1
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Hassan AHE, El-Sayed SM, Yamamoto M, Gohda J, Matsumoto T, Shirouzu M, Inoue JI, Kawaguchi Y, Mansour RMA, Anvari A, Farahat AA. In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses 2023; 15:1171. [PMID: 37243257 PMCID: PMC10223987 DOI: 10.3390/v15051171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and influenza A virus, require the host proteases to mediate viral entry into cells. Rather than targeting the continuously mutating viral proteins, targeting the conserved host-based entry mechanism could offer advantages. Nafamostat and camostat were discovered as covalent inhibitors of TMPRSS2 protease involved in viral entry. To circumvent their limitations, a reversible inhibitor might be required. Considering nafamostat structure and using pentamidine as a starting point, a small set of structurally diverse rigid analogues were designed and evaluated in silico to guide selection of compounds to be prepared for biological evaluation. Based on the results of in silico study, six compounds were prepared and evaluated in vitro. At the enzyme level, compounds 10-12 triggered potential TMPRSS2 inhibition with low micromolar IC50 concentrations, but they were less effective in cellular assays. Meanwhile, compound 14 did not trigger potential TMPRSS2 inhibition at the enzyme level, but it showed potential cellular activity regarding inhibition of membrane fusion with a low micromolar IC50 value of 10.87 µM, suggesting its action could be mediated by another molecular target. Furthermore, in vitro evaluation showed that compound 14 inhibited pseudovirus entry as well as thrombin and factor Xa. Together, this study presents compound 14 as a hit compound that might serve as a starting point for developing potential viral entry inhibitors with possible application against coronaviruses.
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Affiliation(s)
- Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takehisa Matsumoto
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Jun-Ichiro Inoue
- Infection and Advanced Research Center (UTOPIA), The University of Tokyo Pandemic Preparedness, Tokyo 108-8639, Japan
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Reem M A Mansour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abtin Anvari
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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2
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Paul A, Farahat AA, Boykin DW, Wilson WD. Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents. Life (Basel) 2022; 12:life12050681. [PMID: 35629349 PMCID: PMC9147024 DOI: 10.3390/life12050681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
| | - Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
- Correspondence: ; Tel.: +1-404-413-5503; Fax: +1-404-413-5505
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3
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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
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 N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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4
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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5
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
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-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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6
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Guo P, Farahat AA, Paul A, Harika NK, Boykin DW, Wilson WD. Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA. J Am Chem Soc 2018; 140:14761-14769. [PMID: 30353731 PMCID: PMC6399738 DOI: 10.1021/jacs.8b08152] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AT specific heterocyclic cations that bind in the DNA duplex minor groove have had major successes as cell and nuclear stains and as therapeutic agents which can effectively enter human cells. Expanding the DNA sequence recognition capability of the minor groove compounds could also expand their therapeutic targets and have an impact in many areas, such as modulation of transcription factor biological activity. Success in the design of mixed sequence binding compounds has been achieved with N-methylbenzimidazole ( N-MeBI) thiophenes which are preorganized to fit the shape of the DNA minor groove and H-bond to the -NH of G·C base pairs that project into the minor groove. Initial compounds bind strongly to a single G·C base pair in an AT context with a specificity ratio of 50 ( KD AT-GC/ KD AT) or less and this is somewhat low for biological use. We felt that modifications of compound shape could be used to probe local DNA microstructure in target mixed base pair sequences of DNA and potentially improve the compound binding selectivity. Modifications were made by increasing the size of the benzimidazole N-substituent, for example, by using N-isobutyl instead of N-Me, and by changing the molecular twist by introducing substitutions at specific positions on the aromatic core of the compounds. In both cases, we have been able to achieve a dramatic increase in binding specificity, including no detectible binding to pure AT sequences, without a significant loss in affinity to mixed base pair target sequences.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy , Mansoura University , Mansoura 35516 , Egypt
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
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7
