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Bairagya HR. Dynamics of nucleoplasm in human leukemia cells: A thrust towards designing anti-leukemic agents. J Mol Graph Model 2024; 131:108807. [PMID: 38908255 DOI: 10.1016/j.jmgm.2024.108807] [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: 03/04/2024] [Revised: 04/20/2024] [Accepted: 06/02/2024] [Indexed: 06/24/2024]
Abstract
The human inosine monophosphate dehydrogenase (hIMPDH) is a metabolic enzyme that possesses a unique ability to self-assemble into higher-order structures, forming cytoophidia. The hIMPDH II isoform is more active in chronic myeloid leukemia (CML) cancer cells, making it a promising target for anti-leukemic therapy. However, the structural details and molecular mechanisms of the dynamics of hIMPDHcytoophidia assembly in vitro need to be better understood, and it is crucial to reconstitute the computational nucleoplasm model with cytophilic-like polymers in vitro to characterize their structure and function. Finally, a computational model and its dynamics of the nucleoplasm for CML cells have been proposed in this short review. This research on nucleoplasm aims to aid the scientific community's understanding of how metabolic enzymes like hIMPDH function in cancer and normal cells. However, validating and justifying the computational results from modeling and simulation with experimental data is essential. The new insights gained from this research could explain the structure/topology, geometrical, and electronic consequences of hIMPDH inhibitors on leukemic and normal cells. They could lead to further advancements in the knowledge of nucleoplasmic chemical reaction dynamics.
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Affiliation(s)
- Hridoy R Bairagya
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal, 741249, India.
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2
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Nabi Afjadi M, Yazdanparast R, Barzegari E. The Impact of Terminal Peptide Extensions of Retinal Inosine 5´Monophosphate Dehydrogenase 1 Isoforms on their DNA-binding Activities. Protein J 2024; 43:592-602. [PMID: 38733555 DOI: 10.1007/s10930-024-10202-3] [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] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
The main structural difference between the mutation-susceptible retinal isoforms of inosine 5´-monophosphate dehydrogenase-1 (IMPDH-1) with the canonical form resides in the C- and N-terminal peptide extensions with unknown structural/functional impacts. In this report, we aimed to experimentally evaluate the functional impact of these extensions on the specific/non-specific single-stranded DNA (ssDNA)-binding activities relative to those of the canonical form. Our in silico findings indicated the possible contribution of the C-terminal segment to the reduced flexibility of the Bateman domain of the enzyme. In addition, the in silico data indicated that the N-terminal tail acts by altering the distance between the tetramers in the concave octamer complex (the native form) of the enzyme. The overall impact of these predicted structural variations became evident, first, through higher Km values with respect to either of the substrates relative to the canonical isoform, as reported previously (Andashti et al. in Mol Cell Biochem 465(1):155-164, 2020). Secondary, the binding of the recombinant mouse retinal isoform IMPDH1 (603) to its specific Rhodopsin target gene was significantly augmented while its binding to non-specific ssDNA was lower than that of the canonical isoform. The DNA-binding activity of the other mouse retinal isoform, IMPDH1(546), to specific and non-specific ssDNA was lower than that of the canonical form most probably due to the in silico predicted rigidity created in the Bateman domain by the C-terminal peptide extension. Furthermore, the DNA binding to the Rhodopsin target gene by each of the IMPDH isoforms influenced in the presence of GTP (Guanosine triphosphate) and ATP (Adenosine triphosphate).
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Affiliation(s)
- Mohsen Nabi Afjadi
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran
| | - Razieh Yazdanparast
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran.
| | - Ebrahim Barzegari
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran
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3
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Yin Y, Yu H, Wang X, Hu Q, Liu Z, Luo D, Yang X. Cytoophidia: a conserved yet promising mode of enzyme regulation in nucleotide metabolism. Mol Biol Rep 2024; 51:245. [PMID: 38300325 DOI: 10.1007/s11033-024-09208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Nucleotide biosynthesis encompasses both de novo and salvage synthesis pathways, each characterized by significant material and procedural distinctions. Despite these differences, cells with elevated nucleotide demands exhibit a preference for the more intricate de novo synthesis pathway, intricately linked to modes of enzyme regulation. In this study, we primarily scrutinize the biological importance of a conserved yet promising mode of enzyme regulation in nucleotide metabolism-cytoophidia. Cytoophidia, comprising cytidine triphosphate synthase or inosine monophosphate dehydrogenase, is explored across diverse biological models, including yeasts, Drosophila, mice, and human cancer cell lines. Additionally, we delineate potential biomedical applications of cytoophidia. As our understanding of cytoophidia deepens, the roles of enzyme compartmentalization and polymerization in various biochemical processes will unveil, promising profound impacts on both research and the treatment of metabolism-related diseases.
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Affiliation(s)
- Yue Yin
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Huanhuan Yu
- First School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Xinyi Wang
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiaohao Hu
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Zhuoqi Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Daya Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
| | - Xiaohong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
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4
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Hernández-Gómez A, Irisarri I, Fernández-Justel D, Peláez R, Jiménez A, Revuelta JL, Balsera M, Buey RM. GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution. Structure 2023; 31:1526-1534.e4. [PMID: 37875114 DOI: 10.1016/j.str.2023.09.014] [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: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023]
Abstract
IMP dehydrogenase and GMP reductase are enzymes from the same protein family with analogous structures and catalytic mechanisms that have gained attention because of their essential roles in nucleotide metabolism and as potential drug targets. This study focusses on GuaB3, a less-explored enzyme within this family. Phylogenetic analysis uncovers GuaB3's independent evolution from other members of the family and it predominantly occurs in Cyanobacteria. Within this group, GuaB3 functions as a unique IMP dehydrogenase, while its counterpart in Actinobacteria has a yet unknown function. Synechocystis sp. PCC6803 GuaB3 structures demonstrate differences in the active site compared to canonical IMP dehydrogenases, despite shared catalytic mechanisms. These findings highlight the essential role of GuaB3 in Cyanobacteria, provide insights into the diversity and evolution of the IMP dehydrogenase protein family, and reveal a distinctive characteristic in nucleotide metabolism, potentially aiding in combating harmful cyanobacterial blooms-a growing concern for humans and wildlife.
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Affiliation(s)
- Alejandro Hernández-Gómez
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - David Fernández-Justel
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Dpto. Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Mónica Balsera
- Department Abiotic Stress, Instituto de Recursos Naturales y Agrobiología (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain.
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5
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Yazdani M, Zamani J, Fatemi SSA. Identification of a potent dual-function inhibitor for hIMPDH isoforms by computer-aided drug discovery approaches. Front Pharmacol 2022; 13:977568. [PMID: 36386211 PMCID: PMC9643795 DOI: 10.3389/fphar.2022.977568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a key enzyme in de novo biosynthesis of purine nucleotides. Due to this important role, it is a great target to drug discovery for a wide range of activities, especially immunosuppressant in heart and kidney transplantation. Both human IMPDH isoforms are expressed in stimulated lymphocytes. In addition to the side effects of existing drugs, previous studies have mainly focused on the type II isoform. In this study, virtual screening and computer-aided approaches were employed to identify potential drugs with simultaneous inhibitory effects on both human IMPDH isoforms. After Re-docking, Double-step docking, and identification of virtual hits based on the PLANTS scoring function, drug-likeness and ADME-Tox assessments of the topmost ligands were performed. Following further evaluation, the best ligand was selected and, in complex with both isoforms, simulated in monomeric and tetrameric forms using molecular dynamics to evaluate its stability and binding pattern. The results showed a potential drug candidate [(S)-N-(3-hydroxy-1-(4-hydroxyphenyl) propyl)-2-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) acetamide] with a high inhibitory effect on the two human IMPDH isoforms. This drug-like inhibitor could potentially serve as an immunosuppressant to prevent transplant rejection response by inhibiting B- and T-lymphocyte proliferation. In addition, its effect can be evaluated in various therapeutic targets in which IMPDH is known as a therapeutic target, especially in Covid-19 patients.
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Affiliation(s)
- Meysam Yazdani
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Javad Zamani
- Department of Plant Molecular Biotechnology, Institute of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Seyed Safa-Ali Fatemi
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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6
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Xu H, Ma H, Zha L, Li Q, Pan H, Zhang L. Genistein promotes apoptosis of lung cancer cells through the IMPDH2/AKT1 pathway. Am J Transl Res 2022; 14:7040-7051. [PMID: 36398246 PMCID: PMC9641449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE Lung cancer (LC) is a clinically challenging cancer. Genistein is a natural isoflavone product with anti-tumor effects. This study aims to investigate the effect of genistein on A549 cell apoptosis, to provide more experimental evidence for clinical treatment. METHODS Real-time quantitative polymerase chain reaction, western blotting, molecular docking, and target prediction methods were performed to detect the effect of genistein on LC cells. Cell viability of A549 treated by genistein was measured by a CCK-8 assay. The A549 cell apoptosis after genistein treatment was detected by flow cytometry. RESULTS Genistein promoted the apoptosis of LC cells in a time- and concentration-dependent manner. In addition, the low expression of inosine monophosphate dehydrogenase-2 (IMPDH2) inhibited the effect of genistein on LC cells. By predicting IMPDH2 LC-related apoptosis genes and finding the closely related gene protein kinase B (AKT1), it was found that the highly expressed AKT1 inhibited the effect of genistein on LC cell apoptosis and viability. CONCLUSION Genistein may be a promising treatment for LC.
