1
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Katti A, Vega-Pérez A, Foronda M, Zimmerman J, Zafra MP, Granowsky E, Goswami S, Gardner EE, Diaz BJ, Simon JM, Wuest A, Luan W, Fernandez MTC, Kadina AP, Walker JA, Holden K, Lowe SW, Sánchez Rivera FJ, Dow LE. Generation of precision preclinical cancer models using regulated in vivo base editing. Nat Biotechnol 2024; 42:437-447. [PMID: 37563300 DOI: 10.1038/s41587-023-01900-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/10/2023] [Indexed: 08/12/2023]
Abstract
Although single-nucleotide variants (SNVs) make up the majority of cancer-associated genetic changes and have been comprehensively catalogued, little is known about their impact on tumor initiation and progression. To enable the functional interrogation of cancer-associated SNVs, we developed a mouse system for temporal and regulatable in vivo base editing. The inducible base editing (iBE) mouse carries a single expression-optimized cytosine base editor transgene under the control of a tetracycline response element and enables robust, doxycycline-dependent expression across a broad range of tissues in vivo. Combined with plasmid-based or synthetic guide RNAs, iBE drives efficient engineering of individual or multiple SNVs in intestinal, lung and pancreatic organoids. Temporal regulation of base editor activity allows controlled sequential genome editing ex vivo and in vivo, and delivery of sgRNAs directly to target tissues facilitates generation of in situ preclinical cancer models.
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Affiliation(s)
- Alyna Katti
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Adrián Vega-Pérez
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Miguel Foronda
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jill Zimmerman
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Biosanitary Research Institute (IBS)-Granada, Granada, Spain
| | - Elizabeth Granowsky
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Eric E Gardner
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Janelle M Simon
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Wuest
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Luan
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Scott W Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco J Sánchez Rivera
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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2
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Yarnall MTN, Ioannidi EI, Schmitt-Ulms C, Krajeski RN, Lim J, Villiger L, Zhou W, Jiang K, Garushyants SK, Roberts N, Zhang L, Vakulskas CA, Walker JA, Kadina AP, Zepeda AE, Holden K, Ma H, Xie J, Gao G, Foquet L, Bial G, Donnelly SK, Miyata Y, Radiloff DR, Henderson JM, Ujita A, Abudayyeh OO, Gootenberg JS. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol 2023; 41:500-512. [PMID: 36424489 PMCID: PMC10257351 DOI: 10.1038/s41587-022-01527-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads. We demonstrate integration of sequences as large as ~36 kilobases at multiple genomic loci across three human cell lines, primary T cells and non-dividing primary human hepatocytes. To augment PASTE, we discovered 25,614 serine integrases and cognate attachment sites from metagenomes and engineered orthologs with higher activity and shorter recognition sequences for efficient programmable integration. PASTE has editing efficiencies similar to or exceeding those of homology-directed repair and non-homologous end joining-based methods, with activity in non-dividing cells and in vivo with fewer detectable off-target events. PASTE expands the capabilities of genome editing by allowing large, multiplexed gene insertion without reliance on DNA repair pathways.
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Affiliation(s)
- Matthew T N Yarnall
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eleonora I Ioannidi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- ETH Zürich, Zürich, Switzerland
| | - Cian Schmitt-Ulms
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Justin Lim
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Liyang Zhang
- Integrated DNA Technologies, Coralville, IA, USA
| | | | | | | | | | | | - Hong Ma
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jun Xie
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Guangping Gao
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Greg Bial
- Yecuris Corporation, Tualatin, OR, USA
| | | | | | | | | | | | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Rothgangl T, Dennis MK, Lin PJC, Oka R, Witzigmann D, Villiger L, Qi W, Hruzova M, Kissling L, Lenggenhager D, Borrelli C, Egli S, Frey N, Bakker N, Walker JA, Kadina AP, Victorov DV, Pacesa M, Kreutzer S, Kontarakis Z, Moor A, Jinek M, Weissman D, Stoffel M, van Boxtel R, Holden K, Pardi N, Thöny B, Häberle J, Tam YK, Semple SC, Schwank G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol 2021; 39:949-957. [PMID: 34012094 PMCID: PMC8352781 DOI: 10.1038/s41587-021-00933-4] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [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: 02/05/2021] [Accepted: 04/23/2021] [Indexed: 02/02/2023]
Abstract
Most known pathogenic point mutations in humans are C•G to T•A substitutions, which can be directly repaired by adenine base editors (ABEs). In this study, we investigated the efficacy and safety of ABEs in the livers of mice and cynomolgus macaques for the reduction of blood low-density lipoprotein (LDL) levels. Lipid nanoparticle-based delivery of mRNA encoding an ABE and a single-guide RNA targeting PCSK9, a negative regulator of LDL, induced up to 67% editing (on average, 61%) in mice and up to 34% editing (on average, 26%) in macaques. Plasma PCSK9 and LDL levels were stably reduced by 95% and 58% in mice and by 32% and 14% in macaques, respectively. ABE mRNA was cleared rapidly, and no off-target mutations in genomic DNA were found. Re-dosing in macaques did not increase editing, possibly owing to the detected humoral immune response to ABE upon treatment. These findings support further investigation of ABEs to treat patients with monogenic liver diseases.
