1
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Dillenburg M, Smith J, Wagner CR. The Many Faces of Histidine Triad Nucleotide Binding Protein 1 (HINT1). ACS Pharmacol Transl Sci 2023; 6:1310-1322. [PMID: 37854629 PMCID: PMC10580397 DOI: 10.1021/acsptsci.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Indexed: 10/20/2023]
Abstract
The histidine triad nucleotide binding protein 1 (HINT1) is a nucleoside phosphoramidase that has garnered interest due to its widespread expression and participation in a broad range of biological processes. Herein, we discuss the role of HINT1 as a regulator of several CNS functions, tumor suppressor, and mast cell activator via its interactions with multiple G-protein-coupled receptors and transcription factors. Importantly, altered HINT1 expression and mutation are connected to the progression of multiple disease states, including several neuropsychiatric disorders, peripheral neuropathy, and tumorigenesis. Additionally, due to its involvement in the activation of several clinically used phosphoramidate prodrugs, tremendous efforts have been made to better understand the interactions behind nucleoside binding and phosphoramidate hydrolysis by HINT1. We detail the substrate specificity and catalytic mechanism of HINT1 hydrolysis, while highlighting the structural biology behind these efforts. The aim of this review is to summarize the multitude of biological and pharmacological functions in which HINT1 participates while addressing the areas of need for future research.
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Affiliation(s)
- Maxwell Dillenburg
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jacob Smith
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R. Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Fakhri AM, Warner MH, DeGiorgis JA, Cornely K. Mycobacteriophage Rita: a cluster F1 phage discovered in North Easton, Massachusetts. Microbiol Resour Announc 2023; 12:e0051023. [PMID: 37638726 PMCID: PMC10508093 DOI: 10.1128/mra.00510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Mycobacteriophage Rita infects Mycobacterium smegmatis mc2155 and was isolated from a soil sample collected in North Easton, Massachusetts. Assigned to cluster F1 based on sequence similarity to other phages in the same cluster, Rita has a 58,771 bp genome and encodes 104 genes. Rita is 98% similar to phage Bipolar.
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Affiliation(s)
- Anna M. Fakhri
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marcie H. Warner
- Department of Natural Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
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3
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Yao J, Miao Y, Zhu L, Wan M, Lu Y, Tang W. Histidine trinucleotide binding protein 2: from basic science to clinical implications. Biochem Pharmacol 2023; 212:115527. [PMID: 37004779 DOI: 10.1016/j.bcp.2023.115527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Histidine triad nucleotide-binding protein 2 (HINT2) is a dimeric protein that belongs to the histidine triad protein superfamily, predominantly expressed in the liver, pancreas, and adrenal gland, and localised to the mitochondrion. HINT2 binds nucleotides and catalyses the hydrolysis of nucleotidyl substrates. Moreover, HINT2 has been identified as a key regulator of multiple biological processes, including mitochondria-dependent apoptosis, mitochondrial protein acetylation, and steroidogenesis. Genetic manipulation has provided new insights into the physiological roles of HINT2 in several processes, such as inhibition of cancer progression, regulation of hepatic lipid metabolism, and protective effects on the cardiovascular system. The current review outlines the background and functions of HINT2. In addition, it summarises research progress on the correlation between HINT2 and human malignancies, hepatic metabolic diseases, and cardiovascular diseases, with an attempt to provide new research directions emerging in this field and to unveil the therapeutic value of HINT2 as a target in the combat of human diseases.
