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Zhang C, Zhao J, Lu B, Seeman NC, Sha R, Noinaj N, Mao C. Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions. J Am Chem Soc 2023; 145:4853-4859. [PMID: 36791277 DOI: 10.1021/jacs.3c00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Sequence-selective recognition of DNA duplexes is important for a wide range of applications including regulating gene expression, drug development, and genome editing. Many small molecules can bind DNA duplexes with sequence selectivity. It remains as a challenge how to reliably and conveniently obtain the detailed structural information on DNA-molecule interactions because such information is critically needed for understanding the underlying rules of DNA-molecule interactions. If those rules were understood, we could design molecules to recognize DNA duplexes with a sequence preference and intervene in related biological processes, such as disease treatment. Here, we have demonstrated that DNA crystal engineering is a potential solution. A molecule-binding DNA sequence is engineered to self-assemble into highly ordered DNA crystals. An X-ray crystallographic study of molecule-DNA cocrystals reveals the structural details on how the molecule interacts with the DNA duplex. In this approach, the DNA will serve two functions: (1) being part of the molecule to be studied and (2) forming the crystal lattice. It is conceivable that this method will be a general method for studying drug/peptide-DNA interactions. The resulting DNA crystals may also find use as separation matrices, as hosts for catalysts, and as media for material storage.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei 230032, China
| | - Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Anthraquinone: a promising scaffold for the discovery and development of therapeutic agents in cancer therapy. Future Med Chem 2020; 12:1037-1069. [PMID: 32349522 DOI: 10.4155/fmc-2019-0198] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cancer, characterized by uncontrolled malignant neoplasm, is a leading cause of death in both advanced and emerging countries. Although, ample drugs are accessible in the market to intervene with tumor progression, none are totally effective and safe. Natural anthraquinone (AQ) equivalents such as emodin, aloe-emodin, alchemix and many synthetic analogs extend their antitumor activity on different targets including telomerase, topoisomerases, kinases, matrix metalloproteinases, DNA and different phases of cell lines. Nano drug delivery strategies are advanced tools which deliver drugs into tumor cells with minimum drug leakage to normal cells. This review delineates the way AQ derivatives are binding on these targets by abolishing tumor cells to produce anticancer activity and purview of nanoformulations related to AQ analogs.
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Kenney RM, Buxton KE, Glazier S. Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs. Biophys Chem 2016; 216:9-18. [PMID: 27322498 DOI: 10.1016/j.bpc.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
Abstract
Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater<0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater>0 for CT DNA and Δnwater<0 for poly(dG·dC). For poly(dA·dT), Δnwater~0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions.
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Affiliation(s)
- Rachael M Kenney
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Katherine E Buxton
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA; Department of Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Samantha Glazier
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA.
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Shao L, Shi X, Liu W, Gao X, Pu T, Ma B, Wang S. Inactivation and identification of three genes encoding glycosyltransferase required for biosynthesis of nogalamycin. Biotechnol Appl Biochem 2015; 62:765-71. [PMID: 25524457 DOI: 10.1002/bab.1332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 12/10/2014] [Indexed: 11/08/2022]
Abstract
Nogalamycin is an anthracycline antitumor antibiotic, consisting of the aromatic aglycone attached with a nogalose and a nogalamine. At present, the biosynthesis pathway of nogalamycin, especially the glycosylation mechanism of the two deoxysugar moieties, had still not been extensively investigated in vivo. In this study, we inactivated the three glycotransferase genes in the nogalamycin-produced strain, and investigated the function of these genes by analyzing the metabolites profiles in the fermentation broth. The in-frame deletion of snogD and disruption of snogE abolished the production of nogalamycin completely, indicating that the gene products of snogD and snogE are essential to the biosynthesis of nogalamycin. On the other hand, in-frame deletion of snogZ does not abolish the production of nogalamycin, but production yield was reduced to 28% of the wild type, implying that snogZ gene may involved in the activation of other glycotransferases in nogalamycin biosynthesis. This study laid the foundation of modification of nogalamycin biosynthesis/production by genetic engineering methods.
