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Shukla MS, Hoshika S, Benner SA, Georgiadis MM. Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220028. [PMID: 36633282 PMCID: PMC9835606 DOI: 10.1098/rstb.2022.0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA should also be able to adopt B-form. Using a host-guest system in which Moloney murine leukemia virus reverse transcriptase serves as the host and DNA as the guests, we determined high-resolution crystal structures of three complexes including 5'-CTTBPPBBSSZZSAAG, 5'-CTTSSPBZPSZBBAAG and 5'-CTTZZPBSBSZPPAAG with 10 consecutive unnatural nucleobase pairs in B-form within self-complementary 16 bp duplex oligonucleotides. We refer to this ALternative Isoinformational ENgineered (ALIEN) genetic system containing two nucleobase pairs (P:Z, pairing 2-amino-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one with 6-amino-5-nitro-(1H)-pyridin-2-one, and B:S, 6-amino-4-hydroxy-5-(1H)-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one) as ALIEN DNA. We characterized both position- and sequence-specific helical, nucleobase pair and dinucleotide step parameters of P:Z and B:S pairs in the context of B-form DNA. We conclude that ALIEN DNA exhibits structural features that vary with sequence. Further, Z can participate in alternative stacking modes within a similar sequence context as captured in two different structures. This finding suggests that ALIEN DNA may have a larger repertoire of B-form structures than natural DNA. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Madhura S. Shukla
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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2
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Goodwin KD, Lewis MA, Long EC, Georgiadis MM. Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites. Bioorg Med Chem 2023; 77:117113. [PMID: 36516684 DOI: 10.1016/j.bmc.2022.117113] [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: 10/03/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Bleomycins constitute a family of anticancer natural products that bind DNA through intercalation of a C-terminal tail/bithiazole moiety and hydrogen-bonding interactions between the remainder of the drug and the minor groove. The clinical utility of the bleomycins is believed to result from single- and double-strand DNA cleavage mediated by the HOO-Fe(III) form of the drug. The bleomycins also serve as a model system to understand the nature of complex drug-DNA interactions that may guide future DNA-targeted drug discovery. In this study, the impact of the C-terminal tail on bleomycin-DNA interactions was investigated. Toward this goal, we determined two crystal structures of HOO-Co(III)•BLMA2 "green" (a stable structural analogue of the active HOO-Fe(III) drug) bound to duplex DNA containing 5'-TAGTT, one in which the entire drug is bound (fully bound) and a second with only the C-terminal tail/bithiazole bound (partially bound). The structures reported here were captured by soaking HOO-Co(III)•BLMA2 into preformed host-guest crystals including a preferred DNA-binding site. While the overall structure of DNA-bound BLMA2 was found to be similar to those reported earlier at the same DNA site for BLMB2, the intercalated bithiazole of BLMB2 is "flipped" 180˚ relative to DNA-bound BLMA2. This finding highlights an unidentified role for the C-terminal tail in directing the intercalation of the bithiazole. In addition, these analyses identified specific bond rotations within the C-terminal domain of the drug that may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.
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Affiliation(s)
- Kristie D Goodwin
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark A Lewis
- Department of Chemistry & Chemical Biology, Indiana University-Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, USA
| | - Eric C Long
- Department of Chemistry & Chemical Biology, Indiana University-Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, USA.
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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3
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Drug repurposing strategy II: from approved drugs to agri-fungicide leads. J Antibiot (Tokyo) 2023; 76:131-182. [PMID: 36707717 PMCID: PMC9880955 DOI: 10.1038/s41429-023-00594-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023]
Abstract
Epidemic diseases of crops caused by fungi deeply affected the course of human history and processed a major restriction on social and economic development. However, with the enormous misuse of existing antimicrobial drugs, an increasing number of fungi have developed serious resistance to them, making the diseases caused by pathogenic fungi even more challenging to control. Drug repurposing is an attractive alternative, it requires less time and investment in the drug development process than traditional R&D strategies. In this work, we screened 600 existing commercially available drugs, some of which had previously unknown activity against pathogenic fungi. From the primary screen at a fixed concentration of 100 μg/mL, 120, 162, 167, 85, 102, and 82 drugs were found to be effective against Rhizoctonia solani, Sclerotinia sclerotiorum, Botrytis cinerea, Phytophthora capsici, Fusarium graminearum and Fusarium oxysporum, respectively. They were divided into nine groups lead compounds, including quinoline alkaloids, benzimidazoles/carbamate esters, azoles, isothiazoles, pyrimidines, pyridines, piperidines/piperazines, ionic liquids and miscellaneous group, and simple structure-activity relationship analysis was carried out. Comparison with fungicides to identify the most promising drugs or lead structures for the development of new antifungal agents in agriculture.
