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Saikia S, Bordoloi M. Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective. Curr Drug Targets 2020; 20:501-521. [PMID: 30360733 DOI: 10.2174/1389450119666181022153016] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/08/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
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2
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Portugal J. Challenging transcription by DNA-binding antitumor drugs. Biochem Pharmacol 2018; 155:336-345. [PMID: 30040927 DOI: 10.1016/j.bcp.2018.07.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022]
Abstract
Cancer has been associated with altered gene expression. Therefore, transcription and its regulation by transcription factors are considered key points to be explored in the pursuit of more efficient antitumor agents. This paper reviews the effects of DNA-binding drugs on the interaction between transcription factors and DNA, and it discusses recent advances in the understanding of the mechanisms by which small compounds interfere with the activity of transcription factors and gene expression. Many DNA-binding drugs, some of them in clinical use, can compete with a variety of transcription factors for their preferred binding sites in gene promoters, or they can covalently modify DNA, thus preventing transcription factors from recognizing their binding sites. On the other hand, transcription factor activity can be impaired through modification of the protein factors or their complexes. Several "omic" tools have been developed to explore the genome-wide changes in gene expression induced by DNA-binding drugs, which reveal details of the mechanisms of action. Transcriptomic profiles obtained from drug-treated cells and of samples collected from patients upon treatment provide insights into the in vivo mechanisms of drug action related to the inhibition of gene transcription. The information available about the molecular structure and mechanisms of action of both transcription factors and DNA-binding drugs, together with the new opportunities provided by functional genomics, should encourage the development of new more-selective DNA-binding antitumor drugs to target a single gene with little effect on others.
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Affiliation(s)
- José Portugal
- Instituto de Diagnóstico Ambiental y Estudios del Agua, CSIC, E-08034 Barcelona, Spain.
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Ivanov AA, Salyanov VI, Zhuze AL. DNA sequence-specific ligands: XV. Synthesis and spectral characteristics of a new series of dimeric bisbenzimidazoles DB(1, 2, 6, 8, 9, 10, 12). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016020059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Narayanaswamy N, Das S, Samanta PK, Banu K, Sharma GP, Mondal N, Dhar SK, Pati SK, Govindaraju T. Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications. Nucleic Acids Res 2015; 43:8651-63. [PMID: 26350219 PMCID: PMC4605319 DOI: 10.1093/nar/gkv875] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/19/2015] [Indexed: 11/30/2022] Open
Abstract
In molecular biology, understanding the functional and structural aspects of DNA requires sequence-specific DNA binding probes. Especially, sequence-specific fluorescence probes offer the advantage of real-time monitoring of the conformational and structural reorganization of DNA in living cells. Herein, we designed a new class of D2A (one-donor-two-acceptor) near-infrared (NIR) fluorescence switch-on probe named quinone cyanine–dithiazole (QCy–DT) based on the distinctive internal charge transfer (ICT) process for minor groove recognition of AT-rich DNA. Interestingly, QCy–DT exhibited strong NIR-fluorescence enhancement in the presence of AT-rich DNA compared to GC-rich and single-stranded DNAs. We show sequence-specific minor groove recognition of QCy–DT for DNA containing 5′-AATT-3′ sequence over other variable (A/T)4 sequences and local nucleobase variation study around the 5′-X(AATT)Y-3′ recognition sequence revealed that X = A and Y = T are the most preferable nucleobases. The live cell imaging studies confirmed mammalian cell permeability, low-toxicity and selective staining capacity of nuclear DNA without requiring RNase treatment. Further, Plasmodium falciparum with an AT-rich genome showed specific uptake with a reasonably low IC50 value (<4 µM). The ease of synthesis, large Stokes shift, sequence-specific DNA minor groove recognition with switch-on NIR-fluorescence, photostability and parasite staining with low IC50 make QCy–DT a potential and commercially viable DNA probe.
