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Prieto Otoya TD, McQuaid KT, Paterson NG, Cardin DJ, Kellett A, Cardin CJ. Re-pairing DNA: binding of a ruthenium phi complex to a double mismatch. Chem Sci 2024; 15:9096-9103. [PMID: 38903237 PMCID: PMC11186304 DOI: 10.1039/d4sc01448k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024] Open
Abstract
We report a crystal structure at atomic resolution (0.9 Å) of a ruthenium complex bound to a consecutive DNA double mismatch, which results in a TA basepair with flipped out thymine, together with the formation of an adenine bulge. The structure shows a form of metalloinsertion interaction of the Λ-[Ru(phen)2phi]2+ (phi = 9,10-phenanthrenediimine) complex at the bulge site. The metal complex interacts with the DNA via the major groove, where specific interactions between the adenines of the DNA and the phen ligands of the complex are formed. One Δ-[Ru(phen)2phi]2+ complex interacts via the minor groove, which shows sandwiching of its phi ligand between the phi ligands of the other two ruthenium complexes, and no interaction of its phen ligands with DNA. To our knowledge, this binding model represents a new form of metalloinsertion in showing major rather than minor groove insertion.
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Affiliation(s)
| | - Kane T McQuaid
- Department of Chemistry, University of Reading Whiteknights Reading, RG6 6AD UK
| | - Neil G Paterson
- Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - David J Cardin
- Department of Chemistry, University of Reading Whiteknights Reading, RG6 6AD UK
| | - Andrew Kellett
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - Christine J Cardin
- Department of Chemistry, University of Reading Whiteknights Reading, RG6 6AD UK
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2
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Prieto Otoya TD, McQuaid KT, Hennessy J, Menounou G, Gibney A, Paterson NG, Cardin DJ, Kellett A, Cardin CJ. Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ-[Ru(phen) 2 phi] 2. Angew Chem Int Ed Engl 2024; 63:e202318863. [PMID: 38271265 DOI: 10.1002/anie.202318863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ-[Ru(phen)2 phi]2+ , where phi=9,10-phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2 . The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ-enantiomer and show a high affinity for TA/TA steps and, more generally, TA-rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence.
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Affiliation(s)
| | - Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Joseph Hennessy
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Georgia Menounou
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Alex Gibney
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Neil G Paterson
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - David J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Andrew Kellett
- SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland Email
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
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3
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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4
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Satange R, Rode AB, Hou MH. Revisiting recent unusual drug-DNA complex structures: Implications for cancer and neurological disease diagnostics and therapeutics. Bioorg Med Chem 2022; 76:117094. [PMID: 36410206 DOI: 10.1016/j.bmc.2022.117094] [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: 09/14/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
DNA plays a crucial role in various biological processes such as protein production, replication, recombination etc. by adopting different conformations. Targeting these conformations by small molecules is not only important for disease therapy, but also improves our understanding of the mechanisms of disease development. In this review, we provide an overview of some of the most recent ligand-DNA complexes that have diagnostic and therapeutic applications in neurological diseases caused by abnormal repeat expansions and in cancer associated with mismatches. In addition, we have discussed important implications of ligands targeting higher-order structures, such as four-way junctions, G-quadruplexes and triplexes for drug discovery and DNA nanotechnology. We provide an overview of the results and perspectives of such structural studies on ligand-DNA interactions.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Ambadas B Rode
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
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5
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Guin PS, Roy S. Recently Reported Ru-Metal Organic Coordination Complexes and Their Application (A Review). RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222080242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Joaqui-Joaqui MA, Maxwell Z, Raju MVR, Jiang M, Srivastava K, Shao F, Arriaga EA, Pierre VC. Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability. ACS NANO 2022; 16:2928-2941. [PMID: 35133785 PMCID: PMC8926058 DOI: 10.1021/acsnano.1c10084] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Self-assembly of metallointercalators into DNA nanocages is a rapid and facile approach to synthesize discrete bioinorganic host/guest structures with a high load of metal complexes. Turberfield's DNA tetrahedron can accommodate one intercalator for every two base pairs, which corresponds to 48 metallointercalators per DNA tetrahedron. The affinity of the metallointercalator for the DNA tetrahedron is a function of both the structure of the intercalating ligand and the overall charge of the complex, with a trend in affinity [Ru(bpy)2(dppz)]2+ > [Tb-DOTAm-Phen]3+ ≫ Tb-DOTA-Phen. Intercalation of the metal complex stabilizes the DNA tetrahedron, resulting in an increase of its melting temperature and, importantly, a significant increase in its stability in the presence of serum. [Ru(bpy)2(dppz)]2+, which has a greater affinity for DNA than [Tb-DOTAm-Phen]3+, increases the melting point and decreases degradation in serum to a greater extent than the TbIII complex. In the presence of Lipofectamine, the metallointercalator@DNA nanocage assemblies substantially increase the cell uptake of their respective metal complex. Altogether, the facile incorporation of a large number of metal complexes per assembly, the higher stability in serum, and the increased cell penetration of metallointercalator@DNA make these self-assemblies well-suited as metallodrugs.
