Biochemistry and Molecular Biology of Vitamin D and Its Analog

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 31025

Special Issue Editors


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Guest Editor
Department of Pharmaceutical Engineering, Toyama Prefectural University, Toyama 939-0398, Japan
Interests: structure–function analysis and application of cytochromes P450; metabolism and molecular mechanism of vitamin D; production of functional foods; gene therapy; genome editing
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Guest Editor
Faculty of Nutrition, Kobe Gakuin University, Kobe, Japan
Interests: vitamin D
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Previous studies have shown that vitamin D exerts vitamin D receptor (VDR)-mediated genomic and non-genomic actions, as well as VDR-independent effects. Recently, VDR-independent effects of 25(OH)D3 on lipid metabolism by inducing degradation of SREBP/SCAP have been reported, as have ligand-independent effects of the VDR on the hair cycle. Thus, at least five types of effects of vitamin D and/or the VDR should be considered, namely: (1) VDR-dependent effects of 1,25D (VDR-1,25(OH)2D3), (2) VDR-independent effects of 1,25D (non VDR-1,25(OH)2D3), (3) VDR-dependent effects of 25D (VDR-25(OH)D3), (4) VDR-independent effects of 25D (non VDR-25(OH)D3), and (5) ligand-independent effects of VDR (VDR-no ligand).

Several thousand vitamin D analogues have been synthesized, and many have been studied in clinical trials, including for treating type I rickets, osteoporosis, psoriasis, renal osteodystrophy, leukemia, and pancreatic, prostate, and breast cancers. However, in many cases, their precise molecular mechanisms, which may include VDR-dependent and/or -independent pathways, are not fully understood.

In this Special Issue, we focus on the molecular mechanisms of vitamin D, its analogues and/or VDR actions leading to drug discovery, and nutritional supplements for disease prevention in the future.

Prof. Dr. Toshiyuki Sakaki
Prof. Dr. Naoko Tsugawa
Guest Editors

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Keywords

  • vitamin D
  • vitamin D receptor
  • vitamin D analog
  • genomic action
  • non-genomic action
  • bone formation
  • immune response
  • cancer
  • rickets
  • osteoporosis
  • psoriasis
  • drug discovery
  • disease prevention
  • nutrition improvement
  • metabolism of vitamin D or its analogs
  • cytochrome P450

Published Papers (8 papers)

