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Keske N, Özay B, Tükel EY, Menteş M, Yandım C. In silico drug screen reveals potential competitive MTHFR inhibitors for clinical repurposing. J Biomol Struct Dyn 2023; 41:11818-11831. [PMID: 36597898 DOI: 10.1080/07391102.2022.2163697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023]
Abstract
MTHFR (Methylenetetrahydrofolate reductase) is a pivotal enzyme involved in one-carbon metabolism, which is critical for the proliferation of cancer cells. In line with this, published literature showed that MTHFR knockdown caused impaired growth of multiple types of cancer cells. Moreover, higher MTHFR expression levels were linked to shorter overall survival in hepatocellular carcinoma, adrenocortical carcinoma, and low-grade glioma, bringing the need to design MTHFR inhibitors as a possible treatment option. No competitive inhibitors of MTHFR have been reported as of today. This study aimed to identify potential competitive MTHFR inhibitor candidates using an in silico drug screen. A total of 30470 molecules containing biogenic compounds, FDA-approved drugs, and those in clinical trials were screened against the catalytic pocket of MTHFR in the presence and absence of cofactors. Binding energy and ADMET analysis revealed that Vilanterol (β2-adrenergic agonist), Selexipag (prostacyclin receptor agonist), and Ramipril Diketopiperazine (ACE inhibitor) are potential competitive inhibitors of MTHFR. Molecular dynamics analyses and MM-PBSA calculations with these compounds particularly revealed the amino acids between 285-290 for ligand binding and highlighted Vilanterol as the strongest candidate for MTHFR inhibition. Our results could guide the development of novel MTHFR inhibitor compounds, which could be inspired by the drugs brought into the spotlight here. More importantly, these potential candidates could be quhickly tested as a repurposing strategy in pre-clinical and clinical studies of the cancers mentioned above.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nazlıgül Keske
- Faculty of Engineering, Department of Genetics and Bioengineering, İzmir University of Economics, Balçova, İzmir, Turkey
| | - Başak Özay
- Faculty of Engineering, Department of Genetics and Bioengineering, İzmir University of Economics, Balçova, İzmir, Turkey
| | - Ezgi Yağmur Tükel
- Faculty of Engineering, Department of Genetics and Bioengineering, İzmir University of Economics, Balçova, İzmir, Turkey
| | - Muratcan Menteş
- Faculty of Engineering, Department of Genetics and Bioengineering, İzmir University of Economics, Balçova, İzmir, Turkey
| | - Cihangir Yandım
- Faculty of Engineering, Department of Genetics and Bioengineering, İzmir University of Economics, Balçova, İzmir, Turkey
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, İnciraltı, İzmir, Turkey
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Wu MT, Ye WT, Wang YC, Chen PM, Liu JY, Tai CK, Tang FY, Li JR, Liu CC, Chiang EPI. MTHFR Knockdown Assists Cell Defense against Folate Depletion Induced Chromosome Segregation and Uracil Misincorporation in DNA. Int J Mol Sci 2021; 22:ijms22179392. [PMID: 34502300 PMCID: PMC8431311 DOI: 10.3390/ijms22179392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022] Open
Abstract