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Affiliation(s)
- Hao Xu
- Department of Respiratory Medicine, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University Danyang 212300, Jiangsu, P.R. China
| | - Hongda Ma
- Department of Respiratory Medicine, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University Danyang 212300, Jiangsu, P.R. China
| | - Lifen Zha
- Department of Respiratory Medicine, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University Danyang 212300, Jiangsu, P.R. China
| | - Qian Li
- Department of Respiratory Medicine, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University Danyang 212300, Jiangsu, P.R. China
| | - Huiming Pan
- Department of Respiratory Medicine, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University Danyang 212300, Jiangsu, P.R. China
| | - Ladi Zhang
- Department of Respiratory Medicine, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University Danyang 212300, Jiangsu, P.R. China
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7
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Alby-Laurent F, Belaïdouni N, Blanchet B, Rousseau C, Llitjos JF, Sanquer S, Mira JP, Pène F, Toubiana J, Chiche JD. Low-dose mycophenolate mofetil improves survival in a murine model of Staphylococcus aureus sepsis by increasing bacterial clearance and phagocyte function. Front Immunol 2022; 13:939213. [PMID: 35936013 PMCID: PMC9351454 DOI: 10.3389/fimmu.2022.939213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Regulators of TLRs signaling pathways play an important role in the control of the pro-inflammatory response that contributes to sepsis-induced tissue injury. Mycophenolate mofetil, an immunosuppressive drug inhibiting lymphocyte proliferation, has been reported to be a regulator of TLRs signaling pathways. Whether MMF used at infra-immunosuppressive doses has an impact on survival and on innate immune response in sepsis is unknown.C57BL/6J mice were infected intraperitoneally with 108 CFU Staphylococcus aureus, and treated or not with low-dose of MMF (20mg/kg/day during 4 days). Survival rate and bacterial clearance were compared. Cytokine levels, quantitative and qualitative cellular responses were assessed. S. aureus – infected mice treated with MMF exhibited improved survival compared to non-treated ones (48% vs 10%, p<0.001). With the dose used for all experiments, MMF did not show any effect on lymphocyte proliferation. MMF treatment also improved local and systemic bacterial clearance, improved phagocytosis activity of peritoneal macrophages resulting in decreased inflammatory cytokines secretion. MMF-treated mice showed enhanced activation of NF-κB seemed with a suspected TLR4-dependent mechanism. These results suggest that infra-immunosuppressive doses of MMF improve host defense during S. aureus sepsis and protects infected mice from fatal outcome by regulating innate immune responses. The signaling pathways involved could be TLR4-dependent. This work brings new perspectives in pathogenesis and therapeutic approaches of severe infections.
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Affiliation(s)
- Fanny Alby-Laurent
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
| | - Nadia Belaïdouni
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
| | - Benoit Blanchet
- Department of Pharmocology and Toxicology, Cochin Hospital, Assistance Publique des hôpitaux de Paris (APHP), Université de Paris, Paris, France
| | - Christophe Rousseau
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
| | - Jean-François Llitjos
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
- Medical Intensive Care Unit, Cochin Hospital, APHP, Université de Paris, Paris, France
| | - Sylvia Sanquer
- Metabolic and Proteomic Biochemistry Department, Necker-Enfants malades Hospital, Université de Paris, Paris, France
| | - Jean-Paul Mira
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
- Medical Intensive Care Unit, Cochin Hospital, APHP, Université de Paris, Paris, France
| | - Frédéric Pène
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
- Medical Intensive Care Unit, Cochin Hospital, APHP, Université de Paris, Paris, France
| | - Julie Toubiana
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
- Department of General Pediatrics and Infectious Diseases, Necker-Enfants malades Hospital, APHP, Université de Paris, Paris, France
| | - Jean-Daniel Chiche
- Cochin Institute, Department of Infection, Immunity and Inflammation, Inserm U1016, Paris Descartes Sorbonne Paris Cité University UMR-S1016, Centre National de la Recherche Scientifique (CNRS) UMR 8104, Paris, France
- Medical Intensive Care Unit, Cochin Hospital, APHP, Université de Paris, Paris, France
- Department of Intensive Care Medicine, Hospital and University of Lausanne, Lausanne, Switzerland
- *Correspondence: Jean-Daniel Chiche,
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8
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Dobrut A, Brzychczy-Włoch M. Immunogenic Proteins of Group B Streptococcus-Potential Antigens in Immunodiagnostic Assay for GBS Detection. Pathogens 2021; 11:43. [PMID: 35055991 PMCID: PMC8778278 DOI: 10.3390/pathogens11010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen, which asymptomatically colonizes the gastrointestinal and genitourinary tract of up to one third of healthy adults. Nevertheless, GBS carriage in pregnant women may lead to several health issues in newborns causing life threatening infection, such as sepsis, pneumonia or meningitis. Recommended GBS screening in pregnant women significantly reduced morbidity and mortality in infants. Nevertheless, intrapartum antibiotic prophylaxis, recommended following the detection of carriage or in case of lack of a carriage test result for pregnant women who demonstrate certain risk factors, led to the expansion of the adverse phenomenon of bacterial resistance to antibiotics. In our paper, we reviewed some immunogenic GBS proteins, i.e., Alp family proteins, β protein, Lmb, Sip, BibA, FsbA, ScpB, enolase, elongation factor Tu, IMPDH, and GroEL, which possess features characteristic of good candidates for immunodiagnostic assays for GBS carriage detection, such as immunoreactivity and specificity. We assume that they can be used as an alternative diagnostic method to the presently recommended bacteriological cultivation and MALDI.
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Affiliation(s)
| | - Monika Brzychczy-Włoch
- Department of Molecular Medical Microbiology, Faculty of Medicine, Medical College, Jagiellonian University, 31-121 Krakow, Poland;
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9
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Asmare MM, Nitin N, Yun SI, Mahapatra RK. QSAR and deep learning model for virtual screening of potential inhibitors against Inosine 5' Monophosphate dehydrogenase (IMPDH) of Cryptosporidium parvum. J Mol Graph Model 2021; 111:108108. [PMID: 34911011 DOI: 10.1016/j.jmgm.2021.108108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/08/2023]
Abstract
Cryptosporidium parvum (Cp) causes a gastro-intestinal disease called Cryptosporidiosis. C. parvum Inosine 5' monophosphate dehydrogenase (CpIMPDH) is responsible for the production of guanine nucleotides. In the present study, 37 known urea-based congeneric compounds were used to build a 2D and 3D QSAR model against CpIMPDH. The built models were validated based on OECD principles. A deep learning model was adopted from a framework called Deep Purpose. The model was trained with 288 known active compounds and validated using a test set. From the training set of the 3D QSAR, a pharmacophore model was built and the best pharmacophore hypotheses were scored and sorted using a phase-hypo score. A phytochemical database was screened using both the pharmacophore model and a deep learning model. The screened compounds were considered for glide XP docking, followed by quantum polarized ligand docking. Finally, the best compound among them was considered for molecular dynamics simulation study.
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Affiliation(s)
| | - Nitin Nitin
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Soon-Il Yun
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Rajani Kanta Mahapatra
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, 751024, Odisha, India.
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10
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Terminal Peptide Extensions Augment the Retinal IMPDH1 Catalytic Activity and Attenuate the ATP-induced Fibrillation Events. Cell Biochem Biophys 2021; 79:221-229. [PMID: 33733369 DOI: 10.1007/s12013-021-00973-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
Defects in inosine monophosphate dehydrogenase-1 (IMPDH1) lead to insufficient biosyntheses of purine nucleotides. In eyes, these defects are believed to cause retinitis pigmentosa (RP). Major retinal isoforms of IMPDH1 are structurally distinct from those in other tissues, by bearing terminal extensions. Using recombinant mouse IMPDH1 (mH1), we evaluated the kinetics and oligomerization states of the retinal isoforms. Moreover, we adopted molecular simulation tools to study the possible effect of terminal tails on the function of major enzyme isoforms with the aim to find structural evidence in favor of contradictory observations on retinal IMPDH1 function. Our findings indicated higher catalytic activity for the major mouse retinal isoform (mH1603) along with lower fibrillation capacity under the influence of ATP. However, higher mass oligomerization products were formed by the mH1 (603) isoform in the presence of the enzyme inhibitors such as GTP and/or MPA. Collectively, our findings demonstrate that the structural differences between the retinal isoforms have led to functional variations possibly to justify the retinal cells' requirements.
