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Xie X, Yu T, Li X, Zhang N, Foster LJ, Peng C, Huang W, He G. Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials. Signal Transduct Target Ther 2023; 8:335. [PMID: 37669923 PMCID: PMC10480221 DOI: 10.1038/s41392-023-01589-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tingting Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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2
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A novel insight into the cytotoxic effects of Tephrosin with calf thymus DNA: Experimental and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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3
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Portugal J. Insights into DNA-drug interactions in the era of omics. Biopolymers 2020; 112:e23385. [PMID: 32542701 DOI: 10.1002/bip.23385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 01/07/2023]
Abstract
Despite the rise of sophisticated new targeting strategies in cancer chemotherapy, many classic DNA-binding drugs remain on the front line of the therapy against cancer. Based on examples primarily from the author's laboratory, this article reviews the capabilities of several DNA-binding drugs to alter gene expression. Research is ongoing about the molecular bases of the inhibition of gene expression and how alteration of the cellular transcriptome can commit cancer cells to die. The development of a variety of omic techniques allows us to gain insights into the effect of antitumor drugs. Genome-wide approaches provide unbiased genomic data that can facilitate a deeper understanding of the cellular response to DNA-binding drugs. Moreover, the results of large-scale genomic studies are gathered in publicly available databases that can be used in developing precision medicine in cancer treatment.
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Affiliation(s)
- José Portugal
- Instituto de Diagnóstico Ambiental y Estudios del Agua, CSIC, Barcelona, Spain
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4
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Caru M, Curnier D. Sex and Gender Considerations After Surviving Acute Lymphoblastic Leukemia: An Exercise Oncology Context. J Adolesc Young Adult Oncol 2020; 9:441-444. [DOI: 10.1089/jayao.2019.0137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Maxime Caru
- Laboratory of Pathophysiology of Exercise (LPEX), School of Kinesiology and Physical Activity Sciences, Faculty of Medicine, University of Montreal, Montreal, Canada
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Laboratoire EA 4430–Clinique Psychanalyse Developpement (CliPsyD), University of Paris Nanterre, Nanterre, France
| | - Daniel Curnier
- Laboratory of Pathophysiology of Exercise (LPEX), School of Kinesiology and Physical Activity Sciences, Faculty of Medicine, University of Montreal, Montreal, Canada
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
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5
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Vellingiri B, Iyer M, Devi Subramaniam M, Jayaramayya K, Siama Z, Giridharan B, Narayanasamy A, Abdal Dayem A, Cho SG. Understanding the Role of the Transcription Factor Sp1 in Ovarian Cancer: from Theory to Practice. Int J Mol Sci 2020; 21:E1153. [PMID: 32050495 PMCID: PMC7038193 DOI: 10.3390/ijms21031153] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/23/2022] Open
Abstract
Ovarian cancer (OC) is one of the deadliest cancers among women contributing to high risk of mortality, mainly owing to delayed detection. There is no specific biomarker for its detection in early stages. However, recent findings show that over-expression of specificity protein 1 (Sp1) is involved in many OC cases. The ubiquitous transcription of Sp1 apparently mediates the maintenance of normal and cancerous biological processes such as cell growth, differentiation, angiogenesis, apoptosis, cellular reprogramming and tumorigenesis. Sp1 exerts its effects on cellular genes containing putative GC-rich Sp1-binding site in their promoters. A better understanding of the mechanisms underlying Sp1 transcription factor (TF) regulation and functions in OC tumorigenesis could help identify novel prognostic markers, to target cancer stem cells (CSCs) by following cellular reprogramming and enable the development of novel therapies for future generations. In this review, we address the structure, function, and biology of Sp1 in normal and cancer cells, underpinning the involvement of Sp1 in OC tumorigenesis. In addition, we have highlighted the influence of Sp1 TF in cellular reprogramming of iPSCs and how it plays a role in controlling CSCs. This review highlights the drugs targeting Sp1 and their action on cancer cells. In conclusion, we predict that research in this direction will be highly beneficial for OC treatment, and chemotherapeutic drugs targeting Sp1 will emerge as a promising therapy for OC.
