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Crystallographic evidence of Watson-Crick connectivity in the base pair of anionic adenine with thymine. Proc Natl Acad Sci U S A 2020; 117:18224-18230. [PMID: 32680959 PMCID: PMC7414232 DOI: 10.1073/pnas.2008379117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N4444]+) or tetrabutylphosphonium ([P4444]+) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N4444][Ad]·2H2O, and thymine, [P4444][Thy]·2H2O, as well as the double salt cocrystal, [P4444]2[Ad][Thy]·3H2O·2HThy. The cocrystal includes the anionic [Ad-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson-Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.
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2
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Guo C, Asamitsu S, Kashiwazaki G, Sato S, Bando T, Sugiyama H. DNA Interstrand Crosslinks by H-pin Polyamide (S
)-seco
-CBI Conjugates. Chembiochem 2016; 18:166-170. [DOI: 10.1002/cbic.201600425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Chuanxin Guo
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
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Brovarets' OO. [Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?]. UKRAINIAN BIOCHEMICAL JOURNAL 2013; 85:98-103. [PMID: 24319979 DOI: 10.15407/ubj85.04.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.
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4
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Brovarets’ OO, Yurenko YP, Hovorun DM. Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study. J Biomol Struct Dyn 2013; 32:993-1022. [PMID: 23730732 DOI: 10.1080/07391102.2013.799439] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Hopton SR, Thompson AS. Manipulative Interplay of Two Adozelesin Molecules with d(ATTAAT)2 Achieving Ligand-Stacked Watson–Crick and Hoogsteen Base-Paired Duplex Adducts. Biochemistry 2011; 50:4143-54. [DOI: 10.1021/bi101945a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suzanne R. Hopton
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Andrew S. Thompson
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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6
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Nikolova EN, Kim E, Wise AA, O'Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature 2011; 470:498-502. [PMID: 21270796 PMCID: PMC3074620 DOI: 10.1038/nature09775] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Accepted: 01/05/2011] [Indexed: 12/17/2022]
Abstract
Sequence-directed variations in the canonical DNA double helix structure that retain Watson-Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson-Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A•T and G•C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson-Crick base-pairing. The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
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7
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Vincenzi B, Napolitano A, Frezza AM, Schiavon G, Santini D, Tonini G. Wide-spectrum characterization of trabectedin: biology, clinical activity and future perspectives. Pharmacogenomics 2010; 11:865-78. [DOI: 10.2217/pgs.10.69] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ecteinascidin-743 (trabectedin, Yondelis®; PharmaMar, Madrid, Spain), a 25-year-old antineoplastic alkylating agent, has recently shown unexpected and interesting mechanisms of action. Trabectedin causes perturbation in the transcription of inducible genes (e.g., the multidrug resistance gene MDR1) and interaction with DNA repair mechanisms (e.g., the nucleotide excision repair pathway) owing to drug-related DNA double strand breaks and adduct formation. Trabectedin was the first antineoplastic agent from a marine source (namely, the Caribbean tunicate Ecteinascidia turbinata) to receive marketing authorization. This article summarizes the mechanisms of action, the complex metabolism, the main toxicities, the preclinical and clinical evidences of its antineoplastic effects in different types of cancer and, finally, the future perspectives of this promising drug.
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Affiliation(s)
| | - Andrea Napolitano
- University Campus Bio-Medico, Medical Oncology, Via Alvaro del Portillo 200, 00128 Rome, Italy
| | - Anna Maria Frezza
- University Campus Bio-Medico, Medical Oncology, Via Alvaro del Portillo 200, 00128 Rome, Italy
| | - Gaia Schiavon
- University Campus Bio-Medico, Medical Oncology, Via Alvaro del Portillo 200, 00128 Rome, Italy
| | - Daniele Santini
- University Campus Bio-Medico, Medical Oncology, Via Alvaro del Portillo 200, 00128 Rome, Italy
| | - Giuseppe Tonini
- University Campus Bio-Medico, Medical Oncology, Via Alvaro del Portillo 200, 00128 Rome, Italy
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Jensen EA, Allen BD, Kishi Y, O'Leary DJ. Conformational analysis of a covalently cross-linked Watson-Crick base pair model. Bioorg Med Chem Lett 2008; 18:5884-7. [PMID: 18706810 PMCID: PMC2590868 DOI: 10.1016/j.bmcl.2008.07.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/24/2008] [Accepted: 07/28/2008] [Indexed: 11/30/2022]
Abstract
Low-temperature NMR experiments and molecular modeling have been used to characterize the conformational behavior of a covalently cross-linked DNA base pair model. The data suggest that Watson-Crick or reverse Watson-Crick hydrogen bonding geometries have similar energies and can interconvert at low temperatures. This low-temperature process involves rotation about the crosslink CH(2)C(5') (psi) carbon-carbon bond, which is energetically preferred over the alternate CH(2)N(3) (phi) carbon-nitrogen bond rotation.