Folate depletion causes chromosomal instability by increasing DNA strand breakage, uracil misincorporation, and defective repair. Folate mediated one-carbon metabolism has been suggested to play a key role in the carcinogenesis and progression of hepatocellular carcinoma (HCC) through influencing DNA integrity. Methylenetetrahydrofolate reductase (MTHFR) is the enzyme catalyzing the irreversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate that can control folate cofactor distributions and modulate the partitioning of intracellular one-carbon moieties. The association between MTHFR polymorphisms and HCC risk is inconsistent and remains controversial in populational studies. We aimed to establish an in vitro cell model of liver origin to elucidate the interactions between MTHFR function, folate status, and chromosome stability. In the present study, we (1) examined MTHFR expression in HCC patients; (2) established cell models of liver origin with stabilized inhibition of MTHFR using small hairpin RNA delivered by a lentiviral vector, and (3) investigated the impacts of reduced MTHFR and folate status on cell cycle, methyl group homeostasis, nucleotide biosynthesis, and DNA stability, all of which are pathways involved in DNA integrity and repair and are critical in human tumorigenesis. By analyzing the TCGA/GTEx datasets available within GEPIA2, we discovered that HCC cancer patients with higher MTHFR had a worse survival rate. The shRNA of MTHFR (shMTHFR) resulted in decreased MTHFR gene expression, MTHFR protein, and enzymatic activity in human hepatoma cell HepG2. shMTHFR tended to decrease intracellular S-adenosylmethionine (SAM) contents but folate depletion similarly decreased SAM in wildtype (WT), negative control (Neg), and shMTHFR cells, indicating that in cells of liver origin, shMTHFR does not exacerbate the methyl group supply in folate depletion. shMTHFR caused cell accumulations in the G2/M, and cell population in the G2/M was inversely correlated with MTHFR gene level (r = −0.81, p < 0.0001), MTHFR protein expression (r = −0.8; p = 0.01), and MTHFR enzyme activity (r = −0.842; p = 0.005). Folate depletion resulted in G2/M cell cycle arrest in WT and Neg but not in shMTHFR cells, indicating that shMTHFR does not exacerbate folate depletion-induced G2/M cell cycle arrest. In addition, shMTHFR promoted the expression and translocation of nuclei thymidine synthetic enzyme complex SHMT1/DHFR/TYMS and assisted folate-dependent de novo nucleotide biosynthesis under folate restriction. Finally, shMTHFR promoted nuclear MLH1/p53 expression under folate deficiency and further reduced micronuclei formation and DNA uracil misincorporation under folate deficiency. In conclusion, shMTHFR in HepG2 induces cell cycle arrest in G2/M that may promote nucleotide supply and assist cell defense against folate depletion-induced chromosome segregation and uracil misincorporation in the DNA. This study provided insight into the significant impact of MTHFR function on chromosome stability of hepatic tissues. Data from the present study may shed light on the potential regulatory mechanism by which MTHFR modulates the risk for hepatic malignancies.
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Affiliation(s)
- Ming-Tsung Wu
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; (M.-T.W.); (W.-T.Y.); (Y.-C.W.); (P.-M.C.); (J.-Y.L.)
- Department of Civil and Environmental Engineering, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Wei-Ting Ye
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; (M.-T.W.); (W.-T.Y.); (Y.-C.W.); (P.-M.C.); (J.-Y.L.)
| | - Yi-Cheng Wang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; (M.-T.W.); (W.-T.Y.); (Y.-C.W.); (P.-M.C.); (J.-Y.L.)
| | - Po-Ming Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; (M.-T.W.); (W.-T.Y.); (Y.-C.W.); (P.-M.C.); (J.-Y.L.)
| | - Jun-You Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; (M.-T.W.); (W.-T.Y.); (Y.-C.W.); (P.-M.C.); (J.-Y.L.)
| | - Chien-Kuo Tai
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi 62102, Taiwan;
| | - Feng-Yao Tang
- Department of Nutrition, China Medical University, Taichung 40402, Taiwan;
| | - Jian-Rong Li
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan; (J.-R.L.); (C.-C.L.)
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan; (J.-R.L.); (C.-C.L.)
