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Article ; Online: Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.

Paul, Ananya / Nanjunda, Rupesh / Wilson, W David

Current protocols

2023 Volume 3, Issue 4, Page(s) e729

Abstract: Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, have found extensive uses in biotechnology, and are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. ...

Abstract	Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, have found extensive uses in biotechnology, and are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds show that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, compounds can be designed to recognize GC and mixed AT/GC base pair sequences, and stacked dimers can form to recognize specific sequences. © 2023 Wiley Periodicals LLC.
MeSH term(s)	Surface Plasmon Resonance ; Binding Sites ; DNA/chemistry ; DNA/metabolism ; Base Pairing ; Pentamidine
Chemical Substances	DNA (9007-49-2) ; Pentamidine (673LC5J4LQ)
Language	English
Publishing date	2023-04-18
Publishing country	United States
Document type	Review ; Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.729
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Article: Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents.

Paul, Ananya / Farahat, Abdelbasset A / Boykin, David W / Wilson, W David

Life (Basel, Switzerland)

2022 Volume 12, Issue 5

Abstract: Ken Breslauer began studies on the thermodynamics of small cationic molecules binding in the DNA minor groove over 30 years ago, and the studies reported here are an extension of those ground-breaking reports. The goals of this report are to develop a ... ...

Abstract	Ken Breslauer began studies on the thermodynamics of small cationic molecules binding in the DNA minor groove over 30 years ago, and the studies reported here are an extension of those ground-breaking reports. The goals of this report are to develop a detailed understanding of the binding thermodynamics of pyridine-based sequence-specific minor groove binders that have different terminal cationic groups. We apply biosensor-surface plasmon resonance and ITC methods to extend the understanding of minor groove binders in two directions: (i) by using designed, heterocyclic dicationic minor groove binders that can incorporate a G•C base pair (bp), with flanking AT base pairs, into their DNA recognition site, and bind to DNA sequences specifically; and (ii) by using a range of flanking AT sequences to better define molecular recognition of the minor groove. A G•C bp in the DNA recognition site causes a generally more negative binding enthalpy than with most previously used pure AT binding sites. The binding is enthalpy-driven at 25 °C and above. The flanking AT sequences also have a large effect on the binding energetics with the -AAAGTTT- site having the strongest affinity. As a result of these studies, we now have a much better understanding of the effects of the DNA sequence and compound structure on the molecular recognition and thermodynamics of minor groove complexes.
Language	English
Publishing date	2022-05-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life12050681
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Article ; Online: Impact of COVID-19 on Sectors of Indian Economy and Business Survival Strategies

Rakshit, Debdas / Paul, Ananya

SSRN Electronic Journal ; ISSN 1556-5068

2020

Keywords	covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
DOI	10.2139/ssrn.3620727
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.

Ogbonna, Edwin N / Paul, Ananya / Farahat, Abdelbasset A / Terrell, J Ross / Mineva, Ekaterina / Ogbonna, Victor / Boykin, David W / Wilson, W David

ACS bio & med chem Au

2023 Volume 3, Issue 4, Page(s) 335–348

Abstract: The rational design of small molecules that target specific DNA sequences is a promising strategy to modulate gene expression. This report focuses on a diamidinobenzimidazole compound, whose selective binding to the minor groove of AT DNA sequences holds ...