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Affiliation(s)
- Tanja Rothgangl
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Dominik Witzigmann
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Lukas Villiger
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Sabina Egli
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Nina Frey
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Noëlle Bakker
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | | | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Zacharias Kontarakis
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | | | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beat Thöny
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ying K Tam
- Acuitas Therapeutics Inc., Vancouver, BC, Canada
| | | | - Gerald Schwank
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland.
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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4
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Gao P, Lyu Q, Ghanam AR, Lazzarotto CR, Newby GA, Zhang W, Choi M, Slivano OJ, Holden K, Walker JA, Kadina AP, Munroe RJ, Abratte CM, Schimenti JC, Liu DR, Tsai SQ, Long X, Miano JM. Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression. Genome Biol 2021; 22:83. [PMID: 33722289 PMCID: PMC7962346 DOI: 10.1186/s13059-021-02304-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 11/21/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Most single nucleotide variants (SNVs) occur in noncoding sequence where millions of transcription factor binding sites (TFBS) reside. Here, a comparative analysis of CRISPR-mediated homology-directed repair (HDR) versus the recently reported prime editing 2 (PE2) system was carried out in mice over a TFBS called a CArG box in the Tspan2 promoter. RESULTS Quantitative RT-PCR showed loss of Tspan2 mRNA in aorta and bladder, but not heart or brain, of mice homozygous for an HDR-mediated three base pair substitution in the Tspan2 CArG box. Using the same protospacer, mice homozygous for a PE2-mediated single-base substitution in the Tspan2 CArG box displayed similar cell-specific loss of Tspan2 mRNA; expression of an overlapping long noncoding RNA was also nearly abolished in aorta and bladder. Immuno-RNA fluorescence in situ hybridization validated loss of Tspan2 in vascular smooth muscle cells of HDR and PE2 CArG box mutant mice. Targeted sequencing demonstrated variable frequencies of on-target editing in all PE2 and HDR founders. However, whereas no on-target indels were detected in any of the PE2 founders, all HDR founders showed varying levels of on-target indels. Off-target analysis by targeted sequencing revealed mutations in many HDR founders, but none in PE2 founders. CONCLUSIONS PE2 directs high-fidelity editing of a single base in a TFBS leading to cell-specific loss in expression of an mRNA/long noncoding RNA gene pair. The PE2 platform expands the genome editing toolbox for modeling and correcting relevant noncoding SNVs in the mouse.
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Affiliation(s)
- Pan Gao
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Qing Lyu
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Amr R. Ghanam
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38195 USA
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138 USA
| | - Wei Zhang
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Mihyun Choi
- Department of Physiology, Albany Medical College, Albany, NY 12208 USA
| | - Orazio J. Slivano
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Kevin Holden
- Synthego Corporation, Redwood City, CA 94025 USA
| | | | | | - Rob J. Munroe
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853 USA
| | | | - John C. Schimenti
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853 USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138 USA
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38195 USA
| | - Xiaochun Long
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
| | - Joseph M. Miano
- Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA 30912 USA
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5
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Sun S, Błażewska KM, Kadina AP, Kashemirov BA, Duan X, Triffitt JT, Dunford JE, Russell RGG, Ebetino FH, Roelofs AJ, Coxon FP, Lundy MW, McKenna CE. Fluorescent Bisphosphonate and Carboxyphosphonate Probes: A Versatile Imaging Toolkit for Applications in Bone Biology and Biomedicine. Bioconjug Chem 2015; 27:329-40. [PMID: 26646666 DOI: 10.1021/acs.bioconjchem.5b00369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A bone imaging toolkit of 21 fluorescent probes with variable spectroscopic properties, bone mineral binding affinities, and antiprenylation activities has been created, including a novel linking strategy. The linking chemistry allows attachment of a diverse selection of dyes fluorescent in the visible to near-infrared range to any of the three clinically important heterocyclic bisphosphonate bone drugs (risedronate, zoledronate, and minodronate or their analogues). The resultant suite of conjugates offers multiple options to "mix and match" parent drug structure, fluorescence emission wavelength, relative bone affinity, and presence or absence of antiprenylation activity, for bone-related imaging applications.
