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Literature DB >> 26051649

Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair.

Ananya Paul¹, Rupesh Nanjunda¹, Arvind Kumar¹, Sarah Laughlin¹, Raja Nhili², Sabine Depauw², Shelby Sheldon Deuser¹, Yun Chai¹, Arpana S Chaudhary¹, Marie-Hélène David-Cordonnier², David W Boykin¹, W David Wilson³.

Abstract

DNA minor-groove-binding compounds have limited biological applications, in part due to problems with sequence specificity that cause off-target effects. A model to enhance specificity has been developed with the goal of preparing compounds that bind to two AT sites separated by G·C base pairs. Compounds of interest were probed using thermal melting, circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling methods. A new minor groove binder that can strongly and specifically recognize a single G·C base pair with flanking AT sequences has been prepared. This multi-site DNA recognition mode offers novel design principles to recognize entirely new DNA motifs.

Entities: Chemical Disease Gene

Keywords: Biophysical analysis; Heterocyclic diamidines; Mixed DNA recognition; Rational design; Sequence specificity

Mesh：

Substances：
Benzene Derivatives
DNA

Year: 2015 PMID： 26051649 PMCID： PMC4607563 DOI： 10.1016/j.bmcl.2015.05.005

Source DB: PubMed Journal: Bioorg Med Chem Lett ISSN： 0960-894X Impact factor: 2.823

40 in total

Review 1. Transcription factors as targets for cancer therapy.

Authors: James E Darnell
Journal: Nat Rev Cancer Date: 2002-10 Impact factor: 60.716

2. Synthesis and DNA interactions of benzimidazole dications which have activity against opportunistic infections.

Authors: R L Lombardy; F A Tanious; K Ramachandran; R R Tidwell; W D Wilson
Journal: J Med Chem Date: 1996-03-29 Impact factor: 7.446

3. Regulation of gene expression by small molecules.

Authors: J M Gottesfeld; L Neely; J W Trauger; E E Baird; P B Dervan
Journal: Nature Date: 1997-05-08 Impact factor: 49.962

4. Resolution of mixed site DNA complexes with dimer-forming minor-groove binders by using electrospray ionization mass spectrometry: compound structure and DNA sequence effects.

Authors: Sarah Laughlin; Siming Wang; Arvind Kumar; Abdelbasset A Farahat; David W Boykin; W David Wilson
Journal: Chemistry Date: 2015-02-20 Impact factor: 5.236

5. Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/pyrrole-containing polyamides.

Authors: Sameer Chavda; Yang Liu; Balaji Babu; Ryan Davis; Alan Sielaff; Jennifer Ruprich; Laura Westrate; Christopher Tronrud; Amanda Ferguson; Andrew Franks; Samuel Tzou; Chandler Adkins; Toni Rice; Hilary Mackay; Jerome Kluza; Sharjeel A Tahir; Shicai Lin; Konstantinos Kiakos; Chrystal D Bruce; W David Wilson; John A Hartley; Moses Lee
Journal: Biochemistry Date: 2011-03-25 Impact factor: 3.162

6. Targeting the inverted CCAAT box 2 in the topoisomerase IIalpha promoter by JH-37, an imidazole-pyrrole polyamide hairpin: design, synthesis, molecular biology, and biophysical studies.

Authors: James A Henry; N Minh Le; Binh Nguyen; Cameron M Howard; Suzanna L Bailey; Sarah M Horick; Karen L Buchmueller; Minal Kotecha; Daniel Hochhauser; John A Hartley; W David Wilson; Moses Lee
Journal: Biochemistry Date: 2004-09-28 Impact factor: 3.162

7. Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers.

Authors: J C Xuan; I T Weber
Journal: Nucleic Acids Res Date: 1992-10-25 Impact factor: 16.971

8. Structure-dependent inhibition of the ETS-family transcription factor PU.1 by novel heterocyclic diamidines.

Authors: Manoj Munde; Shuo Wang; Arvind Kumar; Chad E Stephens; Abdelbasset A Farahat; David W Boykin; W David Wilson; Gregory M K Poon
Journal: Nucleic Acids Res Date: 2013-10-23 Impact factor: 16.971

9. Phase I and pharmacokinetic study of trabectedin, a DNA minor groove binder, administered as a 24-h continuous infusion in Japanese patients with soft tissue sarcoma.

Authors: Takafumi Ueda; Shigeki Kakunaga; Masashi Ando; Kan Yonemori; Hideshi Sugiura; Kenji Yamada; Akira Kawai
Journal: Invest New Drugs Date: 2014-04-03 Impact factor: 3.850

10. Understanding mixed sequence DNA recognition by novel designed compounds: the kinetic and thermodynamic behavior of azabenzimidazole diamidines.

Authors: Ananya Paul; Yun Chai; David W Boykin; W David Wilson
Journal: Biochemistry Date: 2014-12-24 Impact factor: 3.162

12 in total

1. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences.

Authors: Sarah Laughlin-Toth; E Kathleen Carter; Ivaylo Ivanov; W David Wilson
Journal: Nucleic Acids Res Date: 2017-02-17 Impact factor: 16.971

2. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove.

Authors: Pu Guo; Ananya Paul; Arvind Kumar; Abdelbasset A Farahat; Dhiraj Kumar; Siming Wang; David W Boykin; W David Wilson
Journal: Chemistry Date: 2016-09-14 Impact factor: 5.236

Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair.

Review 1. Transcription factors as targets for cancer therapy.

2. Synthesis and DNA interactions of benzimidazole dications which have activity against opportunistic infections.

3. Regulation of gene expression by small molecules.

4. Resolution of mixed site DNA complexes with dimer-forming minor-groove binders by using electrospray ionization mass spectrometry: compound structure and DNA sequence effects.

5. Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/pyrrole-containing polyamides.

6. Targeting the inverted CCAAT box 2 in the topoisomerase IIalpha promoter by JH-37, an imidazole-pyrrole polyamide hairpin: design, synthesis, molecular biology, and biophysical studies.

7. Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers.

8. Structure-dependent inhibition of the ETS-family transcription factor PU.1 by novel heterocyclic diamidines.

9. Phase I and pharmacokinetic study of trabectedin, a DNA minor groove binder, administered as a 24-h continuous infusion in Japanese patients with soft tissue sarcoma.

10. Understanding mixed sequence DNA recognition by novel designed compounds: the kinetic and thermodynamic behavior of azabenzimidazole diamidines.

1. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences.

2. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove.

3. DNA-Binding Properties of New Fluorescent AzaHx Amides: Methoxypyridylazabenzimidazolepyrroleimidazole/pyrrole.

4. Systematic synthetic and biophysical development of mixed sequence DNA binding agents.

5. Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA.

6. A modular design for minor groove binding and recognition of mixed base pair sequences of DNA.

7. Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove.

Review 8. An overview of recent advances in duplex DNA recognition by small molecules.

Review 9. May the Best Molecule Win: Competition ESI Mass Spectrometry.

10. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition.