1
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Maehigashi T, Lim C, Wade LR, Bowen NE, Knecht KM, Alvarez NN, Kelly WG, Schinazi RF, Kim DH, Xiong Y, Kim B. Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi-Goutières syndrome SAMHD1 dNTPase ortholog. J Biol Chem 2023; 299:105148. [PMID: 37567474 PMCID: PMC10485159 DOI: 10.1016/j.jbc.2023.105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Mutations in sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) are found in a neurodevelopmental disorder, Aicardi-Goutières syndrome, and cancers, and SAMHD1, which is a deoxynucleoside triphosphate (dNTP) triphosphorylase, was identified as a myeloid-specific HIV-1 restriction factor. Here, we characterized the enzymology and structure of an SAMHD1 ortholog of Caenorhabditis elegans, ZK177.8, which also reportedly induces developmental defects upon gene knockdown. We found ZK177.8 protein is a dNTPase allosterically regulated by dGTP. The active site of ZK177.8 recognizes both 2' OH and triphosphate moieties of dNTPs but not base moiety. The dGTP activator induces the formation of the enzymatically active ZK177.8 tetramers, and ZK177.8 protein lowers cellular dNTP levels in a human monocytic cell line. Finally, ZK177.8 tetramers display very similar X-ray crystal structure with human and mouse SAMHD1s except that its lack of the canonical sterile alpha motif domain. This striking conservation in structure, function, and allosteric regulatory mechanism for the hydrolysis of the DNA building blocks supports their host developmental roles.
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Affiliation(s)
- Tatsuya Maehigashi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Lydia R Wade
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Natalie N Alvarez
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - William G Kelly
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Dong-Hyun Kim
- Neurobiota Research Center, College of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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2
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Bowen NE, Tao S, Cho YJ, Schinazi RF, Kim B. Vpx requires active cellular dNTP biosynthesis to effectively counteract the anti-lentivirus activity of SAMHD1 in macrophages. J Biol Chem 2023; 299:104984. [PMID: 37390988 PMCID: PMC10374972 DOI: 10.1016/j.jbc.2023.104984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
HIV-1 replication in primary monocyte-derived macrophages (MDMs) is kinetically restricted at the reverse transcription step due to the low deoxynucleoside triphosphates (dNTP) pools established by host dNTPase, SAM and HD domain containing protein 1 (SAMHD1). Lentiviruses such as HIV-2 and some Simian immunodeficiency virus counteract this restriction using viral protein X (Vpx), which proteosomally degrades SAMHD1 and elevates intracellular dNTP pools. However, how dNTP pools increase after Vpx degrades SAMHD1 in nondividing MDMs where no active dNTP biosynthesis is expected to exists remains unclear. In this study, we monitored known dNTP biosynthesis machinery during primary human monocyte differentiation to MDMs and unexpectedly found MDMs actively express dNTP biosynthesis enzymes such as ribonucleotide reductase, thymidine kinase 1, and nucleoside-diphosphate kinase. During differentiation from monocytes the expression levels of several biosynthesis enzymes are upregulated, while there is an increase in inactivating SAMHD1 phosphorylation. Correspondingly, we observed significantly lower levels of dNTPs in monocytes compared to MDMs. Without dNTP biosynthesis availability, Vpx failed to elevate dNTPs in monocytes, despite SAMHD1 degradation. These extremely low monocyte dNTP concentrations, which cannot be elevated by Vpx, impaired HIV-1 reverse transcription in a biochemical simulation. Furthermore, Vpx failed to rescue the transduction efficiency of a HIV-1 GFP vector in monocytes. Collectively, these data suggest that MDMs harbor active dNTP biosynthesis and Vpx requires this dNTP biosynthesis to elevate dNTP levels to effectively counteract SAMHD1 and relieve the kinetic block to HIV-1 reverse transcription in MDMs.
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Affiliation(s)
- Nicole E Bowen
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Sijia Tao
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Young-Jae Cho
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Baek Kim
- Department of Pediatrics, Center for ViroScience and Cure, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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3
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Menolfi D, Lee BJ, Zhang H, Jiang W, Bowen NE, Wang Y, Zhao J, Holmes A, Gershik S, Rabadan R, Kim B, Zha S. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. Nat Commun 2023; 14:3618. [PMID: 37336885 DOI: 10.1038/s41467-023-39332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication and dNTP levels can be restored in Atr-deficient cells by suppressing origin firing, such as partial inhibition of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and importantly also other replication factors.