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Affiliation(s)
- M. Andrey Joaqui-Joaqui
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Zoe Maxwell
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | | | - Min Jiang
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining, 314400, China
| | - Kriti Srivastava
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Fangwei Shao
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining, 314400, China
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Valérie C. Pierre
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States of America
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7
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Affiliation(s)
- Xin‐Xin Peng
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
- Spin-X Institute, School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510641 P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials Guangzhou 510641 P. R. China
| | - Jun‐Long Zhang
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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8
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Das A, Banik BK. Advances in heterocycles as DNA intercalating cancer drugs. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The insertion of a molecule between the bases of DNA is known as intercalation. A molecule is able to interact with DNA in different ways. DNA intercalators are generally aromatic, planar, and polycyclic. In chemotherapeutic treatment, to suppress DNA replication in cancer cells, intercalators are used. In this article, we discuss the anticancer activity of 10 intensively studied DNA intercalators as drugs. The list includes proflavine, ethidium bromide, doxorubicin, dactinomycin, bleomycin, epirubicin, mitoxantrone, ellipticine, elinafide, and echinomycin. Considerable structural diversities are seen in these molecules. Besides, some examples of the metallo-intercalators are presented at the end of the chapter. These molecules have other crucial properties that are also useful in the treatment of cancers. The successes and limitations of these molecules are also presented.
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Affiliation(s)
- Aparna Das
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
| | - Bimal Krishna Banik
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
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9
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Dayanidhi PD, Vaidyanathan VG. Understanding the ancillary ligand effect on luminescent cyclometalated Ir(III) complex as a reporter for 2-acetylaminofluorene DNA(AAF-dG) adduct. J Biol Inorg Chem 2021; 27:189-199. [PMID: 34843001 DOI: 10.1007/s00775-021-01920-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022]
Abstract
Mutagenic agents such as aromatic amines undergo metabolic activation and produce DNA adducts at C8 position of guanine bases. N-2-acetylaminofluorene (AAF) generates different mutational outcomes when placed at G1, G2, and G3 of a NarI sequence (-G1G2CG3CC/T-). These outcomes are dictated by the conformations adopted by these adducts. Detection of such lesions is of considerable interest owing to their hazardous effects. Here, we report the synthesis of three cyclometalated [Ir(L)2dppz]+ complexes (L = 2-phenylpyridine (ppy) 1; benzo[h]quinoline (bhq) 2; 2-phenylquinoline (pq) 3; dppz = dipyrido[3,2-a:2',3'-c]phenazine) and their interaction with AAF adducted NarI DNA. Remarkably, complexes 1 and 2 displayed dominant 3LC transition characteristic of polar environment despite binding to the adducted sites. On the other hand, complex 3 binds to NarI sequences and behaves as a luminescent reporter for AAF-modified DNA. The results reported here emphasize that molecular light switching phenomenon can be stimulated by switching ancillary ligands and might act as potential probes for covalent-DNA defects.
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Affiliation(s)
- P David Dayanidhi
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - V G Vaidyanathan
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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10
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Andrezálová L, Országhová Z. Covalent and noncovalent interactions of coordination compounds with DNA: An overview. J Inorg Biochem 2021; 225:111624. [PMID: 34653826 DOI: 10.1016/j.jinorgbio.2021.111624] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/30/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022]
Abstract
Deoxyribonucleic acid plays a central role in crucial cellular processes, and many drugs exert their effects through binding to DNA. Since the discovery of cisplatin and its derivatives considerable attention of researchers has been focused on the development of novel anticancer metal-based drugs. Transition metal complexes, due to their great diversity in size and structure, have a big potential to modify DNA through diverse types of interactions, making them the prominent class of compounds for DNA targeted therapy. In this review we describe various binding modes of metal complexes to duplex DNA based on covalent and noncovalent interactions or combination of both. Specific examples of each binding mode as well as possible cytotoxic effects of metal complexes in tumor cells are presented.
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Affiliation(s)
- Lucia Andrezálová
- Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, 813 72 Bratislava, Slovakia; Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Zuzana Országhová
- Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, 813 72 Bratislava, Slovakia
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11
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Nano A, Dai J, Bailis JM, Barton JK. Rhodium Complexes Targeting DNA Mismatches as a Basis for New Therapeutics in Cancers Deficient in Mismatch Repair. Biochemistry 2021; 60:2055-2063. [PMID: 34115466 DOI: 10.1021/acs.biochem.1c00302] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cancers with microsatellite instability (MSI), which include ≤20% of solid tumors, are characterized by resistance to chemotherapy due to deficiency in the DNA mismatch repair (MMR) pathway. Rhodium metalloinsertors make up a class of compounds that bind DNA mismatches with high specificity and show selective cytotoxicity in MSI cancer cells. We determined that rhodium complexes with an N∧O coordination showed significantly increased cell potency compared with that of N∧N-coordinated compounds, and we identified [Rh(chrysi)(phen)(PPO)]2+ (RhPPO) as the most potent, selective compound in this class. Using matched cell lines that are MMR-deficient (HCT116O) and MMR-proficient (HCT116N), we demonstrated that RhPPO preferentially activates the DNA damage response and inhibits DNA replication and cell proliferation in HCT116O cells, leading to cell death by necrosis. Using a fluorescent conjugate of RhPPO, we established that the metalloinsertor localizes to DNA mismatches in the cell nucleus and causes DNA double-strand breaks at or near the mismatch sites. Evaluation of RhPPO across MMR-deficient and MMR-proficient cell lines confirmed the broad potential for RhPPO to target MSI cancers, with cell potency significantly higher than that of platinum complexes used broadly as chemotherapeutics. Moreover, in a mouse xenograft model of MSI cancer, RhPPO shows promising antitumor activity and increased survival. Thus, our studies indicate that RhPPO is a novel DNA-targeted therapy with improved potency and selectivity over standard-of-care platinum-based chemotherapy and, importantly, that DNA mismatches offer a critical new target in the design of chemotherapeutics for MSI cancers.