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11
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Nguyen S, Truong JQ, Bruning JB. Targeting Unconventional Pathways in Pursuit of Novel Antifungals. Front Mol Biosci 2021; 7:621366. [PMID: 33511160 PMCID: PMC7835888 DOI: 10.3389/fmolb.2020.621366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 01/31/2023] Open
Abstract
The impact of invasive fungal infections on human health is a serious, but largely overlooked, public health issue. Commonly affecting the immunocompromised community, fungal infections are predominantly caused by species of Candida, Cryptococcus, and Aspergillus. Treatments are reliant on the aggressive use of pre-existing antifungal drug classes that target the fungal cell wall and membrane. Despite their frequent use, these drugs are subject to unfavorable drug-drug interactions, can cause undesirable side-effects and have compromised efficacy due to the emergence of antifungal resistance. Hence, there is a clear need to develop novel classes of antifungal drugs. A promising approach involves exploiting the metabolic needs of fungi by targeted interruption of essential metabolic pathways. This review highlights potential antifungal targets including enolase, a component of the enolase-plasminogen complex, and enzymes from the mannitol biosynthesis and purine nucleotide biosynthesis pathways. There has been increased interest in the enzymes that comprise these particular pathways and further investigation into their merits as antifungal targets and roles in fungal survival and virulence are warranted. Disruption of these vital processes by targeting unconventional pathways with small molecules or antibodies may serve as a promising approach to discovering novel classes of antifungals.
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Affiliation(s)
- Stephanie Nguyen
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jia Q Truong
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
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12
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Lee S, Ku AF, Vippila MR, Wang Y, Zhang M, Wang X, Hedstrom L, Cuny GD. Mycophenolic anilides as broad specificity inosine-5'-monophosphate dehydrogenase (IMPDH) inhibitors. Bioorg Med Chem Lett 2020; 30:127543. [PMID: 32931912 DOI: 10.1016/j.bmcl.2020.127543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/28/2022]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) is a potential target for microorganisms. However, identifying inhibitor design determinants for IMPDH orthologs continues to evolve. Herein, a series of mycophenolic anilide inhibitors of Cryptosporidium parvum and human IMPDHs are reported. Furthermore, molecular docking of 12 (e.g. SH-19; CpIMPDH Ki,app = 0.042 ± 0.015 µM, HsIMPDH2 Ki,app = 0.13 ± 0.05 µM) supports different binding modes with the two enzymes. For CpIMPDH the inhibitor extends into a pocket in an adjacent subunit. In contrast, docking suggests the inhibitor interacts with Ser276 in the NAD binding site in HsIMPDH2, as well as an adjacent pocket within the same subunit. These results provide further guidance for generating IMPDH inhibitors for enzymes found in an array of pathogenic microorganisms, including Mycobacterium tuberculosis.
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Affiliation(s)
- Seungheon Lee
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Health Building 2, Houston, TX 77204, USA
| | - Angela F Ku
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Health Building 2, Houston, TX 77204, USA; Department of Chemistry, University of Houston, Health Building 2, Houston, TX 77204, USA
| | - Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Health Building 2, Houston, TX 77204, USA
| | - Yong Wang
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Health Building 2, Houston, TX 77204, USA
| | - Minjia Zhang
- Departments of Biology, 415 South St., Waltham, MA 02454, USA
| | - Xingyou Wang
- Departments of Biology, 415 South St., Waltham, MA 02454, USA
| | - Lizbeth Hedstrom
- Departments of Biology, 415 South St., Waltham, MA 02454, USA; Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Health Building 2, Houston, TX 77204, USA.
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13
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Omolabi KF, Agoni C, Olotu FA, Soliman MES. Molecular Basis of P131 Cryptosporidial-IMPDH Selectivity-A Structural, Dynamical and Mechanistic Stance. Cell Biochem Biophys 2020; 79:11-24. [PMID: 33058015 DOI: 10.1007/s12013-020-00950-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2020] [Indexed: 01/10/2023]
Abstract
Cryptosporidiosis accounts for a surge in infant (<5 years) mortality and morbidity. To date, several drug discovery efforts have been put in place to develop effective therapeutic options against the causative parasite. Based on a recent report, P131 spares inosine monophosphate dehydrogenase (IMPDH) in a eukaryotic model (mouse IMPDH (mIMPDH)) while binding selectively to the NAD+ site in Cryptosporidium parvum (CpIMPDH). However, no structural detail exists on the underlining mechanisms of P131-CpIMPDH selective targeting till date. To this effect, we investigate the selective inhibitory dynamics of P131 in CpIMPDH relative to mIMPDH via molecular biocomputation methods. Pairwise sequence alignment revealed prominent variations at the NAD+ binding regions of both proteins that accounted for disparate P131 binding activities. The influence of these variations was further revealed by the MM/PBSA energy estimations coupled with per-residue energy decomposition which monitored the systematic binding of the compound. Furthermore, relative high-affinity interactions occurred at the CpIMPDH NAD+ site which were majorly mediated by SER22, VAL24, PRO26, SER354, GLY357, and TYR358 located on chain D. These residues are unique to the parasite IMPDH form and not in the eukaryotic protein, highlighting variations that account for preferential P131 binding. Molecular insights provided herein corroborate previous experimental reports and further underpin the basis of CpIMPDH inhibitor selectivity. Findings from this study could present attractive prospects toward the design of novel anticryptosporidials with improved selectivity and binding affinity against parasitic targets.
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Affiliation(s)
- Kehinde F Omolabi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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14
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Xu H, Ma H, Zha L, Li Q, Yang G, Pan H, Fei X, Xu X, Xing C, Zhang L. IMPDH2 promotes cell proliferation and epithelial-mesenchymal transition of non-small cell lung cancer by activating the Wnt/β-catenin signaling pathway. Oncol Lett 2020; 20:219. [PMID: 32963625 DOI: 10.3892/ol.2020.12082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Inosine 5'-monophosphate dehydrogenase type II (IMPDH2) is an important enzyme involved in the biosynthesis of guanine nucleotides. Therefore, the present study aimed to investigate the potential and molecular mechanism of IMPDH2 in non-small cell lung cancer (NSCLC). Reverse transcription-quantitative PCR and immunohistochemistry were used to detect IMPDH2 expression levels in NSCLC tissues and cells. A Cell Counting Kit-8 assay, colony formation assay, flow cytometry, wound healing, Transwell assay, western blotting and immunofluorescence analyses were utilized to identify the effects of upregulated IMPDH2 levels on NSCLC cells. The expression levels of IMPDH2 have been discovered to be upregulated in several types of human cancer; however, the biological and clinical value of IMPDH2 in NSCLC remains unclear. The results of the present study revealed that the expression levels of IMPDH2 were significantly upregulated in NSCLC tissues. Furthermore, the genetic knockdown of IMPDH2 significantly hindered the proliferation, apoptosis, invasion, migration and epithelial-mesenchymal transition of NSCLC cells, whereas the overexpression of IMPDH2 achieved the opposite results. In addition, the results of the present study demonstrated that the inhibition of IMPDH2 inhibited the Wnt/β-catenin signaling pathway by decreasing the expression levels of Wnt3a and β-catenin, while increasing the expression levels of phosphorylated glycogen synthase kinase-3β in NSCLC cells. These findings of the present study indicated that IMPDH2 may promote NSCLC progression by activating the Wnt/β-catenin signaling pathway, which suggested that IMPDH2 may be a novel therapeutic target for patients with NSCLC.
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Affiliation(s)
- Hao Xu
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Hongda Ma
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Lifen Zha
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Qian Li
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Guanghui Yang
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Huiming Pan
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Xiangping Fei
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Xingxiang Xu
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Chen Xing
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
| | - Ladi Zhang
- Department of Respiratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu 212300, P.R. China
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15
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Wang W, Wu Y, Chen S, Liu X, He J, Wang S, Lu W, Tang Y, Huang J. Shikonin is a novel and selective IMPDH2 inhibitor that target triple-negative breast cancer. Phytother Res 2020; 35:463-476. [PMID: 32779300 DOI: 10.1002/ptr.6825] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022]
Abstract
Triple-negative breast cancer (TNBC) is heterogeneous disease with a poor prognosis. It is therefore important to explore novel therapeutic agents to improve the clinical efficacy for TNBC. The inosine 5'-monophosphate dehydrogenase 2 (IMPDH2) is a rate-limiting enzyme in the de novo synthesis of guanine nucleotides. It is always overexpressed in many types of tumors, including TNBC and regarded as a potential target for cancer therapy. Through screening a library of natural products, we identified shikonin, a natural bioactive component of Lithospermum erythrorhizon, is a novel and selective IMPDH2 inhibitor. Enzymatic analysis using Lineweaver-Burk plot indicates that shikonin is a competitive inhibitor of IMPDH2. The interaction between shikonin and IMDPH2 was further investigated by thermal shift assay, fluorescence quenching, and molecular docking simulation. Shikonin treatment effectively inhibits the growth of human TNBC cell line MDA-MB-231, and murine TNBC cell line, 4T1 in a dose-dependent manner, which is impaired by exogenous supplementation of guanosine, a salvage pathway of purine nucleotides. Most importantly, IMPDH2 knockdown significantly reduced cell proliferation and conferred resistance to shikonin in TNBC. Collectively, our findings showed the natural product shikonin as a selective inhibitor of IMPDH2 with anti-TNBC activity, impelling its further study in clinical trials.