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Affiliation(s)
- Lei Shao
- State Key Lab of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Xuanwen Shi
- State Key Lab of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Wei Liu
- State Key Lab of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Xiaorong Gao
- State Key Lab of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Tian Pu
- State Key Lab of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Bingji Ma
- Department of Traditional Chinese Medicine, Agronomy College of Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Siyuan Wang
- College of Life Science, Nanjing, People's Republic of China
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Rettig M, Langel W, Kamal A, Weisz K. NMR structural studies on the covalent DNA binding of a pyrrolobenzodiazepine–naphthalimide conjugate. Org Biomol Chem 2010; 8:3179-87. [DOI: 10.1039/c001893g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Banerjee T, Mukhopadhyay R. Structural effects of nogalamycin, an antibiotic antitumour agent, on DNA. Biochem Biophys Res Commun 2008; 374:264-8. [DOI: 10.1016/j.bbrc.2008.07.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 07/03/2008] [Indexed: 11/28/2022]
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Westerlund F, Nordell P, Blechinger J, Santos TM, Nordén B, Lincoln P. Complex DNA Binding Kinetics Resolved by Combined Circular Dichroism and Luminescence Analysis. J Phys Chem B 2008; 112:6688-94. [DOI: 10.1021/jp711116z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pär Nordell
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Julia Blechinger
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Teresa M. Santos
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bengt Nordén
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
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Valls N, Steiner RA, Wright G, Murshudov GN, Subirana JA. Variable role of ions in two drug intercalation complexes of DNA. J Biol Inorg Chem 2005; 10:476-82. [PMID: 15926069 DOI: 10.1007/s00775-005-0655-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 04/21/2005] [Indexed: 10/25/2022]
Abstract
The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-A resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co(2+), Ba(2+) and Na(+) ions. They reveal at least two different types of coordination environments: (1) specific sites for Co(2+) interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.
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Affiliation(s)
- Núria Valls
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028 Barcelona, Spain
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Wilhelmsson LM, Esbjörner EK, Westerlund F, Nordén B, Lincoln P. Meso Stereoisomer as a Probe of Enantioselective Threading Intercalation of Semirigid Ruthenium Complex [μ-(11,11‘-bidppz)(phen)4Ru2]4+. J Phys Chem B 2003. [DOI: 10.1021/jp036302f] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Marcus Wilhelmsson
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE−41296 Gothenburg, Sweden
| | - Elin K. Esbjörner
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE−41296 Gothenburg, Sweden
| | - Fredrik Westerlund
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE−41296 Gothenburg, Sweden
| | - Bengt Nordén
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE−41296 Gothenburg, Sweden
| | - Per Lincoln
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE−41296 Gothenburg, Sweden
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Shinomiya M, Chu W, Carlson RG, Weaver RF, Takusagawa F. Structural, Physical, and Biological Characteristics of RNA.cntdot.DNA Binding Agent N8-Actinomycin D. Biochemistry 2002. [DOI: 10.1021/bi00026a032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Williams HEL, Colgrave ML, Searle MS. Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1726-33. [PMID: 11895443 DOI: 10.1046/j.1432-1327.2002.02819.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two DNA hairpin motifs (5'-GCGAAGC-3' and 5'-ACGA AGT-3'), both stabilized by a 5'-GAA loop, have been used to design novel intramolecular double hairpin structures (5'-GCGAAGCACGAAGT-3' and 5'-ACGAAGTGCG AAGC-3') in which coaxial stacking of the two hairpin components generates a double-stranded stem region effectively with a single-strand break in the middle of the sequence at either the TG or CA step between unconnected 3' and 5' terminal bases. We have investigated by NMR the conformation and dynamics of the DNA at the strand break site. We show that mutual stacking significantly enhances the stability of each hairpin. Further, the anthracycline antibiotic nogalamycin binds cleanly to the 5'-TG (5'-CA) site formed by the mutually stacked hairpins despite the break in the sugar-phosphate backbone on one strand. The complex resembles the structure of nogalamycin-DNA complexes with the drug bound at 5'-TG sites in intact duplex sequences, with pi-stacking interactions probably the single dominant stabilizing interaction.
