Biomedical subjects

Keiko Yamamoto

Publications and source records attributed to Keiko Yamamoto.

At least 19 recordsLinked to original sources

PubMed2007

Alanine scanning mutational analysis of the ligand binding pocket of the human Vitamin D receptor.

We achieved exhaustive alanine scanning mutational analysis of the amino acid residues lining the ligand binding pocket of the Vitamin D receptor to investigate the mechanism of the ligand recognition by the receptor. This is the first exhaustive analysis in the nuclear receptor superfamily. Our results demonstrated the role and importance of all the residues lining the ligand binding pocket. In addition, this analysis was found to indicate ligand-specific ligand-protein interactions, which have key importance in determining the transactivation potency of the individual ligands. Thus, the analysis using 1beta-methyl-1alpha,25-dihydroxyvitamin D(3) revealed the specific van der Waals interactions of 1beta-methyl group with the receptor.

Alanine↗

PubMed2006

Identification of a highly potent vitamin D receptor antagonist: (25S)-26-adamantyl-25-hydroxy-2-methylene-22,23-didehydro-19,27-dinor-20-epi-vitamin D3 (ADMI3).

We synthesized four new vitamin D derivatives, diastereomers at C20 and C25 of 26-adamantyl-1,25-dihydroxy-2-methylene-22,23-didehydro-19,27-dinorvitamin D3 (ADMI1-4), which have the bulky and rigid adamantane ring system at the side chain terminus. These compounds had significant VDR affinity (1/6-1/30 that of the natural hormone) but their efficacies of transactivation in transient transcription assay was low (approximately 1/10). All ADMI compounds antagonized the action of 1,25(OH)2D3 in transient transcription assay in COS-7 cells with ADMI3 (20S,25S-isomer) was the most potent (IC50, 3 nM). ADMI3 (1 microM) suppressed the endogenous CYP24A1 gene expression induced by 1,25(OH)2D3 (10 nM) in HEK293 cells to nearly control level. Thus we have identified 26-adamantyl vitamin D compound as a novel highly potent VDR antagonist/partial agonist. A docking model of ADMI3 reveals that a terminal part of the large adamantane ring crowds the H12 residues (Val318 and Phe422) and this would prevent the H12 adopting the active conformation.

Adamantane↗

PubMed2006

Structure-activity relationships of 19-norvitamin D analogs having a fluoroethylidene group at the C-2 position.

We have synthesized four new geometric isomers of 1alpha,25-dihydroxy-2-(2'-fluoroethylidene)-19-norvitamin D analogs 1 and 2 having a 20R- and 20S-configuration, whose structures are correlated with 2MD possessing high potencies in stimulating bone formation in vitro and in vivo. The E-isomers of (20R)- and (20S)-2-fluoroethylidene analogs 1a and 1b were comparable with the natural hormone 1alpha,25-(OH)(2)D(3) in binding to the vitamin D receptor (VDR), while two Z-isomers 2a and 2b were about 15-20 times less active than the hormone. In inducing expression of the vitamin D responsive element-based luciferase reporter gene, the E-isomers 1a and 1b were 1.2- and 8.6-fold more potent than the hormone, respectively, while the Z-isomers 2a and 2b had 27-55% of the potency. On the basis of the biological activities and a docking simulation based on X-ray crystallographic analysis of the VDR ligand-binding pocket, the structure-activity relationships of the fluorinated 19-norvitamin D analogs are discussed.

Animals↗

PubMed2006

Characterization of rat and human CYP2J enzymes as Vitamin D 25-hydroxylases.

