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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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2
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Lee C. AA mismatched DNAs with a single base difference exhibit a large structural change and a propensity for the parallel-stranded conformation. J Anal Sci Technol 2010. [DOI: 10.5355/jast.2010.37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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3
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Meyer ST, Hergenrother PJ. Small molecule ligands for bulged RNA secondary structures. Org Lett 2010; 11:4052-5. [PMID: 19678613 DOI: 10.1021/ol901478x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay.
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Affiliation(s)
- S Todd Meyer
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61801, USA
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4
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Ma D, Lin Y, Xiao Z, Kappen L, Goldberg IH, Kallmerten AE, Jones GB. Designed DNA probes from the neocarzinostatin family: impact of glycosyl linkage stereochemistry on bulge base binding. Bioorg Med Chem 2009; 17:2428-32. [PMID: 19243952 DOI: 10.1016/j.bmc.2009.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 02/02/2009] [Accepted: 02/03/2009] [Indexed: 10/21/2022]
Abstract
Bulged sites in DNA and RNA have become targets for rational drug design due to their suspected involvement in a number of key biomolecular processes. A lead compound, derived from the enediyne natural product NCS-chrom has been used to inform chemical synthesis of a family of designed probes of DNA bulges, one of which shows 80 nM affinity for a two base bulged target. Key contributors to binding of these spirocyclic compounds have been studied in order to correlate affinity and specificity with structural features. Herein, we demonstrate that the glycosyl linkage stereochemistry of the pendant aminofucosyl group plays a pivotal role in binding, and coupled with insight obtained with various bulged targets, will allow rational design of second generation ligands.
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Affiliation(s)
- Dong Ma
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, 101HT, Boston, MA 02115, USA
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5
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A bulge binding agent with novel wedge-shape topology for stimulation of DNA triplet repeat strand slippage synthesis. Bioorg Med Chem Lett 2008; 18:6184-8. [DOI: 10.1016/j.bmcl.2008.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 09/25/2008] [Accepted: 10/01/2008] [Indexed: 11/15/2022]
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6
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Affiliation(s)
- Jason R Thomas
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61822, USA
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Zhang N, Lin Y, Xiao Z, Jones GB, Goldberg IH. Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA. Biochemistry 2007; 46:4793-803. [PMID: 17388570 PMCID: PMC2569200 DOI: 10.1021/bi602599d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution structure of the complex formed between an oligodeoxynucleotide containing a two-base bulge (5'-CCATCGTCTACCTTTGGTAGGATGG) and SCA-alpha2, a designed spirocyclic helical molecule, has been elucidated. SCA-alpha2, a close mimic of the metabolite, NCSi-gb, of the DNA bulge-specific enediyne antibiotic neocarzinostatin, differs in possessing a more stable spirocyclic ring system and in lacking certain bulky groupings that compromise bulged DNA binding. This study provides a detailed comparison of the binding modes of the two complexes and provides new insights into the importance of shape and space, as opposed to simple nucleotide sequence, in complex formation at the bulge site. The two rigidly held aromatic rings of SCA-alpha2 form a right-handed helical molecular wedge that specifically penetrates the bulge-binding pocket and immobilizes the two bulge residues (GT), which point toward the minor groove, rather than the major groove as in the NCSi-gb.bulged DNA complex. The ligand aromatic ring systems stack on the DNA bulge-flanking base pairs that define the long sides of the triangular prism binding pocket. Like NCSi-gb, SCA-alpha2 possesses the natural N-methylfuranose moiety, alpha-linked to the benzindanol (BI) moiety. The amino sugar anchors in the major groove of the DNA and points toward the 3'-bulge-flanking base pair. Lacking the bulky cyclocarbonate of NCSi-gb, the SCA-alpha2.bulged DNA complex has a much less twisted and buckled 3'-bulge-flanking base pair (dG20.dC8), and the G20 residue stacks directly above the BI ring platform. Also, the absence of the methyl group and the free rotation of the methoxy group on the dihydronaphthanone (NA) moiety of SCA-alpha2 allow better stacking geometry of the NA ring above the 5'-bulge-flanking dG21.dC5 base pair. These and other considerations help to explain why NCSi-gb binds very poorly to bulged RNA and are consistent with the recent observation of good binding with SCA-alpha2. Thus, although the two complexes resemble each other closely, they differ in important local environmental details. SCA-alpha2 has a better hand-in-glove fit at the bulge site, making it an ideal platform for the placement of moieties that can react covalently with the DNA and for generating congeners specific for bulges in RNA.