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4
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Microwave-assisted Catalyzed Synthesis and In vitro Bioactivity Evaluation of Benzimidazoles Bearing Phenolic Hydroxyl. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-0274-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C. Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Hu Zeng
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Manas Mondal
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Ruyi Song
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Bo Xia
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Menghao Liu
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Chenxu Zhu
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Bo He
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Chengqi Yi
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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6
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Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C. Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew Chem Int Ed Engl 2018; 58:130-133. [DOI: 10.1002/anie.201807845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/25/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Hu Zeng
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Manas Mondal
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Ruyi Song
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Bo Xia
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Menghao Liu
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Chenxu Zhu
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Bo He
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Chengqi Yi
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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7
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences; Academia Sinica; 128 Sec. 2, Academia Rd. Nankang Taipei Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center; College of Science; National Taiwan University; No.1, Sec. 4, Roosevelt Rd. Taipei Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology; Chi Mei Medical Center; No.901, Zhonghua Rd. Tainan Taiwan
| | - Stephen Neidle
- The School of Pharmacy; University College London; London WC1N 1AX UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
- Institute of Biotechnology; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
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Richards NGJ, Georgiadis MM. Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System. Acc Chem Res 2017; 50:1375-1382. [PMID: 28594167 DOI: 10.1021/acs.accounts.6b00655] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although the fundamental properties of DNA as first proposed by Watson and Crick in 1953 provided a basic understanding of how duplex DNA was organized and might be replicated, it was not until the first crystal structures of DNA (Z-DNA in 1979, B-DNA in 1980, and A-DNA in 1982) that the true complexity of the molecule began to be appreciated. Many crystal structures of oligonucleotides have since shed light on the helical forms that "Watson-Crick" DNA can adopt, their associated groove widths, and the properties of the nucleobase pairs and their interactions in all three helical forms. Additional understanding of the properties of Watson-Crick DNA has been provided by computational studies employing a variety of theoretical methods. Together with these studies devoted to understanding Watson-Crick DNA, recent efforts to expand the genetic alphabet have founded a new field in synthetic biology. One of these efforts, the artificially expanded genetic information system (AEGIS) developed by Steven Benner and co-workers, takes advantage of orthogonal hydrogen bonding to produce DNA comprised of six nucleobase pairs, of which the most extensively studied is referred to as P:Z with P being 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) and Z being 6-amino-5-nitro-2(1H)-pyridone. P:Z forms three edge-on hydrogen bonds that differ from standard Watson-Crick pairs in the arrangement of acceptors and donor groups; P presents acceptor, acceptor, donor, and Z presents donor, donor, acceptor. Z is unique among the AEGIS nucleobases in having a nitro group present in the major groove. PZ-containing DNA has been exploited in a number of clinical applications and is being used to develop receptors and catalysts. Ultimately, the grand challenge will be to create a semisynthetic organism with an expanded genome. Furthermore, just as our understanding of the properties of natural DNA have benefited from structural and computational characterization, so too will our understanding of artificial DNA. This Account focuses on the structural and biophysical properties of AEGIS DNA containing P:Z pairs. We begin with the fundamental properties of P:Z nucleobase pairs, including their electrostatic potential and hydrogen-bonding energies, as elucidated by quantum mechanical calculations. We then examine the impact of including multiple consecutive P:Z pairs into duplex DNA providing an opportunity to investigate stacking interactions between P:Z pairs. The self-complementary 5'-CTTATPPTAZZATAAG was crystallized in B-form using the host-guest system along with analogous natural sequences including Gs or As. Use of the host-guest system to characterize B-DNA obviates a number of limitations on the structural characterization of sequences of interest; these include the ability to crystallize the desired sequences and to distinguish structural effects imparted by the lattice constraints from those inherent in the sequence itself. On the other hand, 3/6ZP, 5'-CTTATPPPZZZATAAG, was crystallized in A-form in a DNA-only lattice allowing a comparative analysis of P:Z pairs in two of the biologically relevant helical forms: A- and B-DNA. Computational studies on the 3/6ZP sequence starting in A-form provide additional evidence for a more energetically favorable stacking interaction, which we term the "slide" conformer, observed in the A-form crystal structure; this unusual stacking interaction plays a major role in altering the conformational dynamics observed for the PZ-containing duplex as compared to a GC-containing "control" duplex in long time scale molecular dynamics simulations. This combined use of structural and computational strategies paves the way for obtaining a detailed description of artificial DNA, both in how it differs from Watson-Crick DNA and in the rational discovery of proteins, such as endonucleases, transcription factors, and polymerases, which can specifically manipulate DNA containing AEGIS nucleobase pairs.
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Affiliation(s)
- Nigel G. J. Richards
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Alachua, Florida 32615, United States
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department
of Chemistry and Chemical Biology, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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9
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017; 56:8761-8765. [PMID: 28544401 DOI: 10.1002/anie.201703989] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 01/23/2023]
Abstract
Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII (Chro)2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.