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Affiliation(s)
- Adela Nano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Joanne Dai
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Julie M Bailis
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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12
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van der Westhuizen D, Slabber CA, Fernandes MA, Joubert DF, Kleinhans G, van der Westhuizen CJ, Stander A, Munro OQ, Bezuidenhout DI. A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation. Chemistry 2021; 27:8295-8307. [PMID: 33822431 PMCID: PMC8251726 DOI: 10.1002/chem.202100598] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 12/13/2022]
Abstract
The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.
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Affiliation(s)
| | - Cathryn A. Slabber
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Manuel A. Fernandes
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniël F. Joubert
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - George Kleinhans
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
| | - C. Johan van der Westhuizen
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
- Future Production: ChemicalsPharmaceutical Technologies Research GroupCouncil for Scientific and Industrial Research (CSIR)0184PretoriaSouth Africa
| | - André Stander
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - Orde Q. Munro
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniela I. Bezuidenhout
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Laboratory of Inorganic ChemistryEnvironmental and Chemical EngineeringUniversity of Oulu3000OuluFinland
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13
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Dayanidhi PD, Vaidyanathan VG. Structural insights into the recognition of DNA defects by small molecules. Dalton Trans 2021; 50:5691-5712. [PMID: 33949406 DOI: 10.1039/d0dt04289g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Studies on the binding interaction of small molecules and nucleic acids have been explored for their biological applications. With excellent photophysical/chemical properties, numerous metal complexes have been studied as structural probes for nucleic acids. The recognition of DNA defects is of high importance due to their association with various types of cancers. Small molecules that target DNA defects in a specific and selective manner offer a new avenue for developing novel drugs and diagnostic tools. Transition metal complexes have been studied as probes for abasic sites and DNA/RNA mismatches. By changing the ligand structure or metal center, the probing efficiency of the metal complexes varies towards the defects. In this perspective, we have discussed mainly the structural requirement of metal complexes as probes for abasic sites, mismatches, and covalent DNA adducts, followed by the challenges and future directions.
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Affiliation(s)
- P David Dayanidhi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. and Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - V G Vaidyanathan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. and Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
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14
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To WP, Wan Q, Tong GSM, Che CM. Recent Advances in Metal Triplet Emitters with d6, d8, and d10 Electronic Configurations. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2020.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Nano A, Bailis JM, Mariano NF, Pham ED, Threatt SD, Barton JK. Cell-Selective Cytotoxicity of a Fluorescent Rhodium Metalloinsertor Conjugate Results from Irreversible DNA Damage at Base Pair Mismatches. Biochemistry 2020; 59:717-726. [DOI: 10.1021/acs.biochem.9b01037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Adela Nano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Julie M. Bailis
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Natalie F. Mariano
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Elizabeth D. Pham
- Department of Oncology Research, Amgen Research, Amgen, Inc., South San Francisco, California 94080, United States
| | - Stephanie D. Threatt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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16
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An anticancer gold(III)-activated porphyrin scaffold that covalently modifies protein cysteine thiols. Proc Natl Acad Sci U S A 2020; 117:1321-1329. [PMID: 31896586 DOI: 10.1073/pnas.1915202117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cysteine thiols of many cancer-associated proteins are attractive targets of anticancer agents. Herein, we unequivocally demonstrate a distinct thiol-targeting property of gold(III) mesoporphyrin IX dimethyl ester (AuMesoIX) and its anticancer activities. While the binding of cysteine thiols with metal complexes usually occurs via M-S bond formation, AuMesoIX is unique in that the meso-carbon atom of the porphyrin ring is activated by the gold(III) ion to undergo nucleophilic aromatic substitution with thiols. AuMesoIX was shown to modify reactive cysteine residues and inhibit the activities of anticancer protein targets including thioredoxin, peroxiredoxin, and deubiquitinases. Treatment of cancer cells with AuMesoIX resulted in the formation of gold-bound sulfur-rich protein aggregates, oxidative stress-mediated cytotoxicity, and accumulation of ubiquitinated proteins. Importantly, AuMesoIX exhibited effective antitumor activity in mice. Our study has uncovered a gold(III)-induced ligand scaffold reactivity for thiol targeting that can be exploited for anticancer applications.
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17
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Anti-cancer gold, platinum and iridium compounds with porphyrin and/or N-heterocyclic carbene ligand(s). Med Chem 2020. [DOI: 10.1016/bs.adioch.2019.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res 2019; 47:8899-8912. [PMID: 31361900 PMCID: PMC6895262 DOI: 10.1093/nar/gkz653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
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19
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Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH. Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex. Nucleic Acids Res 2019; 46:7396-7404. [PMID: 29741655 PMCID: PMC6101601 DOI: 10.1093/nar/gky345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/25/2018] [Indexed: 12/16/2022] Open
Abstract
Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex. These and other associated changes in DNA conformation allow the formation of a minor groove pocket for tight binding of the second echinomycin molecule. We also show that echinomycin displays enhanced cytotoxicity against mismatch repair-deficient cell lines, raising the possibility of repurposing the drug for detection and treatment of mismatch repair-deficient cancers.
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Affiliation(s)
- Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Shu-Ling Tzeng
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ya-Fen Kao
- Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Michael J Waring
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan.,Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
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20
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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21
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Dayanidhi DPE, Malapati RP, Vaidyanathan Ganesan V. Selective recognition of DNA defects by cyclometalated Ir(iii) complexes. Dalton Trans 2019; 48:13536-13540. [DOI: 10.1039/c9dt01225g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Three different cyclometalated Ir(iii) complexes selectively bind to DNA defects.
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Affiliation(s)
- David Paul Elisa Dayanidhi
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
| | - Rozaria Pinky Malapati
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
| | - Vaidyanathan Vaidyanathan Ganesan
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
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22
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Abstract
Combining metallo-drugs with ionising radiation for synergistic cancer cell killing: chemical design principles, mechanisms of action and emerging applications.
