide insight into its fine structure and mechanism of action.     

The synthesis of 17-alkoxycarbonyl- and 17-carboxamido-13alpha-estra-1,3,5(10),16-tetraene derivatives via palladium-catalyzed carbonylation reactions

17-Alkoxycarbonyl- and 17-carboxamido-13alpha-estra-1,3,5(10),16-tetraenes were synthesized from the 17-iodo-13alpha-estra-1,3,5(10),16-tetraene derivative in palladium-catalyzed alkoxycarbonylation and aminocarbonylation reactions, respectively. The synthesis of the 17-iodo-16-ene derivative, used as substrate, is based on the transformation of the 17-keto derivative (epiestrone methyl ether) to hydrazone, which was treated with iodine in the presence of a base (1,1,3,3-tetramethyl guanidine). 17-Carboxamides were obtained in good yields (up to 88%) not only with simple alkyl/aryl amines but also with amino acid methyl esters as N-nucleophiles. The use of alcohols as O-nucleophiles in alkoxycarbonylation resulted in the corresponding 17-esters; however, yields of synthetic interest were obtained only with methanol.     

3D-structure of human estrogenic 17β-HSD1: binding with various steroids

Human estrogenic dehydrogenase (17β-HSD1) catalyses the last step in the biosynthesis of the active estrogens that stimulate the proliferation of breast cancer cells. While the primary substrate for the enzyme is estrone, the enzyme has some activity for the non-estrogenic substrates. To better understand the structure–function relationships of 17β-HSD1 and to provide a better ground for the design of inhibitors, we have determined the crystal structures of 17β-HSD1 in complex with different steroids.The structure of the complex of estradiol with the enzyme determined previously (Azzi et al., Nature Structural Biology 3, 665–668) showed that the narrow active site was highly complementary to the substrate. The substrate specificity is due to a combination of hydrogen bonding and hydrophobic interactions between the steroid and the enzyme binding pocket. We have now determined structures of 17β-HSD1 in complex with dihydrotestosterone and 20α-OH-progesterone. In the case of the C19 androgen, several residues within the enzyme active site make some small adjustments to accommodate the increased bulk of the substrate. In addition, the C19 steroids bind in a slightly different position from estradiol with shifts in positions of up to 1.4 Å. The altered binding position avoids unfavorable steric interactions between Leu 149 and the C19 methyl group (Han et al., unpublished). The known kinetic parameters for these substrates can be rationalized in light of the structures presented. These results give evidence for the structural basis of steroid recognition by 17β-HSD1 and throw light on the design of new inhibitors for this pivotal steroid enzyme.     

Proprotein convertases process Pmel17 during secretion

Pmel17 is a melanocyte/melanoma-specific protein that traffics to melanosomes where it forms a fibrillar matrix on which melanin gets deposited. Before being cleaved into smaller fibrillogenic fragments the protein undergoes processing by proprotein convertases, a class of serine proteases that typically recognize the canonical motif RX(R/K)R↓. The current model of Pmel17 maturation states that this processing step occurs in melanosomes, but in light of recent reports this issue has become controversial. We therefore addressed this question by thoroughly assessing the processing kinetics of either wild-type Pmel17 or a secreted soluble Pmel17 derivative. Our results demonstrate clearly that processing of Pmel17 occurs during secretion and that it does not require entry of the protein into the endocytic system. Strikingly, processing proceeds even in the presence of the secretion inhibitor monensin, suggesting that Pmel17 is an exceptionally good substrate. In line with this, we find that newly synthesized surface Pmel17 is already quantitatively cleaved. Moreover, we demonstrate that Pmel17 function is independent of the sequence identity of its unconventional proprotein convertase-cleavage motif that lacks arginine in P4 position. The data alter the current view of Pmel17 maturation and suggest that the multistep processing of Pmel17 begins with an early cleavage during secretion that primes the protein for later functional processing.     

Metabolism of [17-2H]pregnenolone into 5-[17 beta-2H, 17 alpha-18O]androstene-3 beta, 17 alpha-diol and other products by incubation with the microsomal fraction of boar testis under 18O2 atmosphere.

[17-2H]Pregnenolone was incubated with the microsomal fraction of boar testis under an 18O2 atmosphere. The metabolites were analyzed by gas chromatography-mass spectrometry, and the following six metabolites labeled with 2H or 18O (or both) were identified: 17 alpha-[17-18O]hydroxypregnenolone, [17-18O]dehydroepiandrosterone, 5-[17-18O]androstene-3 beta, 17 beta-diol, 16 alpha-[16-18O]hydroxy[17-2H]pregnenolone, 5-[17 beta-2H, 17-18O]androstene-3 beta,17 alpha-diol, and 5,16-[17-2H]androstadien-3 beta-ol. The time course of the formation of these metabolites from pregnenolone was also studied using 14C-labeled substrate. The results obtained from these experiments suggest that the first three metabolites were synthesized by a well-documented pathway--pregnenolone yields 17 alpha-hydroxypregnenolone yields dehydroepiandrosterone yields 5-androstene-3 beta,17 beta-diol--, and that 16 alpha-hydroxypregnenolone, 5-androstene-3 beta,17 alpha-diol and 5,16-androstadien-3 beta-ol were synthesized from [17-2H]pregnenolone with retention of 17-2H.     