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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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Harika NK, Wilson WD. Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove. Biochemistry 2018; 57:5050-5057. [PMID: 30048590 DOI: 10.1021/acs.biochem.8b00647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DB2277, a heterocyclic diamidine, is a successful design for mixed base pair (bp) DNA sequence recognition. The compound has a central aza-benzimidazole group that forms two H-bonds with a GC bp that has flanking AT bps. The nuclear magnetic resonance structure of the DB2277-DNA complex with an AAGATA recognition site sequence was determined, and here we report extended molecular dynamics (MD) simulations of the structure. DB2277 has two terminal phenyl-amidine groups, one of which is directly linked to the DB2277 heterocyclic core and the other through a flexible -OCH2- group. The flexibly linked phenyl is too far from the minor groove floor to make direct H-bonds but is linked to an AT bp through water-mediated H-bonds. The flexibly linked phenyl-amidine with water-mediated H-bonds to the bases at the floor of the minor groove suggested that it might rotate in time spans accessible in MD. To test this idea, we conducted multimicrosecond MD simulations to determine if these phenyl rotations could be observed for a bound compound. In a 3 μs simulation, highly dynamic torsional motions were observed for the -OCH2-linked phenyl but not for the other phenyl. The dynamics periodically reached a level to allow 180° rotation of the phenyl while it was still bound in the minor groove. This is the first observation of rotation of a phenyl bound to DNA, and the results provide mechanistic details about how a rotation can occur as well as how mixed bp recognition can occur for monomer compounds bound to the minor groove.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303-3083 , United States
| | - W David Wilson
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303-3083 , United States
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9
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Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem 2018; 14:1051-1086. [PMID: 29977379 PMCID: PMC6009268 DOI: 10.3762/bjoc.14.93] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.
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Affiliation(s)
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research (NIPER), Raebareli 122003, India
| | - Dev P Arya
- NUBAD, LLC, 900B West Faris Rd., Greenville 29605, SC, USA.,Clemson University, Hunter Laboratory, Clemson 29634, SC, USA
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10
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Paul A, Kumar A, Nanjunda R, Farahat AA, Boykin DW, Wilson WD. Systematic synthetic and biophysical development of mixed sequence DNA binding agents. Org Biomol Chem 2018; 15:827-835. [PMID: 27995240 DOI: 10.1039/c6ob02390h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is now well established that, although only about 5% of the human genome codes for protein, most of the DNA has some function, such as synthesis of specific, functional RNAs and/or control of gene expression. These functional sequences open immense possibilities in both biotechnology and therapeutics for the use of cell-permeable, small molecules that can bind mixed-base pair sequences of DNA for regulation of genomic functions. Unfortunately very few types of modules have been designed to recognize mixed DNA sequences and for progress in targeting specific genes, it is essential to have additional classes of compounds. Compounds that can be rationally designed from established modules and which can bind strongly to mixed base pair DNA sequences are especially attractive. Based on extensive experience in design of minor-groove agents for AT recognition, a small library of compounds with two AT specific binding modules, connected through linkers which can recognize the G·C base pairs, were prepared. The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that some pyridyl-linked compounds bind with the target sequence with sub-nanomolar KD, with very slow dissociation kinetics and 200 times selectivity over the related sequence without a G·C base pair. Interestingly, a set of compounds with AT module connected by different linkers shows cooperative dimer recognition of related sequences. This type of design approach can be expanded to additional modules for recognition of a wide variety of sequences.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Janssen Research and Development, 1400 McKean Rd, Spring House, PA 19477, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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11
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Saha A, Kizaki S, Han JH, Yu Z, Sugiyama H. UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258. Bioorg Med Chem 2018; 26:37-40. [PMID: 29170027 DOI: 10.1016/j.bmc.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/15/2023]
Abstract
Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5'-AABrUBrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.
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Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Seiichiro Kizaki
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Ji Hoon Han
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Zutao Yu
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo, Kyoto 606-8502, Japan.