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Affiliation(s)
- Shuting Sun
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,BioVinc LLC , 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Katarzyna M Błażewska
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Faculty of Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland
| | - Anastasia P Kadina
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Xuchen Duan
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford , Nuffield Orthopaedic Centre, Oxford, OX3 7LD, United Kingdom
| | - James T Triffitt
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford , Nuffield Orthopaedic Centre, Oxford, OX3 7LD, United Kingdom
| | - James E Dunford
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford , Nuffield Orthopaedic Centre, Oxford, OX3 7LD, United Kingdom
| | - R Graham G Russell
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford , Nuffield Orthopaedic Centre, Oxford, OX3 7LD, United Kingdom
| | - Frank H Ebetino
- BioVinc LLC , 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Anke J Roelofs
- Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen , Aberdeen, AB25 2ZD, United Kingdom
| | - Fraser P Coxon
- Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen , Aberdeen, AB25 2ZD, United Kingdom
| | - Mark W Lundy
- BioVinc LLC , 6162 Bristol Parkway, Culver City, California 90230, United States
| | - Charles E McKenna
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
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6
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Abstract
Novel α,β-CH2 and β,γ-NH (1a) or α,β-NH and β,γ-CH2 (1b) "Met-Im" dTTPs were synthesized via monodemethylation of triethyl-dimethyl phosphorimido-bisphosphonate synthons (4a, 4b), formed via a base-induced [1,3]-rearrangement of precursors (3a, 3b) in a reaction with dimethyl or diethyl phosphochloridate. Anomerization during final bromotrimethylsilane (BTMS) deprotection after Mitsunobu conjugation with dT was avoided by microwave conditions. 1a was 9-fold more potent in inhibiting DNA polymerase β, attributed to an NH-group interaction with R183 in the active site.
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Affiliation(s)
- Anastasia P. Kadina
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Keriann Oertell
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Vinod K. Batra
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Myron F. Goodman
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
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7
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Seamon KJ, Hansen EC, Kadina AP, Kashemirov BA, McKenna CE, Bumpus NN, Stivers JT. Small molecule inhibition of SAMHD1 dNTPase by tetramer destabilization. J Am Chem Soc 2014; 136:9822-5. [PMID: 24983818 PMCID: PMC4105058 DOI: 10.1021/ja5035717] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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SAMHD1
is a GTP-activated nonspecific dNTP triphosphohydrolase
that depletes dNTP pools in resting CD4+ T cells and macrophages and
effectively restricts infection by HIV-1. We have designed a nonsubstrate
dUTP analogue with a methylene bridge connecting the α phosphate
and 5′ carbon that potently inhibits SAMHD1. Although pppCH2dU shows apparent competitive inhibition, it acts by a surprising
allosteric mechanism that destabilizes active enzyme tetramer.
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Affiliation(s)
- Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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8
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Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH. Stereospecific formation of a ternary complex of (S)-α,β-fluoromethylene-dATP with DNA pol β. Chembiochem 2012; 13:528-30. [PMID: 22315190 DOI: 10.1002/cbic.201100738] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Indexed: 11/07/2022]
Abstract
The influence of water: crystallization of (R/S)-α,β-CHF-dATP with the preorganized pol β-DNA complex shows that (S)-α,β-CHF-dATP is preferentially bound to the active site with the C=F fluorine proximal to a structural water bound to Asp276.
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Affiliation(s)
- Brian T Chamberlain
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, CA 90089, USA
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9
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Kadina AP, Khlebnikov AF, Novikov MS, Pérez PJ, Yufit DS. Intramolecular cycloaddition of azomethine ylides, from imines of O-acylsalicylic aldehyde and ethyl diazoacetate, to ester carbonyl – experimental and DFT computational study. Org Biomol Chem 2012; 10:5582-91. [DOI: 10.1039/c2ob25676b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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