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Xue H, Bhardwaj A, Yin Y, Fijen C, Ephstein A, Zhang L, Ding X, Pascal JM, VanArsdale TL, Rothenberg E. A two-step mechanism governing PARP1-DNA retention by PARP inhibitors. Sci Adv 2022; 8:eabq0414. [PMID: 36070389 PMCID: PMC9451145 DOI: 10.1126/sciadv.abq0414] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
PARP inhibitors (PARPi) have emerged as promising cancer therapeutics capable of targeting specific DNA repair pathways, but their mechanism of action with respect to PARP1-DNA retention remains unclear. Here, we developed single-molecule assays to directly monitor the retention of PARP1 on DNA lesions in real time. Our study reveals a two-step mechanism by which PARPi modulate the retention of PARP1 on DNA lesions, consisting of a primary step of catalytic inhibition via binding competition with NAD+ followed by an allosteric modulation of bound PARPi. While clinically relevant PARPi exhibit distinct allosteric modulation activities that can either increase retention of PARP1 on DNA or induce its release, their retention potencies are predominantly determined by their ability to outcompete NAD+ binding. These findings provide a mechanistic basis for improved PARPi selection according to their characteristic activities and enable further development of more potent inhibitors.
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Affiliation(s)
- Huijun Xue
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Amit Bhardwaj
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Carel Fijen
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anastasiya Ephstein
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lianglin Zhang
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Xia Ding
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - John M. Pascal
- Département de Biochimie and Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal QC H3C 3J7, Canada
| | - Todd L. VanArsdale
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
- Corresponding author. (T.V.); (E.R.)
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Corresponding author. (T.V.); (E.R.)
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8
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Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, Hugel T. Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat Methods 2018; 15:984. [PMID: 30327572 PMCID: PMC7608346 DOI: 10.1038/s41592-018-0193-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Björn Hellenkamp
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.,Engineering and Applied Sciences, Columbia University, New York, NY, USA
| | - Sonja Schmid
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Olga Doroshenko
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Oleg Opanasyuk
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ralf Kühnemuth
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | | | | | - Mikayel Aznauryan
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Mark E Bowen
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Hongtao Chen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Eilert
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Carel Fijen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Markus Götz
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Giorgos Gouridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Taekjip Ha
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Christian A Hanke
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Andreas Hartmann
- B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Leuven, Belgium.,Dynamic Bioimaging Lab, Advanced Optical Microscopy Center and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - Lasse L Hildebrandt
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.,Microspectroscopy Research Facility Wageningen, Wageningen University & Research, Wageningen, The Netherlands
| | - Boyang Hua
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA
| | | | - Eleni Kallis
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Jae-Yeol Kim
- School of Chemistry, Seoul National University, Seoul, South Korea
| | - Georg Krainer
- B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany.,Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nam Ki Lee
- School of Chemistry, Seoul National University, Seoul, South Korea
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Mainz, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brié Levesque
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Marcia Levitus
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - James J McCann
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Nikolaus Naredi-Rainer
- Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Thuy Ngo
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA
| | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Nicole C Robb
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | | | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA
| | - Michael Schlierf
- B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Tim Schröder
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Henning Seidel
- Institute of Physics, University of Lübeck, Lübeck, Germany
| | - Lisa Streit
- Institute for Biophysics, Ulm University, Ulm, Germany
| | - Johann Thurn
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Philip Tinnefeld
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany.,Institute of Physical & Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology, Braunschweig, Germany
| | - Swati Tyagi
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Niels Vandenberk
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Leuven, Belgium
| | - Andrés Manuel Vera
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Bettina Wünsch
- Institute of Physical & Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology, Braunschweig, Germany
| | | | | | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
| | - Timothy D Craggs
- Department of Chemistry, University of Sheffield, Sheffield, UK. .,Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany.
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