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4
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Roy B, Navarro V, Peyrottes S. Prodrugs of Nucleoside 5'-Monophosphate Analogues: Overview of the Recent Literature Concerning their Synthesis and Applications. Curr Med Chem 2023; 30:1256-1303. [PMID: 36093825 DOI: 10.2174/0929867329666220909122820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022]
Abstract
Nucleoside analogues are widely used as anti-infectious and antitumoral agents. However, their clinical use may face limitations associated with their physicochemical properties, pharmacokinetic parameters, and/or their peculiar mechanisms of action. Indeed, once inside the cells, nucleoside analogues require to be metabolized into their corresponding (poly-)phosphorylated derivatives, mediated by cellular and/or viral kinases, in order to interfere with nucleic acid biosynthesis. Within this activation process, the first-phosphorylation step is often the limiting one and to overcome this limitation, numerous prodrug approaches have been proposed. Herein, we will focus on recent literature data (from 2015 and onwards) related to new prodrug strategies, the development of original synthetic approaches and novel applications of nucleotide prodrugs (namely pronucleotides) leading to the intracellular delivery of 5'-monophosphate nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
| | - Valentin Navarro
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
| | - Suzanne Peyrottes
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
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5
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Strom A, Shah R, Dolot R, Rogers MS, Tong CL, Wang D, Xia Y, Lipscomb JD, Wagner CR. Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides. Biochemistry 2022; 61:2648-2661. [PMID: 36398895 PMCID: PMC9854251 DOI: 10.1021/acs.biochem.2c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human histidine triad nucleotide-binding (hHINT) proteins catalyze nucleotide phosphoramidase and acyl-phosphatase reactions that are essential for the activation of antiviral proTides, such as Sofosbuvir and Remdesivir. hHINT1 and hHINT2 are highly homologous but exhibit disparate roles as regulators of opioid tolerance (hHINT1) and mitochondrial activity (hHINT2). NMR studies of hHINT1 reveal a pair of dynamic surface residues (Q62, E100), which gate a conserved water channel leading to the active site 13 Å away. hHINT2 crystal structures identify analogous residues (R99, D137) and water channel. hHINT1 Q62 variants significantly alter the steady-state kcat and Km for turnover of the fluorescent substrate (TpAd), while stopped-flow kinetics indicate that KD also changes. hHINT2, like hHINT1, exhibits a burst phase of adenylation, monitored by fluorescent tryptamine release, prior to rate-limiting hydrolysis and nucleotide release. hHINT2 exhibits a much smaller burst-phase amplitude than hHINT1, which is further diminished in hHINT2 R99Q. Kinetic simulations suggest that amplitude variations can be accounted for by a variable fluorescent yield of the E·S complex from changes in the environment of bound TpAd. Isothermal titration calorimetry measurements of inhibitor binding show that these hHINT variants also alter the thermodynamic binding profile. We propose that these altered surface residues engender long-range dynamic changes that affect the orientation of bound ligands, altering the thermodynamic and kinetic characteristics of hHINT active site function. Thus, studies of the cellular roles and proTide activation potential by hHINTs should consider the importance of long-range interactions and possible protein binding surfaces far from the active site.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rafal Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Cher-Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David Wang
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Youlin Xia
- Department of Structural Biology, St. Jude’s Research Hospital, Memphis, Tennessee 38105, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Carston R. Wagner
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States,Address correspondence to: Carston R. Wagner, University of Minnesota, Department of Medicinal Chemistry, 2231 6th Street S.E., Cancer & Cardiovascular Research Building, Minneapolis, Minnesota 55455, USA,
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6
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Yoshida Y, Ti Z, Tanabe W, Tomoike F, Hashiya F, Suzuki T, Hirota S, Saiki Y, Horii A, Hirayama A, Soga T, Kimura Y, Abe H. Development of Fluorophosphoramidate as a New Biocompatible Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. ChemMedChem 2022; 17:e202200188. [PMID: 35393747 DOI: 10.1002/cmdc.202200188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 11/12/2022]
Abstract
Synthetic phosphate-derived functional groups are important for controlling the function of bioactive molecules in vivo . Herein we describe the development of a new type of biocompatible phosphate analog, a fluorophosphoramidate (FPA) functional group that has characteristic P-F and P-N bonds. We found that FPA with a primary amino group was relatively unstable in aqueous solution and was converted to a monophosphate, while FPA with a secondary amino group was stable. Furthermore, by improving the molecular design of FPA, we developed a reaction in which a secondary amino group is converted to a primary amino group in the intracellular environment, and clarified that the FPA group functions as a phosphate prodrug of nucleoside. Various FPA-gemcitabine derivatives were synthesized and their anticancer activities were evaluated. One of the FPA-gemcitabine derivatives showed superior anticancer activity compared with gemcitabine and its ProTide prodrug, which methodology is widely used in various nucleoside analogs, including anti-cancer and anti-virus drugs.