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Larson ED, Drummond JT. Human mismatch repair and G*T mismatch binding by hMutSalpha in vitro is inhibited by adriamycin, actinomycin D, and nogalamycin. J Biol Chem 2001; 276:9775-83. [PMID: 11134041 DOI: 10.1074/jbc.m006390200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Loss of the human DNA mismatch repair pathway confers cross-resistance to structurally unrelated anticancer drugs. Examples include cisplatin, doxorubicin (adriamycin), and specific alkylating agents. We focused on defining the molecular events that link adriamycin to mismatch repair-dependent drug resistance because adriamycin, unlike drugs that covalently modify DNA, can interact reversibly with DNA. We found that adriamycin, nogalamycin, and actinomycin D comprise a class of drugs that reversibly inhibits human mismatch repair in vitro at low micromolar concentrations. The substrate DNA was not covalently modified by adriamycin treatment in a way that prevents repair, and the inhibition was independent of the number of intercalation sites separating the mismatch and the DNA nick used to direct repair, from 10 to 808 base pairs. Over the broad concentration range tested, there was no evidence for recognition of intercalated adriamycin by MutSalpha as if it were an insertion mismatch. Inhibition apparently results from the ability of the intercalated drug to prevent mismatch binding, shown using a defined mobility shift assay, which occurs at drug concentrations that inhibit repair. These data suggest that adriamycin interacts with the mismatch repair pathway through a mechanism distinct from the manner by which covalent DNA lesions are processed.
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Affiliation(s)
- E D Larson
- Department of Biology, Indiana University, Bloomington 47405, USA
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13
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Williams HE, Searle MS. Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)2Complex determined by NMR and molecular dynamics simulations in solution. J Mol Biol 1999; 290:699-716. [PMID: 10395824 DOI: 10.1006/jmbi.1999.2903] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of the 1:1 nogalamycin:d(ATGCAT)2 complex has been determined in solution from high-resolution NMR data and restrained molecular dynamics (rMD) simulations using an explicit solvation model. The antibiotic intercalates at the 5'-TpG step with the nogalose lying along the minor groove towards the centre of the duplex. Many drug-DNA nuclear Overhauser enhancements (NOEs) in the minor groove are indicative of hydrophobic interactions over the TGCA sequence. Steric occlusion prevents a second nogalamycin molecule from binding at the symmetry-related 5'-CpA site, leading to the conclusion that the observed binding orientation in this complex is the preferred orientation free of the complication of end-effects (drug molecules occupy terminal intercalation sites in all X-ray structures) or steric interactions between drug molecules (other NMR structures have two drug molecules bound in close proximity), as previously suggested. Fluctuations in key structural parameters such as rise, helical twist, slide, shift, buckle and sugar pucker have been examined from an analysis of the final 500 ps of a 1 ns rMD simulation, and reveal that many sequence-dependent structural features previously identified by comparison of different X-ray structures lie within the range of dynamic fluctuations observed in the MD simulations. Water density calculations on MD simulation data reveal a time-averaged pattern of hydration in both the major and minor groove, in good agreement with the extensive hydration observed in two related X-ray structures in which nogalamycin is bound at terminal 5'-TpG sites. However, the pattern of hydration determined from the sign and magnitude of NOE and ROE cross-peaks to water identified in 2D NOESY and ROESY experiments identifies only a few "bound" water molecules with long residence times. These solvate the charged bicycloaminoglucose sugar ring, suggesting an important role for water molecules in mediating drug-DNA electrostatic interactions within the major groove. The high density of water molecules found in the minor groove in X-ray structures and MD simulations is found to be associated with only weakly bound solvent in solution.