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12
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Harika NK, Germann MW, Wilson WD. First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences. Chemistry 2017; 23:17612-17620. [PMID: 29044822 DOI: 10.1002/chem.201704563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 12/24/2022]
Abstract
The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both A⋅T and G⋅C bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the G⋅C base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA
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13
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Laughlin-Toth S, Carter EK, Ivanov I, Wilson WD. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Res 2017; 45:1297-1306. [PMID: 28180310 PMCID: PMC5388402 DOI: 10.1093/nar/gkw1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5΄-AAAGTTT-3΄. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.
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Affiliation(s)
- Sarah Laughlin-Toth
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - E Kathleen Carter
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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14
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Guo P, Paul A, Kumar A, Harika NK, Wang S, Farahat AA, Boykin DW, Wilson WD. A modular design for minor groove binding and recognition of mixed base pair sequences of DNA. Chem Commun (Camb) 2017; 53:10406-10409. [PMID: 28880316 PMCID: PMC5616130 DOI: 10.1039/c7cc06246j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design and synthesis of compounds that target mixed, AT/GC, DNA sequences is described. The design concept connects two N-methyl-benzimidazole-thiophene single GC recognition units with a flexible linker that lets the compound fit the shape and twist of the DNA minor groove while covering a full turn of the double helix.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
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15
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Guo P, Paul A, Kumar A, Farahat AA, Kumar D, Wang S, Boykin DW, Wilson WD. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove. Chemistry 2016; 22:15404-15412. [PMID: 27624927 PMCID: PMC5214980 DOI: 10.1002/chem.201603422] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/10/2022]
Abstract
In spite of its importance in cell function, targeting DNA is under-represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G⋅C base pairs (bp) in DNA sequences. To overcome this barrier, an entirely new design concept for modules that can bind to mixed G⋅C and A⋅T sequences of DNA is reported herein. Because of their successes in biological applications, minor-groove-binding heterocyclic cations were selected as the platform for design. Binding to A⋅T sequences requires hydrogen-bond donors whereas recognition of the G-NH2 requires an acceptor. The concept that we report herein uses pre-organized N-methylbenzimidazole (N-MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma hole (positive electrostatic potential) and the electron-donor nitrogen of N-MeBI preorganizes the conformation for accepting an hydrogen bond from G-NH2 . The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N-MeBI-thiophene monomer compounds can strongly and selectively recognize single G⋅C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma-holes, can lead to new approaches for small molecules in biomolecular interactions.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dhiraj Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA.
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Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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17
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Harika NK, Paul A, Stroeva E, Chai Y, Boykin DW, Germann MW, Wilson WD. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition. Nucleic Acids Res 2016; 44:4519-27. [PMID: 27131382 PMCID: PMC4889958 DOI: 10.1093/nar/gkw353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ekaterina Stroeva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Yun Chai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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18
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Laughlin S, Wilson WD. May the Best Molecule Win: Competition ESI Mass Spectrometry. Int J Mol Sci 2015; 16:24506-31. [PMID: 26501262 PMCID: PMC4632762 DOI: 10.3390/ijms161024506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/18/2015] [Accepted: 10/09/2015] [Indexed: 02/07/2023] Open
Abstract
Electrospray ionization mass spectrometry has become invaluable in the characterization of macromolecular biological systems such as nucleic acids and proteins. Recent advances in the field of mass spectrometry and the soft conditions characteristic of electrospray ionization allow for the investigation of non-covalent interactions among large biomolecules and ligands. Modulation of genetic processes through the use of small molecule inhibitors with the DNA minor groove is gaining attention as a potential therapeutic approach. In this review, we discuss the development of a competition method using electrospray ionization mass spectrometry to probe the interactions of multiple DNA sequences with libraries of minor groove binding molecules. Such an approach acts as a high-throughput screening method to determine important information including the stoichiometry, binding mode, cooperativity, and relative binding affinity. In addition to small molecule-DNA complexes, we highlight other applications in which competition mass spectrometry has been used. A competitive approach to simultaneously investigate complex interactions promises to be a powerful tool in the discovery of small molecule inhibitors with high specificity and for specific, important DNA sequences.
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Affiliation(s)
- Sarah Laughlin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
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