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Affiliation(s)
- Wanyan Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yu Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Si Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xi Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jiacheng He
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuyi Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yong Tang
- Department of Urology, Wuming Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jin Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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16
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The expression and prognostic role of IMPDH2 in ovarian cancer. Ann Diagn Pathol 2020; 46:151511. [PMID: 32305001 DOI: 10.1016/j.anndiagpath.2020.151511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/18/2020] [Indexed: 12/28/2022]
Abstract
OBJECT Inosine 5'-monophosphate dehydrogenase type II (IMPDH2), as an oncogene, is reported to be involved in tumor formation and progression. However, the role of IMPDH2 in ovarian cancer remains unclear. Present study is aimed to investigate the expression and clinical significance of IMPDH2 in ovarian cancer. METHODS The mRNA and protein levels of IMPDH2 were measured in 126 ovarian cancer and matched adjacent normal tissues by quantificational real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC), respectively. Then, the association of IMPDH2 with clinicalpathological characters and prognosis was further evaluated. RESULTS Significant higher mRNA levels of IMPDH2 were observed in ovarian cancer compared with those in normal tissues (P < 0.001). IHC results shown the high-expression rate of IMPDH2 in ovarian cancer was 56.3%, which was obviously higher compared with that in normal tissues (23.8%, P < 0.0001). Moreover, IMPDH2 high-expression significantly correlated with tumor types and Federation International of Gynecology and Obstetrigue (FIGO) stages in ovarian cancer (P < 0.05). IMPDH2 overexpression predicted poorer prognosis and could serve as an independent prognostic factor. CONCLUSIONS IMPDH2 is highly expressed in ovarian cancer and correlates with prognosis, which may serve as a potential prognostic biomarker.
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Kojić V, Popsavin M, Spaić S, Jakimov D, Kovačević I, Svirčev M, Aleksić L, Zelenović BS, Popsavin V. Structure based design, synthesis and in vitro antitumour activity of tiazofurin stereoisomers with nitrogen functions at the C-2' or C-3' positions. Eur J Med Chem 2019; 183:111712. [PMID: 31557614 DOI: 10.1016/j.ejmech.2019.111712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/05/2019] [Accepted: 09/16/2019] [Indexed: 10/26/2022]
Abstract
Three novel tiazofurin analogues having d-arabino stereochemistry and nitrogen functionalities at the C-2' position (5-7) have been designed and synthesized in multistep sequences, starting from d-glucose. The known d-xylo stereoisomer of 1 (compound 2) along with two new analogues bearing nitrogen functions at the C-3' (3 and 4) has also been synthesized from the same sugar precursor. The synthetic sequence consisted of the following three stages: (i) the multistep synthesis of suitably protected pentofuranosyl cyanides, (ii) the construction of ethyl thiazole-4-carboxylate part by cyclocondensation of thus obtained glycofuranosyl cyanides with l-cysteine ethyl ester followed by dehydrogenation, and (iii) the final transformation of the ethyl thiazole-4-carboxylates into the target tiazofurin analogues using the esters ammonolysis. The tiazofurin analogues were evaluated for their antitumour activities in cell-culture-based assays. Compounds 3, 4 (d-xylo) and 7 (d-arabino), showed remarkable antitumour activities, with IC50 values in the range of 4-7 nM. Preliminary structure-activity relationship allowed identification of two analogues with antiproliferative activities exceeding that of the parent compound 1 for several orders of magnitude (e.g. 4: 1354-fold against Raji, 7: 309-fold against K562). Flow cytometry data and Western blot analysis suggested that cytotoxic effects of d-xylo stereoisomers in the culture of K562 cells caused changes in the cell cycle distribution, as well as the induction of apoptosis in caspase-dependent way. The increase of apoptotic cells percentage in treated samples is also confirmed with fluorescent double-staining method. Genotoxicity testing showed that the analogues with the xylo-configuration (2-4) are far less genotoxic than tiazofurin.
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Affiliation(s)
- Vesna Kojić
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi Sad, Put Dr Goldmana 4, 21204, Sremska Kamenica, Serbia
| | - Mirjana Popsavin
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, Serbia.
| | - Saša Spaić
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, Serbia
| | - Dimitar Jakimov
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi Sad, Put Dr Goldmana 4, 21204, Sremska Kamenica, Serbia
| | - Ivana Kovačević
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, Serbia
| | - Miloš Svirčev
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, Serbia
| | - Lidija Aleksić
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi Sad, Put Dr Goldmana 4, 21204, Sremska Kamenica, Serbia
| | - Bojana Srećo Zelenović
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, Serbia
| | - Velimir Popsavin
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, Serbia; Serbian Academy of Sciences and Arts, Knez Mihajlova 35, 11000, Belgrade, Serbia
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18
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Trapero A, Pacitto A, Chan DSH, Abell C, Blundell TL, Ascher DB, Coyne AG. Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH). Bioorg Med Chem Lett 2019; 30:126792. [PMID: 31757668 DOI: 10.1016/j.bmcl.2019.126792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/30/2019] [Indexed: 11/28/2022]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in nucleotide biosynthesis. Because of its critical role in purine biosynthesis, IMPDH is a drug design target for immunosuppressive, anticancer, antiviral and antimicrobial chemotherapy. In this study, we use mass spectrometry and X-ray crystallography to show that the inhibitor 6-Cl-purine ribotide forms a covalent adduct with the Cys-341 residue of Mycobacterium thermoresistibile IMPDH.
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Affiliation(s)
- Ana Trapero
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Angela Pacitto
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom; Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia.
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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19
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Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story. Cancers (Basel) 2019; 11:cancers11091346. [PMID: 31514446 PMCID: PMC6770829 DOI: 10.3390/cancers11091346] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 01/15/2023] Open
Abstract
The purine nucleotides ATP and GTP are essential precursors to DNA and RNA synthesis and fundamental for energy metabolism. Although de novo purine nucleotide biosynthesis is increased in highly proliferating cells, such as malignant tumors, it is not clear if this is merely a secondary manifestation of increased cell proliferation. Suggestive of a direct causative effect includes evidence that, in some cancer types, the rate-limiting enzyme in de novo GTP biosynthesis, inosine monophosphate dehydrogenase (IMPDH), is upregulated and that the IMPDH inhibitor, mycophenolic acid (MPA), possesses anti-tumor activity. However, historically, enthusiasm for employing IMPDH inhibitors in cancer treatment has been mitigated by their adverse effects at high treatment doses and variable response. Recent advances in our understanding of the mechanistic role of IMPDH in tumorigenesis and cancer progression, as well as the development of IMPDH inhibitors with selective actions on GTP synthesis, have prompted a reappraisal of targeting this enzyme for anti-cancer treatment. In this review, we summarize the history of IMPDH inhibitors, the development of new inhibitors as anti-cancer drugs, and future directions and strategies to overcome existing challenges.
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20
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Juvale K, Shaik A, Kirubakaran S. Inhibitors of inosine 5'-monophosphate dehydrogenase as emerging new generation antimicrobial agents. MEDCHEMCOMM 2019; 10:1290-1301. [PMID: 31534651 PMCID: PMC6727467 DOI: 10.1039/c9md00179d] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/01/2019] [Indexed: 12/15/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) is a vital enzyme involved in the de novo synthesis of guanine nucleotides. IMPDH catalyzes a crucial step of converting IMP into XMP that is further converted into GMP. Microbial infections rely on the rapid proliferation of bacteria, and this requires the rate-limiting enzyme IMPDH to expand the guanine nucleotide pool and hence, IMPDH has recently received lots of attention as a potential target for treating infections. Owing to the structural and kinetic differences in the host IMPDH and bacterial IMPDH, a selective targeting is possible and is a crucial feature in the development of new potent and selective inhibitors of bacterial IMPDH. Earlier screening of small molecules revealed a structural requirement for the bacterial/protozoal IMPDH. Early optimization of benzimidazole and benzoxazole scaffolds led to the discovery of new potent and selective inhibitors of pathogenic IMPDH. Further research is vastly focused on the development of highly potent and selective inhibitors of various bacterial IMPDHs. Such studies reveal the importance of this excellent target for treating infectious diseases. The current review focuses on the recent developments in the discovery and development of selective inhibitors of bacterial/protozoal IMPDH with emphasis on the inhibition mechanism and structure-activity relationship.
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Affiliation(s)
- Kapil Juvale
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management , SVKM's NMIMS , V.L. Mehta Road, Vile Parle (W) , Mumbai , 400056 India
| | - Althaf Shaik
- Chemistry , Indian Institute of Technology Gandhinagar , Palaj Village , Gandhinagar , 382355 India .
| | - Sivapriya Kirubakaran
- Chemistry , Indian Institute of Technology Gandhinagar , Palaj Village , Gandhinagar , 382355 India .