Functional aspects of 17beta-hydroxysteroid dehydrogenase 1 determined by comparison to a closely related retinol dehydrogenase

Determining the functional aspects of a gene or protein is a difficult and time-consuming process. De novo analysis is surely the hardest and so it is often quite useful to start with a comparison to functionally or structurally related proteins. Although 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD 1) can hardly be called a new protein but rather the best characterized among the family of 17beta-HSDs some aspects of structure–function relationships remain unclear. We have sought new aspects of 17beta-HSD 1 function through a comparison with its closest homolog, a photoreceptor-associated retinol dehydrogenase (prRDH). Overall amino acid identity and size of the proteins are highly conserved, but major differences occur in the C-termini, where prRDH, but not 17beta-HSD 1, harbors motifs indicative of membrane localization. To gain insight into substrate discrimination by prRDH and 17beta-HSD 1, we constructed 3D-structure models of the corresponding zebrafish enzymes. Investigation of the substrate binding site revealed a few identical amino acids, and suggested a role for G143 in zebrafish 17beta-HSD 1 and M146 and M147 in the two zebrafish paralogs prRDH 1 and prRDH 2, respectively, in substrate specificity. Activity measurements of modified proteins in transiently transfected intact HEK 293 cells hint at a putative role of these amino acids in discrimination between steroid and retinoid substrates.     

A highly selective method for 11 beta-OH protection of steroidal 11 beta, 17 alpha-diols

A highly selective method to protect the 11 beta-OH position of steroid (1) has been developed. This is achieved via double silyl protection of the 11 beta, 17 alpha-diol, followed by selective desilylation of the 17 alpha-OH under basic conditions without the need for a fluoride source.     

Catalytic competence, a new criterion for affinity labeling. Demonstration of the reversible enzymatic interconversion of estrone and estradiol-17 beta covalently bound to human placental estradiol-17 beta dehydrogenase.

Human placental estradiol-17beta dehydrogenase is rapidly inactivated upon treatment with 3-bromoacetoxyestrone. Pseudo-first order kinetic data are obtained and inactivation is accompanied by incorporation of 1 mol of 3-acetoxyestrone/mol of subunit (Mr =34,000). Treatment of the inactivated enzyme with (4S)-[4-2H]DPNH results in the formation of covalently bound [17alpha-2H]estradiol-17beta, which can be released by hydrolysis and identified by gas chromatography-mass sepctrometry. When (4R)-[4-2H]DPNH was used, deuterium was not transferred. Thus, the normal stereochemistry of hydridetransfer is preserved for both partners. After treatment with p-mercuribenzoate, affinity-labeled estradiol-17beta dehyrogenase is no longer able to caralyze reduction its covalently bound estrone; in the presence of DPNH and native enzyme, however, reduction occurs, demonstrating that affinity-labeled enzyme can itself serve as subtrate for native estradiol-17beta dehydrogenase. The reversible enzymatic interconversion of covalently bound estrone was demonstrated using a transhydrogenase assay. The ability of an enzyme to catalyze its normal reaction with a covalently bound substrate is termed catalytic competence, and is considered to be a new criterion for affinity labeling.     

Fingerprinting the substrate specificity of M1 and M17 aminopeptidases of human malaria, Plasmodium falciparum

Background

Plasmodium falciparum, the causative agent of human malaria, expresses two aminopeptidases, PfM1AAP and PfM17LAP, critical to generating a free amino acid pool used by the intraerythrocytic stage of the parasite for proteins synthesis, growth and development. These exopeptidases are potential targets for the development of a new class of anti-malaria drugs.

Methodology/Principal Findings

To define the substrate specificity of recombinant forms of these two malaria aminopeptidases we used a new library consisting of 61 fluorogenic substrates derived both from natural and unnatural amino acids. We obtained a detailed substrate fingerprint for recombinant forms of the enzymes revealing that PfM1AAP exhibits a very broad substrate tolerance, capable of efficiently hydrolyzing neutral and basic amino acids, while PfM17LAP has narrower substrate specificity and preferentially cleaves bulky, hydrophobic amino acids. The substrate library was also exploited to profile the activity of the native aminopeptidases in soluble cell lysates of P. falciparum malaria.

Conclusions/Significance

This data showed that PfM1AAP and PfM17LAP are responsible for majority of the aminopeptidase activity in these extracts. These studies provide specific substrate and mechanistic information important for understanding the function of these aminopeptidases and could be exploited in the design of new inhibitors to specifically target these for anti-malaria treatment.     