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Affiliation(s)
- H E Williams
- Department of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
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Takenaka S, Takagi M. Threading Intercalators as a New DNA Structural Probe. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.327] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Pichierri F, Sarai A. Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00309-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Kapur A, Beck JL, Sheil MM. Observation of daunomycin and nogalamycin complexes with duplex DNA using electrospray ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:2489-2497. [PMID: 10589098 DOI: 10.1002/(sici)1097-0231(19991230)13:24<2489::aid-rcm816>3.0.co;2-f] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The noncovalent binding of the antitumour drugs daunomycin and nogalamycin to duplex DNA has been studied using electrospray ionisation mass spectrometry (ESI-MS). The conditions for the preparation of drug/duplex DNA complexes and for their detection by ESI-MS have been optimised. Ions corresponding to these complexes were most abundant relative to free DNA when prepared in the pH range 8-9, and using gentle ESI interface conditions. Self-complementary oligonucleotides, 5'-d(GGCTAGCC)-3' or 5'-d(CGGCGCCG)-3', annealed in the presence of a 5-fold molar excess of either nogalamycin or daunomycin gave ESI mass spectra in which the most intense ions corresponded to three molecules of drug bound to duplex DNA, with some evidence for four drug molecules bound. For binding to 5'-d(TGAGCTAGCTCA)(2)-3', complexes containing up to four nogalamycin and six daunomycin molecules were observed. These data are consistent with the neighbour exclusion principle whereby intercalation occurs between every other base pair such that up to four bound drugs would be expected for the 8 mers and up to six for the 12 mer. Competition experiments involving a single drug in an equimolar mixture of two oligonucleotides (5'-d(TGAGCTAGCTCA)(2)-3' with either 5'-d(CGGCGCCG)(2)-3' or 5'-d(GGCTAGCC)(2)-3') showed ions arising from complexes of drug/5'-d(CGGCGCCG)(2)-3' were more intense than complexes of drug/5'-d(GGCTAGCC)(2)-3', relative to those from the 12 mer in each mixture. While this suggests ESI-MS has the potential to detect differences in sequence selectivity, more detailed experiments involving a comparison of the relative ionisation efficiency of different oligonucleotides and a wider range of intercalators are required to establish this definitively. ESI mass spectra from experiments in which both drugs were reacted with the same oligonucleotide were more complex, such that a clear preference for one drug could not be established.
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Affiliation(s)
- A Kapur
- Department of Chemistry, University of Wollongong, New South Wales 2522, Australia
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Sim SP, Gatto B, Yu C, Liu AA, Li TK, Pilch DS, LaVoie EJ, Liu LF. Differential poisoning of topoisomerases by menogaril and nogalamycin dictated by the minor groove-binding nogalose sugar. Biochemistry 1997; 36:13285-91. [PMID: 9341219 DOI: 10.1021/bi971261x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The effect of DNA binding on poisoning of human DNA TOP1 has been studied using a pair of related anthracyclines which differ only by a nogalose sugar ring. We show that the nogalose sugar ring of nogalamycin, which binds to the minor groove of DNA, plays an important role in affecting topoisomerase-specific poisoning. Using purified mammalian topoisomerases, menogaril is shown to poison topoisomerase II but not topoisomerase I. By contrast, nogalamycin poisons topoisomerase I but not topoisomerase II. Consistent with the biochemical studies, CEM/VM-1 cells which express drug-resistant TOP2alpha are cross-resistant to menogaril but not nogalamycin. The mechanism by which nogalamycin poisons topoisomerase I has been studied by analyzing a major topoisomerase I-mediated DNA cleavage site induced by nogalamycin. This site is mapped to a sequence embedded in an AT-rich region with four scattered GC base pairs (bps) (at -10, -6, +2, and +12 positions). GC bps embedded in AT-rich regions are known to be essential for nogalamycin binding. Surprisingly, DNase I footprinting analysis of nogalamycin-DNA complexes has revealed a drug-free region from -2 to +9 encompassing the major cleavage site. Our results suggest that nogalamycin, in contrast to camptothecin, may stimulate TOP1 cleavage by binding to a site(s) distal to the site of cleavage.