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Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Rd. Nankang, Taipei, Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, College of Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology, Chi Mei Medical Center, No.901, Zhonghua Rd., Tainan, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
- Institute of Biotechnology, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
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10
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Song D, Ma S. Recent Development of Benzimidazole-Containing Antibacterial Agents. ChemMedChem 2016; 11:646-59. [PMID: 26970352 DOI: 10.1002/cmdc.201600041] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/20/2016] [Indexed: 11/11/2022]
Abstract
Clinically significant antibiotic resistance is one of the greatest challenges of the twenty-first century. However, new antibacterial agents are currently being developed at a much slower pace than our growing need for such drugs. Given their diverse biological activities and clinical applications, many bioactive heterocyclic compounds containing a benzimidazole nucleus have been the focus of interest for many researchers. The benzimidazole nucleus is a structural isostere of naturally occurring nucleotides. This advantage allows benzimidazoles to readily interact with the various biopolymers found in living systems. In view of this situation, much attention has been given to the exploration of benzimidazole-based antibacterial agents, leading to the discovery of many new chemical entities with intriguing profiles. In this minireview we summarize novel benzimidazole derivatives active against various bacterial strains. In particular, we outline the relationship between the structures of variously modified benzimidazoles and their antibacterial activity.
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Affiliation(s)
- Di Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan, 250012, P.R. China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan, 250012, P.R. China.
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11
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Fukuzumi T, Murata A, Aikawa H, Harada Y, Nakatani K. Exploratory Study on the RNA-Binding Structural Motifs by Library Screening Targeting pre-miRNA-29 a. Chemistry 2015; 21:16859-67. [DOI: 10.1002/chem.201502913] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 12/31/2022]
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12
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Sadeghi M, Bayat M, Cheraghi S, Yari K, Heydari R, Dehdashtian S, Shamsipur M. Binding studies of the anti-retroviral drug, efavirenz to calf thymus DNA using spectroscopic and voltammetric techniques. LUMINESCENCE 2015; 31:108-17. [DOI: 10.1002/bio.2931] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/12/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
| | - Maryam Bayat
- Department of Chemistry; Razi University; Kermanshah Iran
| | | | - Khirollah Yari
- Medical Biology Research Center; Kermanshah University of Medical Science; Kermanshah Iran
| | - Rouhollah Heydari
- Razi Herbal, Medicines Research Center; Lorestan University of Medical Sciences; P.O. Box 68149-89468 Khorramabad Iran
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13
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Song Y, Zhong D, Luo J, Tan H, Chen S, Li P, Wang L, Wang T. Binding characteristics and interactive region of 2-phenylpyrazolo[1,5-c]quinazoline with DNA. LUMINESCENCE 2014; 29:1141-7. [DOI: 10.1002/bio.2674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 02/21/2014] [Accepted: 03/03/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Yonghai Song
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Dandan Zhong
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Jinhui Luo
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Hongliang Tan
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Shouhui Chen
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Ping Li
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Li Wang
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
| | - Tao Wang
- Key Laboratory of Chemical Biology; Jiangxi Normal University; Nanchang People's Republic of China
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14
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Singh I, Lian Y, Li L, Georgiadis MM. The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:752-9. [PMID: 24598744 PMCID: PMC3949526 DOI: 10.1107/s1399004713032987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/05/2013] [Indexed: 11/12/2022]
Abstract
The spore photoproduct lesion (SP; 5-thymine-5,6-dihydrothymine) is the dominant photoproduct found in UV-irradiated spores of some bacteria such as Bacillus subtilis. Upon spore germination, this lesion is repaired in a light-independent manner by a specific repair enzyme: the spore photoproduct lyase (SP lyase). In this work, a host-guest approach in which the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) serves as the host and DNA as the guest was used to determine the crystal structures of complexes including 16 bp oligonucleotides with and without the SP lesion at 2.14 and 1.72 Å resolution, respectively. In contrast to other types of thymine-thymine lesions, the SP lesion retains normal Watson-Crick hydrogen bonding to the adenine bases of the complementary strand, with shorter hydrogen bonds than found in the structure of the undamaged DNA. However, the lesion induces structural changes in the local conformation of what is otherwise B-form DNA. The region surrounding the lesion differs significantly in helical form from B-DNA, and the minor groove is widened by almost 3 Å compared with that of the undamaged DNA. Thus, these unusual structural features associated with SP lesions may provide a basis for recognition by the SP lyase.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yajun Lian