| | - En-Pei Isabel Chiang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; (M.-T.W.); (W.-T.Y.); (Y.-C.W.); (P.-M.C.); (J.-Y.L.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung 40227, Taiwan
- Correspondence:
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Bezerra GA, Holenstein A, Foster WR, Xie B, Hicks KG, Bürer C, Lutz S, Mukherjee A, Sarkar D, Bhattacharya D, Rutter J, Talukdar A, Brown PJ, Luo M, Shi L, Froese DS, Yue WW. Identification of small molecule allosteric modulators of 5,10-methylenetetrahydrofolate reductase (MTHFR) by targeting its unique regulatory domain. Biochimie 2021; 183:100-107. [PMID: 33476699 PMCID: PMC8040968 DOI: 10.1016/j.biochi.2021.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
The folate and methionine cycles, constituting one-carbon metabolism, are critical pathways for cell survival. Intersecting these two cycles, 5,10-methylenetetrahydrofolate reductase (MTHFR) directs one-carbon units from the folate to methionine cycle, to be exclusively used for methionine and S-adenosylmethionine (AdoMet) synthesis. MTHFR deficiency and upregulation result in diverse disease states, rendering it an attractive drug target. The activity of MTHFR is inhibited by the binding of AdoMet to an allosteric regulatory domain distal to the enzyme's active site, which we have previously identified to constitute a novel fold with a druggable pocket. Here, we screened 162 AdoMet mimetics using differential scanning fluorimetry, and identified 4 compounds that stabilized this regulatory domain. Three compounds were sinefungin analogues, closely related to AdoMet and S-adenosylhomocysteine (AdoHcy). The strongest thermal stabilisation was provided by (S)-SKI-72, a potent inhibitor originally developed for protein arginine methyltransferase 4 (PRMT4). Using surface plasmon resonance, we confirmed that (S)-SKI-72 binds MTHFR via its allosteric domain with nanomolar affinity. Assay of MTHFR activity in the presence of (S)-SKI-72 demonstrates inhibition of purified enzyme with sub-micromolar potency and endogenous MTHFR from HEK293 cell lysate in the low micromolar range, both of which are lower than AdoMet. Nevertheless, unlike AdoMet, (S)-SKI-72 is unable to completely abolish MTHFR activity, even at very high concentrations. Combining binding assays, kinetic characterization and compound docking, this work indicates the regulatory domain of MTHFR can be targeted by small molecules and presents (S)-SKI-72 as an excellent candidate for development of MTHFR inhibitors.
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Affiliation(s)
- Gustavo A Bezerra
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Alexander Holenstein
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - William R Foster
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Bing Xie
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, USA
| | - Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Seraina Lutz
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Dipika Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, USA
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK.
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Avdović EH, Milenković D, Dimitrić Marković JM, Đorović J, Vuković N, Vukić MD, Jevtić VV, Trifunović SR, Potočňák I, Marković Z. Synthesis, spectroscopic characterization (FT-IR, FT-Raman, and NMR), quantum chemical studies and molecular docking of 3-(1-(phenylamino)ethylidene)-chroman-2,4-dione. Spectrochim Acta A Mol Biomol Spectrosc 2018; 195:31-40. [PMID: 29367024 DOI: 10.1016/j.saa.2018.01.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
The experimental and theoretical investigations of structure of the 3-(1-(phenylamino)ethylidene)-chroman-2,4-dione were performed. X-ray structure analysis and spectroscopic methods (FTIR and FT-Raman, 1H and 13C NMR), along with the density functional theory calculations (B3LYP functional with empirical dispersion corrections D3BJ in combination with the 6-311 + G(d,p) basis set), were used in order to characterize the molecular structure and spectroscopic behavior of the investigated coumarin derivative. Molecular docking analysis was carried out to identify the potency of inhibition of the title molecule against human's Ubiquinol-Cytochrome C Reductase Binding Protein (UQCRB) and Methylenetetrahydrofolate reductase (MTHFR). The inhibition activity was obtained for ten conformations of ligand inside the proteins.
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Affiliation(s)
- Edina H Avdović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Dejan Milenković
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia
| | | | - Jelena Đorović
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia
| | - Nenad Vuković
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Milena D Vukić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Verica V Jevtić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Srećko R Trifunović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Ivan Potočňák
- Institute of Chemistry, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovak Republic
| | - Zoran Marković
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia; Department of Chemical-Technological Sciences, State University of Novi Pazar, Vuka Karadžića bb, 36300 Novi Pazar, Serbia.