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Affiliation(s)
- Demis Menolfi
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Hanwen Zhang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yunyue Wang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Junfei Zhao
- Program for Mathematical Genomics, Department of Systems Biology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Antony Holmes
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Steven Gershik
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
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4
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Menolfi D, Lee BJ, Zhang H, Jiang W, Bowen NE, Wang Y, Zhao J, Holmes A, Gershik S, Rabadan R, Kim B, Zha S. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. bioRxiv 2023:2023.05.26.542515. [PMID: 37292881 PMCID: PMC10246007 DOI: 10.1101/2023.05.26.542515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently in early S phase, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication can be restored in Atr-deficient cells by pathways that suppress origin firing, such as downregulation of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and other replication factors.
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5
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Kapoor-Vazirani P, Rath SK, Liu X, Shu Z, Bowen NE, Chen Y, Haji-Seyed-Javadi R, Daddacha W, Minten EV, Danelia D, Farchi D, Duong DM, Seyfried NT, Deng X, Ortlund EA, Kim B, Yu DS. SAMHD1 deacetylation by SIRT1 promotes DNA end resection by facilitating DNA binding at double-strand breaks. Nat Commun 2022; 13:6707. [PMID: 36344525 PMCID: PMC9640623 DOI: 10.1038/s41467-022-34578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) has a dNTPase-independent function in promoting DNA end resection to facilitate DNA double-strand break (DSB) repair by homologous recombination (HR); however, it is not known if upstream signaling events govern this activity. Here, we show that SAMHD1 is deacetylated by the SIRT1 sirtuin deacetylase, facilitating its binding with ssDNA at DSBs, to promote DNA end resection and HR. SIRT1 complexes with and deacetylates SAMHD1 at conserved lysine 354 (K354) specifically in response to DSBs. K354 deacetylation by SIRT1 promotes DNA end resection and HR but not SAMHD1 tetramerization or dNTPase activity. Mechanistically, K354 deacetylation by SIRT1 promotes SAMHD1 recruitment to DSBs and binding to ssDNA at DSBs, which in turn facilitates CtIP ssDNA binding, leading to promotion of genome integrity. These findings define a mechanism governing the dNTPase-independent resection function of SAMHD1 by SIRT1 deacetylation in promoting HR and genome stability.
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Affiliation(s)
- Priya Kapoor-Vazirani
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Sandip K. Rath
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Xu Liu
- grid.189967.80000 0001 0941 6502Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Zhen Shu
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicole E. Bowen
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Yitong Chen
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Ramona Haji-Seyed-Javadi
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Waaqo Daddacha
- grid.410427.40000 0001 2284 9329Department of Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Elizabeth V. Minten
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Diana Danelia
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Daniela Farchi
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Duc M. Duong
- grid.189967.80000 0001 0941 6502Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- grid.189967.80000 0001 0941 6502Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Xingming Deng
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Eric A. Ortlund
- grid.189967.80000 0001 0941 6502Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Baek Kim
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - David S. Yu
- grid.189967.80000 0001 0941 6502Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322 USA
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6
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Bowen NE, Oo A, Kim B. Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis. Viruses 2022; 14:v14081622. [PMID: 35893688 PMCID: PMC9331428 DOI: 10.3390/v14081622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) has been the primary interest among studies on antiviral discovery, viral replication kinetics, drug resistance, and viral evolution. Following infection and entry into target cells, the HIV-1 core disassembles, and the viral RT concomitantly converts the viral RNA into double-stranded proviral DNA, which is integrated into the host genome. The successful completion of the viral life cycle highly depends on the enzymatic DNA polymerase activity of RT. Furthermore, HIV-1 RT has long been known as an error-prone DNA polymerase due to its lack of proofreading exonuclease properties. Indeed, the low fidelity of HIV-1 RT has been considered as one of the key factors in the uniquely high rate of mutagenesis of HIV-1, which leads to efficient viral escape from immune and therapeutic antiviral selective pressures. Interestingly, a series of studies on the replication kinetics of HIV-1 in non-dividing myeloid cells and myeloid specific host restriction factor, SAM domain, and HD domain-containing protein, SAMHD1, suggest that the myeloid cell tropism and high rate of mutagenesis of HIV-1 are mechanistically connected. Here, we review not only HIV-1 RT as a key antiviral target, but also potential evolutionary and mechanistic crosstalk among the unique enzymatic features of HIV-1 RT, the replication kinetics of HIV-1, cell tropism, viral genetic mutation, and host SAMHD1 protein.
