1
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Guo P, Han D. Targeting Pathogenic DNA and RNA Repeats: A Conceptual Therapeutic Way for Repeat Expansion Diseases. Chemistry 2022; 28:e202201749. [PMID: 35727679 DOI: 10.1002/chem.202201749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/06/2022]
Abstract
Expansions of short tandem repeats (STRs) in the human genome cause nearly 50 neurodegenerative diseases, which are mostly inheritable, nonpreventable and incurable, posing as a huge threat to human health. Non-B DNAs formed by STRs are thought to be structural intermediates that can cause repeat expansions. The subsequent transcripts harboring expanded RNA repeats can further induce cellular toxicity through forming specific structures. Direct targeting of these pathogenic DNA and RNA repeats has emerged as a new potential therapeutic strategy to cure repeat expansion diseases. In this conceptual review, we first introduce the roles of DNA and RNA structures in the genetic instabilities and pathomechanisms of repeat expansion diseases, then describe structural features of DNA and RNA repeats with a focus on the tertiary structures determined by X-ray crystallography and solution nuclear magnetic resonance spectroscopy, and finally discuss recent progress and perspectives of developing chemical tools that target pathogenic DNA and RNA repeats for curing repeat expansion diseases.
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Affiliation(s)
- Pei Guo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| | - Da Han
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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2
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Monsen RC, DeLeeuw LW, Dean WL, Gray RD, Chakravarthy S, Hopkins JB, Chaires JB, Trent JO. Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences. Nucleic Acids Res 2022; 50:4127-4147. [PMID: 35325198 PMCID: PMC9023277 DOI: 10.1093/nar/gkac182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained by an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling and molecular dynamics simulations, to derive self-consistent structural models. The formal resolution of our approach is 18 angstroms, but in some cases structural features of only a few nucleotides can be discerned. We report here five structures of long (34-70 nt) wild-type sequences selected from three cancer-related promoters: c-Myc, c-Kit and k-Ras. Each sequence studied has a unique structure. Three sequences form structures with two contiguous, stacked, G-quadruplex units. One longer sequence from c-Myc forms a structure with three contiguous stacked quadruplexes. A longer c-Kit sequence forms a quadruplex-hairpin structure. Each structure exhibits interfacial regions between stacked quadruplexes or novel loop geometries that are possible druggable targets. We also report methodological advances in our integrated structural biology approach, which now includes quantitative CD for counting stacked G-tetrads, DNaseI cleavage for hairpin detection and SAXS model refinement. Our results suggest that higher-order quadruplex assemblies may be a common feature within the genome, rather than simple single quadruplex structures.
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Affiliation(s)
- Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Lynn W DeLeeuw
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - William L Dean
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Robert D Gray
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
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3
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Zhang C, Liu X, Tan L. Interaction of arene ruthenium(II) complexes [(η 6-C 6H 6)Ru(L)Cl]PF 6 (L = o-fpip and p-fpip) with the RNA triplex poly(U)*poly(A)•poly(U). J Inorg Biochem 2022; 232:111813. [PMID: 35405487 DOI: 10.1016/j.jinorgbio.2022.111813] [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: 03/07/2022] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
To comprehend the binding properties of η6-arene Ru(II) complexes with poly(U)*poly(A)•poly(U) triplex, two arene Ru(II) complexes with different fluorine substituent positions, [(η6-C6H6)Ru(o-fpip)Cl]PF6 (Ru1,η6-C6H6 = benzene ring, o-fpip = 2-(2'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline) and [(η6-C6H6)Ru(p-fpip)Cl]PF6 (Ru2,η6-C6H6 = benzene ring, o-fpip = 2-(4'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline), have been synthesized and characterized in this study. The binding of Ru1 and Ru2 with poly(U)*poly(A)•poly(U) triplex has been investigated by viscosity measurement and spectroscopic methods. Analysis of UV-Vis absorption spectral titrations suggests that Ru1 and Ru2 bind to the triplex through an intercalative mode, but the binding affinity of Ru2 is slightly higher than that of Ru1, which is also verified by viscosity and EB (ethidium bromide) competition measurements. Furthermore, the thermal denaturation experiment shows that Ru1 and Ru2 increase the third-strand stabilization to a similar extent. Interestingly, the two complexes have essentially no effect on the stabilization of the template duplex. Considering the structure of Ru1 and Ru2, conceivably besides the intercalation of ligand, the force stabilizing the triplex should also involve covalent binding and electrostatic interaction. The obtained results will contribute to our understanding of the interaction of arene Ru(II) complexes with the poly(U)*poly(A)•poly(U) triplex.