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Xiao WL, Shi B, Zheng Q, Wang Y, Huang L, Li S, Lu Y, Wu M. Nucleofection is highly efficient for transfecting genes into murine embryonic palatal mesenchymal cells in primary culture. Int J Oral Maxillofac Surg 2007; 36:429-34. [PMID: 17467239 DOI: 10.1016/j.ijom.2006.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 11/08/2006] [Accepted: 12/11/2006] [Indexed: 10/23/2022]
Abstract
Non-syndromic cleft of the lip and/or palate is one of the most common birth defects in humans. Embryonic palatal mesenchymal (EPM) cells are an attractive source for investigating embryonic palatal development. In this study, we developed a highly efficient transfection method for murine EPM (MEPM) cells. MEPM cells were transfected with the plasmid pEGFP-N1 using two non-viral methods: nucleofection and lipofection. Nucleofection provided a much better rate of gene transfer than lipofection particularly in MEPM cells. The methylenetetrahydrofolate reductase (MTHFR) gene is an important candidate for involvement in the pathogenesis of this birth defect. The RNA interference plasmid of MTHFR was constructed and nucleofected into MEPM cells. Successful transfection resulted in a remarkable reduction in the expression of MTHFR. Taken together, the results indicate that nucleofection is highly efficient for MEPM cell transfection, and that this approach may be useful for investigating gene function in the process of palatogenesis.
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Affiliation(s)
- W-L Xiao
- Department of Oral and Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
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Abstract
1,4-Benzothiazine (1,4-BT) derivatives have been reported to exhibit a wide range of pharmacological properties including antifungal, immunostimulating, anti-aldoso-reductase, anti-rheumatic, anti-allergic, vasorelaxant, anti-arrhythmic, anti-hypertensive, neuroprotective and cytotoxic activities. These different effects indicate that 1,4-BT is a template potentially useful in medicinal chemistry research and therapeutic applications.
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Affiliation(s)
- R Fringuelli
- Department of Drug Chemistry and Technology, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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Stankova J, Shang J, Rozen R. Antisense inhibition of methylenetetrahydrofolate reductase reduces cancer cell survival in vitro and tumor growth in vivo. Clin Cancer Res 2005; 11:2047-52. [PMID: 15756031 DOI: 10.1158/1078-0432.ccr-04-2047] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Many cancer lines are methionine dependent and decrease proliferation when methionine supply is limited. Methylenetetrahydrofolate reductase (MTHFR) generates the folate derivative for homocysteine remethylation to methionine. We investigated the effect of antisense-mediated inhibition of MTHFR on survival of human cancer cells. EXPERIMENTAL DESIGN We examined the in vitro and in vivo anticancer effects of a combination of MTHFR antisense and standard cytotoxic drugs. RESULTS Specific antisense against MTHFR (EX5) showed significant inhibitory effects on growth of human colon, lung, breast, prostate, and neuroblastoma tumor cells in vitro compared with that of the control oligonucleotide. Cytotoxic drugs (5-fluorouracil, cisplatin, or paclitaxel) potentiated the effect of EX5. In vivo, antisense alone or in combination with cytotoxic drugs inhibited the growth of human colon and lung carcinoma xenografts. In comparison with control oligonucleotide, treatment with EX5 inhibited growth of colon tumors and lung tumors by 60% and 45%, respectively. EX5 with 5-fluorouracil decreased growth of colon tumors by an additional 30% compared with EX5 alone, and EX5 with cisplatin decreased growth of lung tumors by an additional 40% compared with cisplatin alone. Growth inhibition by EX5 was associated with decreased amounts of MTHFR protein and with increased amounts of an apoptosis marker. CONCLUSIONS Our results confirm that MTHFR inhibition decreases tumor growth and suggest that inhibition of MTHFR by antisense or small molecules may be a novel anticancer approach.
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Affiliation(s)
- Jitka Stankova
- Departments of Human Genetics, Pediatrics and Biology, Research Institute, McGill University-Montreal Children's Hospital, 4060 Saint Catherine Street West, Montreal, Quebec, Canada H3Z 2Z3
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