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| | - Lei Li
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
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15
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Garner ML, Georgiadis TM, Li JB, Wang T, Long EC. Solid-phase synthesis of amidine-substituted phenylbenzimidazoles and incorporation of this DNA binding and recognition motif into amino acid and peptide conjugates. Amino Acids 2014; 46:1297-303. [PMID: 24562478 DOI: 10.1007/s00726-014-1691-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/31/2014] [Indexed: 11/25/2022]
Abstract
Amidine-substituted phenylbenzimidazoles are well-established DNA-binding structural motifs that have contributed to the development of diverse classes of DNA-targeted agents; this ring system not only assists in increasing the overall DNA affinity of an agent, but can also influence its site selectivity. Seeking a means to conveniently exploit these attributes, a protocol for the on-resin synthesis of amino acid- and peptide-phenylbenzimidazole-amidine conjugates was developed to facilitate installation of phenylbenzimidazole-amidines into peptide chains during the course of standard solid-phase syntheses. Building from a resin-bound amino acid or peptide on Rink amide resin, 4-formyl benzoic acid was coupled to the resin-bound free amine followed by introduction of 3,4-diamino-N'-hydroxybenzimidamide (in the presence of 1,4-benzoquinone) to construct the benzimidazole heterocycle. Finally, the resin-bound N'-hydroxybenzimidamide functionality was reduced to an amidine via 1 M SnCl2·2H2O in DMF prior to resin cleavage to release final product. This procedure permits the straightforward synthesis of amino acids or peptides that are N-terminally capped by a phenylbenzimidazole-amidine ring system. Employing this protocol, a series of amino acid-phenylbenzimidazole-amidine (Xaa-R) conjugates was synthesized as well as dipeptide conjugates of the general form Xaa-Gly-R (where R is the phenylbenzimidazole-amidine and Xaa is any amino acid).
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Affiliation(s)
- Matthew L Garner
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN, 46202, USA
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16
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Abstract
Benzimidazole compounds are known to possess varied biological activities and so far various types of benzimidazole drugs have extensively been used in clinic. Benzimidazole compounds as a antibacterial agents has been a quite rapidly developing and is gradually becoming a relatively independent scientific area. In this paper we presented the recent advances of benzimidazole compounds as antibacterial agents. The perspective of the foreseeable future and potential application of benzimidazole as antibacterial agents are also presented.
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17
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Wei D, Wilson WD, Neidle S. Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster. J Am Chem Soc 2013; 135:1369-77. [PMID: 23276263 DOI: 10.1021/ja308952y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
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Affiliation(s)
- DengGuo Wei
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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18
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Umemoto S, Im S, Zhang J, Hagihara M, Murata A, Harada Y, Fukuzumi T, Wazaki T, Sasaoka SI, Nakatani K. Structure-activity studies on the fluorescent indicator in a displacement assay for the screening of small molecules binding to RNA. Chemistry 2012; 18:9999-10008. [PMID: 22763984 DOI: 10.1002/chem.201103932] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 04/04/2012] [Indexed: 11/12/2022]
Abstract
A series of xanthone and thioxanthone derivatives with aminoalkoxy substituents were synthesized as fluorescent indicators for a displacement assay in the study of small-molecule-RNA interactions. The RNA-binding properties of these molecules were investigated in terms of the improved binding selectivity to the loop region in the RNA secondary structure relative to 2,7-bis(2-aminoethoxy)xanthone (X2S) by fluorimetric titration and displacement assay. An 11-mer double-stranded RNA and a hairpin RNA mimicking the stem loop IIB of Rev response element (RRE) RNA of HIV-1 mRNA were used. The X2S derivatives with longer aminoalkyl substituents showed a higher affinity to the double-stranded RNA than the parent molecule. Introduction of a methyl group on the aminoethoxy moiety of X2S effectively modulated the selectivity to the RNA secondary structure. Methyl group substitution at the C1' position suppressed the binding to the loop regions. Substitution with two methyl groups on the amino nitrogen atom resulted in reducing the affinity to the double-stranded region by a factor of 40%. The effect of methyl substitution on the amino nitrogen atom was also observed for a thioxanthone derivative. Titration experiments, however, suggested that thioxanthone derivatives showed a more prominent tendency of multiple binding to RNA than xanthone derivatives. The selectivity index calculated from the affinity to the double-stranded and loop regions suggested that the N,N-dimethyl derivative of X2S would be suitable for the screening of small molecules binding to RRE.