- Bio-engineering , Indian Institute of Technology Gandhinagar , Palaj Village , Gandhinagar , 382355 India
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21
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Yu R, Kim Y, Maltseva N, Braunstein P, Joachimiak A, Hedstrom L. Oxanosine Monophosphate Is a Covalent Inhibitor of Inosine 5'-Monophosphate Dehydrogenase. Chem Res Toxicol 2019; 32:456-466. [PMID: 30746940 DOI: 10.1021/acs.chemrestox.8b00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactive nitrogen species (RNS) are produced during infection and inflammation, and the effects of these agents on proteins, DNA, and lipids are well recognized. In contrast, the effects of RNS damaged metabolites are less appreciated. 5-Amino-3-β-(d-ribofuranosyl)-3 H-imidazo-[4,5- d][1,3]oxazine-7-one (oxanosine) and its nucleotides are products of guanosine nitrosation. Here we demonstrate that oxanosine monophosphate (OxMP) is a potent reversible competitive inhibitor of IMPDH. The value of Ki varies from 50 to 340 nM among IMPDHs from five different organisms. UV spectroscopy and X-ray crystallography indicate that OxMP forms a ring-opened covalent adduct with the active site Cys (E-OxMP*). Unlike the covalent intermediate of the normal catalytic reaction, E-OxMP* does not hydrolyze, but instead recyclizes to OxMP. IMPDH inhibitors block proliferation and can induce apoptosis, so the inhibition of IMPDH by OxMP presents another potential mechanism for RNS toxicity.
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Affiliation(s)
- Runhan Yu
- Department of Chemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Youngchang Kim
- Structural Biology Center, Biosciences , Argonne National Laboratory , Argonne , Illinois 60439 , United States.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering , University of Chicago , Chicago , Illinois 60637 , United States
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering , University of Chicago , Chicago , Illinois 60637 , United States
| | - Philip Braunstein
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences , Argonne National Laboratory , Argonne , Illinois 60439 , United States.,Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering , University of Chicago , Chicago , Illinois 60637 , United States.,Department of Biochemistry and Molecular Biology , University of Chicago , Chicago , Illinois 60557 , United States
| | - Lizbeth Hedstrom
- Department of Chemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
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22
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Juvale K, Purushothaman G, Singh V, Shaik A, Ravi S, Thiruvenkatam V, Kirubakaran S. Identification of selective inhibitors of Helicobacter pylori IMPDH as a targeted therapy for the infection. Sci Rep 2019; 9:190. [PMID: 30655593 PMCID: PMC6336804 DOI: 10.1038/s41598-018-37490-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/30/2018] [Indexed: 12/30/2022] Open
Abstract
Helicobacter pylori (H. pylori), the major cause of several gastric disorders has been recognied as a type I carcinogen. By virtue of resistance developed by H. pylori strains, currently used antibiotic based treatments rather demonstrate high failure rates. Hence, there is an emerging need for identification of new targets to treat H. pylori infection. Inosine-5′-monophosphate dehydrogenase (IMPDH) has been studied as a potential target to treat H. pylori infection. Here, a detailed enzyme kinetic study of recombinant expressed H. pylori inosine-5′-monophosphate dehydrogenase (HpIMPDH) is presented. A new in-house synthesized indole-based scaffold is identified as an inhibitor for HpIMPDH. These indole-based compounds showed non-competitive inhibition against IMP and NAD+ whereas the benzimidazole compounds were found be uncompetitive inhibitors. The new indole scaffold ensures specificity due to its high selectivity for bacterial IMPDH over human IMPDH II. Our work aims to overcome the drawback of existing inhibitors by introducing new indole scaffold for targeting bacterial IMPDH.
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Affiliation(s)
- Kapil Juvale
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India.,Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai, 400056, India
| | - Gayathri Purushothaman
- Biological engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India
| | - Vijay Singh
- Biological engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India
| | - Althaf Shaik
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India
| | - Srimadhavi Ravi
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India
| | - Vijay Thiruvenkatam
- Biological engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India.,Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India
| | - Sivapriya Kirubakaran
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India. .,Biological engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, India.
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23
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Duan S, Huang W, Liu X, Liu X, Chen N, Xu Q, Hu Y, Song W, Zhou J. IMPDH2 promotes colorectal cancer progression through activation of the PI3K/AKT/mTOR and PI3K/AKT/FOXO1 signaling pathways. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:304. [PMID: 30518405 PMCID: PMC6282329 DOI: 10.1186/s13046-018-0980-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
Abstract
Background Inosine 5′-monophosphate dehydrogenase type II (IMPDH2) was originally identified as an oncogene in several human cancers. However, the clinical significance and biological role of IMPDH2 remain poorly understood in colorectal cancer (CRC). Methods Quantitative real-time polymerase chain reaction (qPCR), western blotting analysis, the Cancer Genome Atlas (TCGA) data mining and immunohistochemistry were employed to examine IMPDH2 expression in CRC cell lines and tissues. A series of in-vivo and in-vitro assays were performed to demonstrate the function of IMPDH2 and its possible mechanisms in CRC. Results IMPDH2 was upregulated in CRC cells and tissues at both mRNA and protein level. High IMPDH2 expression was closely associated with T stage, lymph node state, distant metastasis, lymphovascular invasion and clinical stage, and significantly correlated with poor survival of CRC patients. Further study revealed that overexpression of IMPDH2 significantly promoted the proliferation, invasion, migration and epithelial-mesenchymal transition (EMT) of CRC cells in vitro and accelerated xenograft tumour growth in nude mice. On the contrary, knockdown of IMPDH2 achieved the opposite effect. Gene set enrichment analysis (GSEA) showed that the gene set related to cell cycle was linked to upregulation of IMPDH2 expression. Our study verified that overexpressing IMPDH2 could promote G1/S phase cell cycle transition through activation of PI3K/AKT/mTOR and PI3K/AKT/FOXO1 pathways and facilitate cell invasion, migration and EMT by regulating PI3K/AKT/mTOR pathway. Conclusions These results suggest that IMPDH2 plays an important role in the development and progression of human CRC and may serve as a novel prognostic biomarker and therapeutic target for CRC.
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Affiliation(s)
- Shiyu Duan
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Wenqing Huang
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Xiaoting Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Xuming Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Nana Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Xu
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Yukun Hu
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Wen Song
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China
| | - Jun Zhou
- Department of Pathology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China. .,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China. .,Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, China.
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24
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Schiavon CR, Griffin ME, Pirozzi M, Parashuraman R, Zhou W, Jinnah HA, Reines D, Kahn RA. Compositional complexity of rods and rings. Mol Biol Cell 2018; 29:2303-2316. [PMID: 30024290 PMCID: PMC6249804 DOI: 10.1091/mbc.e18-05-0274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Maxwell E Griffin
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Marinella Pirozzi
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Raman Parashuraman
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - H A Jinnah
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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25
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Pua KH, Stiles DT, Sowa ME, Verdine GL. IMPDH2 Is an Intracellular Target of the Cyclophilin A and Sanglifehrin A Complex. Cell Rep 2017; 18:432-442. [PMID: 28076787 DOI: 10.1016/j.celrep.2016.12.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/21/2016] [Accepted: 12/10/2016] [Indexed: 11/16/2022] Open
Abstract
Natural products have demonstrated utility in the clinic and can also act as probes to understand complex cellular pathways. Sanglifehrin A (SFA) is a mixed polyketide and non-ribosomal peptide synthase natural product with sub-nano-molar affinity for its receptor cyclophilin A (PPIA). It has been shown to behave in vitro as an immune suppressant. Here, we identify inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) as an intracellular target of the PPIA-SFA binary complex. The formation of this ternary complex does not inhibit the enzymatic activity of IMPDH2. Rather, ternary complex formation modulates cell growth through interaction with the cystathionine-β-synthase (CBS) domain of IMPDH2. We further demonstrate that the SFA complex is highly isoform selective for IMPDH2 (versus IMPDH1). This work reveals a role for the CBS domains of IMPDH2 in cellular proliferation, suggesting a more complex role than previously suspected for IMPDH2 in T cell activation and proliferation.
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Affiliation(s)
- Khian Hong Pua
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Warp Drive Bio, Cambridge, MA 02139, USA
| | - Dylan T Stiles
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Warp Drive Bio, Cambridge, MA 02139, USA
| | - Mathew E Sowa
- Warp Drive Bio, Cambridge, MA 02139, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory L Verdine
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Warp Drive Bio, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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26
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A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases. Sci Rep 2017; 7:2648. [PMID: 28572600 PMCID: PMC5454003 DOI: 10.1038/s41598-017-02805-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/19/2017] [Indexed: 12/31/2022] Open
Abstract
Inosine-5′-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.
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27
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Chinthakindi PK, Singh J, Gupta S, Nargotra A, Mahajan P, Kaul A, Ahmed Z, Koul S, Sangwan PL. Synthesis of α-santonin derivatives for diminutive effect on T and B-cell proliferation and their structure activity relationships. Eur J Med Chem 2016; 127:1047-1058. [PMID: 27847171 DOI: 10.1016/j.ejmech.2016.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/24/2016] [Accepted: 11/08/2016] [Indexed: 11/18/2022]
Abstract
A new library of 20 compounds from α-santonin was synthesized and tested against Con-A induced T-cell proliferation and LPS-induced B-cell proliferation via MTT assay. The study resulted in the identification of potent immunosuppressant molecules, which were further screened along with α-santonin for Tumor Necrosis Factor Alpha (TNF-α) inhibitory activity. One of the molecules (7) at 10 μM showed equipotency to that of dexamethasone (1 μM conc.) used as a standard. Structure activity relationships of the synthesized compounds along with our earlier reported α-santonin derivatives have been studied. Inferences from the modifications carried out at all the three sites of α-santonin have been elaborated. Computational study of the active compounds shows TNF-α protein as its preferable target rather than Inosine Monophosphate Dehydrogenase (IMPDH).
