Excursions in polynuclear platinum DNA binding.

Polynuclear platinum agents are a structurally unique class of anti-cancer drugs, distinct from the cisplatin family. To describe the chemistry and biology of this class, it was necessary to challenge the accepted paradigms for the structure-activity relationships; design new chemotypes and delineate the structures and consequences of their DNA binding modes. This article summarizes the structural changes induced in DNA by both covalent (bond-forming) and non-covalent (ligand recognition) adducts. Solution (Nuclear Magnetic Resonance), solid state (crystallography) and gas-phase (Electrospray Ionization Mass Spectrometry) techniques have all been used to describe the new DNA structures along with molecular biological techniques. The combined approaches allow molecular description of hitherto unobserved adducts such as long-range major-groove interstrand crosslinks; directional isomers on DNA and a third class of ligand-DNA binding, the phosphate clamp. The phosphate recognition is distinct from ''classic'' minor-groove recognition or intercalation.

[1]  Nicholas P. Farrell,et al.  The phosphate clamp: a small and independent motif for nucleic acid backbone recognition , 2010, Nucleic Acids Res..

[2]  V. Brabec,et al.  Conformation and recognition of DNA modified by a new antitumor dinuclear PtII complex resistant to decomposition by sulfur nucleophiles. , 2010, Biochemical pharmacology.

[3]  V. Brabec,et al.  Factors affecting DNA-DNA interstrand cross-links in the antiparallel 3'-3' sense: a comparison with the 5'-5' directional isomer. , 2009, Chemistry.

[4]  N. Farrell,et al.  Structural consequences of a 3′ → 3′ DNA interstrand cross-link by a trinuclear platinum complex: unique formation of two such cross-links in a 10-mer duplex , 2009, JBIC Journal of Biological Inorganic Chemistry.

[5]  S. Schürch,et al.  The influence of cisplatin on the gas-phase dissociation of oligonucleotides studied by electrospray ionization tandem mass spectrometry , 2009, Journal of the American Society for Mass Spectrometry.

[6]  A. Canals,et al.  DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. , 2009, Dalton transactions.

[7]  Paul J Hergenrother,et al.  DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action. , 2007, Current opinion in biotechnology.

[8]  W. Buchmann,et al.  Noncovalent complexes between DNA and basic polypeptides or polyamines by MALDI-TOF , 2007, Journal of the American Society for Mass Spectrometry.

[9]  N. Farrell,et al.  Pre-association of polynuclear platinum anticancer agents on a protein, human serum albumin. Implications for drug design. , 2007, Dalton transactions.

[10]  L. Kèlland,et al.  The resurgence of platinum-based cancer chemotherapy , 2007, Nature Reviews Cancer.

[11]  D. Stewart,et al.  Mechanisms of resistance to cisplatin and carboplatin. , 2007, Critical reviews in oncology/hematology.

[12]  W. Buchmann,et al.  A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry , 2007, Journal of the American Society for Mass Spectrometry.

[13]  N. Farrell,et al.  A third mode of DNA binding: Phosphate clamps by a polynuclear platinum complex. , 2006, Journal of the American Chemical Society.

[14]  P. Sadler,et al.  Insights into the mechanism of action of platinum anticancer drugs from multinuclear NMR spectroscopy , 2006 .

[15]  V. Brabec,et al.  Deoxyribonuclease I footprinting reveals different DNA binding modes of bifunctional platinum complexes , 2006, The FEBS journal.

[16]  T. Mikkelsen,et al.  Polynuclear platinum anticancer drugs are more potent than cisplatin and induce cell cycle arrest in glioma. , 2006, Neuro-oncology.

[17]  M. Smietana,et al.  Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI , 2006, Journal of the American Society for Mass Spectrometry.

[18]  N. Farrell,et al.  Biological Consequences of Trinuclear Platinum Complexes: Comparison of [{trans-PtCl(NH3)2}2μ-(trans-Pt(NH3)2(H2N(CH2)6-NH2)2)]4+ (BBR 3464) with Its Noncovalent Congeners , 2006, Molecular Pharmacology.