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Affiliation(s)
- Erik A Jensen
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, CA 91711, USA
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9
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Kryachko ES, Nguyen MT. Unnatural Covalent DNA Base Pairing: Quantum Chemical Study. J Phys Chem A 2002. [DOI: 10.1021/jp020810s] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eugene S. Kryachko
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Minh Tho Nguyen
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
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Park HJ. DNA structural perturbation induced by the CPI-derived DNA interstrand cross-linker: molecular mechanisms for the sequence specific recognition. Arch Pharm Res 2001; 24:455-65. [PMID: 11693550 DOI: 10.1007/bf02975194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The highly potent cytotoxic DNA-DNA cross-linker consists of two cyclopropa[c]pyrrolo[3, 4-3]indol-4(5H)-ones indoles [(+)-CPI-I] joined by a bisamido pyrrole (abbreviated to "Pyrrole"). The Pyrrole is a synthetic analog of Bizelesin, which is currently in phase II clinical trials due to its excellent in vivo antitumor activity. The Pyrrole has 10 times more potent cytotoxicity than Bizelesin and mostly form DNA-DNA interstrand cross-links through the N3 of adenines spaced 7 bp apart. The Pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., 5'-T(A/T)2G(A/T)2A*-3'), while Bizelesin prefers purely AT-rich sequences (e.g., 5'-T(A/T)4 or 5A*-3', where T represents the cross-strand adenine alkylation and A* represents an adenine alkylation) (Park et al., 1996). In this study, the high-field 1H-NMR and rMD studies are conducted on the 11-mer DNA duplex adduct of the Pyrrole where the 5'-TTAGTTA*-3' sequence is cross-linked by the drug. A severe structural perturbation is observed in the intervening sequences of cross-linking site, while a normal B-DNA structure is maintained in the region next to the drug-modified adenines. Based upon these observations, we propose that the interplay between the bisamido pyrrole unit of the drug and central G/C base pair (hydrogen-bonding interactions) is involved in the process of cross-linking reaction, and sequence specificity is the outcome of those interactions. This study suggests a mechanism for the sequence specific cross-linking reaction of the Pyrrole, and provides a further insight to develop new DNA sequence selective and distortive cross-linking agents.
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Affiliation(s)
- H J Park
- College of Pharmacy Sungkyunkwan, University, Suwon 440-746, Korea.
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11
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Zhou Q, Duan W, Simmons D, Shayo Y, Raymond MA, Dorr RT, Hurley LH. Design and synthesis of a novel DNA-DNA interstrand adenine-guanine cross-linking agent. J Am Chem Soc 2001; 123:4865-6. [PMID: 11457309 DOI: 10.1021/ja005658r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Q Zhou
- Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, USA
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12
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Li H, Qiu Y, Moyroud E, Kishi Y. Synthesis of DNA Oligomers Possessing a Covalently Cross‐Linked Watson–Crick Base Pair Model. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010417)113:8<1519::aid-ange1519>3.0.co;2-#] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hong‐Yu Li
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617‐495‐5150
| | - Yao‐Ling Qiu
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617‐495‐5150
| | - Elisabeth Moyroud
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617‐495‐5150
| | - Yoshito Kishi
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617‐495‐5150
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Li HY, Qiu YL, Moyroud E, Kishi Y. Synthesis of DNA Oligomers Possessing a Covalently Cross-Linked Watson-Crick Base Pair Model. Angew Chem Int Ed Engl 2001; 40:1471-1475. [PMID: 29712372 DOI: 10.1002/1521-3773(20010417)40:8<1471::aid-anie1471>3.0.co;2-i] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2000] [Revised: 01/18/2001] [Indexed: 11/11/2022]
Abstract
Building bridges: A feasible solid-phase synthesis of antiparallel n-, h-, and H-type DNA oligomers has been demonstrated. The oligomers possess a CH2 -bridged base-pair model that should be conformationally flexible, even after base pairing.