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Affiliation(s)
- Praveen K Chinthakindi
- Bioorganic Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Jasvinder Singh
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IIIM Campus, Jammu, India
| | - Shilpa Gupta
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Priya Mahajan
- Discovery Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Anupurna Kaul
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Zabeer Ahmed
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Surrinder Koul
- Bioorganic Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.
| | - Payare L Sangwan
- Bioorganic Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.
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28
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Smith S, Boitz J, Chidambaram ES, Chatterjee A, Ait-Tihyaty M, Ullman B, Jardim A. The cystathionine-β-synthase domains on the guanosine 5''-monophosphate reductase and inosine 5'-monophosphate dehydrogenase enzymes from Leishmania regulate enzymatic activity in response to guanylate and adenylate nucleotide levels. Mol Microbiol 2016; 100:824-40. [PMID: 26853689 DOI: 10.1111/mmi.13352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2016] [Indexed: 01/24/2023]
Abstract
The Leishmania guanosine 5'-monophosphate reductase (GMPR) and inosine 5'-monophosphate dehydrogenase (IMPDH) are purine metabolic enzymes that function maintaining the cellular adenylate and guanylate nucleotide. Interestingly, both enzymes contain a cystathionine-β-synthase domain (CBS). To investigate this metabolic regulation, the Leishmania GMPR was cloned and shown to be sufficient to complement the guaC (GMPR), but not the guaB (IMPDH), mutation in Escherichia coli. Kinetic studies confirmed that the Leishmania GMPR catalyzed a strict NADPH-dependent reductive deamination of GMP to produce IMP. Addition of GTP or high levels of GMP induced a marked increase in activity without altering the Km values for the substrates. In contrast, the binding of ATP decreased the GMPR activity and increased the GMP Km value 10-fold. These kinetic changes were correlated with changes in the GMPR quaternary structure, induced by the binding of GMP, GTP, or ATP to the GMPR CBS domain. The capacity of these CBS domains to mediate the catalytic activity of the IMPDH and GMPR provides a regulatory mechanism for balancing the intracellular adenylate and guanylate pools.
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Affiliation(s)
- Sabrina Smith
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Jan Boitz
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Ehzilan Subramanian Chidambaram
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Abhishek Chatterjee
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Maria Ait-Tihyaty
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Buddy Ullman
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Armando Jardim
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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29
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Nakabayashi M, Shibata N, Ishido-Nakai E, Kanagawa M, Iio Y, Komori H, Ueda Y, Nakagawa N, Kuramitsu S, Higuchi Y. Crystal structure of a hypothetical protein, TTHA0829 from Thermus thermophilus HB8, composed of cystathionine-β-synthase (CBS) and aspartate-kinase chorismate-mutase tyrA (ACT) domains. Extremophiles 2016; 20:275-82. [DOI: 10.1007/s00792-016-0817-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/14/2016] [Indexed: 01/01/2023]
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30
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Popsavin M, Kojić V, Torović L, Svirčev M, Spaić S, Jakimov D, Aleksić L, Bogdanović G, Popsavin V. Synthesis and in vitro antitumour activity of tiazofurin analogues with nitrogen functionalities at the C-2′ position. Eur J Med Chem 2016; 111:114-25. [DOI: 10.1016/j.ejmech.2016.01.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 01/25/2023]
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31
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Makowska-Grzyska M, Kim Y, Gorla SK, Wei Y, Mandapati K, Zhang M, Maltseva N, Modi G, Boshoff HI, Gu M, Aldrich C, Cuny GD, Hedstrom L, Joachimiak A. Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. PLoS One 2015; 10:e0138976. [PMID: 26440283 PMCID: PMC4594927 DOI: 10.1371/journal.pone.0138976] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/07/2015] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5’-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis (Mtb) is an attractive drug target. The enzyme catalyzes the conversion of inosine 5’-monophosphate into xanthosine 5’-monophosphate with the concomitant reduction of NAD+ to NADH. This reaction controls flux into the guanine nucleotide pool. We report seventeen selective IMPDH inhibitors with antitubercular activity. The crystal structures of a deletion mutant of MtbIMPDH2 in the apo form and in complex with the product XMP and substrate NAD+ are determined. We also report the structures of complexes with IMP and three structurally distinct inhibitors, including two with antitubercular activity. These structures will greatly facilitate the development of MtbIMPDH2-targeted antibiotics.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
| | - Suresh Kumar Gorla
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Yang Wei
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Kavitha Mandapati
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Minjia Zhang
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Gyan Modi
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Minyi Gu
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
| | - Courtney Aldrich
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN, United States of America
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 549A Science and Research Building 2, Houston, TX, United States of America
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America
- * E-mail: (LH); (AJ)
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America
- * E-mail: (LH); (AJ)
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32
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Pankiewicz KW, Felczak K. From ribavirin to NAD analogues and back to ribavirin in search for anticancer agents. HETEROCYCL COMMUN 2015. [DOI: 10.1515/hc-2015-0133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
AbstractRibavirin, a broad-spectrum antiviral agent is used in the clinic alone or in combination with other antivirals and/or interferons. Numerous structural analogues of ribavirin have been developed, among them tiazofurin, which is inactive against viruses but is a potent anticancer drug. Tiazofurin was found to inhibit nicotinamide adenine dinucleotide (NAD)-dependent inosine monophosphate dehydrogenase (IMPDH) after metabolic conversion into tiazofurin adenine dinucleotide (TAD), which binds well but could not serve as IMPDH cofactor. TAD showed high selectivity against human IMPDH vs. other cellular dehydrogenases. Mycophenolic acid (MPA) was even more specific, binding at the cofactor-binding domain of IMPDH. Ribavirin adenine dinucleotide, however, did not show any significant inhibition at the enzymatic level. We synthesized numerous NAD analogues in which natural nicotinamide riboside was replaced by tiazofurin, MPA moiety, or benzamide riboside, and the adenosine moiety as well as the pyrophosphate linker were broadly modified. Some of these compounds were found to be low nanomolar inhibitors of the enzyme and sub-micromolar inhibitors of cancer cell line proliferation. The best were as potent as tyrosine kinase inhibitor gleevec heralded as a ‘magic bullet’ against chronic myelogenous leukemia. In recent years, ribavirin was rediscovered as a potential anticancer agent against number of tumors including leukemia. It was clearly established that its antitumor activity is related to the inhibition of an oncogene, the eukaryotic translation initiation factor (eIF4E).
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Affiliation(s)
- Krzysztof W. Pankiewicz
- 1University of Minnesota Center for Drug Design, MMC 204, 516 Delaware Street NE, Minneapolis, MN 55455, USA
| | - Krzysztof Felczak
- 1University of Minnesota Center for Drug Design, MMC 204, 516 Delaware Street NE, Minneapolis, MN 55455, USA
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33
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Touw WG, Joosten RP, Vriend G. Detection of trans-cis flips and peptide-plane flips in protein structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1604-14. [PMID: 26249342 PMCID: PMC4528797 DOI: 10.1107/s1399004715008263] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/27/2015] [Indexed: 11/13/2022]
Abstract
A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans-cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans-cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure-function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT_CHECK.
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Affiliation(s)
- Wouter G. Touw
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Robbie P. Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands
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34
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Kim Y, Makowska-Grzyska M, Gorla SK, Gollapalli DR, Cuny GD, Joachimiak A, Hedstrom L. Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity. Acta Crystallogr F Struct Biol Commun 2015; 71:531-8. [PMID: 25945705 PMCID: PMC4427161 DOI: 10.1107/s2053230x15000187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/06/2015] [Indexed: 11/10/2022] Open
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) is a promising target for the treatment of Cryptosporidium infections. Here, the structure of C. parvum IMPDH (CpIMPDH) in complex with inosine 5'-monophosphate (IMP) and P131, an inhibitor with in vivo anticryptosporidial activity, is reported. P131 contains two aromatic groups, one of which interacts with the hypoxanthine ring of IMP, while the second interacts with the aromatic ring of a tyrosine in the adjacent subunit. In addition, the amine and NO2 moieties bind in hydrated cavities, forming water-mediated hydrogen bonds to the protein. The design of compounds to replace these water molecules is a new strategy for the further optimization of C. parvum inhibitors for both antiparasitic and antibacterial applications.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Suresh Kumar Gorla
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | | | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Science and Research Building 2, Houston, TX 77204, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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35
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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36
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Makowska-Grzyska M, Kim Y, Maltseva N, Osipiuk J, Gu M, Zhang M, Mandapati K, Gollapalli DR, Gorla SK, Hedstrom L, Joachimiak A. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity. J Biol Chem 2015; 290:5893-911. [PMID: 25572472 PMCID: PMC4342496 DOI: 10.1074/jbc.m114.619767] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD(+), which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD(+) and XMP/NAD(+). In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD(+) adenosine moiety. More importantly, this new NAD(+)-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD(+)-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Youngchang Kim
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Natalia Maltseva
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Jerzy Osipiuk
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637
| | - Minyi Gu
- From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637
| | | | | | | | | | - Lizbeth Hedstrom
- the Departments of Biology and Chemistry, Brandeis University, Waltham, Massachusetts 024549110
| | - Andrzej Joachimiak
- From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637,
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37
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Popsavin M, Kojić V, Spaić S, Svirčev M, Bogdanović G, Jakimov D, Aleksić L, Popsavin V. 2-Substituted thiazole-4-carboxamide derivatives as tiazofurin mimics: synthesis and in vitro antitumour activity. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.02.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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38
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Rostirolla DC, Milech de Assunção T, Bizarro CV, Basso LA, Santos DS. Biochemical characterization of Mycobacterium tuberculosis IMP dehydrogenase: kinetic mechanism, metal activation and evidence of a cooperative system. RSC Adv 2014. [DOI: 10.1039/c4ra02142h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Proposed kinetic mechanism forMtIMPDH in the presence of K+.