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Affiliation(s)
- Shiori Umemoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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19
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Baranauskas A, Paliksa S, Alzbutas G, Vaitkevicius M, Lubiene J, Letukiene V, Burinskas S, Sasnauskas G, Skirgaila R. Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants. Protein Eng Des Sel 2012; 25:657-68. [PMID: 22691702 DOI: 10.1093/protein/gzs034] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vitro synthesis of cDNA is one of the most important techniques in present molecular biology. Faithful synthesis of long cDNA on highly structured RNA templates requires thermostable and processive reverse transcriptases. In a recent attempt to increase the thermostability of the wt Moloney Murine leukemia virus reverse transcriptase (M-MuLV RT), we have employed the compartmentalized ribosome display (CRD) evolution in vitro technique and identified a large set of previously unknown mutations that enabled cDNA synthesis at elevated temperatures. In this study, we have characterized a group of the M-MuLV RT variants (28 novel amino acid positions, 84 point mutants) carrying the individual mutations. The performance of point mutants (thermal inactivation rate, substrate-binding affinity and processivity) correlated remarkably well with the mutation selection frequency in the CRD experiment. By combining the best-performing mutations D200N, L603W, T330P, L139P and E607K, we have generated highly processive and thermostable multiply-mutated M-MuLV RT variants. The processivity of the best-performing multiple mutant increased to 1500 nt (65-fold improvement in comparison to the wt enzyme), and the maximum temperature of the full-length 7.5-kb cDNA synthesis was raised to 62°C (17° higher in comparison with the wt enzyme).
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20
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Lewis EA, Munde M, Wang S, Rettig M, Le V, Machha V, Wilson WD. Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site. Nucleic Acids Res 2011; 39:9649-58. [PMID: 21890907 PMCID: PMC3239193 DOI: 10.1093/nar/gkr699] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Structural results with minor groove binding agents, such as netropsin, have provided detailed, atomic level views of DNA molecular recognition. Solution studies, however, indicate that there is complexity in the binding of minor groove agents to a single site. Netropsin, for example, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of netropsin at single binding sites and (ii) a netropsin induced DNA hairpin to duplex transition. To develop a better understanding of DNA recognition complexity, the two proposals have been tested with several DNAs and the methods of mass spectrometry (MS), polyacrylamide gel electrophoresis (PAGE) and nuclear magnetic resonance spectroscopy in addition to ITC. All of the methods with all of the DNAs investigated clearly shows that netropsin forms two different complexes at AATT sites, and that the proposal for an induced hairpin to duplex transition in this system is incorrect.
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Affiliation(s)
- Edwin A Lewis
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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21
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Fuchs JE, Spitzer GM, Javed A, Biela A, Kreutz C, Wellenzohn B, Liedl KR. Minor groove binders and drugs targeting proteins cover complementary regions in chemical shape space. J Chem Inf Model 2011; 51:2223-32. [PMID: 21819135 DOI: 10.1021/ci200237c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA minor groove binders (MGBs) are known to influence gene expression and are therefore widely studied to explore their therapeutic potential. We identified shape-based virtual screening with ROCS as a highly effective computational approach to enrich known MGBs in top-ranked molecules. Discovery of ten previously unknown MGBs by shape-based screening further confirmed the relevance of ligand shape for minor groove affinity. Based on experimental testing we propose three simple rules (at least two positive charges, four nitrogen atoms, and one aromatic ring) as filters to reach even better enrichment of true positives in ROCS hit lists. Interestingly, shape-based ranking of MGBs versus FDA-approved drugs again leads to high enrichment rates, indicating complementary coverage of chemical shape space and indicating minor groove affinity to be unfavorable for approval of drugs targeting proteins.
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Affiliation(s)
- Julian E Fuchs
- Faculty of Chemistry and Pharmacy, University of Innsbruck, Innsbruck, Austria
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22
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Wang S, Munde M, Wang S, Wilson WD. Minor groove to major groove, an unusual DNA sequence-dependent change in bend directionality by a distamycin dimer. Biochemistry 2011; 50:7674-83. [PMID: 21800847 DOI: 10.1021/bi201010g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequence-dependent conformational changes induced by the minor groove binder, distamycin, have been evaluated by polyacrylamide gel electrophoresis. The distamycin binding affinity, cooperativity, and stoichiometry with three target DNA sequences that have different sizes of alternating AT sites, ATAT, ATATA, and ATATAT, have been determined by mass spectrometry and surface plasmon resonance to help explain the conformational changes. The results show that distamycin binds strongly to and bends five or six AT base pair minor groove sites as a dimer with positive cooperativity, while it binds to ATAT as a weak, slightly anticooperative dimer. The bending direction was evaluated with an in phase A-tract reference sequence. Unlike other similar monomer minor groove binding compounds, such as netropsin, the distamycin dimer changes the directionality of the overall curvature away from the minor groove to the major groove. This distinct structural effect may allow designed distamycin derivatives to have selective therapeutic effects.