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Affiliation(s)
- Yuki Yoshida
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Zheng Ti
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Wataru Tanabe
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Fumiaki Tomoike
- Gakushuin University: Gakushuin Daigaku, Graduate School of Science, JAPAN
| | - Fumitaka Hashiya
- Nagoya University: Nagoya Daigaku, Research Center for Material Science, JAPAN
| | | | - Shuto Hirota
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Yuriko Saiki
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Akira Horii
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Akiyoshi Hirayama
- Keio University: Keio Gijuku Daigaku, Institute for Biosciences, JAPAN
| | - Tomoyoshi Soga
- Keio University: Keio Gijuku Daigaku, Institute for Advance Biosciences, JAPAN
| | - Yasuaki Kimura
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Hiroshi Abe
- Nagoya University, Department of Chemistry, Graduate School of Science, Furo, Chikusa, 464-8602, Nagoya, JAPAN
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7
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Dolot R, Krakowiak A, Kaczmarek R, Włodarczyk A, Pichlak M, Nawrot B. Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A. Biochim Biophys Acta Gen Subj 2021; 1865:129968. [PMID: 34329705 DOI: 10.1016/j.bbagen.2021.129968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 07/25/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Human HINT2 is an important mitochondrial enzyme involved in many processes such as apoptosis and bioenergetics, but its endogenous substrates and the three-dimensional structure of the full-length protein have not been identified yet. METHODS An HPLC assay was used to test the hydrolytic activity of HINT2 against various adenosine, guanosine, and 2'-deoxyguanosine derivatives containing phosphate bonds of different types and different leaving groups. Data on binding affinity were obtained by microscale thermophoresis (MST). Crystal structures of HINT2, in its apo form and with a dGMP ligand, were resolved to atomic resolution. RESULTS HINT2 substrate specificity was similar to that of HINT1, but with the major exception of remarkable discrimination against substrates lacking the 2'-hydroxyl group. The biochemical results were consistent with binding affinity measurements. They showed a similar binding strength of AMP and GMP to HINT2, and much weaker binding of dGMP, in contrast to HINT1. A non-hydrolyzable analog of Ap4A (JB419) interacted with both proteins with similar Kd and Ap4A is the signaling molecule that can interact with hHINT1 and regulate the activity of some transcription factors. CONCLUSIONS Several forms of homo- and heterodimers of different lengths of N-terminally truncated polypeptides resulting from degradation of the full-length protein were described. Ser144 in HINT2 appeared to be functionally equivalent to Ser107 in HINT1 by supporting the protonation of the leaving group in the hydrolytic mechanism of HINT2. SIGNIFICANCE Our results should be considered in future studies on the natural function of HINT2 and its role in nucleotide prodrug processing.
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Affiliation(s)
- Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Artur Włodarczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Marta Pichlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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8
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Vanden Avond MA, Meng H, Beatka MJ, Helbling DC, Prom MJ, Sutton JL, Slick RA, Dimmock DP, Pertusati F, Serpi M, Pileggi E, Crutcher P, Thomas S, Lawlor MW. The nucleotide prodrug CERC-913 improves mtDNA content in primary hepatocytes from DGUOK-deficient rats. J Inherit Metab Dis 2021; 44:492-501. [PMID: 33368311 DOI: 10.1002/jimd.12354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023]
Abstract
Loss-of-function mutations in the deoxyguanosine kinase (DGUOK) gene result in a mitochondrial DNA (mtDNA) depletion syndrome. DGUOK plays an important role in converting deoxyribonucleosides to deoxyribonucleoside monophosphates via the salvage pathway for mtDNA synthesis. DGUOK deficiency manifests predominantly in the liver; the most common cause of death is liver failure within the first year of life and no therapeutic options are currently available. in vitro supplementation with deoxyguanosine or deoxyguanosine monophosphate (dGMP) were reported to rescue mtDNA depletion in DGUOK-deficient, patient-derived fibroblasts and myoblasts. CERC-913, a novel ProTide prodrug of dGMP, was designed to bypass defective DGUOK while improving permeability and stability relative to nucleoside monophosphates. To evaluate CERC-913 for its ability to rescue mtDNA depletion, we developed a primary hepatocyte culture model using liver tissue from DGUOK-deficient rats. DGUOK knockout rat hepatocyte cultures exhibit severely reduced mtDNA copy number (~10%) relative to wild type by qPCR and mtDNA content remains stable for up to 8 days in culture. CERC-913 increased mtDNA content in DGUOK-deficient hepatocytes up to 2.4-fold after 4 days of treatment in a dose-dependent fashion, which was significantly more effective than dGMP at similar concentrations. These early results suggest primary hepatocyte culture is a useful model for the study of mtDNA depletion syndromes and that CERC-913 treatment can improve mtDNA content in this model.