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Affiliation(s)
- Martin R. Gill
- CRUK/MRC Oxford Institute for Radiation Oncology
- Department of Oncology
- University of Oxford
- Oxford
- UK
| | - Katherine A. Vallis
- CRUK/MRC Oxford Institute for Radiation Oncology
- Department of Oncology
- University of Oxford
- Oxford
- UK
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23
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Gabr MT, Pigge FC. Platinum(II) Complexes with Sterically Expansive Tetraarylethylene Ligands as Probes for Mismatched DNA. Inorg Chem 2018; 57:12641-12649. [DOI: 10.1021/acs.inorgchem.8b01782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Moustafa T. Gabr
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - F. Christopher Pigge
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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24
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Boyle KM, Barton JK. A Family of Rhodium Complexes with Selective Toxicity toward Mismatch Repair-Deficient Cancers. J Am Chem Soc 2018; 140:5612-5624. [PMID: 29620877 DOI: 10.1021/jacs.8b02271] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rhodium metalloinsertors are a unique set of metal complexes that bind specifically to DNA base pair mismatches in vitro and kill mismatch repair (MMR)-deficient cells at lower concentrations than their MMR-proficient counterparts. A family of metalloinsertors containing rhodium-oxygen ligand coordination, termed "Rh-O" metalloinsertors, has been prepared and shown to have a significant increase in both overall potency and selectivity toward MMR-deficient cells regardless of structural changes in the ancillary ligands. Here we describe DNA-binding and cellular studies with the second generation of Rh-O metalloinsertors in which an ancillary ligand is varied in both steric bulk and lipophilicity. These complexes, of the form [Rh(L)(chrysi)(PPO)]2+, all include the O-containing PPO ligand (PPO = 2-(pyridine-2-yl)propan-2-ol) and the aromatic inserting ligand chrysi (5,6-chrysene quinone diimine) but differ in the identity of their ancillary ligand L, where L is a phenanthroline or bipyridyl derivative. The Rh-O metalloinsertors in this family all show micromolar binding affinities for a 29-mer DNA hairpin containing a single CC mismatch. The complexes display comparable lipophilic tendencies and p Ka values of 8.1-9.1 for dissociation of an imine proton on the chrysi ligand. In cellular proliferation and cytotoxicity assays with MMR-deficient cells (HCT116O) and MMR-proficient cells (HCT116N), the complexes containing the phenanthroline-derived ligands show highly selective cytotoxic preference for the MMR-deficient cells at nanomolar concentrations. Using mass spectral analyses, it is shown that the complexes are taken into cells through a passive mechanism and exhibit low accumulation in mitochondria, an off-target organelle that, when targeted by parent metalloinsertors, can lead to nonselective cytotoxicity. Overall, these Rh-O metalloinsertors have distinct and improved behavior compared to previous generations of parent metalloinsertors, making them ideal candidates for further therapeutic assessment.
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Affiliation(s)
- Kelsey M Boyle
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
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25
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Bailis JM, Weidmann AG, Mariano NF, Barton JK. Rhodium metalloinsertor binding generates a lesion with selective cytotoxicity for mismatch repair-deficient cells. Proc Natl Acad Sci U S A 2017; 114:6948-6953. [PMID: 28634291 PMCID: PMC5502648 DOI: 10.1073/pnas.1706665114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The DNA mismatch repair (MMR) pathway recognizes and repairs errors in base pairing and acts to maintain genome stability. Cancers that have lost MMR function are common and comprise an important clinical subtype that is resistant to many standard of care chemotherapeutics such as cisplatin. We have identified a family of rhodium metalloinsertors that bind DNA mismatches with high specificity and are preferentially cytotoxic to MMR-deficient cells. Here, we characterize the cellular mechanism of action of the most potent and selective complex in this family, [Rh(chrysi)(phen)(PPO)]2+ (Rh-PPO). We find that Rh-PPO binding induces a lesion that triggers the DNA damage response (DDR). DDR activation results in cell-cycle blockade and inhibition of DNA replication and transcription. Significantly, the lesion induced by Rh-PPO is not repaired in MMR-deficient cells, resulting in selective cytotoxicity. The Rh-PPO mechanism is reminiscent of DNA repair enzymes that displace mismatched bases, and is differentiated from other DNA-targeted chemotherapeutics such as cisplatin by its potency, cellular mechanism, and selectivity for MMR-deficient cells.
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Affiliation(s)
- Julie M Bailis
- Department of Oncology Research, Amgen, Inc., South San Francisco, CA 94080;
| | - Alyson G Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Natalie F Mariano
- Department of Oncology Research, Amgen, Inc., South San Francisco, CA 94080
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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26
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Boynton AN, Marcélis L, McConnell AJ, Barton JK. A Ruthenium(II) Complex as a Luminescent Probe for DNA Mismatches and Abasic Sites. Inorg Chem 2017; 56:8381-8389. [PMID: 28657712 PMCID: PMC5516787 DOI: 10.1021/acs.inorgchem.7b01037] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
[Ru(bpy)2(BNIQ)]2+ (BNIQ = Benzo[c][1,7]naphthyridine-1-isoquinoline), which incorporates the sterically expansive BNIQ ligand, is a
highly selective luminescent probe for DNA mismatches and abasic sites,
possessing a 500-fold higher binding affinity toward these destabilized
regions relative to well-matched base pairs. As a result of this higher
binding affinity, the complex exhibits an enhanced steady-state emission
in the presence of DNA duplexes containing a single base mismatch
or abasic site compared to fully well-matched DNA. Luminescence quenching
experiments with Cu(phen)22+ and [Fe(CN)6]3– implicate binding of the complex to
a mismatch from the minor groove via metalloinsertion. The emission
response of the complex to different single base mismatches, binding
preferentially to the more destabilized mismatches, is also consistent
with binding by metalloinsertion. This work shows that high selectivity
toward destabilized regions in duplex DNA can be achieved through
the rational design of a complex with a sterically expansive aromatic
ligand. The luminescent complex [Ru(bpy)2(BNIQ)]2+ selectivity targets mismatched and abasic sites in duplex
DNA and exhibits an enhanced emission intensity in the presence of
these defect sites relative to well-matched base pairs.