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Affiliation(s)
- Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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23
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Ren TG, Cheng HB, Zhang JL, Li WJ, Guo J, Yang LR. Synthesis of benzimidazoles containing pyrazole group and quantum chemistry calculation of their spectroscopic properties and electronic structure. J Fluoresc 2011; 22:201-12. [PMID: 21826423 DOI: 10.1007/s10895-011-0947-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/02/2011] [Indexed: 10/17/2022]
Abstract
Five benzimidazole compounds containing pyrazole group were synthesized via one-step reaction of o-phenylenediamine and 1-arylpyrazole-4-carbaldehyde in ethanol under mild conditions. The composition and structure of resultant benzimidazole compounds were analyzed by means of elemental analysis, mass spectrometry, (1)H-nuclear magnetic resonance spectroscopy and X-ray single crystal diffraction. The ultraviolet-visible light spectra and fluorescent spectra of the products were measured. Their ground-state (S(0)) equilibrium geometries and vibrational frequencies were determined based on B3LYP method, and their first excited-state (S(1)) geometries were fully optimized based on 6-31G (d, p) basis set of TD-B3LYP method. Besides, the spectroscopic properties of the products were computed based on cc-pVTZ basis set of TD-B3LYP method and compared with corresponding experimental data. It has been found that benzimidazole compounds containing pyrazole group can be readily synthesized in a high yield via one-step reaction of o-phenylenediamine and 1-arylpyrazole-4-carbaldehyde in ethanol solvent. The fluorescence properties of the five synthesized compounds are closely related to their molecular structure; and their computed fluorescence spectra well correspond to their experimental values. Moreover, they have stable structure and strong fluorescence, showing potential application in time-resolved fluoroimmunoassay and DNA probe.
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Affiliation(s)
- Tie-gang Ren
- Fine Chemistry and Engineering Research Institute, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, People's Republic of China.
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24
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Hu L, Kully ML, Boykin DW, Abood N. Synthesis and structure–activity relationship of dicationic diaryl ethers as novel potent anti-MRSA and anti-VRE agents. Bioorg Med Chem Lett 2009; 19:4626-9. [PMID: 19589676 DOI: 10.1016/j.bmcl.2009.06.077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 06/18/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
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25
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Glass LS, Nguyen B, Goodwin KD, Dardonville C, Wilson WD, Long EC, Georgiadis MM. Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA. Biochemistry 2009; 48:5943-52. [PMID: 19405506 PMCID: PMC2740933 DOI: 10.1021/bi900204w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pursuit of small molecules that bind to DNA has led to the discovery of selective and potent antitrypanosomal agents, specifically 4,4'-bis(imidazolinylamino)- and 4,4'-bis(guanidino)diphenylamine compounds, CD27 and CD25, respectively. Although the antitrypanosomal properties of these compounds have been characterized, further development of this series of compounds requires assessment of their DNA site selectivities and affinities. Toward this end, both compounds have been analyzed and found to selectively bind AT sequences. However, CD27 was found to bind with higher affinity to 5'-AATT than 5'-ATAT while CD25 bound more weakly but equally well to either sequence. To detail the nature of its interactions with DNA, the crystal structure of CD27, bound to its preferred DNA-binding site 5'-AATT within a self-complementary oligonucleotide, 5'-d(CTTAATTCGAATTAAG), was determined at 1.75 A using a host-guest approach. Although CD27 is predicted to be highly twisted in its energy-minimized state, it adopts a more planar crescent shape when bound in the minor groove of the DNA. Interactions of CD27 with 5'-AATT include bifurcated hydrogen bonds, providing a basis for selectivity of this site, and favorable van der Waals interactions in a slightly widened minor groove. Thus, an induced fit results from conformational changes in both the ligand and the DNA. Our studies suggest a basis for understanding the mechanism of the antitrypanosomal activity of these symmetric diphenylamine compounds.
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Affiliation(s)
- LaTeca S. Glass
- Department of Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202
| | - Binh Nguyen
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302
| | - Kristie D. Goodwin
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202
| | | | - W. David Wilson
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202,Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302
| | - Eric C. Long
- Department of Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202,To whom correspondence should be addressed. Telephone: (317) 278-8486. Fax (317) 274-4686. E-mail: (M.M.G) or Telephone (317) 274-6888. Fax (317) 274-4701. E-mail: (E.C.L.)
| | - Millie M. Georgiadis
- Department of Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202,Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202,To whom correspondence should be addressed. Telephone: (317) 278-8486. Fax (317) 274-4686. E-mail: (M.M.G) or Telephone (317) 274-6888. Fax (317) 274-4701. E-mail: (E.C.L.)
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26
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Synthesis and affinity to DNA of phenylbenzoimidazoles and benzoimidazo[1,2-c]quinazolines. Eur J Med Chem 2009; 44:3305-12. [PMID: 19349097 PMCID: PMC7115644 DOI: 10.1016/j.ejmech.2009.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 03/02/2009] [Accepted: 03/06/2009] [Indexed: 01/12/2023]
Abstract
Novel N-(benzoimidazophenyl)dialkylaminoalkylamides and 6-dialkylaminoalkylbenzoimidazo[1,2-c]quinazolines were prepared as potential interferon inducers and antiviral agents. They were screened for the DNA affinity by the ethidium bromide displacement assay. It was shown that the lg Ka values of the compounds containing tetracyclic benzoimidazo[1,2-c]quinazoline fragment are approximately one order magnitude greater than those of the corresponding acyclic phenylbenzoimidazole derivatives.