vitamin D is 25-hydroxylated in the liver, before being activated by 1alpha-hydroxylation in the kidney. Recently, the rat cytochrome P450 2J3 (CYP2J3) has been identified as a principal vitamin D 25-hydroxylase in the rat [Yamasaki T, Izumi S, Ide H, Ohyama Y. Identification of a novel rat microsomal vitamin D3 25-hydroxylase. J Biol Chem 2004;279(22):22848-56]. In this study, we examine whether human CYP2J2 that exhibits 73% amino acid homology to rat CYP2J3 has similar catalytic properties. Recombinant human CYP2J2 was overexpressed in Escherichia coli, purified, and assayed for vitamin D 25-hydroxylation activity. We found significant 25-hydroxylation activity toward vitamin D3 (turnover number, 0.087 min(-1)), vitamin D2 (0.16 min(-1)), and 1alpha-hydroxyvitamin D3 (2.2 min(-1)). Interestingly, human CYP2J2 hydroxylated vitamin D2, an exogenous vitamin D, at a higher rate than it did vitamin D3, an endogenous vitamin D, whereas, rat CYP2J3 hydroxylated vitamin D3 (1.4 min(-1)) more efficiently than vitamin D2 (0.86 min(-1)). Our study demonstrated that human CYP2J2 exhibits 25-hydroxylation activity as well as rat CYP2J3, although the activity of human CYP2J2 is weaker than rat CYP2J3. CYP2J2 and CYP2J3 exhibit distinct preferences toward vitamin D3 and D2.

Animals↗

PubMed2006

Structure-function analysis of vitamin D 24-hydroxylase (CYP24A1) by site-directed mutagenesis: amino acid residues responsible for species-based difference of CYP24A1 between humans and rats.

Our previous studies revealed the species-based difference of CYP24A1-dependent vitamin D metabolism. Although human CYP24A1 catalyzes both C-23 and C-24 oxidation pathways, rat CYP24A1 shows almost no C-23 oxidation pathway. We tried to identify amino acid residues that cause the species-based difference by site-directed mutagenesis. In the putative substrate-binding regions, amino acid residue of rat CYP24A1 was converted to the corresponding residue of human CYP24A1. Among eight mutants examined, T416M and I500T showed C-23 oxidation pathway. In addition, the mutant I500F showed quite a different metabolism of 1alpha,25-dihydroxyvitamin D3 [1alpha,25(OH)2D3] from both human and rat CYP24A1. These results strongly suggest that the amino acid residues at positions 416 and 500 play a crucial role in substrate binding and greatly affect substrate orientation. A three-dimensional model of CYP24A1 indicated that the A-ring and triene part of 1alpha,25(OH)2D3 could be located close to amino acid residues at positions 416 and 500, respectively. Our findings provide useful information for the development of new vitamin D analogs for clinical use.

Amino Acid Sequence↗

PubMed2006

Interaction between mitochondrial CYP27B1 and adrenodoxin: role of arginine 458 of mouse CYP27B1.

A molecular modeling study of CYP27B1 suggests that Arg458 of mouse CYP27B1 is involved in interaction with adrenodoxin (ADX). Thus, we generated CYP27B1 mutants R458K and R458Q and revealed their enzymatic properties. Substrate-induced difference spectra and K(m) values for 1alpha-hydroxylation of 25(OH)D3 indicate that the replacement of Arg458 with Lys or Gln does not affect substrate binding. However, these mutants showed remarkable decreases of both kcat values and the ratio of product formation to NADPH oxidation (coupling efficiency). A high K(m) value of R458Q for ADX concentration and a decrease of rate constant of the first electron transfer seem reasonable considering that the conversion from Arg to noncharged Gln abolishes salt-bridge formation with the acidic residue of ADX. On the other hand, R458K showed atypical kinetics for ADX concentration with Hill's constant of 2.0 and high catalytic activity at high ADX concentration by increase of coupling efficiency. These results suggest that conformational change of R458K by binding the two ADX molecules is essential for 1alpha-hydroxylation of 25(OH)D3. On the other hand, binding one ADX molecule is sufficient for the conformational change of the wild-type CYP27B1, judging from its Michaelis-Menten-type kinetics for ADX concentration with high coupling efficiency. These results suggest that ADX functions as an effector for the oxygen transfer reaction in addition to being an electron donor for CYP27B1.

25-Hydroxyvitamin D3 1-alpha-Hydroxylase↗

PubMed2006

Analogs of 1alpha,25-dihydroxyvitamin D3 with high potency in induction of osteoclastogenesis and prevention of dendritic cell differentiation: synthesis and biological evaluation of 2-substituted 19-norvitamin D analogs.