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Affiliation(s)
- S P Sim
- Department of Pharmacology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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18
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Affiliation(s)
- A C Weymouth-Wilson
- Dextra Laboratories Ltd, Innovation Centre, University of Reading, Berkshire, UK
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19
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Cruse WB, Saludjian P, Leroux Y, Léger G, Manouni DE, Prangé T. A continuous transition from A-DNA to B-DNA in the 1:1 complex between nogalamycin and the hexamer dCCCGGG. J Biol Chem 1996; 271:15558-67. [PMID: 8662899 DOI: 10.1074/jbc.271.26.15558] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The antibiotic nogalamycin, a drug with high specificity for TG and CG steps in double-stranded DNA, has been crystallized as a 1:1 complex with the hexamer d(CCCGGG). The antibiotic is inserted at the central CG step of the duplex, with the two sugars oriented in the same direction and with strong interactions with the DNA within the grooves. The amino-glucose residue makes an integral part of a well defined major groove hydration network with van der Waals contacts and several strong hydrogen bonds to the duplex. The nogalose residue resides in the minor groove, making primarily van der Waals contacts. The single site allows an accurate molecular description of the intercalation, without perturbations from end effects observed previously. The local unwinding induced by nogalamycin is completely relaxed 2 base pairs away from the intercalation site. The two strands of the DNA show a continuous deformation from the A to the B form: 1) the cytosines toward the 5' end of the nogalomycin site in each strand have c3'-endo conformations while 5 guanosines toward the 3' ends have c2'-endo conformations; 2) within each strand, the phosphate-phosphate distances increase in a continuous manner from 5.7 A (A-form) to 7.1 A (B-form).
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Affiliation(s)
- W B Cruse
- "Chimie Structurale et Spectroscopie Biomoléculaire" (URA 1430 CNRS) UFR-Biomédicale, 74, rue M. Cachin, 93012 Bobigny Cedex, France
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Rehn C, Pindur U. Model building and molecular mechanics calculations of mitoxantrone-deoxytetranucleotide complexes: Molecular foundations of DNA intercalation as cytostatic active principle. MONATSHEFTE FUR CHEMIE 1996. [DOI: 10.1007/bf00817255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Smith CK, Davies GJ, Dodson EJ, Moore MH. DNA-nogalamycin interactions: the crystal structure of d(TGATCA) complexed with nogalamycin. Biochemistry 1995; 34:415-25. [PMID: 7819233 DOI: 10.1021/bi00002a005] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structure of the self-complementary deoxyoligonucleotide d5'(TGATCA) complexed with nogalamycin, an antitumor anthracycline, has been solved to 1.8 A resolution using X-ray crystallographic methods. The technique of single isomorphous replacement, utilizing the anomalous signal of bromine in derivative data collected at three different wavelengths, Cu K alpha, Mo K alpha, and 0.91 A synchroton radiation, was used. The complex crystallized in space group P4(1)2(1)2 with unit cell dimensions a = 37.2 A and c = 70.1 A. The final structure including 116 water molecules has an overall R factor of 19.5% for the 4767 reflections with F > or = 1 sigma F in the resolution range 10.0-1.8 A. One nogalamycin molecule intercalates between each of the d5'(TpG) steps at both ends of a distorted B DNA double helix. This structure provides the first three-dimensional picture of nogalamycin bound to the triplet sequence d5'(TGA), one of its favorable natural binding sites. The drug exhibits a strict requirement for binding to the 3' side of a pyrimidine and the 5' side of a purine. Nogalamycin has bulky sugar groups at either end of a planar aglycon chromophore; therefore, in order for intercalation to occur, the DNA must either transiently open or flex along the helix axis to allow insertion of the chromophore between the base pairs. Conformational change in nogalamycin is observed in the drug-DNA complex with respect to free nogalamycin. Nogalamycin binding to DNA induces severe deformation to the intercalation site base pairs. In comparison to previously reported anthracycline-DNA structures significant differences in base-pair geometry, drug hydrogen-bonding patterns, and the extent of hydration are observed. The position of the drug in this complex is stabilized by a number of nonbonded forces including van der Waals interactions and extensive direct and solvent-mediated hydrogen bonds to the DNA duplex.