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27
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Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL. Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine. J Am Chem Soc 2008; 130:11570-1. [PMID: 18686953 DOI: 10.1021/ja8025328] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The predominant product of aberrant DNA methylation is the genotoxic lesion N7-methyl-2'-deoxyguanosine (m7dG). M7dG is recognized and excised by lesion-specific DNA glycosylases, namely AlkA in E. coli and Aag in humans. Structural studies of m7dG recognition and catalysis by these enzymes have been hampered due to a lack of efficient means by which to incorporate the chemically labile m7dG moiety site-specifically into DNA on a preparative scale. Here we report a solution to this problem. We stabilized the lesion toward acid-catalyzed and glycosylase-catalyzed depurination by 2'-fluorination and toward base-catalyzed degradation using mild, nonaqueous conditions in the DNA deprotection reaction. Duplex DNA containing 2'-fluoro-m7dG (Fm7dG) cocrystallized with AlkA as a host-guest complex in which the lesion-containing segment of DNA was nearly devoid of protein contacts, thus enabling the first direct visualization of the N7-methylguanine lesion nucleobase in DNA. The structure reveals that the base-pairing mode of Fm7dG:C is nearly identical to that of G:C, and Fm7dG does not induce any apparent structural disturbance of the duplex structure. These observations suggest that AlkA and Aag must perform a structurally invasive interrogation of DNA in order to detect the presence of intrahelical m7dG lesions.
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Affiliation(s)
- Seongmin Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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28
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Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding. Proc Natl Acad Sci U S A 2008; 105:5052-6. [PMID: 18362349 DOI: 10.1073/pnas.0708143105] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bleomycins constitute a widely studied class of complex DNA cleaving natural products that are used to treat various cancers. Since their first isolation, the bleomycins have provided a paradigm for the development and discovery of additional DNA-cleaving chemotherapeutic agents. The bleomycins consist of a disaccharide-modified metal-binding domain connected to a bithiazole/C-terminal tail via a methylvalerate-Thr linker and induce DNA damage after oxygen activation through site-selective cleavage of duplex DNA at 5'-GT/C sites. Here, we present crystal structures of two different 5'-GT containing oligonucleotides in both the presence and absence of bound Co(III).bleomycin B(2). Several findings from our studies impact the current view of bleomycin binding to DNA. First, we report that the bithiazole intercalates in two distinct modes and can do so independently of well ordered minor groove binding of the metal binding/disaccharide domains. Second, the Co(III)-coordinating equatorial ligands in our structure include the imidazole, histidine amide, pyrimidine N1, and the secondary amine of the beta aminoalanine, whereas the primary amine acts as an axial ligand. Third, minor groove binding of Co(III).bleomycin involves direct hydrogen bonding interactions of the metal binding domain and disaccharide with the DNA. Finally, modeling of a hydroperoxide ligand coordinated to Co(III) suggests that it is ideally positioned for initiation of C4'-H abstraction.
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29
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Nelson SM, Ferguson LR, Denny WA. Non-covalent ligand/DNA interactions: minor groove binding agents. Mutat Res 2007; 623:24-40. [PMID: 17507044 DOI: 10.1016/j.mrfmmm.2007.03.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 03/31/2007] [Indexed: 05/15/2023]
Abstract
An understanding of the mechanism by which minor groove binding agents interact with DNA has led to the design of agents that can reversibly bind with high selectivity to extended DNA target sequences. Simple compounds, such as the polypyrroles and the bis-benzimidazoles, have been used as carriers for alkylating agents effectively directing alkylation to specific DNA sequences. The spectrum of DNA alkylation and mutation by classical alkylators, such as nitrogen mustards, has been profoundly modified by such attachment. The observed "side-by-side" binding of small polypyrrole antibiotics has led to the design of synthetic hairpin polyamides with programmable DNA sequence selectivity. These compounds are able to compete with natural substrates, such as specific transcription factors, and alter gene expression. They are being developed as artificial transcription factors, able to deliver activating peptides to specific recognition sequences, and as potential protein-DNA dimerization agents. Hairpin polyamides are also being used as carriers for the delivery of alkylators to defined DNA sites. The degree of control of gene expression thus offered by the hairpin polyamides suggests enormous promise for their clinical utility. Recent developments with other minor groove binding small molecules and technological advances are also discussed.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand.