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Affiliation(s)
- Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India
| | - Mahalaxmi Iyer
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641043, India; (M.I.); (K.J.)
| | - Mohana Devi Subramaniam
- Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, India;
| | - Kaavya Jayaramayya
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641043, India; (M.I.); (K.J.)
| | - Zothan Siama
- Department of Zoology, School of Life-science, Mizoram University, Aizawl 796004, Mizoram, India;
| | - Bupesh Giridharan
- R&D Wing, Sree Balaji Medical College and Hospital (SBMCH), BIHER, Chromepet, Chennai 600044, Tamil Nadu, India;
| | - Arul Narayanasamy
- Disease Proteomics Laboratory, Department of Zoology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India;
| | - Ahmed Abdal Dayem
- Molecular & Cellular Reprogramming Center, Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea;
| | - Ssang-Goo Cho
- Molecular & Cellular Reprogramming Center, Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea;
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6
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Caru M, Samoilenko M, Drouin S, Lemay V, Kern L, Romo L, Bertout L, Lefebvre G, Andelfinger G, Krajinovic M, Laverdiere C, Sinnett D, Curnier D. Childhood Acute Lymphoblastic Leukemia Survivors Have a Substantially Lower Cardiorespiratory Fitness Level Than Healthy Canadians Despite a Clinically Equivalent Level of Physical Activity. J Adolesc Young Adult Oncol 2019; 8:674-683. [DOI: 10.1089/jayao.2019.0024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Maxime Caru
- Laboratory of Pathophysiology of EXercise (LPEX), School of Kinesiology and Physical Activity Sciences, Faculty of Medicine, University of Montreal, Montreal, Canada
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Laboratoire EA 4430–Clinique Psychanalyse Developpement (CliPsyD), University of Paris Nanterre, Nanterre, France
| | - Mariia Samoilenko
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Department of Mathematics, Université du Québec à Montréal, Montreal, Canada
| | - Simon Drouin
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
| | - Valérie Lemay
- Laboratory of Pathophysiology of EXercise (LPEX), School of Kinesiology and Physical Activity Sciences, Faculty of Medicine, University of Montreal, Montreal, Canada
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
| | - Laurence Kern
- Laboratoire EA 4430–Clinique Psychanalyse Developpement (CliPsyD), University of Paris Nanterre, Nanterre, France
| | - Lucia Romo
- Laboratoire EA 4430–Clinique Psychanalyse Developpement (CliPsyD), University of Paris Nanterre, Nanterre, France
| | - Laurence Bertout
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
| | - Geneviève Lefebvre
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
| | - Gregor Andelfinger
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Maja Krajinovic
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Caroline Laverdiere
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Daniel Sinnett
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Daniel Curnier
- Laboratory of Pathophysiology of EXercise (LPEX), School of Kinesiology and Physical Activity Sciences, Faculty of Medicine, University of Montreal, Montreal, Canada
- Sainte-Justine University Health Center, Research Center, Montreal, Canada
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7
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Silva S, Shimizu JF, Oliveira DMD, Assis LRD, Bittar C, Mottin M, Sousa BKDP, Mesquita NCDMR, Regasini LO, Rahal P, Oliva G, Perryman AL, Ekins S, Andrade CH, Goulart LR, Sabino-Silva R, Merits A, Harris M, Jardim ACG. A diarylamine derived from anthranilic acid inhibits ZIKV replication. Sci Rep 2019; 9:17703. [PMID: 31776405 PMCID: PMC6881388 DOI: 10.1038/s41598-019-54169-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-transmitted Flavivirus, originally identified in Uganda in 1947 and recently associated with a large outbreak in South America. Despite extensive efforts there are currently no approved antiviral compounds for treatment of ZIKV infection. Here we describe the antiviral activity of diarylamines derived from anthranilic acid (FAMs) against ZIKV. A synthetic FAM (E3) demonstrated anti-ZIKV potential by reducing viral replication up to 86%. We analyzed the possible mechanisms of action of FAM E3 by evaluating the intercalation of this compound into the viral dsRNA and its interaction with the RNA polymerase of bacteriophage SP6. However, FAM E3 did not act by these mechanisms. In silico results predicted that FAM E3 might bind to the ZIKV NS3 helicase suggesting that this protein could be one possible target of this compound. To test this, the thermal stability and the ATPase activity of the ZIKV NS3 helicase domain (NS3Hel) were investigated in vitro and we demonstrated that FAM E3 could indeed bind to and stabilize NS3Hel.