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Affiliation(s)
- C K Smith
- Department of Chemistry, University of York, Heslington, England
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Missailidis S, Hester RE. FTIR spectra of deoxyoligonucleotide-nogalamycin complexes. ACTA ACUST UNITED AC 1995. [DOI: 10.1002/bspy.350010202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Robinson H, Yang D, Wang AH. Structure and dynamics of the antitumor drugs nogalamycin and disnogalamycin complexed to d(CGTACG)2: comparison of crystal and solution structures. Gene 1994; 149:179-88. [PMID: 7958983 DOI: 10.1016/0378-1119(94)90427-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nuclear magnetic resonance (NMR) solution structures of the 2:1 complexes of nogalamycin-d(CGTACG)2 (Ng-CGTACG) and disnogalamycin-d(CGTACG)2 (DNg-CGTACG) have been determined by a quantitative treatment of two-dimensional nuclear Overhauser effect (2D-NOE) crosspeak intensities. The 1.3 A resolution crystal structure of the 2:1 complex of Ng-CGTACG was used as a starting model for refinement using the procedure, SPEDREF [Robinson and Wang, Biochemistry 31 (1992) 3524-3533], which incorporates full matrix relaxation theory and simulated annealing minimization. The refined solution structures have R-factors of 16.1 and 19.6% between the observed and simulated NOEs for Ng-CGTACG and DNg-CGTACG, respectively. The refined NMR structures retain major features of the crystal structure in which the elongated aglycone chromophore is intercalated between the CpG steps with its nogalose and aminoglucose lying in the minor and major grooves, respectively. The root mean square deviation between the solution and crystal structure for the complexes is 1.01 A (Ng-CGTACG) and 1.20 A (DNg-CGTACG) for the drug, plus the three base pairs surrounding the drug, indicating a very similar local structure at the intercalation site. In the NMR structure, the two G:C Watson-Crick base pairs (C1:G12 and G2:C11) that wrap around the aglycone have large buckles, as do those seen in the crystal structure. There is a 22 degree bend at the T3-A4 step in the refined solution structure. This rearrangement of the solution conformation is likely due to the absence of crystal packing. Specific hydrogen bonds between the drug and G:C bases in both grooves of the helix are preserved in the solution structure. A separate study of the 2:1 complex at low pH showed that the terminal G-C base pairing is destabilized.
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Affiliation(s)
- H Robinson
- Biophysics Division, University of Illinois at Urbana-Champaign, 61801
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Kennard O. From data to knowledge—Use of the Cambridge Structural Database for studying molecular interactions. Supramol Chem 1993. [DOI: 10.1080/10610279308035171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fox KR, Alam Z. Footprinting studies of DNA-sequence recognition by nogalamycin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 209:31-6. [PMID: 1396706 DOI: 10.1111/j.1432-1033.1992.tb17257.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have studied the DNA sequence binding preference of the antitumour antibiotic nogalamycin by DNase-I footprinting using a variety of DNA fragments. The DNA fragments were obtained by cloning synthetic oligonucleotides into longer DNA fragments and were designed to contain isolated ligand-binding sites surrounded by repetitive sequences such as (A)n.(T)n and (AT)n. Within regions of (A)n.(T)n, clear footprints are observed with low concentrations of nogalamycin (< 5 microM), with apparent binding affinities for tetranucleotide sequences which decrease in the order TGCA > AGCT = ACGT > TCGA. In contrast, within regions of (AT)n, the ligand binds best to AGCT; binding to TCGA and TGCA is no stronger than to alternating AT. Within (ATT)n, the preference is for ACGT > TCGA. Although each of these binding sites contains all four base pairs, there is no apparent consensus sequence, suggesting that the selectivity is affected by local DNA dynamic and structural effects. At higher drug concentrations (> 25 microM), nogalamycin prevents DNAse-I cleavage of (AT)n but shows no interaction with regions of (AC)n.(GT)n. Regions of (A)n.(T)n, which are poorly cut by DNase I, show enhanced rates of cleavage in the presence of low concentrations of nogalamycin, but are protected from cleavage at higher concentrations. We suggest that this arises because drug binding to adjacent regions distorts the DNA to a structure which is more readily cut by the enzyme and which is better able to bind further ligand molecules.