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Affiliation(s)
- Chengqing Zhang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China.
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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: 43] [Impact Index Per Article: 10.8] [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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Stanzione F, Giangreco I, Cole JC. Use of molecular docking computational tools in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:273-343. [PMID: 34147204 DOI: 10.1016/bs.pmch.2021.01.004] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular docking has become an important component of the drug discovery process. Since first being developed in the 1980s, advancements in the power of computer hardware and the increasing number of and ease of access to small molecule and protein structures have contributed to the development of improved methods, making docking more popular in both industrial and academic settings. Over the years, the modalities by which docking is used to assist the different tasks of drug discovery have changed. Although initially developed and used as a standalone method, docking is now mostly employed in combination with other computational approaches within integrated workflows. Despite its invaluable contribution to the drug discovery process, molecular docking is still far from perfect. In this chapter we will provide an introduction to molecular docking and to the different docking procedures with a focus on several considerations and protocols, including protonation states, active site waters and consensus, that can greatly improve the docking results.
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Affiliation(s)
| | - Ilenia Giangreco
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
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6
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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7
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Li N, Wang J, Ma K, Liang L, Mi L, Huang W, Ma X, Wang Z, Zheng W, Xu L, Chen JH, Yu Z. The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics. Nucleic Acids Res 2019; 47:e86. [PMID: 31114915 PMCID: PMC6735771 DOI: 10.1093/nar/gkz464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 05/06/2019] [Accepted: 05/15/2019] [Indexed: 11/21/2022] Open
Abstract
A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3' overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson-Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.
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Affiliation(s)
- Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Junli Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Kangkang Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lipei Mi
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Xiaofeng Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Wei Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Linyan Xu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
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8
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Krafcikova M, Dzatko S, Caron C, Granzhan A, Fiala R, Loja T, Teulade-Fichou MP, Fessl T, Hänsel-Hertsch R, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. J Am Chem Soc 2019; 141:13281-13285. [PMID: 31394899 DOI: 10.1021/jacs.9b03031] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studies on DNA-ligand interactions in the cellular environment are problematic due to the lack of suitable biophysical tools. To address this need, we developed an in-cell NMR-based approach for monitoring DNA-ligand interactions inside the nuclei of living human cells. Our method relies on the acquisition of NMR data from cells electroporated with preformed DNA-ligand complexes. The impact of the intracellular environment on the integrity of the complexes is assessed based on in-cell NMR signals from unbound and ligand-bound forms of a given DNA target. This technique was tested on complexes of two model DNA fragments and four ligands, namely, a representative DNA minor-groove binder (netropsin) and ligands binding DNA base-pairing defects (naphthalenophanes). In the latter case, we demonstrate that two of the three in vitro-validated ligands retain their ability to form stable interactions with their model target DNA in cellulo, whereas the third one loses this ability due to off-target interactions with genomic DNA and cellular metabolites. Collectively, our data suggest that direct evaluation of the behavior of drug-like molecules in the intracellular environment provides important insights into the development of DNA-binding ligands with desirable biological activity and minimal side effects resulting from off-target binding.