In our previous papers, we found that introduction of a substituent at C(2) into 1alpha,25-dihydroxy-19-norvitamin D(3) (2a) caused dramatic changes in binding affinity for the vitamin D receptor (VDR) and in transcriptional activity compared with the parent compound. To investigate the broad biological activity of 2-substituted 19-norvitamin D analogs, we synthesized two new (20S)-2-hydroxyethylidene-19-norvitamin D derivatives (3b and 4b) and a total of 16 A-ring-modified analogs including 3b and 4b were tested for the following in vitro and in vivo biological activities: (1) affinity for the VDR, (2) transcriptional activity, (3) osteoclast formation, (4) bone calcium mobilization in rats, and (5) effects on differentiation of dendritic cells (DCs). The biological effects of the analogs were compared with those of 1alpha,25-dihydroxyvitamin D(3) (1a) and 2MD, which is being developed for the treatment of osteoporosis. The efficacy of the (20S)-19-norvitamin D analogs with 2-hydroxyethylidene, 2-hydroxyethoxy, and 2-methyl moieties (3b, 5b, 6b, and 9b) was more than 10-fold stronger than that of 1a with respect to transcriptional activity, ability to induce osteoclast formation, and ability to inhibit CD86 expression, a marker of mature DCs, and was similar to that of 2MD. The (20S)-2beta-hydroxyethoxy derivative 6b was 2 orders of magnitude more active than 1a and approximately twice as potent as 2MD in preventing CD86 production. The 2-epoxy derivatives 7 and 8 were relatively poor ligands for the VDR and exhibited activity lower than that of the natural hormone 1a.

Animals↗

PubMed2006

Synthesis and biological activities of new 1alpha,25-dihydroxy-19-norvitamin D3 analogs with modifications in both the A-ring and the side chain.

In a series of studies on structure-activity relationships of 2-substituted 19-norvitamin D analogs, we found that 1alpha,25-dihydroxy-19-norvitamin D3 analogs with 2beta-hydroxyethoxy or 2E-hydroxyethylidene moieties show strong binding affinity for the vitamin D receptor (VDR) as well as marked transcriptional activity. To further examine the effects of side chain structure on the activity of 2-substituted 19-norvitamin D analogs, we have synthesized new 19-norvitamin D3 analogs with modifications in both the A-ring at the C(2) position and the side chain. The side chains of these analogs contained a double bond between C(22) and C(23) or an oxygen atom at C(22). The biological activity of the analogs was evaluated in vitro. All the side chain-modified analogs were less active than 1alpha,25-dihydroxyvitamin D31e and the parent compounds 3-6e possessing a natural 20R-configuration in binding to the VDR, but, except for the (20R)-22-oxa analogs 3-6d, were significantly more potent in transcriptional activity. Of the side-chain-modified analogs 4 and 5, the 2beta-hydroxyethoxy- and 2E-hydroxyethylidene-22,24-diene-24a,26a,27a-trihomo analogs showed markedly higher transcriptional activity (25- and 17.5-fold, respectively) compared with 1e. Elongation of the side chain at the C-24, C-26, and C-27 positions and introduction of a 22,24-diene moiety strongly increased transcriptional activity, as seen in the 20-epi analogs 3-6f.

Animals↗

PubMed2006

Vitamin D receptor: ligand recognition and allosteric network.

To investigate the allosteric effects of ligands in the function of nuclear receptors, we performed exhaustive alanine scanning mutational analysis (ASMA) of the residues lining the ligand-binding pocket (LBP) of the human vitamin D receptor. The effects of ligands were examined in this system (termed two-dimensional (2D) ASMA) using 10 structurally and biologically characteristic ligands that included agonists, partial agonists, and a full antagonist. The results clearly revealed the role and importance of all the amino acid residues lining the LBP and the relationships between ligand binding and transcriptional potency. 2D ASMA indicated ligand-specific ligand-protein interactions, which have key importance in determining the transactivation potency of the ligand. Taking the results as a whole, we suggest a ligand-mediated allosteric network through which information from ligands is transmitted to the interfaces with protein cofactors and which was shown to be linked to part of the network found by statistical coupling analysis.