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Affiliation(s)
- K R Fox
- Department of Physiology and Pharmacology, University of Southampton, England
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Abstract
Molecular dynamics simulations have been undertaken for a B-form dodecanucleotide duplex in solution with and without an intercalated proflavine molecule between the central C.G base pairs. The introduction of this simple intercalator affects both the conformational features and dynamic properties of the oligonucleotide double helix. Changes are seen in the rms atomic fluctuations and anisotropy of phosphate, sugar and base atoms. The backbone conformation is slightly changed on average and more sugars adopt the C3' endo conformation in the simulation of the complex compared with the simulation of the oligonucleotide alone. Both major and minor grooves becomes wider on average with the addition of the intercalating drug. Flanking A.T base pairs on both sides of the intercalation site have undergone an increase in flexibility, with the base pairs, especially at the 5' side, having the N1...N3 hydrogen bonds being broken.
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Affiliation(s)
- P Herzyk
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK
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Kamitori S, Takusagawa F. Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D. J Mol Biol 1992; 225:445-56. [PMID: 1593629 DOI: 10.1016/0022-2836(92)90931-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The crystal structures of the 2:1 complex of the self-complementary DNA octamer d(GAAGCTTC) with actinomycin D has been determined at 3.0 A resolution. This is the first example of a crystal structure of a DNA-drug complex in which the drug intercalates into the middle of a relatively long DNA segment. The results finally confirmed the DNA-actinomycin intercalation model proposed by Sobell & co-workers in 1971. The DNA molecule adopts a severely distorted and slightly kinked B-DNA-like structure with an actinomycin D molecule intercalated in the middle sequence, GC. The two cyclic depsipeptides, which differ from each other in overall conformation, lie in the minor groove. The complex is further stabilized by forming base-peptide and chromophore-backbone hydrogen bonds. The DNA helix appears to be unwound by rotating one of the base-pairs at the intercalation site. This single base-pair unwinding motion generates a unique asymmetrically wound helix at the binding site of the drug, i.e. the helix is loosened at one end of the intercalation site and tightened at the other end. The large unwinding of the DNA by the drug intercalation is absorbed mostly in a few residues adjacent to the intercalation site. The asymmetrical twist of the DNA helix, the overall conformation of the two cyclic depsipeptides and their interaction mode with DNA are correlated to each other and rationally explained.
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Affiliation(s)
- S Kamitori
- X-ray Crystallography Laboratory, University of Kansas, Lawrence 66045-0046
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Monnot M, Mauffret O, Lescot E, Fermandjian S. Probing intercalation and conformational effects of the anticancer drug 2-methyl-9-hydroxyellipticinium acetate in DNA fragments with circular dichroism. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 204:1035-9. [PMID: 1551384 DOI: 10.1111/j.1432-1033.1992.tb16725.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Circular dichroism was applied to the analysis of drug-DNA associations. With the octanucleotide d(TGACGTCA) (octanucleotide I), which is the cAMP-responsive element (CRE) in gene promoters and its reverse d(ACTGCAGT) (octanucleotide II), it was demonstrated that the anticancer polyaromatic agent celiptium intercalates into DNA base pairs with its long direction perpendicular to both the DNA-helix axis and the base-pair long axis and induces larger conformational changes in the CpG-containing octanucleotide I CRE than in its reverse-sequence octanucleotide II. It was concluded that CD is a powerful and sensitive technique to discriminate between drug-binding modes of DNA, to define the geometry of the chromophore inserted into base pairs and, finally, to measure sequence-dependent conformational changes induced by intercalation in DNA. We anticipate that these studies will contribute to a better understanding of the molecular bases that underlie the mechanism of action of those cytotoxic drugs which interfere with the DNA-nuclear-protein recognition.