Abstract	The rational design of small molecules that target specific DNA sequences is a promising strategy to modulate gene expression. This report focuses on a diamidinobenzimidazole compound, whose selective binding to the minor groove of AT DNA sequences holds broad significance in the molecular recognition of AT-rich human promoter sequences. The objective of this study is to provide a more detailed and systematized understanding, at an atomic level, of the molecular recognition mechanism of different AT-specific sequences by a rationally designed minor groove binder. The specialized method of X-ray crystallography was utilized to investigate how the sequence-dependent recognition properties in general, A-tract, and alternating AT sequences affect the binding of diamidinobenzimidazole in the DNA minor groove. While general and A-tract AT sequences give a narrower minor groove, the alternating AT sequences intrinsically have a wider minor groove which typically constricts upon binding. A strong and direct hydrogen bond between the N-H of the benzimidazole and an H-bond acceptor atom in the minor groove is essential for DNA recognition in all sequences described. In addition, the diamidine compound specifically utilizes an interfacial water molecule for its DNA binding. DNA complexes of AATT and AAAAAA recognition sites show that the diamidine compound can bind in two possible orientations with a preference for water-assisted hydrogen bonding at either cationic end. The complex structures of AAATTT, ATAT, ATATAT, and AAAA are bound in a singular orientation. Analysis of the helical parameters shows a minor groove expansion of about 1 Å across all the nonalternating DNA complexes. The results from this systematic approach will convey a greater understanding of the specific recognition of a diverse array of AT-rich sequences by small molecules and more insight into the design of small molecules with enhanced specificity to AT and mixed DNA sequences.
Language	English
Publishing date	2023-04-05
Publishing country	United States
Document type	Journal Article
ISSN	2694-2437
ISSN (online)	2694-2437
DOI	10.1021/acsbiomedchemau.3c00002
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Article ; Online: Investigation of the effect of structure modification of furamidine on the DNA minor groove binding and antiprotozoal activity.

Farahat, Abdelbasset A / Kumar, Arvind / Wenzler, Tanja / Brun, Reto / Paul, Ananya / Guo, Pu / Wilson, W David / Boykin, David W

European journal of medicinal chemistry

2023 Volume 252, Page(s) 115287

Abstract: New analogs of the antiprotozoal agent Furamidine were prepared utilizing Stille coupling reactions and amidation of the bisnitrile intermediate using lithium bis-trimethylsilylamide. Both the phenyl groups and the furan moiety of furamidine were ... ...

Abstract	New analogs of the antiprotozoal agent Furamidine were prepared utilizing Stille coupling reactions and amidation of the bisnitrile intermediate using lithium bis-trimethylsilylamide. Both the phenyl groups and the furan moiety of furamidine were replaced by heterocycles including thiophene, selenophene, indole or benzimidazole. Based upon the ΔTm and the CD results, the new compounds showed strong binding to the DNA minor groove. The new analogues are also more active both in vitro and in vivo than furamidine. Compounds 7a, 7b, and 7f showed the highest activity in vivo by curing 75% of animals, and this merits further evaluation.
MeSH term(s)	Animals ; Benzamidines/pharmacology ; Benzamidines/chemistry ; Benzamidines/metabolism ; Antiprotozoal Agents/pharmacology ; DNA/metabolism
Chemical Substances	furamidine (73819-26-8) ; Benzamidines ; Antiprotozoal Agents ; DNA (9007-49-2)
Language	English
Publishing date	2023-03-20
Publishing country	France
Document type	Journal Article
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2023.115287
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Zs.B 784: Show issues

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Article: Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove.

Guo, Pu / Farahat, Abdelbasset A / Paul, Ananya / Boykin, David W / Wilson, W David

Chemical science

2021 Volume 12, Issue 48, Page(s) 15849–15861

Abstract: This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. ...

Abstract	This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an
Language	English
Publishing date	2021-11-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d1sc04720e
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Article ; Online: Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines.

Ogbonna, Edwin N / Paul, Ananya / Ross Terrell, J / Fang, Ziyuan / Chen, Cen / Poon, Gregory M K / Boykin, David W / Wilson, W David

Bioorganic & medicinal chemistry

2022 Volume 68, Page(s) 116861

Abstract: The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically ...