Alanine↗

PubMed2006

Possible connections among job stress, depressive symptoms, lipid modulation and antioxidants.

BACKGROUND: Oxidative/antioxidative status may be related to psychological stress or pathogenesis of depression. SUBJECTS AND METHODS: Participants were selected from 381 female nurses working in a university hospital, and the Brief Job Stress Questionnaire was utilized to assess them. Nurses with high job stress (JS) (n = 18) and with low JS (n = 15) consented to participate in this study. Depressive symptoms were assessed by the Centre for Epidemiologic Studies Depression scale (CES-D). Cholesterols, lipid peroxidation (malondialdehyde, MDA) and antioxidants in the plasma were measured. RESULTS: High JS participants exhibited significantly higher CES-D scores (t = 3.34, p < 0.005), and significantly lower concentrations of total cholesterol (TC), low density+very low density lipoprotein cholesterols (LDL+VLDL), alpha-tocopherol, and beta-carotene compared with low JS participants (t = 2.69, p < 0.05; t = 3.46, p < 0.005; t = 2.96, p < 0.05; t = 2.98, p < 0.05, respectively). However, the reductions in plasma indicators were substantially weakened after controlling for lifestyle factors with the exception of LDL+VLDL and alpha-tocopherol. In addition, the significance of alpha-tocopherol concentrations appeared to depend on cholesterol levels. CES-D scores correlated positively with plasma MDA levels, the MDA/TC ratio and the MDA/LDL+VLDL ratio among the low JS group (r = 0.69, p < 0.001; r = 0.79, p < 0.001; r = 0.75, p < 0.005, respectively), whereas there were no correlations among the high JS group. After controlling for lifestyle covariates, the relationship between CES-D scores and the MDA/LDL+VLDL ratio remained significant (beta = 0.95, p < 0.05) using a multiple linear regression model (F = 3.61, p < 0.05). LIMITATIONS: Sample numbers in each JS group were relatively small. CONCLUSIONS: Psychological stress may reduce the plasma levels of LDL+VLDL accompanying an alpha-tocopherol decrease. There appeared to be a correlation between elevated MDA and depressive symptoms in low JS participants.

Adult↗

PubMed2006

Ligand recognition by vitamin D receptor: total alanine scanning mutational analysis of the residues lining the ligand binding pocket of vitamin D receptor.

We performed total alanine scanning mutational analysis (ASMA) of the residues lining the ligand binding pocket (LBP) of the human vitamin D receptor (hVDR) to investigate allosteric effects of ligands in the function of nuclear receptors (NRs). This was accomplished for the first time in the NR superfamily. The effects of ligand structure were also examined in this system (termed 2D-ASMA) using 8 representative VDR ligands. The results clearly revealed the role and importance of all amino acid residues lining the LBP and the relationships between ligand binding and transcriptional potency. 2D-ASMA indicated ligand-specific ligand-protein interactions, which are essential in determining the transactivation potency of the ligand. Taking the results as a whole, we suggest a ligand-mediated allosteric network, which allows transmission of information from ligands to the interfaces of the VDR in association with protein cofactors and was shown to be linked to a part of the network identified by statistical coupling analysis (SCA).

Alanine↗

PubMed2005

Synthesis of docosahexaenoic acid derivatives designed as novel PPARgamma agonists and antidiabetic agents.

To discover novel peroxisome proliferator-activated receptor gamma (PPARgamma) agonists that could be used as antidiabetic agents, we designed docosahexaenoic acid (DHA) derivatives (2 and 3), which have a hydrophilic substituent at the C4-position, based on the crystal structure of the ligand-binding pocket of PPARgamma. These compounds were synthesized via iodolactone as a key intermediate. We found that both DHA derivatives (2 and 3) showed PPARgamma transactivation higher than, or comparable to, that of pioglitazone, which is a TZD derivative used as an antidiabetic agent. DHA derivatives related to these potent compounds 2 and 3 were also synthesized to study structure-activity relationships. Furthermore, 4-OH DHA 2, which shows strong PPARgamma transcriptional activity, was separated as an optically pure form.