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Affiliation(s)
- Nicole E. Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
- Correspondence:
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7
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Bowen NE, Temple J, Shepard C, Oo A, Arizaga F, Kapoor-Vazirani P, Persaud M, Yu CH, Kim DH, Schinazi RF, Ivanov DN, Diaz-Griffero F, Yu DS, Xiong Y, Kim B. Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins. J Biol Chem 2021; 297:101170. [PMID: 34492268 PMCID: PMC8497992 DOI: 10.1016/j.jbc.2021.101170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Elevated intracellular levels of dNTPs have been shown to be a biochemical marker of cancer cells. Recently, a series of mutations in the multifunctional dNTP triphosphohydrolase (dNTPase), sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), have been reported in various cancers. Here, we investigated the structure and functions of SAMHD1 R366C/H mutants, found in colon cancer and leukemia. Unlike many other cancer-specific mutations, the SAMHD1 R366 mutations do not alter cellular protein levels of the enzyme. However, R366C/H mutant proteins exhibit a loss of dNTPase activity, and their X-ray structures demonstrate the absence of dGTP substrate in their active site, likely because of a loss of interaction with the γ-phosphate of the substrate. The R366C/H mutants failed to reduce intracellular dNTP levels and restrict HIV-1 replication, functions of SAMHD1 that are dependent on the ability of the enzyme to hydrolyze dNTPs. However, these mutants retain dNTPase-independent functions, including mediating dsDNA break repair, interacting with CtIP and cyclin A2, and suppressing innate immune responses. Finally, SAMHD1 degradation in human primary-activated/dividing CD4+ T cells further elevates cellular dNTP levels. This study suggests that the loss of SAMHD1 dNTPase activity induced by R366 mutations can mechanistically contribute to the elevated dNTP levels commonly found in cancer cells.
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Affiliation(s)
- Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Caitlin Shepard
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Fidel Arizaga
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Priya Kapoor-Vazirani
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Dong-Hyun Kim
- School of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David S Yu
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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8
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Lin ZP, Al Zouabi NN, Xu ML, Bowen NE, Wu TL, Lavi ES, Huang PH, Zhu YL, Kim B, Ratner ES. In silico screening identifies a novel small molecule inhibitor that counteracts PARP inhibitor resistance in ovarian cancer. Sci Rep 2021; 11:8042. [PMID: 33850183 PMCID: PMC8044145 DOI: 10.1038/s41598-021-87325-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Poly ADP-ribose polymerase (PARP) inhibitors are promising targeted therapy for epithelial ovarian cancer (EOC) with BRCA mutations or defective homologous recombination (HR) repair. However, reversion of BRCA mutation and restoration of HR repair in EOC lead to PARP inhibitor resistance and reduced clinical efficacy of PARP inhibitors. We have previously shown that triapine, a small molecule inhibitor of ribonucleotide reductase (RNR), impaired HR repair and sensitized HR repair-proficient EOC to PARP inhibitors. In this study, we performed in silico screening of small molecule libraries to identify novel compounds that bind to the triapine-binding pocket on the R2 subunit of RNR and inhibit RNR in EOC cells. Following experimental validation of selected top-ranking in silico hits for inhibition of dNTP and DNA synthesis, we identified, DB4, a putative RNR pocket-binding inhibitor markedly abrogated HR repair and sensitized BRCA-wild-type EOC cells to the PARP inhibitor olaparib. Furthermore, we demonstrated that the combination of DB4 and olaparib deterred the progression of BRCA-wild type EOC xenografts and significantly prolonged the survival time of tumor-bearing mice. Herein we report the discovery of a putative small molecule inhibitor of RNR and HR repair for combination with PARP inhibitors to treat PARP inhibitor-resistant and HR repair-proficient EOC.
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Affiliation(s)
- Z Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06510, USA.
| | - Nour N Al Zouabi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Mark L Xu
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Terence L Wu
- Yale West Campus Analytical Core, Yale University, West Haven, CT, 06516, USA
| | - Ethan S Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Pamela H Huang
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Yong-Lian Zhu
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Elena S Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06510, USA.
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9
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El-Sayed WMM, Gombolay AL, Xu P, Yang T, Jeon Y, Balachander S, Newnam G, Tao S, Bowen NE, Brůna T, Borodovsky M, Schinazi RF, Kim B, Chen Y, Storici F. Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii. iScience 2020; 24:102005. [PMID: 33490913 PMCID: PMC7809514 DOI: 10.1016/j.isci.2020.102005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/29/2020] [Accepted: 12/23/2020] [Indexed: 11/02/2022] Open
Abstract
Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. We discovered a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the corresponding nucleotide content of these C. reinhardtii organelle genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. We reveal specific biases and patterns in rNMP distributions in the algal mitochondrial, chloroplast, and nuclear DNA. Moreover, we identified the C. reinhardtii orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.
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Affiliation(s)
- Waleed M M El-Sayed
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Marine Microbiology Department, National Institute of Oceanography and Fisheries, Red Sea, 84517, Egypt
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sijia Tao
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Tomáš Brůna
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mark Borodovsky
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30309, USA
| | - Yongsheng Chen
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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