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Hendi NN, Nemer G. In silico characterization of the novel SDR42E1 as a potential vitamin D modulator. J Steroid Biochem Mol Biol 2024; 238:106447. [PMID: 38160768 DOI: 10.1016/j.jsbmb.2023.106447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily encompasses enzymes that play essential roles in the metabolism of steroid hormones and lipids. Despite an enigmatic function, recent genetic studies have linked the novel SDR 42 extended-1 (SDR42E1) gene to 25-hydroxyvitamin D levels. This study investigated the potential SDR42E1 functions and interactions with vitamin D using bioinformatics and molecular docking studies. Phylogenetic analysis unveiled that the nucleotide sequences of human SDR42E1 exhibit high evolutionary conservation across nematodes and fruit flies. Molecular docking analysis identified strong binding affinities between SDR42E1 and its orthologs with vitamin D3 and essential precursors, 8-dehydrocholesterol, followed by 7-dehydrocholesterol and 25-hydroxyvitamin D. The hydrophobic interactions observed between the protein residues and vitamin D compounds supported the predicted transmembrane localization of SDR42E1. Our investigation provides valuable insights into the potential role of SDR42E1 in skin vitamin D biosynthesis throughout species. This provides the foundation for future research and development of targeted therapies for vitamin D deficiency and related health conditions.
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Affiliation(s)
- Nagham Nafiz Hendi
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar; Department of Biochemistry and Molecular Genetics, American University of Beirut, P.O. Box 110236, Beirut, Lebanon.
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Ohkawara B, Tomita H, Inoue T, Zhang S, Kanbara S, Koshimizu H, Miyasaka Y, Takeda JI, Nishiwaki H, Nakashima H, Ito M, Masuda A, Ishiguro N, Ogi T, Ohno T, Imagama S, Ohno K. Calcitriol ameliorates motor deficits and prolongs survival of Chrne-deficient mouse, a model for congenital myasthenic syndrome, by inducing Rspo2. Neurotherapeutics 2024; 21:e00318. [PMID: 38233267 DOI: 10.1016/j.neurot.2024.e00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
Signal transduction at the neuromuscular junction (NMJ) is compromised in a diverse array of diseases including congenital myasthenic syndromes (CMS). Germline mutations in CHRNE encoding the acetylcholine receptor (AChR) ε subunit are the most common cause of CMS. An active form of vitamin D, calcitriol, binds to vitamin D receptor (VDR) and regulates gene expressions. We found that calcitriol enhanced MuSK phosphorylation, AChR clustering, and myotube twitching in co-cultured C2C12 myotubes and NSC34 motor neurons. RNA-seq analysis of co-cultured cells showed that calcitriol increased the expressions of Rspo2, Rapsn, and Dusp6. ChIP-seq of VDR revealed that VDR binds to a region approximately 15 kbp upstream to Rspo2. Biallelic deletion of the VDR-binding site of Rspo2 by CRISPR/Cas9 in C2C12 myoblasts/myotubes nullified the calcitriol-mediated induction of Rspo2 expression and MuSK phosphorylation. We generated Chrne knockout (Chrne KO) mouse by CRISPR/Cas9. Intraperitoneal administration of calcitriol markedly increased the number of AChR clusters, as well as the area, the intensity, and the number of synaptophysin-positive synaptic vesicles, in Chrne KO mice. In addition, calcitriol ameliorated motor deficits and prolonged survival of Chrne KO mice. In the skeletal muscle, calcitriol increased the gene expressions of Rspo2, Rapsn, and Dusp6. We propose that calcitriol is a potential therapeutic agent for CMS and other diseases with defective neuromuscular signal transmission.