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Research

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14 pages, 2289 KiB  
Article
Therapeutic Potential of a Novel Vitamin D3 Oxime Analogue, VD1-6, with CYP24A1 Enzyme Inhibitory Activity and Negligible Vitamin D Receptor Binding
by Ali K. Alshabrawy, Yingjie Cui, Cyan Sylvester, Dongqing Yang, Emilio S. Petito, Kate R. Barratt, Rebecca K. Sawyer, Jessica K. Heatlie, Ruhi Polara, Matthew J. Sykes, Gerald J. Atkins, Shane M. Hickey, Michael D. Wiese, Andrea M. Stringer, Zhaopeng Liu and Paul H. Anderson
Biomolecules 2022, 12(7), 960; https://doi.org/10.3390/biom12070960 - 08 Jul 2022
Cited by 4 | Viewed by 1956
Abstract
The regulation of vitamin D3 actions in humans occurs mainly through the Cytochrome P450 24-hydroxylase (CYP24A1) enzyme activity. CYP24A1 hydroxylates both 25-hydroxycholecalciferol (25(OH)D3) and 1,25-dihydroxycholecalciferol (1,25(OH)2D3), which is the first step of vitamin D catabolism. An [...] Read more.
The regulation of vitamin D3 actions in humans occurs mainly through the Cytochrome P450 24-hydroxylase (CYP24A1) enzyme activity. CYP24A1 hydroxylates both 25-hydroxycholecalciferol (25(OH)D3) and 1,25-dihydroxycholecalciferol (1,25(OH)2D3), which is the first step of vitamin D catabolism. An abnormal status of the upregulation of CYP24A1 occurs in many diseases, including chronic kidney disease (CKD). CYP24A1 upregulation in CKD and diminished activation of vitamin D3 contribute to secondary hyperparathyroidism (SHPT), progressive bone deterioration, and soft tissue and cardiovascular calcification. Previous studies have indicated that CYP24A1 inhibition may be an effective strategy to increase endogenous vitamin D activity and decrease SHPT. This study has designed and synthesized a novel C-24 O-methyloxime analogue of vitamin D3 (VD1-6) to have specific CYP24A1 inhibitory properties. VD1-6 did not bind to the vitamin D receptor (VDR) in concentrations up to 10−7 M, assessed by a VDR binding assay. The absence of VDR binding by VD1-6 was confirmed in human embryonic kidney HEK293T cultures through the lack of CYP24A1 induction. However, in silico docking experiments demonstrated that VD1-6 was predicted to have superior binding to CYP24A1, when compared to that of 1,25(OH)2D3. The inhibition of CYP24A1 by VD1-6 was also evident by the synergistic potentiation of 1,25(OH)2D3-mediated transcription and reduced 1,25(OH)2D3 catabolism over 24 h. A further indication of CYP24A1 inhibition by VD1-6 was the reduced accumulation of the 24,25(OH)D3, the first metabolite of 25(OH)D catabolism by CYP24A1. Our findings suggest the potent CYP24A1 inhibitory properties of VD1-6 and its potential for testing as an alternative therapeutic candidate for treating SHPT. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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16 pages, 1880 KiB  
Article
Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists
by Ayana Yoshihara, Haru Kawasaki, Hiroyuki Masuno, Koki Takada, Nobutaka Numoto, Nobutoshi Ito, Naoya Hirata, Yasunari Kanda, Michiyasu Ishizawa, Makoto Makishima, Hiroyuki Kagechika and Aya Tanatani
Biomolecules 2022, 12(1), 130; https://doi.org/10.3390/biom12010130 - 14 Jan 2022
Cited by 5 | Viewed by 2337
Abstract
1α,25-Dihydroxyvitamin D3 [1α,25(OH)2D3, 1] is an active form of vitamin D3 and regulates various biological phenomena, including calcium and phosphate homeostasis, bone metabolism, and immune response via binding to and activation of vitamin D receptor (VDR). [...] Read more.
1α,25-Dihydroxyvitamin D3 [1α,25(OH)2D3, 1] is an active form of vitamin D3 and regulates various biological phenomena, including calcium and phosphate homeostasis, bone metabolism, and immune response via binding to and activation of vitamin D receptor (VDR). Lithocholic acid (LCA, 2) was identified as a second endogenous agonist of VDR, though its potency is very low. However, the lithocholic acid derivative 3 (Dcha-20) is a more potent agonist than 1α,25(OH)2D3, (1), and its carboxyl group has similar interactions to the 1,3-dihydroxyl groups of 1 with amino acid residues in the VDR ligand-binding pocket. Here, we designed and synthesized amide derivatives of 3 in order to clarify the role of the carboxyl group. The synthesized amide derivatives showed HL-60 cell differentiation-inducing activity with potency that depended upon the substituent on the amide nitrogen atom. Among them, the N-cyanoamide 6 is more active than either 1 or 3. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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11 pages, 1267 KiB  
Article
Synthesis of C2-Alkoxy-Substituted 19-Nor Vitamin D3 Derivatives: Stereoselectivity and Biological Activity
by Yuka Mizumoto, Ryota Sakamoto, Akiko Nagata, Suzuka Sakane, Atsushi Kittaka, Minami Odagi, Masayuki Tera and Kazuo Nagasawa
Biomolecules 2022, 12(1), 69; https://doi.org/10.3390/biom12010069 - 04 Jan 2022
Cited by 1 | Viewed by 1787
Abstract
The active form of vitamin D3 (D3), 1a,25-dihydroxyvitamn D3 (1,25D3), plays a central role in calcium and bone metabolism. Many structure–activity relationship (SAR) studies of D3 have been conducted, with the aim of separating the biological [...] Read more.
The active form of vitamin D3 (D3), 1a,25-dihydroxyvitamn D3 (1,25D3), plays a central role in calcium and bone metabolism. Many structure–activity relationship (SAR) studies of D3 have been conducted, with the aim of separating the biological activities of 1,25D3 or reducing its side effects, such as hypercalcemia, and SAR studies have shown that the hypercalcemic activity of C2-substituted derivatives and 19-nor type derivatives is significantly suppressed. In the present paper, we describe the synthesis of 19-nor type 1,25D3 derivatives with alkoxy groups at C2, by means of the Julia–Kocienski type coupling reaction between a C2 symmetrical A ring ketone and a CD ring synthon. The effect of C2 substituents on the stereoselectivity of the coupling reaction was evaluated. The biological activities of the synthesized derivatives were evaluated in an HL-60 cell-based assay. The a-methoxy-substituted C2α-7a was found to show potent cell-differentiating activity, with an ED50 value of 0.38 nM, being 26-fold more potent than 1,25D3. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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13 pages, 1295 KiB  
Article
New Variants of the Cytochrome P450 2R1 (CYP2R1) Gene in Individuals with Severe Vitamin D-Activating Enzyme 25(OH)D Deficiency
by Martyna Fronczek, Joanna Katarzyna Strzelczyk, Krzysztof Biernacki, Silvia Salatino, Tadeusz Osadnik and Zofia Ostrowska
