1
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Effects of N-terminus modified Hx-amides on DNA binding affinity, sequence specificity, cellular uptake, and gene expression. Bioorg Med Chem Lett 2021; 47:128158. [PMID: 34058343 DOI: 10.1016/j.bmcl.2021.128158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Five X-HxIP (Hx-amides) 6a-e, in which the N-terminus p-anisyl moiety is modified, were designed and synthesised with the purpose of optimising DNA binding, improving cellular uptake/nuclear penetration, and enhancing the modulation of the topoisomerase IIα (TOP2A) gene expression. The modifications include a fluorophenyl group and other heterocycles bearing different molecular shapes, size, and polarity. Like their parent compound HxIP 3, all five X-HxIP analogues bind preferentially to their cognate sequence 5'-TACGAT-3', which is found embedded on the 5' flank of the inverted CCAAT box-2 (ICB2) site in the TOP2A gene promoter, and inhibit protein complex binding. Interestingly, the 4-pyridyl analog 6a exhibits greater binding affinity for the target DNA sequence and abolishes the protein:ICB2 interaction in vitro, at a lower concentration, compared to the prototypical compound HxIP 3. Analogues 6b-e, display improved DNA sequence specificity, but reduced binding affinity for the cognate sequence, relative to the unmodified HxIP 3, with polyamides 6b and 6e being the most sequence selective. However, unlike 3 and 6b, 6a was unable to enter cells, access the nucleus and thereby affect TOP2A gene expression in confluent human lung cancer cells. These results show that while DNA binding affinity and sequence selectivity are important, consideration of cellular uptake and concentration in the nucleus are critical when exerting biological activity is the desired outcome. By characterising the DNA binding, cellular uptake and gene regulatory properties of these small molecules, we can elucidate the determinants of the elicited biological activity, which can be impacted by even small structural modifications in the polyamide molecular design.
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2
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Liu B, Pett L, Kiakos K, Patil PC, Satam V, Hartley JA, Lee M, Wilson WD. DNA-Binding Properties of New Fluorescent AzaHx Amides: Methoxypyridylazabenzimidazolepyrroleimidazole/pyrrole. Chembiochem 2018; 19:1979-1987. [PMID: 29974647 DOI: 10.1002/cbic.201800273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Indexed: 11/11/2022]
Abstract
DNA minor groove binding polyamides have been extensively developed to control abnormal gene expression. The establishment of novel, inherently fluorescent 2-(p-anisyl)benzimidazole (Hx) amides has provided an alternative path for studying DNA binding in cells by direct observation of cell localization. Because of the 2:1 antiparallel stacking homodimer binding mode of these molecules to DNA, modification of Hx amides to 2-(p-anisyl)-4-azabenzimidazole (AzaHx) amides has successfully extended the DNA-recognition repertoire from central CG [recognized by Hx-I (I=N-methylimidazole)] to central GC [recognized by AzaHx-P (P=N-methylpyrrole)] recognition. For potential targeting of two consecutive GG bases, modification of the AzaHx moiety to 2- and 3-pyridyl-aza-benzimidazole (Pyr-AzaHx) moieties was explored. The newly designed molecules are also small-sized, fluorescent amides with the Pyr-AzaHx moiety connected to two conventional five-membered heterocycles. Complementary biophysical methods were performed to investigate the DNA-binding properties of these molecules. The results showed that neither 3-Pyr-AzaHx nor 2-Pyr-AzaHx was able to mimic I-I=N-methylimidazole-N-methylimidazole to target GG dinucleotides specifically. Rather, 3-Pyr-AzaHx was found to function like AzaHx, f-I (f=formamide), or P-I as an antiparallel stacked dimer. 3-Pyr-AzaHx-PI (2) binds 5'-ACGCGT'-3' with improved binding affinity and high sequence specificity in comparison to its parent molecule AzaHx-PI (1). However, 2-Pyr-AzaHx is detrimental to DNA binding because of an unfavorable steric clash upon stacking in the minor groove.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA
| | - Luke Pett
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Pravin C Patil
- Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA
| | - Vijay Satam
- Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA
| | - John A Hartley
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Moses Lee
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA.,Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA.,Current address: M. J. Murdock Charitable Trust, 703 Broadway Street, Suite, 710, Vancouver, WA, 98660, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA
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3
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Kiakos K, Englinger B, Yanow SK, Wernitznig D, Jakupec MA, Berger W, Keppler BK, Hartley JA, Lee M, Patil PC. Design, synthesis, nuclear localization, and biological activity of a fluorescent duocarmycin analog, HxTfA. Bioorg Med Chem Lett 2018; 28:1342-1347. [PMID: 29548574 DOI: 10.1016/j.bmcl.2018.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/23/2018] [Accepted: 03/05/2018] [Indexed: 01/20/2023]
Abstract
HxTfA 4 is a fluorescent analog of a potent cytotoxic and antimalarial agent, TfA 3, which is currently being investigated for the development of an antimalarial vaccine, PlasProtect®. HxTfA contains a p-anisylbenzimidazole or Hx moiety, which is endowed with a blue emission upon excitation at 318 nm; thus enabling it to be used as a surrogate for probing the cellular fate of TfA using confocal microscopy, and addressing the question of nuclear localization. HxTfA exhibits similar selectivity to TfA for A-tract sequences of DNA, alkylating adenine-N3, albeit at 10-fold higher concentrations. It also possesses in vitro cytotoxicity against A549 human lung carcinoma cells and Plasmodium falciparum. Confocal microscopy studies showed for the first time that HxTfA, and by inference TfA, entered A549 cells and localized in the nucleus to exert its biological activity. At biologically relevant concentrations, HxTfA elicits DNA damage response as evidenced by a marked increase in the levels of γH2AX observed by confocal microscopy and immunoblotting studies, and ultimately induces apoptosis.