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Affiliation(s)
- Adam N Boynton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Lionel Marcélis
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Anna J McConnell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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27
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Spinello A, Magistrato A. An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era. Expert Opin Drug Discov 2017; 12:813-825. [DOI: 10.1080/17460441.2017.1340272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Angelo Spinello
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
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28
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Galliot A, Gil A, Calhorda MJ. Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study. Phys Chem Chem Phys 2017. [PMID: 28621352 DOI: 10.1039/c7cp00532f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.
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Affiliation(s)
- Aurellia Galliot
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Adrià Gil
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Maria José Calhorda
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
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29
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Hall JP, Keane PM, Beer H, Buchner K, Winter G, Sorensen TL, Cardin DJ, Brazier JA, Cardin CJ. Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes. Nucleic Acids Res 2016; 44:9472-9482. [PMID: 27599841 PMCID: PMC5100598 DOI: 10.1093/nar/gkw753] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/20/2016] [Indexed: 01/01/2023] Open
Abstract
[Ru(phen)2(dppz)]2+ has been studied since the 1990s due to its 'light-switch' properties. It can be used as a luminescent DNA probe, with emission switched on through DNA binding. The luminescence observed is dependent on the solvent accessibility of the pyrazine nitrogen atoms, and therefore is sensitive to changes in both binding site of the cation and chromophore orientation. The compound is also chiral, and there are distinct differences between the enantiomers in terms of the emission behaviour when bound to a variety of DNA sequences. Whilst a number of binary DNA-complex X-ray crystal structures are available, most include the Λ enantiomer and there is very little structural information about binding of the Δ enantiomer. Here, we present the first X-ray crystal structure of a Δ enantiomer bound to well-matched DNA, in the absence of the other, Λ enantiomer. We show how the binding site observed here can be related to a more general pattern of motifs in the crystallographic literature and propose that the Δ enantiomer can bind with five different binding modes, offering a new hypothesis for the interpretation of solution data.
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Affiliation(s)
- James P Hall
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK .,Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, OX11 0DE, UK
| | - Páraic M Keane
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Hanna Beer
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Katrin Buchner
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, OX11 0DE, UK
| | - Thomas L Sorensen
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, OX11 0DE, UK
| | - David J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - John A Brazier
- Department of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
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30
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Boynton AN, Marcélis L, Barton JK. [Ru(Me4phen)2dppz](2+), a Light Switch for DNA Mismatches. J Am Chem Soc 2016; 138:5020-3. [PMID: 27068529 DOI: 10.1021/jacs.6b02022] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Ru(Me4phen)2dppz](2+) serves as a luminescent "light switch" for single base mismatches in DNA. The preferential luminescence enhancement observed with mismatches results from two factors: (i) the complex possesses a 26-fold higher binding affinity toward the mismatch compared to well-matched base pairs, and (ii) the excited state emission lifetime of the ruthenium bound to the DNA mismatch is 160 ns versus 35 ns when bound to a matched site. Results indicate that the complex binds to the mismatch through a metalloinsertion binding mode. Cu(phen)2(2+) quenching experiments show that the complex binds to the mismatch from the minor groove, characteristic of metalloinsertion. Additionally, the luminescence intensity of the complex with DNA containing single base mismatches correlates with the thermodynamic destabilization of the mismatch, also consistent with binding through metalloinsertion. This complex represents a potentially new early cancer diagnostic for detecting deficiencies in mismatch repair.
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Affiliation(s)
- Adam N Boynton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Lionel Marcélis
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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31
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Fung SK, Zou T, Cao B, Chen T, To WP, Yang C, Lok CN, Che CM. Luminescent platinum(II) complexes with functionalized N-heterocyclic carbene or diphosphine selectively probe mismatched and abasic DNA. Nat Commun 2016; 7:10655. [PMID: 26883164 PMCID: PMC4757794 DOI: 10.1038/ncomms10655] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/06/2016] [Indexed: 01/09/2023] Open
Abstract
The selective targeting of mismatched DNA overexpressed in cancer cells is an appealing strategy in designing cancer diagnosis and therapy protocols. Few luminescent probes that specifically detect intracellular mismatched DNA have been reported. Here we used Pt(II) complexes with luminescence sensitive to subtle changes in the local environment and report several Pt(II) complexes that selectively bind to and identify DNA mismatches. We evaluated the complexes' DNA-binding characteristics by ultraviolet/visible absorption titration, isothermal titration calorimetry, nuclear magnetic resonance and quantum mechanics/molecular mechanics calculations. These Pt(II) complexes show up to 15-fold higher emission intensities upon binding to mismatched DNA over matched DNA and can be utilized for both detecting DNA abasic sites and identifying cancer cells and human tissue samples with different levels of mismatch repair. Our work highlights the potential of luminescent Pt(II) complexes to differentiate between normal cells and cancer cells which generally possess more aberrant DNA structures. DNA pairing defects such as mismatched and abasic DNA are prevalent in cancer cells. Here, the authors present luminescent platinum based probes capable of preferentially binding to mismatched and abasic DNA, and reporting this by a significant luminescence enhancement
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Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation Shenzhen, Shenzhen 518053, China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Wai-Pong To
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chen Yang
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation Shenzhen, Shenzhen 518053, China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation Shenzhen, Shenzhen 518053, China
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32
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Abstract
DNA has been exploited as a biological target of chemotherapeutics since the 1940s. Traditional chemotherapeutics, such as cisplatin and DNA-alkylating agents, rely primarily on increased uptake by rapidly proliferating cancer cells for therapeutic effects, but this strategy can result in off-target toxicity in healthy tissue. Recently, research interests have shifted towards targeted chemotherapeutics, in which a drug targets a specific biological signature of cancer, resulting in selective toxicity towards cancerous cells. Here, we review a family of complexes, termed rhodium metalloinsertors, that selectively target DNA base pair mismatches, a hallmark of mismatch-repair (MMR) deficient cancers. These rhodium metalloinsertors, bind DNA mismatches with high specificity and display high selectively in killing MMR-deficient versus MMR-proficient cells. This cell selectivity is unique for small molecules that bind DNA. Current generations of rhodium metalloinsertors have shown nanomolar potency along with high selectivity towards MMR-deficient cells, and show promise as a foundation for a new family of chemotherapeutics for MMR-deficient cancers.