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Affiliation(s)
- Hong-Yu Li
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617-495-5150
| | - Yao-Ling Qiu
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617-495-5150
| | - Elisabeth Moyroud
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617-495-5150
| | - Yoshito Kishi
- Department of Chemistry and Chemical Biology Harvard University, Cambridge, MA 02138 (USA) Fax: (+1) 617-495-5150
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14
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Abstract
In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.
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Affiliation(s)
- B S Reddy
- Department of Chemistry, University of Alberta, Edmonton, Canada
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Seaman FC, Hurley LH. Molecular Basis for the DNA Sequence Selectivity of Ecteinascidin 736 and 743: Evidence for the Dominant Role of Direct Readout via Hydrogen Bonding. J Am Chem Soc 1998. [DOI: 10.1021/ja983091x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frederick C. Seaman
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
| | - Laurence H. Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
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Lee SJ, Seaman FC, Sun D, Xiong H, Kelly RC, Hurley LH. Replacement of the Bizelesin Ureadiyl Linkage by a Guanidinium Moiety Retards Translocation from Monoalkylation to Cross-Linking Sites on DNA. J Am Chem Soc 1997. [DOI: 10.1021/ja963873v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seung-Joo Lee
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074, the Institute for Drug Development, 14960 Omicron Drive, San Antonio, Texas 78245-3217, and The Pharmacia Upjohn Company, 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Frederick C. Seaman
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074, the Institute for Drug Development, 14960 Omicron Drive, San Antonio, Texas 78245-3217, and The Pharmacia Upjohn Company, 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Daekyu Sun
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074, the Institute for Drug Development, 14960 Omicron Drive, San Antonio, Texas 78245-3217, and The Pharmacia Upjohn Company, 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Heping Xiong
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074, the Institute for Drug Development, 14960 Omicron Drive, San Antonio, Texas 78245-3217, and The Pharmacia Upjohn Company, 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Robert C. Kelly
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074, the Institute for Drug Development, 14960 Omicron Drive, San Antonio, Texas 78245-3217, and The Pharmacia Upjohn Company, 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Laurence H. Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074, the Institute for Drug Development, 14960 Omicron Drive, San Antonio, Texas 78245-3217, and The Pharmacia Upjohn Company, 301 Henrietta Street, Kalamazoo, Michigan 49001
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Boger DL, Garbaccio RM. Catalysis of the CC-1065 and duocarmycin DNA alkylation reaction: DNA binding induced conformational change in the agent results in activation. Bioorg Med Chem 1997; 5:263-76. [PMID: 9061191 DOI: 10.1016/s0968-0896(96)00238-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A number of indirect observations are summarized that suggest the rate acceleration for the CC-1065 and duocarmycin. DNA alkylation reaction is derived in part from a DNA binding-induced conformational change in the agents which substantially increases their inherent reactivity. This ground-state destabilization of the agent, which we suggest results from a binding-induced twist in the linking N2 amide and requires a rigid extended N2 amide substituent, disrupts the vinylogous amide stabilization and activates the agents for DNA alkylation.