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Affiliation(s)
- Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Hiroyuki Tomita
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taro Inoue
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shaochuan Zhang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Kanbara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Koshimizu
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Miyasaka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Nishiwaki
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Nakashima
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naoki Ishiguro
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shiro Imagama
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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Antifungal activity of vitamin D 3 against Candida albicans in vitro and in vivo. Microbiol Res 2022; 265:127200. [PMID: 36162148 DOI: 10.1016/j.micres.2022.127200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/04/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022]
Abstract
The incidence of intra-abdominal candidiasis (IAC), characterized by high morbidity and mortality, has become a serious concern. The limitations of current antifungal drugs on the market underscores the importance of the development of novel antifungal agents. In the present study, the antifungal activity of vitamin D3 (VD3) against various Candida species was investigated. In vitro, the broth microdilution method and solid plate assay confirmed that VD3 inhibited the growth of Candida spp. in a broad-spectrum, dose-dependent manner. VD3 also had a significant antifungal effect on the initiation, development, and maturation phases of biofilm formation in Candida albicans. The mechanism of VD3 action was explored by transcriptomics and reverse transcription quantitative PCR (RT-qPCR) analysis, and showed that VD3 affects ribosome biogenesis, coenzyme metabolism, and carbon metabolism. These results suggested that VD3 may have multitarget effects against C. albicans. In the murine IAC model, VD3 reduced the fungal burden in the liver, kidneys, and small intestine. Further histopathological analysis and quantification of plasma cytokine levels confirmed that VD3 treatment significantly decreased the infiltration of inflammatory cells and the levels of plasma interferon (IFN)-γ and tumor necrosis factor (TNF)-α. Taken together, these findings suggest a new antifungal mechanism for VD3 and indicate that VD3 could be an effective therapeutic agent for use in IAC treatment.
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Wu J, Hu B, Lu S, Duan R, Deng H, Li L, He L, Zhao Y, Wang J, Yu Z. Identification of raloxifene as a novel α-glucosidase inhibitor using a systematic drug repurposing approach in combination with cross molecular docking-based virtual screening and experimental verification. Carbohydr Res 2021; 511:108478. [PMID: 34801925 DOI: 10.1016/j.carres.2021.108478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/14/2023]
Abstract
α-Glucosidase is a promising target for the treatment of diabetes. Drug repurposing can increase the chances of discovering an active inhibitor. Therefore, this study aimed to identify potential α-glucosidase inhibitor using drug repurposing and in silico strategies. We identified critical amino acid residues of the three α-glucosidase proteins. Based on cross molecular docking studies of three α-glucosidase proteins and drugs in the FDA database, we screened hits with the favorable binding affinities and modes targeting the three proteins. Subsequently, an in vitro activity assay showed that raloxifene was an excellent inhibitor of α-glucosidase. Moreover, molecular dynamics simulations of raloxifene and three proteins were performed to assess the stability of the protein-hit systems in physiological conditions and clarify protein-hit interactions. We also performed the binding free energy calculation, Hirshfeld surface and alanine scanning mutagenesis analyses. These results demonstrated that binding between raloxifene and the three proteins was stable, and the critical amino acid residues of the three proteins formed stable contacts with raloxifene. The molecular mechanisms agree well with its activity, reinforcing that raloxifene is a candidate α-glucosidase inhibitor. Our study smoothes the path for the development of novel a-glucosidase inhibitors with high efficacy and low toxicity for the treatment of diabetes.
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Affiliation(s)
- Jiaofeng Wu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Baichun Hu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China; Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Shuaizhong Lu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China; Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Rong Duan
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Haoran Deng
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Lele Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Lijuan He
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Yunli Zhao
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Jian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China; Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, PR China.
| | - Zhiguo Yu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, PR China.
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Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. PLoS One 2021; 16:e0257206. [PMID: 34506566 PMCID: PMC8432871 DOI: 10.1371/journal.pone.0257206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.
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Affiliation(s)
- R. V. Sriram Uday
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Rajdip Misra
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Annaram Harika
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, Kolkata, West Bengal, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - V. Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
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Wu J, Hu B, Sun X, Wang H, Huang Y, Zhang Y, Liu M, Liu Y, Zhao Y, Wang J, Yu Z. In silico study reveals existing drugs as α-glucosidase inhibitors: Structure-based virtual screening validated by experimental investigation. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sharma S, Gupta J, Prabhakar PK, Gupta P, Solanki P, Rajput A. Phytochemical Repurposing of Natural Molecule: Sabinene for Identification of Novel Therapeutic Benefits UsingIn SilicoandIn VitroApproaches. Assay Drug Dev Technol 2019; 17:339-351. [DOI: 10.1089/adt.2019.939] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Shamini Sharma
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jeena Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Pranav Kumar Prabhakar
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Pawan Gupta
- Department of Pharmacology, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
- Department of Research Facilitation, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, India
| | - Preeti Solanki
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anuradha Rajput
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
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Drug Repurposing Identifies New Promising Treatment Options for Invasive Fungal Diseases. Clin Ther 2019; 41:2454-2459. [PMID: 31526654 DOI: 10.1016/j.clinthera.2019.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 11/21/2022]
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