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Affiliation(s)
- Kelsey M Boyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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33
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Draksharapu A, Boersma AJ, Leising M, Meetsma A, Browne WR, Roelfes G. Binding of copper(II) polypyridyl complexes to DNA and consequences for DNA-based asymmetric catalysis. Dalton Trans 2015; 44:3647-55. [PMID: 25476597 DOI: 10.1039/c4dt02733g] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interaction between salmon testes DNA (st-DNA) and a series of Cu(II) polypyridyl complexes, i.e. [Cu(dmbpy)(NO3)2] (1) (dmbpy = 4,4'-dimethyl-2,2'-bipyridine), [Cu(bpy)(NO3)2] (2) (bpy = 2,2'-bipyridine), [Cu(phen)(NO3)2] (3) (phen = phenanthroline), [Cu(terpy)(NO3)2]·H2O (4) (terpy = 2,2':6',2″-terpyridine), [Cu(dpq)(NO3)2] (5) (dpq = dipyrido-[3,2-d:2',3'-f]-quinoxaline) and [Cu(dppz)(NO3)2] (6) (dppz = dipyrido[3,2-a:2',3'-c]phenazine) was studied by UV/Vis absorption, Circular Dichroism, Linear Dichroism, EPR, Raman and (UV and vis) resonance Raman spectroscopies and viscometry. These complexes catalyse enantioselective C-C bond forming reactions in water with DNA as the source of chirality. Complex 1 crystallizes as an inorganic polymer with nitrate ligands bridging the copper ions, which adopt essentially a distorted square pyramidal structure with a fifth bridging nitrate ligand at the axial position. Raman spectroscopy indicates that in solution the nitrate ligands in 1, 2, 3 and 4 are displaced by solvent (H2O). For complex 1, multiple supramolecular species are observed in the presence of st-DNA in contrast to the other complexes, which appear to interact relatively uniformly as a single species predominantly, when st-DNA is present. Overall the data suggest that complexes 1 and 2 engage primarily through groove binding with st-DNA while 5 and 6 undergo intercalation. For complexes 3 and 4 the data indicates that both groove binding and intercalation takes place, albeit primarily intercalation. Although it is tempting to conclude that the groove binders give highest ee and rate acceleration, it is proposed that the flexibility and dynamics in binding of Cu(II) complexes to DNA are key parameters that determine the outcome of the reaction. These findings provide insight into the complex supramolecular structure of these DNA-based catalysts.
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Affiliation(s)
- Apparao Draksharapu
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Weidmann AG, Barton JK. A monofunctional platinum complex coordinated to a rhodium metalloinsertor selectively binds mismatched DNA in the minor groove. Inorg Chem 2015; 54:9626-36. [PMID: 26397309 DOI: 10.1021/acs.inorgchem.5b01722] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh-O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA nonclassically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and it triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors.
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Affiliation(s)
- Alyson G Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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35
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Wragg A, Gill MR, McKenzie L, Glover C, Mowll R, Weinstein JA, Su X, Smythe C, Thomas JA. Serum Albumin Binding Inhibits Nuclear Uptake of Luminescent Metal-Complex-Based DNA Imaging Probes. Chemistry 2015; 21:11865-71. [PMID: 26133680 DOI: 10.1002/chem.201501675] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 11/07/2022]
Abstract
The DNA binding and cellular localization properties of a new luminescent heterobimetallic Ir(III) Ru(II) tetrapyridophenazine complex are reported. Surprisingly, in standard cell media, in which its tetracationic, isostructural Ru(II) Ru(II) analogue is localized in the nucleus, the new tricationic complex is poorly taken up by live cells and demonstrates no nuclear staining. Consequent cell-free studies reveal that the Ir(III) Ru(II) complex binds bovine serum albumin, BSA, in Sudlow's Site I with a similar increase in emission and binding affinity to that observed with DNA. Contrastingly, in serum-free conditions the complex is rapidly internalized by live cells, where it localizes in cell nuclei and functions as a DNA imaging agent. The absence of serum proteins also greatly alters the cytotoxicity of the complex, where high levels of oncosis/necrosis are observed due to this enhanced uptake. This suggests that simply increasing the lipophilicity of a DNA imaging probe to enhance cellular uptake can be counterproductive as, due to increased binding to serum albumin protein, this strategy can actually disrupt nuclear targeting.