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Affiliation(s)
- Diana Carolina Rostirolla
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
| | | | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
| | - Diogenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
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39
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Carcamo WC, Calise SJ, von Mühlen CA, Satoh M, Chan EKL. Molecular cell biology and immunobiology of mammalian rod/ring structures. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:35-74. [PMID: 24411169 DOI: 10.1016/b978-0-12-800097-7.00002-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleotide biosynthesis is a highly regulated process necessary for cell growth and replication. Cytoplasmic structures in mammalian cells, provisionally described as rods and rings (RR), were identified by human autoantibodies and recently shown to include two key enzymes of the CTP/GTP biosynthetic pathways, cytidine triphosphate synthetase (CTPS) and inosine monophosphate dehydrogenase (IMPDH). Several studies have described CTPS filaments in mammalian cells, Drosophila, yeast, and bacteria. Other studies have identified IMPDH filaments in mammalian cells. Similarities among these studies point to a common evolutionarily conserved cytoplasmic structure composed of a subset of nucleotide biosynthetic enzymes. These structures appear to be a conserved metabolic response to decreased intracellular GTP and/or CTP pools. Antibodies to RR were found to develop in some hepatitis C patients treated with interferon-α and ribavirin. Additionally, the presence of anti-RR antibodies was correlated with poor treatment outcome.
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Affiliation(s)
- Wendy C Carcamo
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - S John Calise
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | | | - Minoru Satoh
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Florida, Gainesville, Florida, USA; Department of Clinical Nursing, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA.
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40
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Felczak K, Vince R, Pankiewicz KW. NAD-based inhibitors with anticancer potential. Bioorg Med Chem Lett 2013; 24:332-6. [PMID: 24269162 DOI: 10.1016/j.bmcl.2013.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/01/2013] [Accepted: 11/05/2013] [Indexed: 11/27/2022]
Abstract
Three classes of novel inhibitors of inosine monophosphate dehydrogenase have been prepared and their anti-proliferative properties were evaluated against several cancer cell lines. (1) Mycophenolic adenine dinucleotide analogues (8-13) containing a substituent at the C2 of adenine ring were found to be potent inhibitors of IMPDH (Ki's in range of 0.6-82nM) and sub-μM inhibitors of leukemic K562 cell proliferation. (2) Mycophenolic adenosine (d and l) esters (20 and 21) showed a potent inhibition of IMPDH2 (Ki=102 and Ki=231nM, respectively) and inhibition of K562 cell growth (IC50=0.5 and IC50=1.6μM). These compounds serve both as inhibitors of the enzyme and as a depot form of mycophenolic acid. The corresponding amide analogue 22, also a potent inhibitor of IMPDH (Ki=84nM), did not inhibit cancer cell proliferation. (3) Mycophenolic-(l)- and (d)-valine adenine di-amide derivatives 25 (Ki=9nM) and 28 (Ki=3nM) were found to be very potent enzymatically, but did not inhibit proliferation of cancer cells.
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Affiliation(s)
- Krzysztof Felczak
- Center for Drug Design, University of Minnesota, 516 Delaware Street S.E., Minneapolis, MN 55455, USA
| | - Robert Vince
- Center for Drug Design, University of Minnesota, 516 Delaware Street S.E., Minneapolis, MN 55455, USA
| | - Krzysztof W Pankiewicz
- Center for Drug Design, University of Minnesota, 516 Delaware Street S.E., Minneapolis, MN 55455, USA.
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41
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Bairagya HR, Mukhopadhyay BP, Sekar K. Conserved water mediated H-bonding dynamics of inhibitor, cofactor, Asp 364 and Asn 303 in human IMPDH II. J Biomol Struct Dyn 2013; 26:497-507. [PMID: 19108589 DOI: 10.1080/07391102.2009.10507265] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The IMPDH (Inosine monophosphate dehydrogenase)-II is largely produced in cancer cells. Extensive MD-simulation (2 ns) of the 1B3O, 1NFB, 1NF7, 1LRT, and 1MEW PDB-structures revealed the presence of a conserved water molecule, which is H-bonded and stabilized by the surrounding ribose hydroxyl (O2) of inhibitor, nitrogen (NN) of cofactor, carboxyl oxygen (OD2) and amide nitrogen atoms of the active site Asp 364 and Asn 303 of human. These water-mediated interaction are partially supported in the solvated and X-ray structures. The stereochemistry of the four- centered H-bonds around the conserved water center may be exploited to design a better model inhibitor for IMPDH-II.
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Affiliation(s)
- Hridoy R Bairagya
- Department of Chemistry, National Institute of Technology-Durgapur, West Bengal, Durgapur-713209, India
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42
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Bairagya HR, Mishra DK, Mukhopadhyay BP, Sekar K. Conserved water-mediated recognition and dynamics of NAD+ (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor. J Biomol Struct Dyn 2013; 32:1248-62. [PMID: 23829371 DOI: 10.1080/07391102.2013.812982] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10 ns simulation of the IMP-NAD(+) complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD(+). Three conserved water molecules (W1, W, and W1') in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD(+)) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP-NAD(+)-enzyme complexes and their recognition to NAD(+), some covalent modification at carboxamide group of di-nucleotide (NAD(+)) has been made by substituting the -CONH2group by -CONHNH2 (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II.
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Affiliation(s)
- Hridoy R Bairagya
- a Department of Chemistry , National Institute of Technology , Durgapur , West Bengal , 713209 , India
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43
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Bairagya HR, Mukhopadhyay BP. An insight to the dynamics of conserved water-mediated salt bridge interaction and interdomain recognition in hIMPDH isoforms. J Biomol Struct Dyn 2013; 31:788-808. [DOI: 10.1080/07391102.2012.712458] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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44
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MgATP regulates allostery and fiber formation in IMPDHs. Structure 2013; 21:975-85. [PMID: 23643948 DOI: 10.1016/j.str.2013.03.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 11/22/2022]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in nucleotide biosynthesis studied as an important therapeutic target and its complex functioning in vivo is still puzzling and debated. Here, we highlight the structural basis for the regulation of IMPDHs by MgATP. Our results demonstrate the essential role of the CBS tandem, conserved among almost all IMPDHs. We found that Pseudomonas aeruginosa IMPDH is an octameric enzyme allosterically regulated by MgATP and showed that this octameric organization is widely conserved in the crystal structures of other IMPDHs. We also demonstrated that human IMPDH1 adopts two types of complementary octamers that can pile up into isolated fibers in the presence of MgATP. The aggregation of such fibers in the autosomal dominant mutant, D226N, could explain the onset of the retinopathy adRP10. Thus, the regulatory CBS modules in IMPDHs are functional and they can either modulate catalysis or macromolecular assembly.
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45
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Rao VA, Shepherd SM, Owen R, Hunter WN. Structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:243-7. [PMID: 23519796 PMCID: PMC3606566 DOI: 10.1107/s1744309113002352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/23/2013] [Indexed: 05/29/2023]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) represents a potential antimicrobial drug target. The crystal structure of recombinant Pseudomonas aeruginosa IMPDH has been determined to a resolution of 2.25 Å. The structure is a homotetramer of subunits dominated by a (β/α)8-barrel fold, consistent with other known structures of IMPDH. Also in common with previous work, the cystathionine β-synthase domains, residues 92-204, are not present in the model owing to disorder. However, unlike the majority of available structures, clearly defined electron density exists for a loop that creates part of the active site. This loop, composed of residues 297-315, links α8 and β9 and carries the catalytic Cys304. P. aeruginosa IMPDH shares a high level of sequence identity with bacterial and protozoan homologues, with residues involved in binding substrate and the NAD+ cofactor being conserved. Specific differences that have been proven to contribute to selectivity against the human enzyme in a study of Cryptosporidium parvum IMPDH are also conserved, highlighting the potential value of IMPDH as a drug target.