[19]  P. Miller,et al.  Formation and repair of interstrand cross-links in DNA. , 2006, Chemical reviews.

[20]  B. Van Houten,et al.  Prokaryotic nucleotide excision repair: the UvrABC system. , 2006, Chemical reviews.

[21]  N. Farrell,et al.  Synthesis, characterization, and cytotoxicity of a novel highly charged trinuclear platinum compound. Enhancement of cellular uptake with charge. , 2005, Inorganic chemistry.

[22]  A. Rich,et al.  Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases , 2005, Nature.

[23]  A. Woods,et al.  Study of the fragmentation patterns of the phosphate-arginine noncovalent bond. , 2005, Journal of proteome research.

[24]  Eddie Reed ERCC1 and Clinical Resistance to Platinum-Based Therapy , 2005, Clinical Cancer Research.

[25]  N. Farrell,et al.  Cross-links of quadruplex structures from human telomeric DNA by dinuclear platinum complexes show the flexibility of both structures. , 2005, Biochemistry.

[26]  S. Ferré,et al.  Amazing stability of the arginine-phosphate electrostatic interaction. , 2005, Journal of proteome research.

[27]  A. Noronha,et al.  Structure, flexibility, and repair of two different orientations of the same alkyl interstrand DNA cross-link. , 2005, Biochemistry.

[28]  Dong Wang,et al.  Cellular processing of platinum anticancer drugs , 2005, Nature Reviews Drug Discovery.

[29]  N. Farrell,et al.  Unique cooperative binding interaction observed between a minor groove binding Pt antitumor agent and Hoechst dye 33258. , 2005, Inorganic chemistry.

[30]  S. A. McLuckey,et al.  Gas-phase fragmentation of oligonucleotide ions , 2004 .

[31]  N. Farrell,et al.  Comparison of structural effects in 1,4 DNA-DNA interstrand cross-links formed by dinuclear and trinuclear platinum complexes. , 2004, Journal of inorganic biochemistry.

[32]  N. Farrell,et al.  Long range 1,4 and 1,6-interstrand cross-links formed by a trinuclear platinum complex. Minor groove preassociation affects kinetics and mechanism of cross-link formation as well as adduct structure. , 2004, Journal of the American Chemical Society.

[33]  Alexander Rich,et al.  The double helix: a tale of two puckers , 2003, Nature Structural Biology.

[34]  Adam P. Silverman,et al.  2.4-Å Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex* , 2002, The Journal of Biological Chemistry.

[35]  V. Brabec,et al.  DNA Interstrand Cross-links of the Novel Antitumor Trinuclear Platinum Complex BBR3464 , 2002, The Journal of Biological Chemistry.

[36]  Laurence H. Hurley,et al.  DNA and its associated processes as targets for cancer therapy , 2002, Nature Reviews Cancer.

[37]  N. Farrell,et al.  Kinetic and equilibria studies of the aquation of the trinuclear platinum phase II anticancer agent [(trans-PtCl(NH(3))(2))(2)(mu-trans-Pt(NH(3))(2)(NH(2)(CH(2))(6)NH(2))(2))](4+) (BBR3464). , 2002, Inorganic chemistry.

[38]  V. Brabec,et al.  A comparison of DNA binding profiles of dinuclear platinum compounds with polyamine linkers and the trinuclear platinum phase II clinical agent BBR3464 , 2002, JBIC Journal of Biological Inorganic Chemistry.

[39]  S. Lippard,et al.  2.4 A crystal structure of an oxaliplatin 1,2-d(GpG) intrastrand cross-link in a DNA dodecamer duplex. , 2001, Inorganic chemistry.

[40]  C. Prives,et al.  The C-terminus of p53: the more you learn the less you know , 2001, Nature Structural Biology.

[41]  C. Manzotti,et al.  The novel trinuclear platinum complex BBR3464 induces a cellular response different from cisplatin. , 2001, European journal of cancer.