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Affiliation(s)
- Ashley Wragg
- Department of Chemistry, University of Chemistry, Sheffield S3 7HF (UK), Fax: (+44) 114-222-9346
| | - Martin R Gill
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN (UK)
| | - Luke McKenzie
- Department of Chemistry, University of Chemistry, Sheffield S3 7HF (UK), Fax: (+44) 114-222-9346
| | - Caroline Glover
- Department of Chemistry, University of Chemistry, Sheffield S3 7HF (UK), Fax: (+44) 114-222-9346
| | - Rachel Mowll
- Department of Chemistry, University of Chemistry, Sheffield S3 7HF (UK), Fax: (+44) 114-222-9346
| | - Julia A Weinstein
- Department of Chemistry, University of Chemistry, Sheffield S3 7HF (UK), Fax: (+44) 114-222-9346
| | - Xiaodi Su
- Institute of Material Research and Engineering, A*STAR (Agency for Science, Technology and Research), Singapore 117602
| | - Carl Smythe
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN (UK)
| | - Jim A Thomas
- Department of Chemistry, University of Chemistry, Sheffield S3 7HF (UK), Fax: (+44) 114-222-9346.
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36
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Gil A, Melle-Franco M, Branchadell V, Calhorda MJ. How the Intercalation of Phenanthroline Affects the Structure, Energetics, and Bond Properties of DNA Base Pairs: Theoretical Study Applied to Adenine–Thymine and Guanine–Cytosine Tetramers. J Chem Theory Comput 2015; 11:2714-28. [DOI: 10.1021/ct5006104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adrià Gil
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Vicenç Branchadell
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Calhorda
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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37
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Galindo-Murillo R, García-Ramos JC, Ruiz-Azuara L, Cheatham TE, Cortés-Guzmán F. Intercalation processes of copper complexes in DNA. Nucleic Acids Res 2015; 43:5364-76. [PMID: 25958394 PMCID: PMC4477671 DOI: 10.1093/nar/gkv467] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022] Open
Abstract
The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | - Juan Carlos García-Ramos
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México. Avenida Universidad 3000, 04510 México City, Mexico
| | - Lena Ruiz-Azuara
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México. Avenida Universidad 3000, 04510 México City, Mexico
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México, DF 04510, Mexico Centro Conjunto de Investigación en Química Sustentable UAEMex-UNAM, carretera Toluca-Atlacomulco km 14.5, Toluca, México 50200, Mexico
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38
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Komor AC, Barton JK. An unusual ligand coordination gives rise to a new family of rhodium metalloinsertors with improved selectivity and potency. J Am Chem Soc 2014; 136:14160-72. [PMID: 25254630 PMCID: PMC4195389 DOI: 10.1021/ja5072064] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Rhodium
metalloinsertors are octahedral complexes that bind DNA
mismatches with high affinity and specificity and exhibit unique cell-selective
cytotoxicity, targeting mismatch repair (MMR)-deficient cells over
MMR-proficient cells. Here we describe a new generation of metalloinsertors
with enhanced biological potency and selectivity, in which the complexes
show Rh–O coordination. In particular, it has been found that
both Δ- and Λ-[Rh(chrysi)(phen)(DPE)]2+ (where
chrysi =5,6 chrysenequinone diimmine, phen =1,10-phenanthroline, and
DPE = 1,1-di(pyridine-2-yl)ethan-1-ol) bind to DNA containing a single
CC mismatch with similar affinities and without racemization. This
is in direct contrast with previous metalloinsertors and suggests
a possible different binding disposition for these complexes in the
mismatch site. We ascribe this difference to the higher pKa of the coordinated immine of the chrysi ligand in these
complexes, so that the complexes must insert into the DNA helix with
the inserting ligand in a buckled orientation; spectroscopic studies
in the presence and absence of DNA along with the crystal structure
of the complex without DNA support this assignment. Remarkably, all
members of this new family of compounds have significantly increased
potency in a range of cellular assays; indeed, all are more potent
than cisplatin and N-methyl-N′-nitro-nitrosoguanidine
(MNNG, a common DNA-alkylating chemotherapeutic agent). Moreover,
the activities of the new metalloinsertors are coupled with high levels
of selective cytotoxicity for MMR-deficient versus proficient colorectal
cancer cells.
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Affiliation(s)
- Alexis C Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena California 91125, United States
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39
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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40
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Franco D, Vargiu AV, Magistrato A. Ru[(bpy)2(dppz)]2+ and Rh[(bpy)2(chrysi)]3+ Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation. Inorg Chem 2014; 53:7999-8008. [DOI: 10.1021/ic5008523] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Duvan Franco
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
| | - Attilio V. Vargiu
- Dipartimento
di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.700, I-09042 Monserrato, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
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41
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Abstract
We report the synthesis and characterization of a bimetallic conjugate (RhPt) in which an oxaliplatin derivative is tethered to a rhodium metalloinsertor through an aminomalonate leaving group ligand. The complex interacts with DNA through metalloinsertion at a base pair mismatch followed by formation of a covalent Pt-DNA adduct. Characterization of RhPt in mismatch repair-deficient HCT116O cells reveals increased cytotoxicity compared to cisplatin and oxaliplatin as well as relative to the unconjugated rhodium and platinum counterparts. Caspase and poly-ADP ribose polymerase inhibition assays indicate that RhPt induces apoptotic cell death. Inductively coupled plasma mass spectrometry (ICP-MS) experiments reveal that RhPt exhibits enhanced cellular uptake properties that contribute to its increased efficacy.