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Affiliation(s)
- Michaela Krafcikova
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
| | - Simon Dzatko
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Coralie Caron
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Tomas Loja
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Tomas Fessl
- Faculty of Science , University of South Bohemia , Ceske Budejovice CZ-370 05 , Czech Republic
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute , University of Cambridge , Cambridge CB2 0RE , United Kingdom
| | - Jean-Louis Mergny
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
| | | | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
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9
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del Mundo IMA, Cho EJ, Dalby KN, Vasquez KM. A tunable assay for modulators of genome-destabilizing DNA structures. Nucleic Acids Res 2019; 47:e73. [PMID: 30949695 PMCID: PMC6648359 DOI: 10.1093/nar/gkz237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 11/24/2022] Open
Abstract
Regions of genomic instability are not random and often co-localize with DNA sequences that can adopt alternative DNA structures (i.e. non-B DNA, such as H-DNA). Non-B DNA-forming sequences are highly enriched at translocation breakpoints in human cancer genomes, representing an endogenous source of genetic instability. However, a further understanding of the mechanisms involved in non-B DNA-induced genetic instability is needed. Small molecules that can modulate the formation/stability of non-B DNA structures, and therefore the subsequent mutagenic outcome, represent valuable tools to study DNA structure-induced genetic instability. To this end, we have developed a tunable Förster resonance energy transfer (FRET)-based assay to detect triplex/H-DNA-destabilizing and -stabilizing ligands. The assay was designed by incorporating a fluorophore-quencher pair in a naturally-occurring H-DNA-forming sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. By tuning triplex stability via buffer composition, the assay functions as a dual-reporter that can identify stabilizers and destabilizers, simultaneously. The assay principle was demonstrated using known triplex stabilizers, BePI and coralyne, and a complementary oligonucleotide to mimic a destabilizer, MCRa2. The potential of the assay was validated in a 384-well plate with 320 custom-assembled compounds. The discovery of novel triplex stabilizers/destabilizers may allow the regulation of genetic instability in human genomes.
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Affiliation(s)
- Imee M A del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX, USA
| | - Eun Jeong Cho
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX, USA
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10
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Challenges and current status of computational methods for docking small molecules to nucleic acids. Eur J Med Chem 2019; 168:414-425. [PMID: 30831409 DOI: 10.1016/j.ejmech.2019.02.046] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 01/29/2023]
Abstract
Since the development of the first docking program in 1982, the use of docking-based in silico screening for potentially bioactive molecule discovery has become a common strategy in academia and pharmaceutical industry. Up until recently, application of docking programs has largely focused on drugs binding to proteins. However, with the discovery of promising drug targets in nucleic acids, including RNA riboswitches, DNA G-quadruplexes, and extended repeats in RNA, there has been greater interests in developing drugs for nucleic acids. However, due to major biochemical and physical differences in charges, binding pockets, and solvation, existing docking programs, developed for proteins, face difficulties when adopted directly for nucleic acids. In this review, we cover the current field of in silico docking to nucleic acids, available programs, as well as challenges faced in the field.
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11
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Tutuncu S, Guloglu S, Kucukakdag A, Cetinkol OP. Selective High Binding Affinity of Azacyanines to polyd(A) polyd(T)⋅polyd(T) Triplex: The Effect of Chain Length and Branching on Stabilization, Selectivity and Affinity. ChemistrySelect 2018. [DOI: 10.1002/slct.201802802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Serra Tutuncu
- Biomedical Engineering ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
| | - Sercan Guloglu
- Biochemistry ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
| | - Ayca Kucukakdag
- Department of ChemistryMiddle East Technical University 06800 Çankaya Ankara Turkey
| | - Ozgul Persil Cetinkol
- Biomedical Engineering ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
- Biochemistry ProgramMiddle East Technical University 06800, Çankaya Ankara Turkey
- Department of ChemistryMiddle East Technical University 06800 Çankaya Ankara Turkey
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12
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del Villar-Guerra R, Gray RD, Trent JO, Chaires JB. A rapid fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity. Nucleic Acids Res 2018; 46:e41. [PMID: 29361140 PMCID: PMC6283418 DOI: 10.1093/nar/gky019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/12/2017] [Accepted: 01/09/2018] [Indexed: 12/23/2022] Open
Abstract
We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal component analysis and hierarchical clustering analysis to interpret the results obtained. This analysis classified compounds based on selectivity for AT-rich, GC-rich and G4 structures. We used the FID assay as a secondary screen to test the binding selectivity of an additional 20 compounds selected from the NCI Diversity Set III library that were identified as G4 binders using a thermal shift assay. The results showed G4 binding selectivity for only a few of the 20 compounds. Overall, we show that this R-FID assay, coupled with PCA and HCA, provides a useful tool for the discovery of ligands selective for particular nucleic acid structures.