Animals↗

PubMed2005

Ethanol production from cellobiose by Zymobacter palmae carrying the Ruminocuccus albus beta-glucosidase gene.

Its metabolic characteristics suggest Zymobacter palmae gen. nov., sp. nov. could serve as a useful new ethanol-fermenting bacterium, but its biotechnological exploitation would require certain genetic improvements. We therefore established a method for transforming Z. palmae using the broad-host vector plasmids pRK290, pMFY31 and pMFY40 as a source of transforming DNA. Using electroporation, the frequency of transformation was 10(5) to 10(6) transformants/mug of DNA. To confer the ability to ferment cellobiose, which is a hydrolysis product from cellulosic materials treated enzymatically or with acid, the beta-glucosidase gene from Ruminococcus albus was introduced into Z. palmae, where its expression was driven by its endogenous promoter. About 56% of the enzyme expressed was localized on the cell-surface or in the periplasm. The recombinant Z. palmae could ferment 2% cellobiose to ethanol, producing 95% of the theoretical yield with no accumulation of organic acids as metabolic by-products. Thus, expression of beta-glucosidase in Z. palmae expanded the substrate spectrum of the strain, enabling ethanol production from cellulosic materials.

Cellobiose↗

PubMed2005

Identification of the amino acid residue of CYP27B1 responsible for binding of 25-hydroxyvitamin D3 whose mutation causes vitamin D-dependent rickets type 1.

We previously reported the three-dimensional structure of human CYP27B1 (25-hydroxyvitamin D3 1alpha-hydroxylase) constructed by homology modeling. Using the three-dimensional model we studied the docking of the substrate, 25-hydroxyvitamin D3, into the substrate binding pocket of CYP27B1. In this study, we focused on the amino acid residues whose point mutations cause vitamin D-dependent rickets type 1, especially unconserved residues among mitochondrial CYPs such as Gln65 and Thr409. Recently, we successfully overexpressed mouse CYP27B1 by using a GroEL/ES co-expression system. In a mutation study of mouse CYP27B1 that included spectroscopic analysis, we concluded that in a 1alpha-hydroxylation process, Ser408 of mouse CYP27B1 corresponding to Thr409 of human CYP27B1 forms a hydrogen bond with the 25-hydroxyl group of 25-hydroxyvitamin D3. This is the first report that shows a critical amino acid residue recognizing the 25-hydroxyl group of the vitamin D3.

25-Hydroxyvitamin D3 1-alpha-Hydroxylase↗

PubMed2005

New derivatives of 1alpha,25-dihydroxy-19-norvitamin D3 with two substituents at C-2: synthesis and biological activity.

To examine the effect of 2,2-disubstitution on the biological activities of 19-norvitamin D analogs, novel 2,2-disubstituted-(20R)- and (20S)-1alpha,25-dihydroxy-19-norvitamin D3 analogs were prepared and their biological activities were studied. All the synthesized analogs possessing hydrophobic 2alpha-substituents were more active than the corresponding 2beta-isomers both in binding to the vitamin D receptor and in activating gene transcription. The 2alpha-methyl-2beta-hydroxy analog 9b was found to have markedly higher transcriptional activity (32-fold) than the natural ligand 1a, although the two had the same binding affinity to the vitamin D receptor. To our knowledge, this analog is among the most potent of 19-norvitamin D analogs.

Animals↗

PubMed2005

Identification of putative metabolites of docosahexaenoic acid as potent PPARgamma agonists and antidiabetic agents.

We found that putative metabolites of docosahexaenoic acid (DHA) are strong PPARgamma activators and potential antidiabetic agents. We designed DHA derivatives based on the crystal structure of PPARgamma, synthesized them and evaluated their activities in vitro and in vivo. The efficacy of 5E-4-hydroxy-DHA 2a as a PPARgamma activator was about fourfold stronger than that of pioglitazone. Furthermore, the 4-keto derivative (10b) showed antidiabetic activity in animal models without producing undesirable effects such as obesity and hepatotoxicity.

Animals↗

PubMed2005

The distinct agonistic properties of the phenylpyrazolosteroid cortivazol reveal interdomain communication within the glucocorticoid receptor.