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Affiliation(s)
- D L Boger
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
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19
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Park HJ, Kelly RC, Hurley LH. The Chemical Evolution of DNA−DNA Interstrand Cross-Linkers That Recognize Defined Mixed AT and GC Sequences. J Am Chem Soc 1996. [DOI: 10.1021/ja961678a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Hyun-Ju Park
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Robert C. Kelly
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Laurence H. Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
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20
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Seaman FC, Hurley L. Manipulative Interplay of the Interstrand Cross-Linker Bizelesin with d(TAATTA)2 To Achieve Sequence Recognition of DNA. J Am Chem Soc 1996. [DOI: 10.1021/ja961924i] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frederick C. Seaman
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
| | - Laurence Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
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21
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Boger DL, Johnson DS. CC-1065 und die Duocarmycine: mechanistische Studien zum Verständnis ihrer biologischen Funktion. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961081306] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Seaman FC, Chu J, Hurley L. Cross-Linkage by “Intact” Bizelesin and Bisalkylation by the “Separated Halves” of the Bizelesin Dimer: Contrasting Drug Manipulation of DNA Conformation (5‘-TAATTA-3‘) Directs Alkylation toward Different Adenine Targets. J Am Chem Soc 1996. [DOI: 10.1021/ja960017a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frederick C. Seaman
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074
| | - Jianxiong Chu
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074
| | - Laurence Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712-1074
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23
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Escudé C, Mohammadi S, Sun JS, Nguyen CH, Bisagni E, Liquier J, Taillandier E, Garestier T, Hélène C. Ligand-induced formation of hoogsteen-paired parallel DNA. CHEMISTRY & BIOLOGY 1996; 3:57-65. [PMID: 8807829 DOI: 10.1016/s1074-5521(96)90085-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Based on molecular modeling studies, a model has been proposed for intercalation of triple-helix-specific ligands (benzopyridoindole (BPI) derivatives) into triple helices, in which the intercalating compounds interact mainly with the Hoogsteen-paired strands of the triple helix. We set out to test this model experimentally using DNA duplexes capable of forming parallel Hoogsteen base-paired structures. RESULTS We have investigated the possible formation of a parallel DNA structure involving Hoogsteen hydrogen bonds by thermal denaturation, FTIR spectroscopy and gel-shift experiments. We show that BPI derivatives bind to Hoogsteen base-paired duplexes and stabilize them. The compounds induce a reorganization from a non-perfectly matched antiparallel Watson- Crick duplex into a perfectly matched parallel Hoogsteen-paired duplex. CONCLUSIONS These results suggest that preferential intercalation of BPI derivatives in triple helices is due to their ability to interact specifically with the Hoogsteen-paired bases. The results are consistent with a model proposed on the basis of molecular modeling studies using energy minimization, and they open a new field of investigations regarding the biological relevance of Hoogsteen base-pairing.
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Affiliation(s)
- C Escudé
- Laboratoire de Biophysique, INSERM U201 CNRS URA481, Muséum National d'Histoire Naturelle, 43, rue Cuvier, 75231 Paris Cedex 05, France
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Thompson AS, Fan JY, Sun D, Hansen M, Hurley LH. Determination of the structural role of the internal guanine-cytosine base pair in recognition of a seven-base-pair sequence cross-linked by bizelesin. Biochemistry 1995; 34:11005-16. [PMID: 7669758 DOI: 10.1021/bi00035a006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Bizelesin (formerly U77,779, The Upjohn Co.) is a bifunctional DNA cross-linking antitumor antibiotic consisting of two open-ring homologs of the (+)-CC-1065 cyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one (CPI) subunits connected by a rigid linking moiety. Previous studies have shown that Bizelesin most often forms an interstrand cross-link through the N3 of two adenines 6 base pairs (bp) apart (inclusive of the modified adenines). However, gel electrophoresis studies have also indicated that Bizelesin forms 7-bp cross-links in specific sequences. In most of these sequences the cross-linked adenines represent the only possible cross-link site (i.e., no 6-bp site is available); however, in several sequences, a 7-bp sequence is selected in overwhelming preference to a possible 6-bp sequence. In this study, we demonstrate the unique requirement for a G.C base pair within this sequence and the critical presence of the exocyclic 2-amino group of guanine. In a subsequent two-dimensional 1H-NMR study that concentrates on the 7-bp cross-link formed with the sequence 5'-TTAGTTA-3', the role of the central G.C base pairs in the formation of a 7-bp cross-link is probed. 1H-NMR analysis coupled with restrained molecular dynamics (rMD) provides evidence for distortion around the covalently modified adenines. Because of this distortion, the modified bases are twisted toward the center of the duplex adduct, effectively reducing the cross-linked distance. The rMD study also indicates that a hydrogen bond is formed between the exocyclic amine of the central guanine and the carbonyl of the ureylene linker. On the basis of the observation of the distortion in the duplex and the hydrogen bonding between the drug and DNA, it is possible to speculate on the role of the central G.C bases in this sequence preference and propose a mechanism by which Bizelesin forms a 7-bp rather than a 6-bp cross-link with this sequence.