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Affiliation(s)
- Alyson G Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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42
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Fu C, Harms K, Zhang L, Meggers E. DNA Mismatch Recognition by a Hexacoordinate Silicon Sandwich–Ruthenium Hybrid Complex. Organometallics 2014. [DOI: 10.1021/om500367a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Chen Fu
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Klaus Harms
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Lilu Zhang
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Eric Meggers
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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Abstract
Classical chemotherapeutics, such as cisplatin and its analogues, have been highly successful in the clinic, yet improvements can certainly be made, given the significant side effects associated with the killing of healthy cells. Recent advances in the field of chemotherapy include the development of targeted anticancer agents, compounds that are directed towards a specific biomarker of cancer, with the hopes that such targeted therapies might have reduced side effects given their greater selectivity. Here we discuss several transition metal complexes that are tailored towards various biomolecules associated with cancer. Most notably, the success of rhodium metalloinsertors, which specifically bind to nucleic acid base mismatches in DNA, highlight the enormous potential of this exciting new strategy.
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Affiliation(s)
- Alyson G Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Alexis C Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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44
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Akerman KJ, Fagenson AM, Cyril V, Taylor M, Muller MT, Akerman MP, Munro OQ. Gold(III) macrocycles: nucleotide-specific unconventional catalytic inhibitors of human topoisomerase I. J Am Chem Soc 2014; 136:5670-82. [PMID: 24694294 PMCID: PMC4004252 DOI: 10.1021/ja412350f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
Topoisomerase
IB (Top1) is a key eukaryotic nuclear enzyme that
regulates the topology of DNA during replication and gene transcription.
Anticancer drugs that block Top1 are either well-characterized interfacial
poisons or lesser-known catalytic inhibitor compounds. Here we describe
a new class of cytotoxic redox-stable cationic Au3+ macrocycles
which, through hierarchical cluster analysis of cytotoxicity data
for the lead compound, 3, were identified as either poisons
or inhibitors of Top1. Two pivotal enzyme inhibition assays prove
that the compounds are true catalytic inhibitors of Top1. Inhibition
of human topoisomerase IIα (Top2α) by 3 was
2 orders of magnitude weaker than its inhibition of Top1, confirming
that 3 is a type I-specific catalytic inhibitor. Importantly,
Au3+ is essential for both DNA intercalation and enzyme
inhibition. Macromolecular simulations show that 3 intercalates
directly at the 5′-TA-3′ dinucleotide sequence targeted
by Top1 via crucial electrostatic interactions, which include π–π
stacking and an Au···O contact involving a thymine
carbonyl group, resolving the ambiguity of conventional (drug binds
protein) vs unconventional (drug binds substrate) catalytic inhibition
of the enzyme. Surface plasmon resonance studies confirm the molecular
mechanism of action elucidated by the simulations.
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Affiliation(s)
- Kate J Akerman
- School of Chemistry and Physics, University of KwaZulu-Natal , Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
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45
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Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev 2014; 43:3630-65. [DOI: 10.1039/c3cs60455a] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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McConnell AJ, Song H, Barton JK. Luminescence of [Ru(bpy)2(dppz)]2+ bound to RNA mismatches. Inorg Chem 2013; 52:10131-6. [PMID: 23968195 DOI: 10.1021/ic401531r] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The luminescence of rac-[Ru(bpy)2(dppz)](2+) (bpy = 2,2'-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) was explored in the presence of RNA oligonucleotides containing a single RNA mismatch (CA and GG) in order to develop a probe for RNA mismatches. While there is minimal luminescence of [Ru(bpy)2(dppz)](2+) in the presence of matched RNA due to weak binding, the luminescence is significantly enhanced in the presence of a single CA mismatch. The luminescence differential between CA mismatched and matched RNA is substantially higher compared to the DNA analogue, and therefore, [Ru(bpy)2(dppz)](2+) appears to be also a sensitive light switch probe for a CA mismatch in duplex RNA. Although the luminescence intensity is lower in the presence of RNA than DNA, Förster resonance energy transfer (FRET) between the donor ruthenium complex and FRET acceptor SYTO 61 is successfully exploited to amplify the luminescence in the presence of the mismatch. Luminescence and quenching studies with sodium iodide suggest that [Ru(bpy)2(dppz)](2+) binds to these mismatches via metalloinsertion from the minor groove. This work provides further evidence that metalloinsertion is a general binding mode of octahedral metal complexes to thermodynamically destabilized mismatches not only in DNA but also in RNA.
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Affiliation(s)
- Anna J McConnell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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47
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Weidmann AG, Komor AC, Barton JK. Biological effects of simple changes in functionality on rhodium metalloinsertors. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120117. [PMID: 23776288 PMCID: PMC3685451 DOI: 10.1098/rsta.2012.0117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors-bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex-our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure-function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus.
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Abstract
The discovery of cisplatin as a therapeutic agent stimulated a new era in the application of transition metal complexes for therapeutic design. Here we describe recent results on a variety of transition metal complexes targeted to DNA to illustrate many of the issues involved in new therapeutic design. We describe first structural studies of complexes bound covalently and non-covalently to DNA to identify potential lesions within the cell. We then review the biological fates of these complexes, illustrating the key elements in obtaining potent activity, the importance of uptake and subcellular localization of the complexes, as well as the techniques used to delineate these characteristics. Genomic DNA provides a challenging but valuable target for new transition metal-based therapeutics.
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Affiliation(s)
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA. Fax: 626-577-4976; Tel: 626-395-6075;
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49
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Bag SS, Kundu R, Jana S. Sensing of biomolecules and label-free discrimination of DNA containing a triple T–C/T–G mismatch pair with a fluorescence light-up probe, triazolylpyrene (TNDMBPy). Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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50
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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