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30
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Tanious FA, Laine W, Peixoto P, Bailly C, Goodwin KD, Lewis MA, Long EC, Georgiadis MM, Tidwell RR, Wilson WD. Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water. Biochemistry 2007; 46:6944-56. [PMID: 17506529 PMCID: PMC2519038 DOI: 10.1021/bi700288g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RT29 is a dicationic diamidine derivative that does not obey the classical "rules" for shape and functional group placement that are expected to result in strong binding and specific recognition of the DNA minor groove. The compound contains a benzimidazole diphenyl ether core that is flanked by the amidine cations. The diphenyl ether is highly twisted and gives the entire compound too much curvature to fit well to the shape of the minor groove. DNase I footprinting, fluorescence intercalator displacement studies, and circular dichroism spectra, however, indicate that the compound is an AT specific minor groove binding agent. Even more surprisingly, quantitative biosensor-surface plasmon resonance and isothermal titration calorimetric results indicate that the compound binds with exceptional strength to certain AT sequences in DNA with a large negative enthalpy of binding. Crystallographic results for the DNA complex of RT29 compared to calculated results for the free compound show that the compound undergoes significant conformational changes to enhance its minor groove interactions. In addition, a water molecule is incorporated directly into the complex to complete the compound-DNA interface, and it forms an essential link between the compound and base pair edges at the floor of the minor groove. The calculated DeltaCp value for complex formation is substantially less than the experimentally observed value, which supports the idea of water being an intrinsic part of the complex with a major contribution to the DeltaCp value. Both the induced fit conformational changes of the compound and the bound water are essential for strong binding to DNA by RT29.
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Affiliation(s)
- Farial A. Tanious
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098
| | - William Laine
- INSERM U-814, ‡ Institute for Cancer Research, Lille 59045, France
| | - Paul Peixoto
- INSERM U-814, ‡ Institute for Cancer Research, Lille 59045, France
| | - Christian Bailly
- INSERM U-814, ‡ Institute for Cancer Research, Lille 59045, France
| | - Kristie D. Goodwin
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine
| | - Mark A. Lewis
- Department of Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202 and
| | - Eric C. Long
- Department of Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202 and
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine
| | - Richard R. Tidwell
- Department of Pathology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - W. David Wilson
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098
- * To whom correspondence should be addressed, Tel: 404-651-3903, Fax: 404-651-1416, and
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31
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Spillane CB, Smith JA, Morgan JL, Keene FR. DNA affinity binding studies using a fluorescent dye displacement technique: the dichotomy of the binding site. J Biol Inorg Chem 2007; 12:819-24. [PMID: 17486377 DOI: 10.1007/s00775-007-0235-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
We have observed a number of discrepancies and contradictions in the use of a fluorescent intercalator displacement assay in surveying the binding affinities of dinuclear polypyridyl ruthenium(II) complexes with DNA. By a modification of the assay using the fluorescent minor-groove binder 4',6-diamidino-2-phenylindole, rather than intercalating dyes (ethidium bromide or thiazole orange), results were obtained for all complexes studied which were consistent with relative affinities and stereoselectivities observed with other techniques, including NMR, affinity chromatography and equilibrium dialysis. It is believed that the difference in binding mode between the minor groove-binding Ru(II) complexes and the intercalating fluorescent dyes they are displacing may contribute to these discrepancies.
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Affiliation(s)
- Caitriona B Spillane
- School of Pharmacy and Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia
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Montaño SP, Coté ML, Roth MJ, Georgiadis MM. Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus. Nucleic Acids Res 2006; 34:5353-60. [PMID: 17003051 PMCID: PMC1636480 DOI: 10.1093/nar/gkl693] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the first step of retroviral integration, integrase cleaves the linear viral DNA within its long terminal repeat (LTR) immediately 3′ to the CA dinucleotide step, resulting in a reactive 3′ OH on one strand and a 5′ two base overhang on the complementary strand. In order to investigate the structural properties of the 3′ end processing site within the Moloney murine leukemia virus (MMLV) LTR d(TCTTTCATT), a host-guest crystallographic method was employed to determine the structures of four self-complementary 16 bp oligonucleotides including LTR sequences (underlined), d(TTTCATTGCAATGAAA), d(CTTTCATTAATGAAAG), d(TCTTTCATATGAAAGA) and d(CACAATGATCATTGTG), the guests, complexed with the N-terminal fragment of MMLV reverse transcriptase, the host. The structures of the LTR-containing oligonucleotides were compared to those of non-LTR oligonucleotides crystallized in the same lattice. Properties unique to the CA dinucleotide step within the LTR sequence, independent of its position from the end of the duplex, include a positive roll angle and negative slide value. This propensity for the CA dinucleotide step within the MMLV LTR sequence to adopt only positive roll angles is likely influenced by the more rigid, invariable 3′ and 5′ flanking TT dinucleotide steps and may be important for specific recognition and/or cleavage by the MMLV integrase.
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Affiliation(s)
| | - Marie L. Coté
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Monica J. Roth
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Millie M. Georgiadis
- To whom correspondence should be addressed. Tel: +1 317 278 8486; Fax: +1 317 274 4686;
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