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Affiliation(s)
- Rafael del Villar-Guerra
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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13
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Shahabadi N, Shiri F, Hadidi S. The effect of dimerization on the interaction of ibuprofen drug with calf thymus DNA: Molecularmodeling and spectroscopic investigation. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:147-168. [PMID: 29465331 DOI: 10.1080/15257770.2018.1438617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The interaction between the dimer structure of ibuprofen drug (D-IB) and calf thymus DNA under simulative physiological conditions was investigated with the use of Hoechst 33258 and methylene blue dye as spectral probes by the methods of UV-visible absorption, fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling study.Using the Job's plot, a single class of binding sites for theD-IB on DNA was put in evidence. The Stern-Volmer analysis of fluorescence quenching data shows the presence of both the static and dynamic quenching mechanisms. The binding constants, Kb were calculated at different temperatures, and the thermodynamic parameters ∆G∘, ∆H∘ and ∆S∘ were given. The experimental results showed that D-IB molecules could bind with DNA via groove binding mode as evidenced by: I. DNA binding constant from spectrophotometric studies of the interaction of D-IB with DNA is comparable to groove binding drugs. II. Competitive fluorimetric studies with Hoechst 33258 have shown that D-IB exhibits the ability of this complex to displace with DNA-bounded Hoechst, indicating that it binds to DNA in strong competition with Hoechst for the groove binding. III. There is no significantly change in the absorption of the MB-DNA system upon adding the D-IB, indicates that MB molecules are not released from the DNA helix after addition of the D-IB and are indicative of a non-intercalative mode of binding. IV. Small changes in DNA viscosity in the presence of D-IB, indicating weak link to DNA, which is consistent with DNA groove binding. As well as, induced CD spectral changes, and the docking results revealed that groove mechanism is followed by D-IB to bind with DNA.
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Affiliation(s)
- Nahid Shahabadi
- a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Farshad Shiri
- a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran
| | - Saba Hadidi
- a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
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14
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Yang H, Yao W, Wang Y, Shi L, Su R, Wan D, Xu N, Lian W, Chen C, Liu S. High-throughput screening of triplex DNA binders from complicated samples by 96-well pate format in conjunction with peak area-fading UHPLC-Orbitrap MS. Analyst 2017; 142:670-675. [DOI: 10.1039/c6an01974a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Screening triplex DNA binders from complicated samples in a high-throughput fashion with good reproducibility without the requirement of an extra releasing step.
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Affiliation(s)
- Hongmei Yang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
| | - Wenbin Yao
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Yihan Wang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Lei Shi
- High Temperature Reactor Holdings Co
- Ltd
- China Nuclear Engineering Group Co
- Beijing 100037
- China
| | - Rui Su
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Debin Wan
- Department of Entomology and Comprehensive Cancer Center
- University of California
- Davis
- USA
| | - Niusheng Xu
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- China
| | - Wenhui Lian
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Changbao Chen
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Shuying Liu
- Changchun University of Chinese Medicine
- Changchun 130117
- China
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
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15
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Discovery of novel dual VEGFR2 and Src inhibitors using a multistep virtual screening approach. Future Med Chem 2016; 9:7-24. [PMID: 27995811 DOI: 10.4155/fmc-2016-0162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AIM Simultaneous inhibition of VEGFR2 and Src may enhance the efficacy of VEGFR2-targeted cancer therapeutics. Hence, development of dual inhibitors on VEGFR2 and Src can be a useful strategy for such treatments. MATERIALS & METHODS A multistep virtual screening protocol, comprising ligand-based support vector machines method, drug-likeness rules filter and structure-based molecular docking, was developed and employed to identify dual inhibitors of VEGFR2 and Src from a large commercial chemical library. Kinase inhibitory assays and cell viability assays were then used for experimental validation. RESULTS A set of compounds belonging to six different molecular scaffolds was identified and sent for biological evaluation. Compound 3c belonging to the 2-amino-3-cyanopyridine scaffold exhibited good antiproliferative effect and dual-target activities against VEGFR2 and Src. CONCLUSION This study demonstrated the ability of the multistep virtual screening approach to identify novel multitarget agents.