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Affiliation(s)
- Mark A Vanden Avond
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Hui Meng
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Margaret J Beatka
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Daniel C Helbling
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mariah J Prom
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jessica L Sutton
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebecca A Slick
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Elisa Pileggi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | | | | | - Michael W Lawlor
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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9
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Yoshida Y, Honma M, Kimura Y, Abe H. Structure, Synthesis and Inhibition Mechanism of Nucleoside Analogues as HIV-1 Reverse Transcriptase Inhibitors (NRTIs). ChemMedChem 2021; 16:743-766. [PMID: 33230979 DOI: 10.1002/cmdc.202000695] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/31/2020] [Indexed: 12/13/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by infection with the human immunodeficiency virus (HIV). Although treatments against HIV infection are available, AIDS remains a serious disease that causes many deaths annually. Although a variety of anti-HIV drugs have been synthesized and marketed to treat HIV-infected patients, nucleoside analogue reverse transcriptase inhibitors (NRTIs), which mimic nucleosides, are used extensively and remain a subject of interest to medicinal chemists. However, HIV has acquired drug resistance against NRTIs, and thus the struggle to find novel therapies continues. In this review, we trace the trajectory of NRTIs, focusing on the synthesis, mechanisms of action and applications of NRTIs that have been developed.
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Affiliation(s)
- Yuki Yoshida
- Graduate School of Science, Department of Chemistry, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Masakazu Honma
- Nucleic Acid Medicine Research Laboratories, Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, >, Tokyo, 194-8533, Japan
| | - Yasuaki Kimura
- Graduate School of Science, Department of Chemistry, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Graduate School of Science, Department of Chemistry, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
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10
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Strom A, Shah R, Wagner CR. "Switching On" Enzyme Substrate Specificity Analysis with a Fluorescent Competitive Inhibitor. Biochemistry 2021; 60:440-450. [PMID: 33513008 DOI: 10.1021/acs.biochem.0c00954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatically driven change to the spectroscopic properties of a chemical substrate or product has been a linchpin in the development of continuous enzyme kinetics assays. These assays inherently necessitate substrates or products that naturally comply with the constraints of the spectroscopic technique being used, or they require structural changes to the molecules involved to make them observable. Here we demonstrate a new analytical kinetics approach with enzyme histidine triad nucleotide binding protein 1 (HINT1) that allows us to extract both useful kcat values and a rank-ordered list of substrate specificities without the need to track substrates or products directly. Instead, this is accomplished indirectly using a "switch on" competitive inhibitor that fluoresces maximally only when bound to the HINT1 enzyme active site. Kinetic information is extracted from the duration of the diminished fluorescence when the monitorable inhibitor-bound enzyme is challenged with saturating concentrations of a nonfluorescent substrate. We refer to the loss of fluorescence, while the substrate competes for the fluorescent probe in the active site, as the substrate's residence transit time (RTT). The ability to assess kcat values and substrate specificity by monitoring the RTTs for a set of substrates with a competitive "switch on" inhibitor should be broadly applicable to other enzymatic reactions in which the "switch on" inhibitor has sufficient binding affinity over the enzymatic product.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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11
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Jovanovic D, Tremmel P, Pallan PS, Egli M, Richert C. The Enzyme‐Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dejana Jovanovic
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Peter Tremmel
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Pradeep S. Pallan
- Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 USA
| | - Martin Egli
- Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 USA
| | - Clemens Richert
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
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12
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Jovanovic D, Tremmel P, Pallan PS, Egli M, Richert C. The Enzyme-Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid. Angew Chem Int Ed Engl 2020; 59:20154-20160. [PMID: 32757352 PMCID: PMC7436718 DOI: 10.1002/anie.202008665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/04/2020] [Indexed: 12/23/2022]
Abstract
Phosphoramidates composed of an amino acid and a nucleotide analogue are critical metabolites of prodrugs, such as remdesivir. Hydrolysis of the phosphoramidate liberates the nucleotide, which can then be phosphorylated to become the pharmacologically active triphosphate. Enzymatic hydrolysis has been demonstrated, but a spontaneous chemical process may also occur. We measured the rate of enzyme-free hydrolysis for 17 phosphoramidates of ribonucleotides with amino acids or related compounds at pH 7.5. Phosphoramidates of proline hydrolyzed fast, with a half-life time as short as 2.4 h for Pro-AMP in ethylimidazole-containing buffer at 37 °C; 45-fold faster than Ala-AMP and 120-fold faster than Phe-AMP. Crystal structures of Gly-AMP, Pro-AMP, βPro-AMP and Phe-AMP bound to RNase A as crystallization chaperone showed how well the carboxylate is poised to attack the phosphoramidate, helping to explain this reactivity. Our results are significant for the design of new antiviral prodrugs.