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Affiliation(s)
- Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, United Kingdom; Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria.
| | - Bernhard Englinger
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | | | - Debora Wernitznig
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Michael A Jakupec
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Walter Berger
- Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria; Research Cluster "Translational Cancer Therapy Research", University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin C Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
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4
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Satam V, Babu B, Patil P, Brien KA, Olson K, Savagian M, Lee M, Mepham A, Jobe LB, Bingham JP, Pett L, Wang S, Ferrara M, Bruce CD, Wilson WD, Lee M, Hartley JA, Kiakos K. AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide. Bioorg Med Chem Lett 2015; 25:3681-5. [PMID: 26122210 DOI: 10.1016/j.bmcl.2015.06.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 11/30/2022]
Abstract
The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔT(M), and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5'-ACGCGT-3', the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (K(eq) 4.0±0.2×10(7) M(-1)).
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Affiliation(s)
- Vijay Satam
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Balaji Babu
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kimberly A Brien
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kevin Olson
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Mia Savagian
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Megan Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Andrew Mepham
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Laura Beth Jobe
- Department of Chemistry, Erskine College, Due West, SC 29639, United States
| | - John P Bingham
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Luke Pett
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Maddi Ferrara
- Department of Chemistry, John Carroll University, University Heights, OH 44118, United States
| | - Chrystal D Bruce
- Department of Chemistry, John Carroll University, University Heights, OH 44118, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States; Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States.
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
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5
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Laughlin S, Wang S, Kumar A, Farahat AA, Boykin DW, Wilson WD. Resolution of mixed site DNA complexes with dimer-forming minor-groove binders by using electrospray ionization mass spectrometry: compound structure and DNA sequence effects. Chemistry 2015; 21:5528-39. [PMID: 25703690 PMCID: PMC4732565 DOI: 10.1002/chem.201406322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/18/2022]
Abstract
Small-molecule targeting of the DNA minor groove is a promising approach to modulate genomic processes necessary for normal cellular function. For instance, dicationic diamindines, a well-known class of minor groove binding compounds, have been shown to inhibit interactions of transcription factors binding to genomic DNA. The applications of these compounds could be significantly expanded if we understand sequence-specific recognition of DNA better and could use the information to design more sequence-specific compounds. Aside from polyamides, minor groove binders typically recognize DNA at A-tract or alternating AT base pair sites. Targeting sites with GC base pairs, referred to here as mixed base pair sequences, is much more difficult than those rich in AT base pairs. Compound 1 is the first dicationic diamidine reported to recognize a mixed base pair site. It binds in the minor groove of ATGA sequences as a dimer with positive cooperativity. Due to the well-characterized behavior of 1 with ATGA and AT rich sequences, it provides a paradigm for understanding the elements that are key for recognition of mixed sequence sites. Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to screen DNA complexes formed by analogues of 1 for specific recognition. We also report a novel approach to determine patterns of recognition by 1 for cognate ATGA and ATGA-mutant sequences. We found that functional group modifications and mutating the DNA target site significantly affect binding and stacking, respectively. Both compound conformation and DNA sequence directionality are crucial for recognition.
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Affiliation(s)
- Sarah Laughlin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Abdelbasset A. Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - David W. Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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6
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Satam V, Patil P, Babu B, Rice T, Porte A, Alger S, Zeller M, Lee M. Orthogonally Positioned Diamino Pyrrole- and Imidazole-Containing Polyamides: Synthesis of 1-(3-Substituted-propyl)-4-nitropyrrole-2-carboxylic Acid and 1-(3-Chloropropyl)-4-nitroimidazole-2-carboxylic Acid. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.839795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Vijay Satam
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Pravin Patil
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Balaji Babu
- b Department of Chemistry , Youngstown State University , Youngstown , Ohio , USA
| | - Toni Rice
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Alexander Porte
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Shannon Alger
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Matthias Zeller
- b Department of Chemistry , Youngstown State University , Youngstown , Ohio , USA
| | - Moses Lee
- a Department of Chemistry , Hope College , Holland , Michigan , USA
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