Abstract	The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding K
MeSH term(s)	Benzimidazoles/chemistry ; Binding Sites ; DNA/chemistry ; Drug Design ; Indoles/pharmacology ; Models, Molecular ; Nucleic Acid Conformation ; Pentamidine/chemistry ; Surface Plasmon Resonance ; Thiophenes/chemistry ; Thiophenes/pharmacology ; Transcription Factors
Chemical Substances	Benzimidazoles ; Indoles ; Thiophenes ; Transcription Factors ; Pentamidine (673LC5J4LQ) ; DNA (9007-49-2)
Language	English
Publishing date	2022-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2022.116861
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Article ; Online: A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context.

Paul, Ananya / Guo, Pu / Boykin, David W / Wilson, W David

Molecules (Basel, Switzerland)

2019 Volume 24, Issue 5

Abstract: We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology ... ...

Abstract	We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-
MeSH term(s)	Base Pairing ; Base Sequence ; DNA/chemistry ; Heterocyclic Compounds/chemical synthesis ; Heterocyclic Compounds/chemistry ; Nucleic Acid Conformation ; Surface Plasmon Resonance
Chemical Substances	Heterocyclic Compounds ; DNA (9007-49-2)
Language	English
Publishing date	2019-03-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules24050946
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Article ; Online: Biosensor-Surface Plasmon Resonance: Label-Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid Interactions.

Paul, Ananya / Musetti, Caterina / Nanjunda, Rupesh / Wilson, W David

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2035, Page(s) 63–85

Abstract: Biosensor-surface plasmon resonance (SPR) technology is now well established as a quantitative approach for the study of nucleic acid interactions in real time, without the need for labeling any components of the interaction. The method provides real- ... ...

Abstract	Biosensor-surface plasmon resonance (SPR) technology is now well established as a quantitative approach for the study of nucleic acid interactions in real time, without the need for labeling any components of the interaction. The method provides real-time equilibrium and kinetic characterization for quadruplex DNA interactions and requires small amounts of materials and no external probe. A detailed protocol for quadruplex-DNA interaction analyses with a variety of binding molecules using biosensor-SPR methods is presented. Explanations of the SPR method with basic fundamentals for use and analysis of results are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples. Details of experimental design, quantitative and qualitative data analyses, and presentation are described. Some specific examples of small molecule-DNA quadruplex interactions are presented with results evaluated by both kinetic and steady-state SPR methods.
MeSH term(s)	Biosensing Techniques ; Kinetics ; Nucleic Acids/chemistry ; Surface Plasmon Resonance
Chemical Substances	Nucleic Acids
Language	English
Publishing date	2019-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9666-7_4
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Article ; Online: Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove.

Guo, Pu / Farahat, Abdelbasset A / Paul, Ananya / Kumar, Arvind / Boykin, David W / Wilson, W David

Biochemistry

2020 Volume 59, Issue 18, Page(s) 1756–1768

Abstract: The majority of current drugs against diseases, such as cancer, can bind to one or more sites in a protein and inhibit its activity. There are, however, well-known limits on the number of druggable proteins, and complementary current drugs with compounds ...

Abstract	The majority of current drugs against diseases, such as cancer, can bind to one or more sites in a protein and inhibit its activity. There are, however, well-known limits on the number of druggable proteins, and complementary current drugs with compounds that could selectively target DNA or RNA would greatly enhance the availability of cellular probes and therapeutic progress. We are focusing on the design of sequence-specific DNA minor groove binders that, for example, target the promoter sites of transcription factors involved in a disease. We have started with AT-specific minor groove binders that are known to enter human cells and have entered clinical trials. To broaden the sequence-specific recognition of these compounds, several modules that have H-bond acceptors that strongly and specifically recognize G·C base pairs were identified. A lead module is a thiophene-
MeSH term(s)	Amidines/chemistry ; Base Pairing ; Benzimidazoles/chemistry ; DNA/analysis ; DNA/chemistry ; Humans ; Molecular Structure ; Thiophenes/chemistry
Chemical Substances	Amidines ; Benzimidazoles ; Thiophenes ; DNA (9007-49-2) ; benzimidazole (E24GX49LD8)
Language	English
Publishing date	2020-04-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.0c00090
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