[42]  N. Farrell,et al.  Kinetic analysis of the stepwise formation of a long-range DNA interstrand cross-link by a dinuclear platinum antitumor complex: evidence for aquated intermediates and formation of both kinetically and thermodynamically controlled conformers. , 2001, Journal of the American Chemical Society.

[43]  R. Griffey,et al.  Analysis of noncovalent complexes of DNA and RNA by mass spectrometry. , 2001, Chemical reviews.

[44]  V. Brabec,et al.  Sequence Specificity, Conformation, and Recognition by HMG1 Protein of Major DNA Interstrand Cross-links of Antitumor Dinuclear Platinum Complexes* , 2000, The Journal of Biological Chemistry.

[45]  N. Farrell,et al.  Platinum-Based Drugs in Cancer Therapy , 2000, Cancer Drug Discovery and Development.

[46]  N. Farrell,et al.  Equilibrium and kinetic studies of the aquation of the dinuclear platinum complex [[trans-PtCl(NH3)2]2(mu-NH2(CH2)6NH2)]2+: pKa determinations of aqua ligands via [1H,15N] NMR spectroscopy. , 2000, Inorganic chemistry.

[47]  N. Farrell,et al.  Consequences of nucleic acid conformation on the binding of a trinuclear platinum drug. , 1999, Biochemistry.

[48]  John D. Roberts,et al.  Cellular pharmacology of polynuclear platinum anti-cancer agents. , 1999, Journal of inorganic biochemistry.

[49]  N. Farrell,et al.  Comparison of cytotoxicity and cellular accumulation of polynuclear platinum complexes in L1210 murine leukemia cell lines. , 1999, Journal of inorganic biochemistry.

[50]  N. Farrell,et al.  A novel charged trinuclear platinum complex effective against cisplatin-resistant tumours: hypersensitivity of p53-mutant human tumour xenografts , 1999, British Journal of Cancer.

[51]  C. Pabo,et al.  Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins , 1999, Nature.

[52]  V. Brabec,et al.  DNA modifications by a novel bifunctional trinuclear platinum phase I anticancer agent. , 1999, Biochemistry.

[53]  W. Shepard,et al.  Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site. , 1999, Nucleic acids research.

[54]  S. Rajski,et al.  DNA Cross-Linking Agents as Antitumor Drugs. , 1998, Chemical reviews.

[55]  S. Lippard,et al.  NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin. , 1998, Biochemistry.

[56]  S. Lippard,et al.  Binding of tsHMG, a mouse testis-specific HMG-domain protein, to cisplatin-DNA adducts. , 1997, Biochemistry.

[57]  P. Sadler,et al.  Platination of a GG site on single-stranded and double-stranded forms of a 14-base oligonucleotide with diaqua cisplatin followed by NMR and HPLC -- influence of the platinum ligands and base sequence on 5'-G versus 3'-G platination selectivity. , 1997, European journal of biochemistry.

[58]  C. Burrows,et al.  Cytosine-specific chemical probing of DNA using bromide and monoperoxysulfate. , 1996, Nucleic acids research.

[59]  P. Sadler,et al.  Kinetic Analysis of the Stepwise Platination of Single‐ and Double‐Stranded GG Oligonucleotides with Cisplatin and cis‐[PtCl(H2O)(NH3)2]+ , 1996 .

[60]  H. Berman,et al.  Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative. , 1996, Biochemistry.

[61]  Huifang Huang,et al.  Solution Structure of a Cisplatin-Induced DNA Interstrand Cross-Link , 1995, Science.

[62]  Y. Zou,et al.  Effects of geometric isomerism and ligand substitution in bifunctional dinuclear platinum complexes on binding properties and conformational changes in DNA. , 1995, Biochemistry.

[63]  S. Lippard,et al.  Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin , 1995, Nature.

[64]  S. Neidle,et al.  Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2. , 1995, Nucleic acids research.