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16
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Hu Y, Lin F, Wu T, Wang Y, Zhou XS, Shao Y. Fluorescently Sensing of DNA Triplex Assembly Using an Isoquinoline Alkaloid as Selector, Stabilizer, Inducer, and Switch-On Emitter. Chem Asian J 2016; 11:2041-8. [DOI: 10.1002/asia.201600459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Yuehua Hu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Fan Lin
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Ying Wang
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Xiao-Shun Zhou
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
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17
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Chaires JB. A small molecule--DNA binding landscape. Biopolymers 2016; 103:473-9. [PMID: 25913470 DOI: 10.1002/bip.22660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/16/2015] [Indexed: 02/03/2023]
Abstract
This brief account traces the development of a "competition dialysis" method used to characterize the structural and sequence selectivity of DNA binding compounds. The method was inspired by a simple "differential dialysis" method pioneered by Don Crothers to explore base-selective intercalator binding. Results from compiled competition dialysis studies provide a small-molecule DNA binding landscape that shows a rich diversity of interactions and molecular recognition.
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Affiliation(s)
- Jonathan B Chaires
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
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18
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van der Watt PJ, Chi A, Stelma T, Stowell C, Strydom E, Carden S, Angus L, Hadley K, Lang D, Wei W, Birrer MJ, Trent JO, Leaner VD. Targeting the Nuclear Import Receptor Kpnβ1 as an Anticancer Therapeutic. Mol Cancer Ther 2016; 15:560-73. [PMID: 26832790 DOI: 10.1158/1535-7163.mct-15-0052] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 01/15/2016] [Indexed: 11/16/2022]
Abstract
Karyopherin beta 1 (Kpnβ1) is a nuclear transport receptor that imports cargoes into the nucleus. Recently, elevated Kpnβ1 expression was found in certain cancers and Kpnβ1 silencing with siRNA was shown to induce cancer cell death. This study aimed to identify novel small molecule inhibitors of Kpnβ1, and determine their anticancer activity. An in silico screen identified molecules that potentially bind Kpnβ1 and Inhibitor of Nuclear Import-43, INI-43 (3-(1H-benzimidazol-2-yl)-1-(3-dimethylaminopropyl)pyrrolo[5,4-b]quinoxalin-2-amine) was investigated further as it interfered with the nuclear localization of Kpnβ1 and known Kpnβ1 cargoes NFAT, NFκB, AP-1, and NFY and inhibited the proliferation of cancer cells of different tissue origins. Minimum effect on the proliferation of noncancer cells was observed at the concentration of INI-43 that showed a significant cytotoxic effect on various cervical and esophageal cancer cell lines. A rescue experiment confirmed that INI-43 exerted its cell killing effects, in part, by targeting Kpnβ1. INI-43 treatment elicited a G2-M cell-cycle arrest in cancer cells and induced the intrinsic apoptotic pathway. Intraperitoneal administration of INI-43 significantly inhibited the growth of subcutaneously xenografted esophageal and cervical tumor cells. We propose that Kpnβ1 inhibitors could have therapeutic potential for the treatment of cancer. Mol Cancer Ther; 15(4); 560-73. ©2016 AACR.
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Affiliation(s)
- Pauline J van der Watt
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alicia Chi
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tamara Stelma
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Catherine Stowell
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Erin Strydom
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sarah Carden
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Liselotte Angus
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kate Hadley
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Dirk Lang
- Confocal and Light Microscope Imaging Facility, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Wei Wei
- Center for Cancer Research, The Gillette Center for Gynecologic Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael J Birrer
- Center for Cancer Research, The Gillette Center for Gynecologic Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - John O Trent
- Department of Medicine, J.G. Brown Cancer Center, University of Louisville, Louisville, Kentucky
| | - Virna D Leaner
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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19
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Wang Y, Hu Y, Wu T, Zhou X, Shao Y. Triggered Excited-State Intramolecular Proton Transfer Fluorescence for Selective Triplex DNA Recognition. Anal Chem 2015; 87:11620-4. [DOI: 10.1021/acs.analchem.5b02851] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
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20
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In silico identification of novel ligands for G-quadruplex in the c-MYC promoter. J Comput Aided Mol Des 2014; 29:339-48. [PMID: 25527072 DOI: 10.1007/s10822-014-9826-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
G-quadruplex DNA formed in NHEIII1 region of oncogene promoter inhibits transcription of the genes. In this study, virtual screening combining pharmacophore-based search and structure-based docking screening was conducted to discover ligands binding to G-quadruplex in promoter region of c-MYC. Several hit ligands showed the selective PCR-arresting effects for oligonucleotide containing c-MYC G-quadruplex forming sequence. Among them, three hits selectively inhibited cell proliferation and decreased c-MYC mRNA level in Ramos cells, where NHEIII1 is included in translocated c-MYC gene for overexpression. Promoter assay using two kinds of constructs with wild-type and mutant sequences showed that interaction of these ligands with the G-quadruplex resulted in turning-off of the reporter gene. In conclusion, combined virtual screening methods were successfully used for discovery of selective c-MYC promoter G-quadruplex binders with anticancer activity.