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Affiliation(s)
- Suely Silva
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Jacqueline Farinha Shimizu
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Débora Moraes de Oliveira
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil
| | - Leticia Ribeiro de Assis
- Laboratory of Antibiotics and Chemotherapeutics, São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Cintia Bittar
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Melina Mottin
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goias, Goiânia, GO, 74605- 170, Brazil
| | - Bruna Katiele de Paula Sousa
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goias, Goiânia, GO, 74605- 170, Brazil
| | | | - Luis Octávio Regasini
- Laboratory of Antibiotics and Chemotherapeutics, São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Paula Rahal
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Alexander Luke Perryman
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
- Repare Therapeutics, 7210 Rue Frederick-Banting, Suite 100, Montreal, QC, H4S 2A1, Canada
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, United States
| | - Carolina Horta Andrade
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goias, Goiânia, GO, 74605- 170, Brazil
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Federal University of Uberlandia, Uberlândia, MG, Brasil
| | - Robinson Sabino-Silva
- Integrative Physiology and Salivary Nanobiotechnology Group, Federal University of Uberlandia, Uberlândia, MG, Brasil
| | - Andres Merits
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil.
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil.
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8
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Abstract
Mutated or dysregulated transcription factors represent a unique class of drug targets that mediate aberrant gene expression, including blockade of differentiation and cell death gene expression programmes, hallmark properties of cancers. Transcription factor activity is altered in numerous cancer types via various direct mechanisms including chromosomal translocations, gene amplification or deletion, point mutations and alteration of expression, as well as indirectly through non-coding DNA mutations that affect transcription factor binding. Multiple approaches to target transcription factor activity have been demonstrated, preclinically and, in some cases, clinically, including inhibition of transcription factor-cofactor protein-protein interactions, inhibition of transcription factor-DNA binding and modulation of levels of transcription factor activity by altering levels of ubiquitylation and subsequent proteasome degradation or by inhibition of regulators of transcription factor expression. In addition, several new approaches to targeting transcription factors have recently emerged including modulation of auto-inhibition, proteolysis targeting chimaeras (PROTACs), use of cysteine reactive inhibitors, targeting intrinsically disordered regions of transcription factors and combinations of transcription factor inhibitors with kinase inhibitors to block the development of resistance. These innovations in drug development hold great promise to yield agents with unique properties that are likely to impact future cancer treatment.
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Affiliation(s)
- John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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9
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Caru M, Petrykey K, Drouin S, Beaulieu P, St-Onge P, Lemay V, Bertout L, Laverdiere C, Andelfinger G, Krajinovic M, Sinnett D, Curnier D. Identification of genetic association between cardiorespiratory fitness and the trainability genes in childhood acute lymphoblastic leukemia survivors. BMC Cancer 2019; 19:443. [PMID: 31088516 PMCID: PMC6515640 DOI: 10.1186/s12885-019-5651-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 04/29/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The progress of treatments of childhood acute lymphoblastic leukemia (ALL) has made it possible to reach a survival rate superior to 80%. However, the treatments lead to several long-term adverse effects, including cardiac toxicity. Although studies have reported associations between genetic variants and cardiorespiratory fitness, none has been performed on childhood ALL survivors. METHODS We performed whole-exome sequencing in 239 childhood ALL survivors from the PETALE cohort. Germline variants (both common and rare) in selected set of genes (N = 238) were analyzed for an association with cardiorespiratory fitness. RESULTS Our results showed that the common variant in the TTN gene was significantly associated with a low cardiorespiratory fitness level (p = 0.0005) and that the LEPR, IGFBPI and ENO3 genes were significantly associated with a low cardiorespiratory fitness level in female survivors (p ≤ 0.002). Also, we detected an association between the low cardiorespiratory fitness level in participants that were stratified to the "high risk" prognostic group and functionally predicted rare variants in the SLC22A16 gene (p = 0.001). Positive associations between cardiorespiratory fitness level and trainability genes were mainly observed in females. CONCLUSIONS For the first time, we observed that low cardiorespiratory fitness in childhood ALL survivors can be associated with variants in genes related to subjects' trainability. These findings could allow better childhood ALL patient follow-up tailored to their genetic profile and cardiorespiratory fitness, which could help reduce at least some of the burden of long-term adverse effects of treatments.