[65]  J. H. Boom,et al.  A novel DNA structure induced by the anticancer bisplatinum compound crosslinked to a GpC site in DNA , 1995, Nature Structural Biology.

[66]  P. S. Ho,et al.  The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[67]  M. Waring,et al.  Localized chemical reactivity in DNA associated with the sequence-specific bisintercalation of echinomycin. , 1994, The Biochemical journal.

[68]  H. D. Showalter,et al.  Anticancer activity in murine and human tumor cell lines of bis(platinum) complexes incorporating straight-chain aliphatic diamine linker groups. , 1992, Journal of medicinal chemistry.

[69]  K. Kinzler,et al.  Definition of a consensus binding site for p53 , 1992, Nature Genetics.

[70]  B Tidor,et al.  Arginine-mediated RNA recognition: the arginine fork , 1991, Science.

[71]  R. V. van Breemen,et al.  Characterization of cisplatin adducts of oligonucleotides by fast atom bombardment mass spectrometry. , 1991, Analytical biochemistry.

[72]  N. Farrell,et al.  Cytotoxicity and antitumor activity of bis(platinum) complexes. A novel class of platinum complexes active in cell lines resistant to both cisplatin and 1,2-diaminocyclohexane complexes. , 1990, Journal of medicinal chemistry.

[73]  John D. Roberts,et al.  Interaction of novel bis(platinum) complexes with DNA. , 1989, Nucleic acids research.

[74]  N. Farrell,et al.  Bis(platinum) Complexes Containing Two Platinum cis-Diammine Units. Synthesis and Initial DNA-Binding Studies. , 1988 .

[75]  N. Farrell,et al.  Bis(platinum) complexes containing two platinum cis-diammine units. Synthesis and initial DNA-binding studies , 1988 .

[76]  Dietrich Suck,et al.  Structure of DNase I at 2.0 Å resolution suggests a mechanism for binding to and cutting DNA , 1986, Nature.

[77]  W. Mcgregor,et al.  Nucleotide Excision Repair , 2020, Definitions.

[78]  M. Fojta,et al.  Differential recognition by the tumor suppressor protein p53 of DNA modified by the novel antitumor trinuclear platinum drug BBR3464 and cisplatin. , 2004, Nucleic acids research.

[79]  A. Sancar,et al.  Nucleotide excision repair in E. coli and man. , 2004, Advances in protein chemistry.

[80]  A. Noronha,et al.  Preparation of interstrand cross-linked DNA oligonucleotide duplexes. , 2004, Frontiers in bioscience : a journal and virtual library.

[81]  N. Farrell,et al.  The nature of the DNA template (single- versus double-stranded) affects the rate of aquation of a dinuclear Pt anticancer drug. , 2003, Chemical communications.

[82]  V. Brabec DNA modifications by antitumor platinum and ruthenium compounds: their recognition and repair. , 2002, Progress in nucleic acid research and molecular biology.

[83]  N. Farrell,et al.  Cooperative effects in long-range 1,4 DNA-DNA interstrand cross-links formed by polynuclear platinum complexes: an unexpected syn orientation of adenine bases outside the binding sites , 2002, JBIC Journal of Biological Inorganic Chemistry.

[84]  M. Waring,et al.  High-resolution footprinting studies of drug-DNA complexes using chemical and enzymatic probes. , 2001, Methods in enzymology.

[85]  M. Waring,et al.  Diethylpyrocarbonate and osmium tetroxide as probes for drug-induced changes in DNA conformation in vitro. , 1997, Methods in molecular biology.

[86]  J. Loo,et al.  Studying noncovalent protein complexes by electrospray ionization mass spectrometry. , 1997, Mass spectrometry reviews.

[87]  Gary L. Glish,et al.  Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides , 1992, Journal of the American Society for Mass Spectrometry.

[88]  D. Suck,et al.  Structure of DNase I , 1991 .

[89]  N. Farrell,et al.  Bis(Platinum) Complexes. Chemistry, Antitumor Activity and DNA-Binding , 1990 .