1
|
Nilov DK, Pushkarev SV, Gushchina IV, Manasaryan GA, Kirsanov KI, Švedas VK. Modeling of the Enzyme-Substrate Complexes of Human Poly(ADP-Ribose) Polymerase 1. BIOCHEMISTRY (MOSCOW) 2020; 85:99-107. [PMID: 32079521 DOI: 10.1134/s0006297920010095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is a key DNA repair enzyme and an important target in cancer treatment. Conventional methods of studying the reaction mechanism of PARP-1 have limitations because of the complex structure of PARP-1 substrates; however, the necessary data can be obtained by molecular modeling. In this work, a molecular dynamics model for the PARP-1 enzyme-substrate complex containing NAD+ molecule and the end of the poly(ADP-ribose) chain in the form of ADP molecule was obtained for the first time. Interactions with the active site residues have been characterized where Gly863, Lys903, Glu988 play a crucial role, and the SN1-like mechanism for the enzymatic ADP-ribosylation reaction has been proposed. Models of PARP-1 complexes with more sophisticated two-unit fragments of the growing polymer chain as well as competitive inhibitors 3-aminobenzamide and 7-methylguanine have been obtained by molecular docking.
Collapse
Affiliation(s)
- D K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S V Pushkarev
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - I V Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - G A Manasaryan
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, 119991, Russia
| | - K I Kirsanov
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478, Russia
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| |
Collapse
|
2
|
Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3. Int J Mol Sci 2019; 21:ijms21010214. [PMID: 31892271 PMCID: PMC6982223 DOI: 10.3390/ijms21010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.
Collapse
|
3
|
Bolderson E, Burgess JT, Li J, Gandhi NS, Boucher D, Croft LV, Beard S, Plowman JJ, Suraweera A, Adams MN, Naqi A, Zhang SD, Sinclair DA, O'Byrne KJ, Richard DJ. Barrier-to-autointegration factor 1 (Banf1) regulates poly [ADP-ribose] polymerase 1 (PARP1) activity following oxidative DNA damage. Nat Commun 2019; 10:5501. [PMID: 31796734 PMCID: PMC6890647 DOI: 10.1038/s41467-019-13167-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/22/2019] [Indexed: 01/19/2023] Open
Abstract
The DNA repair capacity of human cells declines with age, in a process that is not clearly understood. Mutation of the nuclear envelope protein barrier-to-autointegration factor 1 (Banf1) has previously been shown to cause a human progeroid disorder, Néstor–Guillermo progeria syndrome (NGPS). The underlying links between Banf1, DNA repair and the ageing process are unknown. Here, we report that Banf1 controls the DNA damage response to oxidative stress via regulation of poly [ADP-ribose] polymerase 1 (PARP1). Specifically, oxidative lesions promote direct binding of Banf1 to PARP1, a critical NAD+-dependent DNA repair protein, leading to inhibition of PARP1 auto-ADP-ribosylation and defective repair of oxidative lesions, in cells with increased Banf1. Consistent with this, cells from patients with NGPS have defective PARP1 activity and impaired repair of oxidative lesions. These data support a model whereby Banf1 is crucial to reset oxidative-stress-induced PARP1 activity. Together, these data offer insight into Banf1-regulated, PARP1-directed repair of oxidative lesions. Mutation of the nuclear envelope protein, barrier-to-autointegration factor 1 (Banf1), has previously been associated with the development of ageing associated diseases in a human progeria syndrome. Here, the authors reveal the functional link between Banf1-regulated, PARP1-directed repair of oxidative lesions.
Collapse
Affiliation(s)
- Emma Bolderson
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia. .,Princess Alexandra Hospital, Ipswich Road, Woolloongabba, Brisbane, Queensland, 4102, Australia.
| | - Joshua T Burgess
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Jun Li
- Department of Genetics, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, 02115, USA.,National Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Neha S Gandhi
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, 4000, Queensland, Australia
| | - Didier Boucher
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Laura V Croft
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Samuel Beard
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Jennifer J Plowman
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Amila Suraweera
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Mark N Adams
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Ali Naqi
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, University of Ulster, Londonderry, UK
| | - David A Sinclair
- Department of Genetics, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, 02115, USA.,The Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Kenneth J O'Byrne
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Princess Alexandra Hospital, Ipswich Road, Woolloongabba, Brisbane, Queensland, 4102, Australia
| | - Derek J Richard
- Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), Queensland University of Technology (QUT), Brisbane, Queensland, Australia. .,Princess Alexandra Hospital, Ipswich Road, Woolloongabba, Brisbane, Queensland, 4102, Australia.
| |
Collapse
|