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Affiliation(s)
- Na Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Yiqing Lin
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Ziwei Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Graham B. Jones
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Irving H. Goldberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
- To whom correspondence should be addressed: Irving H. Goldberg, Telephone: (617) 432−1787; Fax: (617) 432−0471, E-mail:
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Kappen LS, Lin Y, Jones GB, Goldberg IH. Probing DNA bulges with designed helical spirocyclic molecules. Biochemistry 2007; 46:561-7. [PMID: 17209566 PMCID: PMC2569198 DOI: 10.1021/bi061744d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because bulged structures (unpaired bases) in nucleic acids are of general biological significance, it has been of interest to design small molecules as specific probes of bulge function. On the basis of our earlier work with the specific DNA bulge-binding metabolite obtained from the enediyne antitumor antibiotic neocarzinostatin chromophore (NCS-chrom), we have prepared three small helical spirocyclic molecules that most closely mimic the natural product. These wedge-shaped molecules resemble the natural product in having the sugar residue attached to the same five-membered ring system. In one instance, the sugar is aminoglucose in beta-glycosidic linkage, and in the other, two enantiomers have the natural sugar N-methylfucosamine in alpha-glycosidic linkage. All three analogues were found to interfere with bulge-specific cleavage by NCS-chrom and the ability of bulged DNA to serve as a template for DNA polymerase 1 in accordance with their binding affinities for DNA containing a two-base bulge. Comparable results were obtained with the analogues for the less efficiently cleaved three-base bulge DNA structures. In each situation, the enantiomers possessing the natural sugar in alpha-glycosidic linkage are the most potent inhibitors of the cleavage reaction. In the DNA polymerase reactions, again, the closest natural product mimics were the most effective in selectively impeding nucleotide extension at the bulge site, presumably by complex formation. These results demonstrate the potential usefulness of bulge-binding compounds in modifying DNA structure and function and support efforts to design and prepare reactive species of these molecules that can covalently modify bulged DNA.
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Affiliation(s)
- Lizzy S. Kappen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Massachusetts 02115
| | - Yiqing Lin
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Graham B. Jones
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Irving H. Goldberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Massachusetts 02115
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Jones GB, Lin Y, Xiao Z, Kappen L, Goldberg IH. Molecular probes of DNA bulges: Functional assay and spectroscopic analysis. Bioorg Med Chem 2007; 15:784-90. [PMID: 17085052 DOI: 10.1016/j.bmc.2006.10.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 10/22/2006] [Accepted: 10/23/2006] [Indexed: 11/30/2022]
Abstract
Bulged structures in DNA and RNA have been linked to biomolecular processes involved in numerous diseases, thus probes with affinity for these nucleic acid targets would be of considerable utility to chemical biologists. Herein, we report guided chemical synthesis of small molecules capable of binding to DNA bulges by virtue of their unique (spirocyclic) geometry. The agents, modeled on a natural product congener, show pronounced selectivity for specific bulged motifs and are able to enhance slipped DNA synthesis, a hallmark functional assay of bulge binding. Significantly, bulge-agent complexes demonstrate characteristic fluorescent signatures depending on bulge and flanking sequence in the oligo. It is anticipated that these signature patterns can be harnessed as molecular probes of bulged hotspots in DNA and RNA.
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Affiliation(s)
- Graham B Jones
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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Gaikwad NW, Hwang GS, Goldberg IH. Synthesis and NMR binding study of a chiral spirocyclic helical analogue of a natural DNA bulge binder. Org Lett 2006; 6:4833-6. [PMID: 15606078 DOI: 10.1021/ol048152c] [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] [Indexed: 01/26/2023]
Abstract
[reaction: see text] Synthesis of chiral spirocyclic helical compounds which mimic the molecular architecture of the potent DNA bulge binder obtained from the antitumor agent NCS-chrom has been accomplished. Structural analysis of the compounds by CD and NMR is presented. NMR titration study indicates binding of P,alpha-helimer (1d) at a two-base bulge site in a DNA oligomer, providing insight to the design of agents as specific probes of a bulged structure in nucleic acids.