Recent structural analyses of the nuclear receptors establish a paradigm of receptor activation, in which agonist binding induces the ligand binding domain (LBD)/activation function-2 helix to form a charge clamp for coactivator recruitment. However, these analyses have not sufficiently addressed the mechanisms for differential actions of various synthetic steroids in terms of fine tuning of multiple functions of whole receptor molecules. In the present study, we used the glucocorticoid receptor (GR)-specific agonist cortivazol (CVZ) to probe the plasticity and functional modularity of the GR. Structural docking analysis revealed that although CVZ is more bulky than other agonists, it can be accommodated in the ligand binding pocket of the GR by reorientation of several amino acid side chains but without major alterations in the active conformation of the LBD. In this induced fit model, the phenylpyrazole A-ring of CVZ establishes additional contacts with helices 3 and 5 of the LBD that may contribute to a more stable LBD configuration. Structural and functional analysis revealed that CVZ is able to compensate for the deleterious effects of a C-terminal deletion of the LBD in a manner that mimics the stabilizing influence of the F602S point mutation. CVZ-mediated productive recruitment of transcriptional intermediary factor 2 to the C-terminally deleted LBD requires the receptor's own DNA binding domain and is positively influenced by the N-terminal regions of GR or progesterone receptor. These results support a model where ligand-dependent conformational changes in the LBD play a role in GR-mediated gene regulation via modular interaction with the DBD and activation function-1.

Amino Acid Sequence↗

PubMed2005

Metabolism of vitamin D3 by cytochromes P450.

The vitamin D3 25-hydroxylase (CYP27A1), 25-hydroxyvitamin D3 1alpha-hydroxylase (CYP27B1) and 1alpha,25-dihydroxyvitamin D3 24-hydroxylase (CYP24A1) are members of the cytochrome P450 superfamily, and key enzymes of vitamin D3 metabolism. Using the heterologous expression in E. coli, enzymatic properties of the P450s were recently investigated in detail. Upon analyses of the metabolites of vitamin D3 by the reconstituted system, CYP27A1 surprisingly produced at least seven forms of minor metabolites including 1alpha,25(OH)2D3 in addition to the major metabolite 25(OH)D3. These results indicated that human CYP27A1 catalyzes multiple reactions involved in the vitamin D3 metabolism. In contrast, CYP27B1 only catalyzes the hydroxylation at C-1alpha position of 25(OH)D3 and 24R,25(OH)2D3. Enzymatic studies on substrate specificity of CYP27B1 suggest that the 1alpha-hydroxylase activity of CYP27B1 requires the presence of 25-hydroxyl group of vitamin D3 and is enhanced by 24-hydroxyl group while the presence of 23-hydroxyl group greatly reduced the activity. Eight types of missense mutations in the CYP27B1 gene found in vitamin D-dependent rickets type I (VDDR-I) patients completely abolished the 1alpha-hydroxylase activity. A three-dimensional model of CYP27B1 structure simulated on the basis of the crystal structure of rabbit CYP2C5 supports the experimental data from mutagenesis study of CYP27B1 that the mutated amino acid residues may be involved in protein folding, heme-propionate binding or activation of molecular oxygen. CYP24A1 expressed in E. coli showed a remarkable metabolic processes of 25(OH)D3 and 1alpha,25(OH)2D3. Rat CYP24A1 catalyzed six sequential monooxygenation reactions that convert 1alpha,25(OH)2D3 into calcitroic acid, a known final metabolite of C-24 oxidation pathway. In addition to the C-24 oxidation pathway, human CYP24A1 catalyzed also C-23 oxidation pathway to produce 1alpha,25(OH)2D3-26,23-lactone. Surprisingly, more than 70 % of the vitamin D metabolites observed in a living body were found to be the products formed by the activities of CYP27A1, CYP27B1 and CYP24A1. The species-based difference was also observed in the metabolism of vitamin D analogs by CYP24A1, suggesting that the recombinant system for human CYP24A1 may be of great use for the prediction of the metabolism of vitamin D analogs in humans.

25-Hydroxyvitamin D3 1-alpha-Hydroxylase↗