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Affiliation(s)
- Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, India
| | - Shubhajit Das
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Khadija Banu
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | | | - Neelima Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suman K Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Swapan K Pati
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - T Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, India
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Abstract
PARP-1 is a nuclear enzyme regulating transcription, chromatin restructuring, and DNA repair. PARP-1 is activated by interaction with NAD+, DNA, and core histones. Each route of PARP-1 activation leads to somewhat different outcomes. PARP-1 interactions with core histones control PARP-1 functions during transcriptional activation in euchromatin. DNA-dependent regulation of PARP-1 determines its localization in heterochromatin and PARP-1-dependent silencing. Here we address the biological significance of DNA-dependent PARP-1 regulation in vitro and in vivo. We report that minor grove binding ligands (MGBLs) specifically target PARP-1 interaction with DNA, and, hence, the DNA-dependent pathway of PARP-1 activation. By obstructing its interaction with DNA molecules, MGBLs block PARP-1 activity in vitro and in vivo, as we demonstrate using Drosophila, as well as human cancer-derived cells. We also demonstrate synergistic inhibition of PARP-1, combining MGBLs with conventional NAD+-dependent inhibitors in human cancer cells. These results suggest that combining different classes of PARP-1 inhibitors can precisely modulate PARP-1 activity in living cells, thus holding promise for new avenues of cancer treatment.
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Lauria A, Alfio A, Bonsignore R, Gentile C, Martorana A, Gennaro G, Barone G, Terenzi A, Almerico AM. New benzothieno[3,2-d]-1,2,3-triazines with antiproliferative activity: synthesis, spectroscopic studies, and biological activity. Bioorg Med Chem Lett 2014; 24:3291-7. [PMID: 24986661 DOI: 10.1016/j.bmcl.2014.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 10/25/2022]
Abstract
New benzothieno[3,2-d]-1,2,3-triazines, together with precursors triazenylbenzo[b]thiophenes, were designed, synthesized and screened as anticancer agents. The structural features of these compounds prompted us to investigate their DNA binding capability through UV-vis absorption titrations, circular dichroism, and viscometry, pointing out the occurrence of groove-binding. The derivative 3-(4-methoxy-phenyl)benzothieno[3,2-d]-1,2,3-triazin-4(3H)-one showed the highest antiproliferative effect against HeLa cells and was also tested in cell cycle perturbation experiments. The obtained results assessed for the first time the anticancer activity of benzothieno[3,2-d]-1,2,3-triazine nucleus, and we related it to its DNA-binding properties.
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Affiliation(s)
- Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy.
| | - Alessia Alfio
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Riccardo Bonsignore
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Giuseppe Gennaro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Alessio Terenzi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo-Via Archirafi, 32-90123 Palermo, Italy
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Yang YT, Lin CY, Jeng J, Ong CW. Impact of pyrrolidine-bispyrrole DNA minor groove binding agents and chirality on global proteomic profile in Escherichia Coli. Proteome Sci 2013; 11:23. [PMID: 23702249 PMCID: PMC3669006 DOI: 10.1186/1477-5956-11-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecules for rational drug design has attracted increasing attention due to the chirality of DNA. Yet, there is limited research on the chirality effect of minor groove binders on DNA interaction, especially at the protein expression level. This paper is an attempt to illustrate that DNA binding affinity might not provide a full picture on the biological activities. Drug interacting at the genomic level can be translated to the proteomic level. Here we have illustrated that although the chiral bispyrrole-pyrrolidine-oligoamides, PySSPy and PyRSPy, showed low binding affinity to DNA, their influence at the proteomic level is significant. More importantly, the chirality also plays a role. Two-dimensional proteomic profile to identify the differentially expressed protein in Escherichia coli DH5α (E coli DH5α) were investigated. RESULTS E coli DH5α incubated with the chiral PySSPy and PyRSPy, diastereomeric at the pyrrolidine ring, showed differential expression of eighteen proteins as observed through two dimensional proteomic profiling. These eighteen proteins identified by MALDI_TOF/TOF MS include antioxidant defense, DNA protection, protein synthesis, chaperone, and stress response proteins. No statistically significant toxicity was observed at the tested drug concentrations as measured via MTT assay. CONCLUSION The current results showed that the chiral PySSPy and PyRSPy impact on the proteomic profiling of E coli DH5α, implicating the importance of drug chirality on biological activities at the molecular level.
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Affiliation(s)
- Ya-Ting Yang
- Department of Chemistry, National Sun Yat-sen University, No, 70, Lienhai Rd,, Kaohsiung, 80424, Taiwan.