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Affiliation(s)
- Dejana Jovanovic
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Peter Tremmel
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
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13
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Schwarz DC, Williams SK, Dillenburg M, Wagner CR, Gestwicki JE. A Phosphoramidate Strategy Enables Membrane Permeability of a Non-nucleotide Inhibitor of the Prolyl Isomerase Pin1. ACS Med Chem Lett 2020; 11:1704-1710. [PMID: 32944137 PMCID: PMC7488286 DOI: 10.1021/acsmedchemlett.0c00170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
The membrane permeability of nucleotide-based drugs, such as sofosbuvir (Sovaldi), requires installation of phosphate-caging groups. One strategy, termed "ProTide", masks the anionic phosphate through an N-linked amino ester and an O-linked aromatic phospho-ester, such that release of the active drug requires consecutive enzymatic liberation by an esterase and then a phosphoramidase, such as Hint1. Because Hint1 is known to be selective for nucleotides, it was not clear if the ProTide approach could be deployed for non-nucleotides. Here, we demonstrate that caging of a phosphate-containing inhibitor of the prolyl isomerase Pin1 increases its permeability. Moreover, this compound was processed by both esterase and phosphoramidase activity, releasing the active molecule to bind and inhibit Pin1 in cells. Thus, Hint1 appears to recognize a broader set of substrates than previously appreciated. It seems possible that other potent, but impermeable, phosphate-containing inhibitors might likewise benefit from this approach.
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Affiliation(s)
- Daniel
M. C. Schwarz
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Sarah K. Williams
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Maxwell Dillenburg
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R. Wagner
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason E. Gestwicki
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
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14
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Matos de Souza MR, Cunha MS, Okon A, Monteiro FLL, Campanati L, Wagner CR, da Costa LJ. In Vitro and In Vivo Characterization of the Anti-Zika Virus Activity of ProTides of 2'-C-β-Methylguanosine. ACS Infect Dis 2020; 6:1650-1658. [PMID: 32525653 DOI: 10.1021/acsinfecdis.0c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ProTide approach has emerged as a powerful tool to improve the intracellular delivery of nucleotide analogs with antiviral and anticancer activity. Here, we characterized the anti-ZIKV (ZIKV, Zika virus) activity of two ProTides of 2'-C-β-methylguanosine. ProTide UMN-1001 is a 2'-C-β-methylguanosine tryptamine phosphoramidate monoester, and ProTide UMN-1002 is a 2-(methylthio)-ethyl-2'-C-β-methylguanosine tryptamine phosphoramidate diester. UMN-1002 undergoes stepwise intracellular activation to the corresponding nucleotide monophosphate followed by P-N bond cleavage by intracellular histidine triad nucleotide binding protein 1 (Hint1). UMN-1001 is activated by Hint1 but is less cell-permeable than UMN-1002. UMN-1001 and UMN-1002 were found to be more potent than 2'-C-β-methylguanosine against ZIKV in human-derived microvascular endothelial and neuroblastoma cells and in reducing ZIKV RNA replication. Studies with a newborn mouse model of ZIKV infection demonstrated that, while treatment with 2'-C-β-methylguanosine and UMN-1001 was lethal, treatment with UMN-1002 was nontoxic and significantly reduced ZIKV infection. Our data suggests that anchimeric activated ProTides of 2'-C-β-methyl nucleosides should be further investigated for their potential as anti-ZIKV therapeutics.