Biomolecules 2021, 11(12), 1867; https://doi.org/10.3390/biom11121867 - 12 Dec 2021
Cited by 5 | Viewed by 2689
Abstract
Background: Vitamin D is a fat-soluble cholesterol derivative found in two forms, vitamin D2, and vitamin D3. Cytochrome P450 2R1 (CYP2R1) encoded by the CYP2R1 gene is the major hydroxylase that activates vitamin D by catalyzing the formation of 25-hydroxyvitamin D (25(OH)D). Methods: [...] Read more.
Background: Vitamin D is a fat-soluble cholesterol derivative found in two forms, vitamin D2, and vitamin D3. Cytochrome P450 2R1 (CYP2R1) encoded by the CYP2R1 gene is the major hydroxylase that activates vitamin D by catalyzing the formation of 25-hydroxyvitamin D (25(OH)D). Methods: We collected 89 (100%) subjects, 46 of which (51.69%) had a documented severe deficiency of 25(OH)D (<10 ng/mL) and 43 (48.31%) in the control group with documented optimum levels of 25(OH)D (>30 ng/mL). We performed Sanger sequencing of three selected fragments of the CYP2R1 gene (Ch11: 14878000–14878499; Ch11: 14880058–14880883 and Ch11: 14885321–14886113) that affect the binding of substrates to this enzyme and analyzed the possible involvement of genetic variation in these regions with an increased risk of vitamin D deficiency in healthy Polish individuals. Results: Two substitutions were found within the three fragments. Bioinformatic analysis suggested that one of these (NC_000011.10: g.14878291G>A) may influence the structure and function of CYP2R1. Conclusions: Variant NC_000011.10: g.14878291G>A may have a perturbing effect on heme binding in the active site of CYP2R1 and on the function of 25-hydroxylase and probably affects the concentration of 25(OH)D in vivo. We intend to perform functional verification in a larger patient population to confirm and extend these results. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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23 pages, 20961 KiB  
Article
Impact of Vitamin D3 Deficiency on Phosphatidylcholine-/Ethanolamine, Plasmalogen-, Lyso-Phosphatidylcholine-/Ethanolamine, Carnitine- and Triacyl Glyceride-Homeostasis in Neuroblastoma Cells and Murine Brain
by Anna Andrea Lauer, Lea Victoria Griebsch, Sabrina Melanie Pilz, Daniel Janitschke, Elena Leoni Theiss, Jörg Reichrath, Christian Herr, Christoph Beisswenger, Robert Bals, Teresa Giovanna Valencak, Dorothea Portius, Heike Sabine Grimm, Tobias Hartmann and Marcus Otto Walter Grimm
Biomolecules 2021, 11(11), 1699; https://doi.org/10.3390/biom11111699 - 15 Nov 2021
Cited by 2 | Viewed by 3712
Abstract
Vitamin D3 hypovitaminosis is associated with several neurological diseases such as Alzheimer’s disease, Parkinson’s disease or multiple sclerosis but also with other diseases such as cancer, diabetes or diseases linked to inflammatory processes. Importantly, in all of these diseases lipids have at [...] Read more.
Vitamin D3 hypovitaminosis is associated with several neurological diseases such as Alzheimer’s disease, Parkinson’s disease or multiple sclerosis but also with other diseases such as cancer, diabetes or diseases linked to inflammatory processes. Importantly, in all of these diseases lipids have at least a disease modifying effect. Besides its well-known property to modulate gene-expression via the VDR-receptor, less is known if vitamin D hypovitaminosis influences lipid homeostasis and if these potential changes contribute to the pathology of the diseases themselves. Therefore, we analyzed mouse brain with a mild vitamin D hypovitaminosis via a targeted shotgun lipidomic approach, including phosphatidylcholine, plasmalogens, lyso-phosphatidylcholine, (acyl-/acetyl-) carnitines and triglycerides. Alterations were compared with neuroblastoma cells cultivated in the presence and with decreased levels of vitamin D. Both in cell culture and in vivo, decreased vitamin D level resulted in changed lipid levels. While triglycerides were decreased, carnitines were increased under vitamin D hypovitaminosis suggesting an impact of vitamin D on energy metabolism. Additionally, lyso-phosphatidylcholines in particular saturated phosphatidylcholine (e.g., PC aa 48:0) and plasmalogen species (e.g., PC ae 42:0) tended to be increased. Our results suggest that vitamin D hypovitaminosis not only may affect gene expression but also may directly influence cellular lipid homeostasis and affect lipid turnover in disease states that are known for vitamin D hypovitaminosis. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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11 pages, 791 KiB  
Article
A Novel Method for the Determination of Vitamin D Metabolites Assessed at the Blood-Cerebrospinal Fluid Barrier
by Sieglinde Zelzer, Andreas Meinitzer, Markus Herrmann, Walter Goessler and Dietmar Enko
Biomolecules 2021, 11(9), 1288; https://doi.org/10.3390/biom11091288 - 29 Aug 2021
Cited by 5 | Viewed by 1914
Abstract
The brain’s supply with vitamin D is poorly understood. Therefore, the present study aimed to determine 25-hydroxy vitamin D3 (25(OH)D) and 24,25-dihydroxy vitamin D (24,25(OH)2D3) in serum and cerebrospinal fluid (CSF) from individuals with intact and disturbed brain-CSF-barrier (BCB) [...] Read more.
The brain’s supply with vitamin D is poorly understood. Therefore, the present study aimed to determine 25-hydroxy vitamin D3 (25(OH)D) and 24,25-dihydroxy vitamin D (24,25(OH)2D3) in serum and cerebrospinal fluid (CSF) from individuals with intact and disturbed brain-CSF-barrier (BCB) function. In 292 pairs of serum and CSF samples the vitamin D metabolites were measured with liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). CSF/serum ratios (QALB, Q25(OH)D, Q24,25(OH)2D3) were calculated. Median (IQR) serum concentrations of 25(OH)D and 24,25(OH)2D3 were 63.8 (43.4–83.9) nmol/L and 4.2 (2.2–6.2) nmol/L. The CSF concentrations of both metabolites accounted for 3.7 and 3.3% of the respective serum concentrations. Serum 25(OH)D correlated inversely with Q25(OH)D and Q24,25(OH)2D3 implying a more efficient transport of both metabolites across the BCB when the serum concentration of 25(OH)D is low. In patients with BCB dysfunction, the CSF concentrations and the CSF/serum ratios of both vitamin D metabolites were higher than in individuals with intact BCB. The CSF concentrations of 25(OH)D and 24,25(OH)2D3 depend on BCB function and the respective serum concentrations of both metabolites. Higher vitamin D metabolite concentrations in CSF of patients with impaired BCB function may be due to passive diffusion across the BCB. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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Review