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Ning J, Chen W, Li J, Peng Z, Wang J, Ni Z. Structural and energetic insights into sequence-specific interaction in DNA–drug recognition: development of affinity predictor and analysis of binding selectivity. J Mol Model 2012; 19:1573-82. [DOI: 10.1007/s00894-012-1722-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/03/2012] [Indexed: 11/28/2022]
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Leung CH, Chan DSH, Ma VPY, Ma DL. DNA-Binding Small Molecules as Inhibitors of Transcription Factors. Med Res Rev 2012; 33:823-46. [DOI: 10.1002/med.21266] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | | | - Victor Pui-Yan Ma
- Department of Chemistry; Hong Kong Baptist University; Kowloon Tong; Hong Kong
| | - Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University; Kowloon Tong; Hong Kong
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Williams AK, Dasilva SC, Bhatta A, Rawal B, Liu M, Korobkova EA. Determination of the drug–DNA binding modes using fluorescence-based assays. Anal Biochem 2012; 422:66-73. [DOI: 10.1016/j.ab.2011.12.041] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 12/12/2011] [Accepted: 12/29/2011] [Indexed: 01/04/2023]
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New insight into the molecular mechanisms of the biological effects of DNA minor groove binders. PLoS One 2011; 6:e25822. [PMID: 21998702 PMCID: PMC3187808 DOI: 10.1371/journal.pone.0025822] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 09/12/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Bisbenzimides, or Hoechst 33258 (H258), and its derivative Hoechst 33342 (H342) are archetypal molecules for designing minor groove binders, and widely used as tools for staining DNA and analyzing side population cells. They are supravital DNA minor groove binders with AT selectivity. H342 and H258 share similar biological effects based on the similarity of their chemical structures, but also have their unique biological effects. For example, H342, but not H258, is a potent apoptotic inducer and both H342 and H258 can induce transgene overexpression in in vitro studies. However, the molecular mechanisms by which Hoechst dyes induce apoptosis and enhance transgene overexpression are unclear. METHODOLOGY/PRINCIPAL FINDINGS To determine the molecular mechanisms underlying different biological effects between H342 and H258, microarray technique coupled with bioinformatics analyses and multiple other techniques has been utilized to detect differential global gene expression profiles, Hoechst dye-specific gene expression signatures, and changes in cell morphology and levels of apoptosis-associated proteins in malignant mesothelioma cells. H342-induced apoptosis occurs in a dose-dependent fashion and is associated with morphological changes, caspase-3 activation, cytochrome c mitochondrial translocation, and cleavage of apoptosis-associated proteins. The antagonistic effect of H258 on H342-induced apoptosis indicates a pharmacokinetic basis for the two dyes' different biological effects. Differential global gene expression profiles induced by H258 and H342 are accompanied by unique gene expression signatures determined by DNA microarray and bioinformatics software, indicating a genetic basis for their different biological effects. CONCLUSIONS/SIGNIFICANCE A unique gene expression signature associated with H342-induced apoptosis provides a new avenue to predict and classify the therapeutic class of minor groove binders in the drug development process. Further analysis of H258-upregulated genes of transcription regulation may identify the genes that enhance transgene overexpression in gene therapy and promote recombinant protein products in biopharmaceutical companies. DATA DEPOSITION The microarray data reported in this article have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no.GSE28616).
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Derudas M, Pala N, Sanna V, Dallocchio R, Dessì A, Roggio AM, Sechi M. Design and synthesis of novel polycycles based on the 3H-pyrrolo/6,7-dihydropyrido[1,2-a]indole scaffold as templates for pharmaceutical development. J Heterocycl Chem 2011. [DOI: 10.1002/jhet.710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Anuradha, Alam MS, Chaudhury NK. Osmolyte Changes the Binding Affinity and Mode of Interaction of Minor Groove Binder Hoechst 33258 with Calf Thymus DNA. Chem Pharm Bull (Tokyo) 2010; 58:1447-54. [DOI: 10.1248/cpb.58.1447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Anuradha
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
| | | | - Nabo Kumar Chaudhury
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
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Ojha H, Murari BM, Anand S, Hassan MI, Ahmad F, Chaudhury NK. Interaction of DNA Minor Groove Binder Hoechst 33258 with Bovine Serum Albumin. Chem Pharm Bull (Tokyo) 2009; 57:481-6. [DOI: 10.1248/cpb.57.481] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Himanshu Ojha
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
| | | | - Sneh Anand
- Center for Biomedical Engineering, Indian Institute of Technology
| | | | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia
| | - Nabo Kumar Chaudhury
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
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Abstract
Designed, synthetic heterocyclic diamidines have excellent activity against eukaryotic parasites that cause diseases such as sleeping sickness and leishmania and adversely affect millions of people each year. The most active compounds bind specifically and strongly in the DNA minor groove at AT sequences. The compounds enter parasite cells rapidly and appear first in the kinetoplast that contains the mitochondrial DNA of the parasite. With time the compounds are also generally seen in the cell nucleus but are not significantly observed in the cytoplasm. The kinetoplast decays over time and disappears from the mitochondria of treated cells. At this point the compounds begin to be observed in other regions of the cell, such as the acidocalcisomes. The cells typically die in 24-48h after treatment. Active compounds appear to selectively target extended AT sequences and induce changes in kinetoplast DNA minicircles that cause a synergistic destruction of the catenated kinetoplast DNA network and cell death.