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Affiliation(s)
- A S Thompson
- Drug Dynamics Institute, College of Pharmacy, University of Texas at Austin 78712, USA
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Jebaratnam DJ, Arya DP, Chen H, Kugabalasooriar S, Duc Vo. A single precursor approach to new DNA cleaving and crosslinking agents. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00193-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Remias MG, Lee CS, Haworth IS. Molecular dynamics simulations of chlorambucil/DNA adducts. A structural basis for the 5'-GNC interstrand DNA crosslink formed by nitrogen mustards. J Biomol Struct Dyn 1995; 12:911-36. [PMID: 7779307 DOI: 10.1080/07391102.1995.10508784] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The alkylation of DNA by chlorambucil has been studied using a computational approach. Molecular dynamics simulations were performed on the fully solvated non-covalent complex, two monoadducts and a crosslinked diadduct of chlorambucil with the d(CGG3G2CGC).-d(GCG1CCCG) duplex, in which the N7 atoms of G1, G2 and G3 are potential alkylation sites. The results provide a structural basis for the preference of nitrogen mustards to crosslink DNA duplexes at a 5'-GNC site (a 1,3 crosslink, G1-G3) rather than at a 5'-GC sites (a 1,2 crosslink, G1-G2). In the non-covalent complex simulation the drug reoriented from a non-interstrand crosslinking location to a position favorable for G1-G3 diadduct formation. It proved possible to construct a G1-G3 diadduct from a structure from the non-covalent simulation, and continue the molecular dynamics calculation without further disruption of the DNA structure. A crosslinked diadduct developed with four BII conformations on the 3' side of each alkylated guanine and of their respective complementary cytosine. In the first monoadduct simulation the starting point was the same DNA conformation used in the crosslinked diadduct simulation with alkylation at G1. In this simulation the DNA deformation was reduced, with the helix returning to a more canonical form. A second monoadduct simulation was started from a canonical DNA conformation alkylated at G3. Here, no significant motion towards a potential crosslinking conformation occurred. Collectively, the results suggest that crosslink formation is dependent upon the drug orientation prior to alkylation and the required deformation of the DNA to permit 1,3 crosslinking can largely be achieved in the non-covalent complex.
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Affiliation(s)
- M G Remias
- Dept. of Pharmaceutical Sciences, University of Southern California, Los Angeles 90033, USA
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Gallego J, Luque FJ, Orozco M, Gago F. Binding of echinomycin to d(GCGC)2 and d(CCGG)2: distinct stacking interactions dictate the sequence-dependent formation of Hoogsteen base pairs. J Biomol Struct Dyn 1994; 12:111-29. [PMID: 7848562 DOI: 10.1080/07391102.1994.10508091] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular dynamics simulations have been used to explore the behavior of the complexes of echinomycin with the DNA tetramers d(GCGC)2 and d(CCGG)2 in which the terminal bases have been paired according to either a Hoogsteen or a Watson-Crick hydrogen bonding scheme. The energy of the four resulting complexes has been monitored along the dynamics trajectories and the interaction energy between echinomycin and DNA has been decomposed into contributions arising from the planar aromatic systems and the depsipeptide part of the antibiotic. Our calculations predict a large increase in overall stabilization upon protonation of the terminal cytosines and subsequent Hoogsteen pair formation in the complex of echinomycin with d(GCGC)2 but not with d(CCGG)2, in agreement with the experimental evidence [Gao and Patel, Quart. Rev. Biophys. 22, 93-138 (1989)]. The conformational preferences appear to arise mainly from differential stacking interactions in which the electrostatic component is shown to play a dominant role. Differences in hydrogen bonding patterns are also found among the complexes and these are compared in relation to available crystal structures. The binding of echinomycin to DNA appears as a complex process involving many interrelated variables.
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Affiliation(s)
- J Gallego
- Departamento de Fisiología y Farmacologia, Universidad de Alcalá de Henares, Madrid, Spain
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