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21
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Synthesis andIn VitroEvaluation of Bis-intercalators with Varied Linkers between Aminochloropyrimidine Rings. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.1767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Feinstein WP, Brylinski M. eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models. Mol Inform 2014; 33:135-50. [PMID: 27485570 DOI: 10.1002/minf.201300143] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/06/2013] [Indexed: 12/26/2022]
Abstract
A standard practice for lead identification in drug discovery is ligand virtual screening, which utilizes computing technologies to detect small compounds that likely bind to target proteins prior to experimental screens. A high accuracy is often achieved when the target protein has a resolved crystal structure; however, using protein models still renders significant challenges. Towards this goal, we recently developed eFindSite that predicts ligand binding sites using a collection of effective algorithms, including meta-threading, machine learning and reliable confidence estimation systems. Here, we incorporate fingerprint-based virtual screening capabilities in eFindSite in addition to its flagship role as a ligand binding pocket predictor. Virtual screening benchmarks using the enhanced Directory of Useful Decoys demonstrate that eFindSite significantly outperforms AutoDock Vina as assessed by several evaluation metrics. Importantly, this holds true regardless of the quality of target protein structures. As a first genome-wide application of eFindSite, we conduct large-scale virtual screening of the entire proteome of Escherichia coli with encouraging results. In the new approach to fingerprint-based virtual screening using remote protein homology, eFindSite demonstrates its compelling proficiency offering a high ranking accuracy and low susceptibility to target structure deformations. The enhanced version of eFindSite is freely available to the academic community at http://www.brylinski.org/efindsite.
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Affiliation(s)
- Wei P Feinstein
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. .,Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA.
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23
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Stefan L, Bertrand B, Richard P, Le Gendre P, Denat F, Picquet M, Monchaud D. Assessing the Differential Affinity of Small Molecules for Noncanonical DNA Structures. Chembiochem 2012; 13:1905-12. [DOI: 10.1002/cbic.201200396] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 01/19/2023]
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24
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Ma DL, Chan DSH, Lee P, Kwan MHT, Leung CH. Molecular modeling of drug–DNA interactions: Virtual screening to structure-based design. Biochimie 2011; 93:1252-66. [PMID: 21514356 DOI: 10.1016/j.biochi.2011.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/01/2011] [Indexed: 12/11/2022]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
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25
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Abstract
A DNA duplex can be recognized sequence-specifically in the major groove by an oligodeoxynucleotide (ODN). The resulting structure is a DNA triple helix, or triplex. The scientific community has invested significant research capital in the study of DNA triplexes because of their robust potential for providing new applications, including molecular biology tools and therapeutic agents. The triplex structures have inherent instabilities, however, and the recognition of DNA triplexes by small molecules has been attempted as a means of strengthening the three-stranded complex. Over the decades, the majority of work in the field has focused on heterocycles that intercalate between the triplex bases. In this Account, we present an alternate approach to recognition and stabilization of DNA triplexes. We show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the TAT triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (TAT and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson-Hoogsteen groove, making it the first molecule that selectively recognizes a triplex groove over a duplex groove. The groove recognition of aminoglycosides is not limited to DNA triplexes, but also extends to RNA and hybrid triple helical structures. Intercalator-neomycin conjugates are shown to simultaneously probe the base stacking and groove surface in the DNA triplex. Calorimetric and spectrosocopic studies allow the quantification of the effect of surface area of the intercalating moiety on binding to the triplex. These studies outline a novel approach to the recognition of DNA triplexes that incorporates the use of noncompeting binding sites. These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity.