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Eckdahl TT, Brown AD, Hart SN, Malloy KJ, Shott M, Yiu G, Hoopes LLM, Heyer LJ. Microarray analysis of the in vivo sequence preferences of a minor groove binding drug. BMC Genomics 2008; 9:32. [PMID: 18215295 PMCID: PMC2254601 DOI: 10.1186/1471-2164-9-32] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2007] [Accepted: 01/23/2008] [Indexed: 01/24/2023] Open
Abstract
Background Minor groove binding drugs (MGBDs) interact with DNA in a sequence-specific manner and can cause changes in gene expression at the level of transcription. They serve as valuable models for protein interactions with DNA and form an important class of antitumor, antiviral, antitrypanosomal and antibacterial drugs. There is a need to extend knowledge of the sequence requirements for MGBDs from in vitro DNA binding studies to living cells. Results Here we describe the use of microarray analysis to discover yeast genes that are affected by treatment with the MGBD berenil, thereby allowing the investigation of its sequence requirements for binding in vivo. A novel approach to sequence analysis allowed us to address hypotheses about genes that were directly or indirectly affected by drug binding. The results show that the sequence features of A/T richness and heteropolymeric character discovered by in vitro berenil binding studies are found upstream of genes hypothesized to be directly affected by berenil but not upstream of those hypothesized to be indirectly affected or those shown to be unaffected. Conclusion The data support the conclusion that effects of berenil on gene expression in yeast cells can be explained by sequence patterns discovered by in vitro binding experiments. The results shed light on the sequence and structural rules by which berenil binds to DNA and affects the transcriptional regulation of genes and contribute generally to the development of MGBDs as tools for basic and applied research.
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Affiliation(s)
- Todd T Eckdahl
- Biology Department, Missouri Western State University, Saint Joseph, MO, 64507, USA.
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Hurst SJ, Han MS, Lytton-Jean AKR, Mirkin CA. Screening the Sequence Selectivity of DNA-Binding Molecules Using a Gold Nanoparticle-Based Colorimetric Approach. Anal Chem 2007; 79:7201-5. [PMID: 17696406 DOI: 10.1021/ac071253e] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a novel competition assay that uses a gold nanoparticle (Au NP)-based, high-throughput colorimetric approach to screen the sequence selectivity of DNA-binding molecules. This assay hinges on the observation that the melting behavior of DNA-functionalized Au NP aggregates is sensitive to the concentration of the DNA-binding molecule in solution. When short, oligomeric hairpin DNA sequences were added to a reaction solution consisting of DNA-functionalized Au NP aggregates and DNA-binding molecules, these molecules may either bind to the Au NP aggregate interconnects or the hairpin stems based on their relative affinity for each. This relative affinity can be measured as a change in the melting temperature (Tm) of the DNA-modified Au NP aggregates in solution. As a proof of concept, we evaluated the selectivity of 4',6-diamidino-2-phenylindone (an AT-specific binder), ethidium bromide (a nonspecific binder), and chromomycin A (a GC-specific binder) for six sequences of hairpin DNA having different numbers of AT pairs in a five-base pair variable stem region. Our assay accurately and easily confirmed the known trends in selectivity for the DNA binders in question without the use of complicated instrumentation. This novel assay will be useful in assessing large libraries of potential drug candidates that work by binding DNA to form a drug/DNA complex.