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Affiliation(s)
| | | | - Aniekan Okon
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | | | - Carston R. Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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15
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Strom A, Tong CL, Wagner CR. Histidine triad nucleotide-binding proteins HINT1 and HINT2 share similar substrate specificities and little affinity for the signaling dinucleotide Ap4A. FEBS Lett 2020; 594:1497-1505. [PMID: 31990367 DOI: 10.1002/1873-3468.13745] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 11/07/2022]
Abstract
Human histidine triad nucleotide-binding protein 2 (hHINT2) is an important player in human mitochondrial bioenergetics, but little is known about its catalytic capabilities or its nucleotide phosphoramidate prodrug (proTide)-activating activity akin to the cytosolic isozyme hHINT1. Here, a similar substrate specificity profile (kcat /Km ) for model phosphoramidate substrates was found for hHINT2 but with higher kcat and Km values when compared with hHINT1. A broader pH range for maximum catalytic activity was determined for hHINT2 (pK1 = 6.76 ± 0.16, pK2 = 8.41 ± 0.07). In addition, the known hHINT1-microphthalmia-inducing transcription factor-regulating molecule Ap4 A was found to have no detectable binding to HINT1 nor HINT2 by isothermal titration calorimetry. These results demonstrate that despite differences in their sequence and localization, HINT1 and HINT2 have similar nucleotide substrate specificities, which should be considered in future proTide design and in studies of their natural function.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Cher Ling Tong
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Carston R Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
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16
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Jung A, Yun JS, Kim S, Kim SR, Shin M, Cho DH, Choi KS, Chang JH. Crystal Structure of Histidine Triad Nucleotide-Binding Protein from the Pathogenic Fungus Candida albicans. Mol Cells 2019; 42:56-66. [PMID: 30622225 PMCID: PMC6354057 DOI: 10.14348/molcells.2018.0377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Accepted: 11/14/2018] [Indexed: 12/19/2022] Open
Abstract
Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of 2.5 Å. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (α1-β1) and with the α3 helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.
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Affiliation(s)
- Ahjin Jung
- Department of Biology Education, Kyungpook National University, Daegu 41566,
Korea
| | - Ji-Sook Yun
- Department of Biology Education, Kyungpook National University, Daegu 41566,
Korea
| | - Shinae Kim
- Department of Biology Education, Kyungpook National University, Daegu 41566,
Korea
| | - Sang Ryong Kim
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566,
Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41566,
Korea
| | - Dong Hyung Cho
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566,
Korea
| | - Kwang Shik Choi
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566,
Korea
- Research Institute for Dokdo and Ulleungdo Island, Kyungpook National University, Daegu 41566,
Korea
- Research Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566,
Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566,
Korea
- Research Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566,
Korea
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17
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Wang Z, Lin J, Qiao K, Cai S, Zhang VW, Zhao C, Lu J. Novel mutations in HINT1 gene cause the autosomal recessive axonal neuropathy with neuromyotonia. Eur J Med Genet 2018; 62:190-194. [PMID: 30006059 DOI: 10.1016/j.ejmg.2018.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/01/2018] [Accepted: 07/09/2018] [Indexed: 01/29/2023]
Abstract
Autosomal recessive axonal neuropathy with neuromyotonia (ARAN-NM) is a rare form of hereditary neuropathy. Mutations in HINT1 gene have been identified to be the cause of this disorder. We report two unrelated patients who presented gait impairment, progressive distal muscle weakness and atrophy, neuromyotonia and foot deformities. Electrophysiological studies showed axonal motor neuropathy and neuromyotonic discharges. Using Next-generation sequencing, we identified two homozygous mutations, NM_005340.6: c.112T > C; p.(Cys38Arg) and NM_005340.6: c.289G > A; p.(Val97Met) in HINT1 gene. Based on the clinical presentation and molecular genetic analyses, ARAN-NM was diagnosed in both patients and NM_005340.6: c.112T > C; p.(Cys38Arg) and NM_005340.6: c.289G > A; p.(Val97Met) in HINT1 gene were believe to be causative for the disorder.
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Affiliation(s)
- Zhangyang Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jie Lin
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shuang Cai
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Victor W Zhang
- AmCare Genomics Lab, Guangzhou, China; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China.
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