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Affiliation(s)
- Vincenzo A. Rao
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Sharon M. Shepherd
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Richard Owen
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
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46
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Characterization of the novel Trypanosoma brucei inosine 5'-monophosphate dehydrogenase. Parasitology 2013; 140:735-45. [PMID: 23369253 DOI: 10.1017/s0031182012002090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There is an alarming rate of human African trypanosomiasis recrudescence in many parts of sub-Saharan Africa. Yet, the disease has no successful chemotherapy. Trypanosoma lacks the enzymatic machinery for the de novo synthesis of purine nucleotides, and is critically dependent on salvage mechanisms. Inosine 5'-monophosphate dehydrogenase (IMPDH) is responsible for the rate-limiting step in guanine nucleotide metabolism. Here, we characterize recombinant Trypanosoma brucei IMPDH (TbIMPDH) to investigate the enzymatic differences between TbIMPDH and host IMPDH. Size-exclusion chromatography and analytical ultracentrifugation sedimentation velocity experiments reveal that TbIMPDH forms a heptamer, different from type 1 and 2 mammalian tetrameric IMPDHs. Kinetic analysis reveals calculated K m values of 30 and 1300 μ m for IMP and NAD, respectively. The obtained K m value of TbIMPDH for NAD is approximately 20-200-fold higher than that of mammalian enzymes and indicative of a different NAD binding mode between trypanosomal and mammalian IMPDHs. Inhibition studies show K i values of 3·2 μ m, 21 nM and 3·3 nM for ribavirin 5'-monophosphate, mycophenolic acid and mizoribine 5'-monophosphate, respectively. Our results show that TbIMPDH is different from its mammalian counterpart and thus may be a good target for further studies on anti-trypanosomal drugs.
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47
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Thomas EC, Gunter JH, Webster JA, Schieber NL, Oorschot V, Parton RG, Whitehead JP. Different characteristics and nucleotide binding properties of inosine monophosphate dehydrogenase (IMPDH) isoforms. PLoS One 2012; 7:e51096. [PMID: 23236438 PMCID: PMC3517587 DOI: 10.1371/journal.pone.0051096] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
We recently reported that Inosine Monophosphate Dehydrogenase (IMPDH), a rate-limiting enzyme in de novo guanine nucleotide biosynthesis, clustered into macrostructures in response to decreased nucleotide levels and that there were differences between the IMPDH isoforms, IMPDH1 and IMPDH2. We hypothesised that the Bateman domains, which are present in both isoforms and serve as energy-sensing/allosteric modules in unrelated proteins, would contribute to isoform-specific differences and that mutations situated in and around this domain in IMPDH1 which give rise to retinitis pigmentosa (RP) would compromise regulation. We employed immuno-electron microscopy to investigate the ultrastructure of IMPDH macrostructures and live-cell imaging to follow clustering of an IMPDH2-GFP chimera in real-time. Using a series of IMPDH1/IMPDH2 chimera we demonstrated that the propensity to cluster was conferred by the N-terminal 244 amino acids, which includes the Bateman domain. A protease protection assay suggested isoform-specific purine nucleotide binding characteristics, with ATP protecting IMPDH1 and AMP protecting IMPDH2, via a mechanism involving conformational changes upon nucleotide binding to the Bateman domain without affecting IMPDH catalytic activity. ATP binding to IMPDH1 was confirmed in a nucleotide binding assay. The RP-causing mutation, R224P, abolished ATP binding and nucleotide protection and this correlated with an altered propensity to cluster. Collectively these data demonstrate that (i) the isoforms are differentially regulated by AMP and ATP by a mechanism involving the Bateman domain, (ii) communication occurs between the Bateman and catalytic domains and (iii) the RP-causing mutations compromise such regulation. These findings support the idea that the IMPDH isoforms are subject to distinct regulation and that regulatory defects contribute to human disease.
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Affiliation(s)
- Elaine C. Thomas
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (ECT); (JPW)
| | - Jennifer H. Gunter
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
| | - Julie A. Webster
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
- Metabolic Medicine, Mater Medical Research Institute, South Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Viola Oorschot
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Robert G. Parton
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Jonathan P. Whitehead
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia
- Metabolic Medicine, Mater Medical Research Institute, South Brisbane, Queensland, Australia
- * E-mail: (ECT); (JPW)
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48
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Bairagya HR, Mukhopadhyay BP, Bera AK. Role of salt bridge dynamics in inter domain recognition of human IMPDH isoforms: an insight to inhibitor topology for isoform-II. J Biomol Struct Dyn 2012; 29:441-62. [PMID: 22066532 DOI: 10.1080/07391102.2011.10507397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in the biosynthesis pathway of guanosine nucleotide. Type II isoform of the enzyme is selectively upregulated in neoplastic fast replicating lymphocytes and CML cancer cells. The hIMPDH-II is an excellent target for antileukemic agent. The detailed investigation during MD-Simulation (15 ns) of three different unliganded structures (1B3O, 1JCN and 1JR1) have clearly explored the salt bridge mediated stabilization of inter or intra domain (catalytic domains I(N), I(C) with res. Id. 28-111 and 233-504, whereas two CBS domains C₁, C₂ are 112-171 and 172-232) in IMPDH enzyme which are mostly inaccessible in their X-rays structures. The salt bridge interaction in I(N)---C₁ inter-domain of hIMPDH-I, I(N)---C₂ of IMPDH-II and C₁---I(C) of nhIMPDH-II are discriminative features among the isoforms. The I(N)---C₂ recognition in hIMPDH-II (1B3O) is missing in type-I isoform (1JCN). The salt bridge interaction D232---K238 at the surface of protein and the involvement of three conserved water molecules or the hydrophilic centers (WA²³²(OD1), WB ²³²(OD2) and W²³⁸(NZ)) to those acidic and basic residues seem to be unique in hIMPDH-II. The hydrophilic susceptibility, geometrical and electronic consequences of this salt bridge interaction could be useful to design the topology of specific inhibitor for hIMPDH-II which may not be effective for hIMPDH-I. Possibly, the aliphatic ligand containing carboxyl, amide or hydrophilic groups with flexible structure may be implicated for hIMPDH-II inhibitor design using the conserved water mimic drug design protocol.
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Affiliation(s)
- Hridoy R Bairagya
- Department of Chemistry, National Institute of Technology-Durgapur, West Bengal, Durgapur-713209, India
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Midtkandal RR, Redpath P, Trammell SAJ, Macdonald SJF, Brenner C, Migaud ME. Novel synthetic route to the C-nucleoside, 2-deoxy benzamide riboside. Bioorg Med Chem Lett 2012; 22:5204-7. [PMID: 22795628 PMCID: PMC3683580 DOI: 10.1016/j.bmcl.2012.06.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 11/30/2022]
Abstract
2-Deoxy-C-nucleosides are a subcategory of C-nucleosides that has not been explored extensively, largely because the synthesis is less facile. Flexible synthetic procedures giving access to 2-deoxy-C-nucleosides are therefore of interest. To exemplify the versatility and highlight the limitations of a synthetic route recently developed to that effect, the first synthesis of 2-deoxy benzamide riboside is reported. Biological properties of this novel C-nucleoside are also discussed.
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Affiliation(s)
- Rebecca R Midtkandal
- Queen's University Belfast, John King Laboratory, School of Pharmacy, Lisburn Road, Belfast, BT9 7BL, Northern Ireland, UK
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50
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Makowska-Grzyska M, Kim Y, Wu R, Wilton R, Gollapalli DR, Wang XK, Zhang R, Jedrzejczak R, Mack JC, Maltseva N, Mulligan R, Binkowski TA, Gornicki P, Kuhn ML, Anderson WF, Hedstrom L, Joachimiak A. Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes. Biochemistry 2012; 51:6148-63. [PMID: 22788966 DOI: 10.1021/bi300511w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first unique step of the GMP branch of the purine nucleotide biosynthetic pathway. This enzyme is found in organisms of all three kingdoms. IMPDH inhibitors have broad clinical applications in cancer treatment, as antiviral drugs and as immunosuppressants, and have also displayed antibiotic activity. We have determined three crystal structures of Bacillus anthracis IMPDH, in a phosphate ion-bound (termed "apo") form and in complex with its substrate, inosine 5'-monophosphate (IMP), and product, xanthosine 5'-monophosphate (XMP). This is the first example of a bacterial IMPDH in more than one state from the same organism. Furthermore, for the first time for a prokaryotic enzyme, the entire active site flap, containing the conserved Arg-Tyr dyad, is clearly visible in the structure of the apoenzyme. Kinetic parameters for the enzymatic reaction were also determined, and the inhibitory effect of XMP and mycophenolic acid (MPA) has been studied. In addition, the inhibitory potential of two known Cryptosporidium parvum IMPDH inhibitors was examined for the B. anthracis enzyme and compared with those of three bacterial IMPDHs from Campylobacter jejuni, Clostridium perfringens, and Vibrio cholerae. The structures contribute to the characterization of the active site and design of inhibitors that specifically target B. anthracis and other microbial IMPDH enzymes.
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Affiliation(s)
- Magdalena Makowska-Grzyska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
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