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Affiliation(s)
- Sarah J Hurst
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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Necula M, Chirita CN, Kuret J. Cyanine dye N744 inhibits tau fibrillization by blocking filament extension: implications for the treatment of tauopathic neurodegenerative diseases. Biochemistry 2005; 44:10227-37. [PMID: 16042400 DOI: 10.1021/bi050387o] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tau fibrillization is a potential therapeutic target for Alzheimer's and other neurodegenerative diseases. Small molecules capable of both inhibiting aggregation and promoting filament disaggregation have been discovered, but knowledge of their mechanism of action and potential for testing in biological models is fragmentary. To clarify these issues, the interaction between a small-molecule inhibitor of tau fibrillization, 3,3'-bis(beta-hydroxyethyl)-9-ethyl-5,5'-dimethoxythiacarbocyanine iodide (N744), and full-length four-repeat tau protein was characterized in vitro using transmission electron microscopy and fluorescence spectroscopy. Analysis of reaction time courses performed in the presence of anionic fibrillization inducers revealed that increasing concentrations of N744 decreased the total filament length without modulating lag time, indicating that filament extension but not nucleation was affected by inhibitor under the conditions that were investigated. Critical concentration measurements confirmed that N744 shifted equilibria at filament ends away from the fibrillized state, resulting in endwise filament disaggregation when it was added to synthetic filaments. Both increasing bulk tau concentrations and filament stabilizing modifications such as pseudophosphorylation and glycation antagonized N744 activity. The results illustrate the importance of mechanism for the design and interpretation of pharmacological studies in biological models of tau aggregation.
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Affiliation(s)
- Mihaela Necula
- Biophysics Program, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
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Gniazdowski M, Denny WA, Nelson SM, Czyz M. Effects of anticancer drugs on transcription factor–DNA interactions. Expert Opin Ther Targets 2005; 9:471-89. [PMID: 15948668 DOI: 10.1517/14728222.9.3.471] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
DNA-interacting anticancer drugs are able to affect the propensity of DNA to interact with proteins through either reversible binding or covalent bond formation. The effect of the drugs on transcription factor interactions with DNA is reviewed. These effects can be classified as (i) competition between a drug and regulatory protein for target sequences; (ii) weakening of this interaction; (iii) enhancement of this interaction by chemical modification of the DNA and the creation of non-natural binding sites; and (iv) a 'suicide' mechanism, which is observed when a transcription factor induces changes in DNA structure, allowing a drug to bind to a target sequence. Several new strategies -- the antigene approach with oligonucleotides, peptide nucleic acids or locked nucleic acids, and sequence-specific polyamides -- are also reviewed.
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Affiliation(s)
- Marek Gniazdowski
- Department of Medicinal Chemistry, Institute of Physiology and Biochemistry, Medical University of Lódz, Mazowiecka 6/8, 92-215 Lódz, Poland.
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Wu J, Ling X, Pan D, Apontes P, Song L, Liang P, Altieri DC, Beerman T, Li F. Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence-selective DNA binding antitumor agent, hedamycin: evidence of survivin down-regulation associated with drug sensitivity. J Biol Chem 2005; 280:9745-51. [PMID: 15637054 PMCID: PMC2826138 DOI: 10.1074/jbc.m409350200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Expression of the antiapoptotic protein survivin is associated with cancer cell viability and drug resistance. Thus, control of its expression in cancer cells has significant consequences for cancer therapeutics. Here we have shown that hedamycin, a GC-rich DNA binding drug, down-regulated survivin expression. Using a series of survivin promoter-luciferase constructs, we have identified an 86-bp GC-rich DNA element (-124 to -39) that mediates the ability of hedamycin to down-regulate survivin expression. Furthermore, both in vivo foot-printing and in vitro gel mobility shift experiments revealed that hedamycin bound to a 21-bp GC-rich DNA element (-115 to -95) in the survivin promoter. This drug-DNA interaction abrogated the binding of Sp-1 or Sp1-like proteins to the 21-bp cis-acting DNA element, and mutagenesis of this region consistently diminished survivin promoter activity. Finally, down-regulation of survivin transcription by hedamycin modulated the viability of cancer cells. These data suggest that abrogation of Sp-1 or Sp1-like protein binding to the 21-bp DNA element in the survivin promoter contributes at least in part to the inhibitory effect of hedamycin on survivin gene transcription. Drug-induced modulation of survivin gene expression may provide novel approaches for cancer therapeutics.