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26
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Holt PA, Buscaglia R, Trent JO, Chaires JB. A Discovery Funnel for Nucleic Acid Binding Drug Candidates. Drug Dev Res 2010; 72:178-186. [PMID: 21566705 DOI: 10.1002/ddr.20414] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Computational approaches are becoming increasingly popular for the discovery of drug candidates against a target of interest. Proteins have historically been the primary targets of many virtual screening efforts. While in silico screens targeting proteins has proven successful, other classes of targets, in particular DNA, remain largely unexplored using virtual screening methods. With the realization of the functional importance of many non-cannonical DNA structures such as G-quadruplexes, increased efforts are underway to discover new small molecules that can bind selectively to DNA structures. Here, we describe efforts to build an integrated in silico and in vitro platform for discovering compounds that may bind to a chosen DNA target. Millions of compounds are initially screened in silico for selective binding to a particular structure and ranked to identify several hundred best hits. An important element of our strategy is the inclusion of an array of possible competing structures in the in silico screen. The best hundred or so hits are validated experimentally for binding to the actual target structure by a high-throughput 96-well thermal denaturation assay to yield the top ten candidates. Finally, these most promising candidates are thoroughly characterized for binding to their DNA target by rigorous biophysical methods, including isothermal titration calorimetry, differential scanning calorimetry, spectroscopy and competition dialysis.This platform was validated using quadruplex DNA as a target and a newly discovered quadruplex binding compound with possible anti-cancer activity was discovered. Some considerations when embarking on virtual screening and in silico experiments are also discussed.
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Affiliation(s)
- Patrick A Holt
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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27
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Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010; 24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 223] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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28
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Musmuca I, Caroli A, Mai A, Kaushik-Basu N, Arora P, Ragno R. Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors. J Chem Inf Model 2010; 50:662-76. [PMID: 20225870 DOI: 10.1021/ci9004749] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The viral NS5B RNA-dependent RNA-polymerase (RdRp) is one of the best-studied and promising targets for the development of novel therapeutics against hepatitis C virus (HCV). Allosteric inhibition of this enzyme has emerged as a viable strategy toward blocking replication of viral RNA in cell based systems. Herein, we describe how the combination of a complete computational procedure together with biological studies led to the identification of novel molecular scaffolds, hitherto untested toward NS5B polymerase. Structure based 3-D quantitative structure-activity relationship (QSAR) models were generated employing NS5B non-nucleoside inhibitors (NNIs), whose bound conformations were readily available from the protein database (PDB). These were grouped into two training sets of structurally diverse NS5B NNIs, based on their binding to the enzyme thumb (15 NNIs) or palm (10 NNIs) domains. Ligand based (LB) and structure based (SB) alignments were rigorously investigated to assess the reliability on the correct molecular alignment for unknown binding mode modeled compounds. Both Surflex and Autodock programs were able to reproduce with minimal errors the experimental binding conformations of 24 experimental NS5B allosteric inhibitors. Eighty-one (thumb) and 223 (palm) modeled compounds taken from literature were LB and SB aligned and used as external validation sets for the development of 3-D QSAR models. Low error of prediction proved the 3-D QSARs to be useful scoring functions for the in silico screening procedure. Finally, the virtual screening of the NCI Diversity Set led to the selection for enzymatic assays of 20 top-scoring molecules for each final model. Among the 40 selected molecules, preliminary data yielded four derivatives exhibiting IC(50) values ranging between 45 and 75 microM. Binding mode analysis of hit compounds within the NS5B polymerase thumb domain showed that one of them, NSC 123526, exhibited a docked conformation which was in good agreement with the thumb training set most active compound (6).
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Affiliation(s)
- Ira Musmuca
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Universita di Roma, P le A Moro 5, 00185 Rome, Italy
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29
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Jain AK, Bhattacharya S. Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA. Bioconjug Chem 2010; 21:1389-403. [PMID: 20509695 DOI: 10.1021/bc900247s] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Akash K. Jain
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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