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21 pages, 17965 KiB  
Review
The Synthesis and Biological Evaluation of D-Ring-Modified Vitamin D Analogues
by Fumihiro Kawagoe, Sayuri Mototani and Atsushi Kittaka
Biomolecules 2021, 11(11), 1639; https://doi.org/10.3390/biom11111639 - 04 Nov 2021
Cited by 6 | Viewed by 1884
Abstract
The vitamin D3 structure consists of the A-ring, a linker originating from the B-ring, C-ring, D-ring, and side-chain moieties. Each unit has its unique role in expressing the biological activities of vitamin D3. Many efforts have been made to date [...] Read more.
The vitamin D3 structure consists of the A-ring, a linker originating from the B-ring, C-ring, D-ring, and side-chain moieties. Each unit has its unique role in expressing the biological activities of vitamin D3. Many efforts have been made to date to assess the possible clinical use of vitamin D. Some organic chemists focused on the D-ring structure of vitamin D and synthesized D-ring-modified vitamin D analogues, and their biological activities were studied. This review summarizes the synthetic methodologies of D-ring-modified vitamin D analogues, except for seco-D, and their preliminary biological profiles. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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9 pages, 718 KiB  
Review
The Effects of Vitamin D on Immune System and Inflammatory Diseases
by Tomoka Ao, Junichi Kikuta and Masaru Ishii
Biomolecules 2021, 11(11), 1624; https://doi.org/10.3390/biom11111624 - 03 Nov 2021
Cited by 117 | Viewed by 13031
Abstract
Immune cells, including dendritic cells, macrophages, and T and B cells, express the vitamin D receptor and 1α-hydroxylase. In vitro studies have shown that 1,25-dihydroxyvitamin D, the active form of vitamin D, has an anti-inflammatory effect. Recent epidemiological evidence has indicated a significant [...] Read more.
Immune cells, including dendritic cells, macrophages, and T and B cells, express the vitamin D receptor and 1α-hydroxylase. In vitro studies have shown that 1,25-dihydroxyvitamin D, the active form of vitamin D, has an anti-inflammatory effect. Recent epidemiological evidence has indicated a significant association between vitamin D deficiency and an increased incidence, or aggravation, of infectious diseases and inflammatory autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, and multiple sclerosis. However, the impact of vitamin D on treatment and prevention, particularly in infectious diseases such as the 2019 coronavirus disease (COVID-19), remains controversial. Here, we review recent evidence associated with the relationship between vitamin D and inflammatory diseases and describe the underlying immunomodulatory effect of vitamin D. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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