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Affiliation(s)
- Jianguo Wu
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Xiang Ling
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Dalin Pan
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Pasha Apontes
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Lei Song
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Ping Liang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Dario C. Altieri
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Terry Beerman
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Fengzhi Li
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
- To whom correspondence should be addressed: Dept. of Pharmacology and Therapeutics, Roswell Park Cancer Inst., Elm and Carlton Sts., Buffalo, NY 14263. Tel.: 716-845-4398; Fax: 716-845-8857;
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22
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Csuk R, Barthel A, Brezesinski T, Raschke C. Synthesis of pathogen inactivating nucleic acid intercalators. Eur J Med Chem 2004; 39:975-88. [PMID: 15501547 DOI: 10.1016/j.ejmech.2004.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Revised: 07/19/2004] [Accepted: 07/30/2004] [Indexed: 11/22/2022]
Abstract
A series of antiviral compounds consisting of an intercalating acridine derived part, a spacer region and a reactive EDTA-derived conjugate was synthesized in an easy sequence starting from 1,omega-alkyldiamines. As shown in model screenings, in the presence of ascorbic acid the Fe-complexes of these compounds reduced the phage-titer of MS2-phages by several logarithmic decades.
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Affiliation(s)
- René Csuk
- Institut für Organische Chemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120 Halle (Saale), Germany.
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23
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Rajarao GK, Nekhotiaeva N, Good L. Peptide-mediated delivery of green fluorescent protein into yeasts and bacteria. FEMS Microbiol Lett 2002; 215:267-72. [PMID: 12399045 DOI: 10.1111/j.1574-6968.2002.tb11401.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Stringent microbial cell barriers limit the application of many substances in research and therapeutics. Carrier peptides that penetrate or translocate across cell membranes may help overcome this problem. To assess peptide-mediated delivery into two yeast and three bacterial species, a range of cell penetrating and signal peptide sequences were fused to green fluorescent protein (GFP), expressed in Escherichia coli, partially purified and incubated with growing cells. Fluorescence microscopy indicated several peptides that mediated delivery. In particular, VLTNENPFSDP efficiently delivered GFP into Candida albicans and Staphylococcus aureus, while YKKSNNPFSD was most efficient for Bacillus subtilis and CFFKDEL for Escherichia coli. Carrier peptides may improve delivery of certain large molecular mass molecules into microorganisms for research and therapeutic applications.
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Affiliation(s)
- Gunaratna Kuttuva Rajarao
- Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, 17177 Stockholm, Sweden
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24
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25
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Gonzalez C, Moore M, Ribeiro S, Schmitz U, Schroth GP, Turin L, Bruice TW. The hybridization-stabilization assay: a solution-based isothermal method for rapid screening and determination of sequence preference of ligands that bind to duplexed nucleic acids. Nucleic Acids Res 2001; 29:E85. [PMID: 11504893 PMCID: PMC55869 DOI: 10.1093/nar/29.16.e85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2001] [Revised: 07/01/2001] [Accepted: 07/01/2001] [Indexed: 11/13/2022] Open
Abstract
The gene-to-drug quest will be most directly served by the discovery and development of small molecules that bind to nucleic acids and modulate gene expression at the level of transcription and/or inhibit replication of infectious agents. Full realization of this potential will require implementation of a complete suite of modern drug discovery technologies. Towards this end, here we describe our initial results with a new assay for identification and characterization of novel nucleic acid binding ligands. It is based on the well recognized property of stabilization of hybridization of complementary oligonucleotides by groove and/or intercalation binding ligands. Unlike traditional thermal melt methodologies, this assay is isothermal and, unlike gel-based footprinting techniques, the assay also is performed in solution and detection can be by any number of highly sensitive, non-radioisotopic modalities, such as fluorescence resonance energy transfer, described herein. Thus, the assay is simple to perform, versatile in design and amenable to miniaturization and high throughput automation. Assay validation was performed using various permutations of direct and competitive binding formats and previously well studied ligands, including pyrrole polyamide and intercalator natural products, designed hairpin pyrrole-imidazole polyamides and furan-based non-polyamide dications. DNA specific ligands were identified and their DNA binding site size and sequence preference profiles were determined. A systematic approach to studying the relationship of binding sequence specificity with variation in ligand structure was demonstrated, and preferred binding sites in longer DNA sequences were found by pseudo-footprinting, with results that are in accord with established findings. This assay methodology should promote a more rapid discovery of novel nucleic acid ligands and potential drug candidates.
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Affiliation(s)
- C Gonzalez
- Genelabs Technologies Inc., 505 Penobscot Drive, Redwood City, CA 94063, USA
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