Highly efficient synthesis of steroid-17-spiro-5'-oxazolidine-2',4'-diones from 17-keto steroids

Spiro[androst-4-en-17 alpha,5'-oxazolidine]-2',3,4'-trione 8a and spiro[androst-4-en-17 alpha,5'-oxazolidine]-2',3,4',11-tetraone 8b, two potentially bioactive spiranes, were prepared from the parent 17-ketones in four steps (64% and 49.5% yield, respectively). The key intermediates were the hydroxyimidates 5a and 5b, which easily underwent cyclization to the corresponding spirooxazolinone 4'-enol ethers when treated with alkylchlorocarbonates. The respective N-amyl derivatives of the spiranes 8a and 8b were obtained with n-pentyl bromide in the presence of KF. A new method for the synthesis of steroid 17 alpha-hydroxy-17-carboxyesters and 17 alpha-hydroxy-17-carboxamides is described. Attempts to synthesize the title compounds from these products were unsuccessful.     

Development of a plasma 17alpha-hydroxyprogesterone time resolved-fluorescence immunoassay involving a new biotinylated tracer

A biotinylated 17alpha-hydroxyprogesterone probe (3) was prepared from 17alpha-hydroxyprogesterone-3-carboxymethyloxime and conjugate obtained by acylation of biotinylaminopropylammonium trifluroacetate. This new tracer was used in the development of a 17alpha-hydroxyprogesterone time-resolved fluoroimmunoassay using streptavidin-europium. The new method was compared to a long-standing radioimmunoassay method and found to be more sensitive and economical.     

Molecular mechanisms of estrogen recognition and 17-keto reduction by human 17beta-hydroxysteroid dehydrogenase 1

The reduction of inactive estrone (E1) to the active estrogen 17beta-estradiol (E2) is catalyzed by type 1 17beta-hydroxysteroid dehydrogenase (17HSD1). Crystallographic studies, modeling and activity measurement of mutants and chimeric enzymes have led to the understanding of its mechanism of action and the molecular basis for the estrogenic specificity. An electrophilic attack on the C17-keto oxygen by the Tyr 155 hydroxyl is proposed for initiation of the transition state. The active site is a hydrophobic pocket with catalytic residues at one end and the recognition machinery on the other. Tyr 155, Lys 159 and Ser 142 are essential for the activity. The presence of certain other amino acids near the substrate recognition end of the active site including His 152 and Pro 187 is critical to the shape complementarity of estrogenic ligands. His 221 and Glu 282 form hydrogen bonds with 3-hydroxyl of the aromatic A-ring of the ligand. This mechanism of recognition of E1 by 17HSD1 is similar to that of E2 by estrogen receptor alpha. In a ternary complex with NADP(+) and equilin, an equine estrogen with C7=C8 double bond, the orientation of C17=O of equilin relative to the C4-hydride is more acute than the near normal approach of the hydride for the substrate. In the apo-enzyme structure, a substrate-entry loop (residues 186-201) is in an open conformation. The loop is closed in this complex and Phe 192 and Met 193 make contacts with the ligand. Residues of the entry loop could be partially responsible for the estrogenic specificity.     

A facile synthesis of C(2)-symmetric 17 beta-estradiol dimers

A rapid and efficient synthesis of a series of C(2)-symmetric 17 beta-estradiol dimers is described. The new molecules are linked at position 17 alpha of the steroid nucleus with either an alkyl chain or a polyethylene glycol chain. They are made from estrone in five chemical steps with an overall yield exceeding 30%. The biological activity of these compounds was evaluated in vitro on estrogen dependent and independent (ER(+) and ER(-)) human breast tumor cell lines: MCF-7 and MDA-MB-231. Some of the dimers present selective cytotoxic activity against the ER(+) cell line.     

Evidence of an enzymatic 17alpha leads to 21 hydroxyl transfer in the biosynthesis of cortexolone from 17alpha-hydroperoxyprogesterone by adrenal cortex microsomes.

The concept of a possible biogenetic intramolecular relationship between several pairs of hydroxylated positions of corticosteroids, in particular between positions 17alpha and 21, has been proposed by us some time ago. We now present evidence that to a certain extent such a relationship can indeed exist. 18O-labelled 17alpha-hydroperoxyprogesterone was incubated under ordinary oxygen atmosphere with the microsomal fractions of bovine adrenal cortex. Following extensive purifications by thin-layer chromatography, we have isolated a metabolite with mobility characteristics corresponding to those of authentic 17,21-dihydroxy-4-pregnene-3,20-dione (cortexolone). According to its mass spectrum, this metabolite has a molecular weight of 350, i.e. 4 atomic mass units higher than the molecular weight of non-labelled cortexolone. No conversion of 17alpha-hydroperoxyprogesterone to cortexolone was observed with a previously heat-inactivated preparation. The presence of 4 additional mass units in the cortexolone metabolite means that the latter has preserved two 18O-labels in the molecule, one at position 17alpha and the other one at position 21. This can only be explained by a rearrangement reaction of the hydroperoxide group in such a way that it is accompanied by a C-17alpha to C-21 hydroxyl transfer. In the inverse case, when non-labelled 17alpha-hydroperoxyprogesterone was incubated under 99% 18O2-atmosphere, non-labelled cortexolone of molecular weight 346 was also found.