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Affiliation(s)
- Nilesh W Gaikwad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Xiao Z, Kappen LS, Goldberg IH. Development of new simple molecular probes of DNA bulged structures. Bioorg Med Chem Lett 2006; 16:2895-9. [PMID: 16546380 DOI: 10.1016/j.bmcl.2006.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 02/28/2006] [Accepted: 03/01/2006] [Indexed: 10/24/2022]
Abstract
NCSi-gb is a neocarzinostatin chromophore (NCS-chrom) metabolite which binds strongly to certain two-base DNA bulges. Compared with previously reported NCSi-gb analogues, a new analogue with a different aminoglycoside position was synthesized, and it showed strong fluorescence and improved binding and sequence selectivity to DNA bulges. The N-dimethylated form of this analogue had a similar binding pattern, and it competitively inhibited bulge-specific cleavage by NCS-chrom.
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Affiliation(s)
- Ziwei Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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12
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Xi Z, Ouyang D, Mu HT. Stimulation on DNA triplet repeat strand slippage synthesis by the designed spirocycles. Bioorg Med Chem Lett 2006; 16:1180-4. [PMID: 16364637 DOI: 10.1016/j.bmcl.2005.11.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 11/08/2005] [Accepted: 11/24/2005] [Indexed: 11/24/2022]
Abstract
The designed simpler chiral spirocyclic helical compounds that mimic the molecular architecture of the DNA bulge binder NCSi-gb have been prepared. It has been found that the synthesized spirocyclic compounds have strong stimulation effect on DNA slippage synthesis. Their stimulation activities on DNA strand slippage suggest that they may bind to or induce the formation of a non Watson-Crick structure during in vitro replication of DNA triplet repeats.
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Affiliation(s)
- Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, Nankai University, Tianjin 300071, China.
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Xi Z, Ouyang D, Mu HT. Interaction of bulged DNA with leucine-containing mimics of NCS-chrom. Bioorg Med Chem Lett 2006; 16:1185-90. [PMID: 16406515 DOI: 10.1016/j.bmcl.2005.11.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 11/08/2005] [Accepted: 11/24/2005] [Indexed: 10/25/2022]
Abstract
Synthesis of chiral spirocyclic helical compounds containing leucine that mimic the molecular architecture of the potent DNA bulge binder obtained from the natural product metabolite NCSi-gb has been accomplished. The interaction between the compounds and DNA was studied by circular dichroism (CD) method. The results suggested that the two synthetic diastereoisomers specifically targeted the bulge site of DNA and induced conformational change of bulged DNA greatly.
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Affiliation(s)
- Zhen Xi
- Institute of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, Tianjin 300071, China.
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14
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Xiao Z, Zhang N, Lin Y, Jones GB, Goldberg IH. Spirocyclic helical compounds as binding agents for bulged RNA, including HIV-2 TAR. Chem Commun (Camb) 2006:4431-3. [PMID: 17057867 DOI: 10.1039/b610007d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on fluorescence binding studies and 1D 1H NMR studies, designed synthetic analogues of NCSi-gb bind specifically with two-base bulged RNA, including HIV-2 TAR RNA, making them potential lead compounds for antiviral drug development.
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Affiliation(s)
- Ziwei Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Fouad FS, Xi Z, Goldberg IH, Jones GB. Preparation of alkylation agents for bulged DNA microenvironments. Bioorg Med Chem Lett 2004; 14:3337-9. [PMID: 15149702 DOI: 10.1016/j.bmcl.2004.03.092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Accepted: 03/14/2004] [Indexed: 10/26/2022]
Abstract
A designed molecule with capacity to alkylate DNA bulges has been prepared from readily available starting materials. The spirocyclic template utilized was designed on the basis of established architectures, and equipped with a mustard alkylating group. Preliminary studies confirm alkylation of specific bulged sequences, paving the way for second generation substrates with higher affinity.
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Affiliation(s)
- Farid S Fouad
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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