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Affiliation(s)
- M Monnot
- Institut Gustave Roussy, Laboratoire de Biochimie-Enzymologie, URA 147 Centre National de la Recherche Scientifique, Villejuif, France
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Leonard GA, Brown T, Hunter WN. Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 204:69-74. [PMID: 1740157 DOI: 10.1111/j.1432-1033.1992.tb16606.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Crystallographic methods have been applied to determine the high-resolution structure of the complex formed between the self-complementary oligonucleotide d(TGTACA) and the anthracycline antibiotic 4'-epiadriamycin. The complex crystallises in the tetragonal system, space group P4(1)2(1)2 with a = 2.802 nm and c = 5.293 nm, and an asymmetric unit consisting of a single DNA strand, one drug molecule and 34 solvent molecules. The refinement converged with an R factor of 0.17 for the 2381 reflections with F greater than or equal to 3 sigma F in the resolution range 0.70-0.14 nm. Two asymmetric units associate such that a distorted B-DNA-type hexanucleotide duplex is formed incorporating two drug molecules that are intercalated at the TpG steps. The amino sugar of 4'-epiadriamycin binds in the minor groove of the duplex and displays different interactions from those observed in previously determined structures. Interactions between the hydrophilic groups of the amino sugar and the oligonucleotide are all mediated by solvent molecules. Ultraviolet melting measurements and comparison with other anthracycline-DNA complexes suggest that these indirect interactions have a powerful stabilising effect on the complex.
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Affiliation(s)
- G A Leonard
- Department of Chemistry, University of Edinburgh, Scotland
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The role of medicinal chemistry in the discovery of DNA-active anticancer drugs: from random searching, through lead development, to de novo design. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/978-94-009-0385-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Kennard O, Hunter WN. Einkristall-Röntgenstrukturanalysen von Oligonucleotiden und Oligonucleotid-Wirkstoff-Komplexen. Angew Chem Int Ed Engl 1991. [DOI: 10.1002/ange.19911031007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sriram M, Liaw YC, Gao YG, Wang AH. Molecular structure of antitumor drug steffimycin and modelling of its binding to DNA. J Biomol Struct Dyn 1991; 9:251-69. [PMID: 1741962 DOI: 10.1080/07391102.1991.10507911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The molecular and crystal structure of steffimycin have been determined by single crystal X-ray diffraction to 0.9 angstrom resolution. The triclinic crystals are in the space group P1, with the unit cell dimensions of a = 8.606(3) angstrom, b = 22.168(7) angstrom, c = 8.448(2) angstrom, alpha = 97.56(3) degrees, beta = 95.97(2) degrees, gamma = 87.94(3) degrees, Z = 2. The structure was solved by direct methods and refined by the full-matrix least-squares method to a final R value of 0.065 with 3405 (Inet greater than 2.0 sigma (Inet] observed reflections using the NRCVAX software package. The crystal lattice includes 2 independent steffimycin, 3 water and one 2-methyl-2,4-pentanediol molecules. The conformation of steffimycin is grossly similar to other anthracycline antibiotics including daunorubicin. The crystal packing interactions of steffimycin suggest a preferred stacking of the aglycone chromophore of the antibiotic which resembles the intercalative interactions seen in the daunorubicin-d(CGTACG) (Wang et al., Biochemistry 26, 1152 (1987] and nogalamycin-d(CGT(pS)ACG) (Liaw et al., Biochemistry 28, 9913 (1989] complexes. The atomic coordinates data from these complexes were used to model the intercalative binding of steffimycin to DNA. The models were then stereochemically idealized by the constraint refinement program NUCLSQ. Subsequently XPLOR software package was used for energy minimization of these models in vacuo. The model building studies suggest that steffimycin has a higher CpG base sequence specificity over the TpA step, similar to that of daunorubicin and nogalamycin.
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Affiliation(s)
- M Sriram
- Department of Physiology and Biophysics, University of Illinois, Urbana-Champaign 61801
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Abstract
This review assimilates up-to-date information on the biochemical pharmacology of nogalamycin and selected derivatives that have shown good biological activities and/or received a relatively detailed investigation. The structure and chemical preparation of these derivatives from nogalamycin is described and the nomenclature which has been rather perplexing in the literature is clarified. The interaction of this class of compounds, particularly nogalamycin, with DNA is extensively reviewed. The biochemical mechanism of action of nogalamycin and its structurally closely-related derivatives is described. Among nogalamycin derivatives, menogaril showed distinct biochemical effects as well as superior cytotoxicity and antitumor activity and also proved to be effective against breast cancer clinically.
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Affiliation(s)
- L H Li
- Upjohn Laboratories, Upjohn Company, Kalamazoo, MI 49001
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