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Affiliation(s)
- Maxime Caru
- Laboratoire de Physiopathologie de l'EXercice (LPEX), École de Kinésiologie et des Sciences de l'Activité physique, Faculté de Médecine, Université de Montréal, CEPSUM, 2100, boulevard Édouard Montpetit, Montréal, QC, H3C 3J7, Canada. .,Department of psychology, Laboratoire EA 4430 - Clinique Psychanalyse Developpement (CliPsyD), University of Paris Nanterre, Nanterre, Ile-de-France, France. .,Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada.
| | - Kateryna Petrykey
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada.,Department of pharmacology and physiology, University of Montreal, Montreal, Quebec, Canada
| | - Simon Drouin
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Patrick Beaulieu
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Pascal St-Onge
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Valérie Lemay
- Laboratoire de Physiopathologie de l'EXercice (LPEX), École de Kinésiologie et des Sciences de l'Activité physique, Faculté de Médecine, Université de Montréal, CEPSUM, 2100, boulevard Édouard Montpetit, Montréal, QC, H3C 3J7, Canada.,Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Laurence Bertout
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Caroline Laverdiere
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Gregor Andelfinger
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Maja Krajinovic
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada.,Department of pharmacology and physiology, University of Montreal, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Daniel Curnier
- Laboratoire de Physiopathologie de l'EXercice (LPEX), École de Kinésiologie et des Sciences de l'Activité physique, Faculté de Médecine, Université de Montréal, CEPSUM, 2100, boulevard Édouard Montpetit, Montréal, QC, H3C 3J7, Canada.,Research Center, Sainte-Justine University Health Center, Montreal, Quebec, Canada
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10
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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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11
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Congras A, Caillet N, Torossian N, Quelen C, Daugrois C, Brousset P, Lamant L, Meggetto F, Hoareau-Aveilla C. Doxorubicin-induced loss of DNA topoisomerase II and DNMT1- dependent suppression of MiR-125b induces chemoresistance in ALK-positive cells. Oncotarget 2018; 9:14539-14551. [PMID: 29581862 PMCID: PMC5865688 DOI: 10.18632/oncotarget.24465] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 11/20/2017] [Indexed: 12/04/2022] Open
Abstract
Systemic anaplastic large-cell lymphoma (ALCL) is a childhood T cell neoplasm defined by the presence or absence of translocations that lead to the ectopic expression of anaplastic lymphoma kinase (ALK), with nucleophosmin-ALK (NPM-ALK) fusions being the most common. Polychemotherapy involving doxorubicin is the standard first-line treatment but for the 25 to 35% of patients who relapse and develop resistance the prognosis remains poor. We studied the potential role of the microRNA miR-125b in the development of resistance to doxorubicin in NPM-ALK(+) ALCL. Our results show that miR-125b expression is repressed in NPM-ALK(+) cell lines and patient samples through hypermethylation of its promoter. NPM-ALK activity, in cooperation with DNA topoisomerase II (Topo II) and DNA methyltransferase 1 (DNMT1), is responsible for miR-125b repression through DNA hypermethylation. MiR-125b repression was reversed by the inhibition of DNMTs with decitabine or the inhibition of DNA topoisomerase II with either doxorubicin or etoposide. In NPM-ALK(+) cell lines, doxorubicin treatment led to an increase in miR-125b levels by inhibiting the binding of DNMT1 to the MIR125B1 promoter and downregulating the pro-apoptotic miR-125b target BAK1. Reversal of miR-125b silencing, increased miR-125b levels and reduced BAK1 expression also led to a lower efficacy of doxorubicin, suggestive of a pharmacoresistance mechanism. In line with this, miR-125b repression and increased BAK1 expression correlated with early relapse in human NPM-ALK(+) ALCL primary biopsies. Collectively our findings suggest that miR-125b could be used to predict therapeutic outcome in NPM-ALK(+) ALCL.
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Affiliation(s)
- Annabelle Congras
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
| | - Nina Caillet
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
| | - Nouritza Torossian
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France
| | - Cathy Quelen
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
| | - Camille Daugrois
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France
| | - Pierre Brousset
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Institut Carnot Lymphome-CALYM, 31024, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31024, Toulouse, France.,European Research Initiative on ALK-related malignancies (ERIA) (http://www.erialcl.net/).,Equipe Labelisée LIGUE 2017
| | - Laurence Lamant
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Institut Carnot Lymphome-CALYM, 31024, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31024, Toulouse, France.,European Research Initiative on ALK-related malignancies (ERIA) (http://www.erialcl.net/).,Equipe Labelisée LIGUE 2017
| | - Fabienne Meggetto
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Institut Carnot Lymphome-CALYM, 31024, Toulouse, France.,Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31024, Toulouse, France.,European Research Initiative on ALK-related malignancies (ERIA) (http://www.erialcl.net/).,Equipe Labelisée LIGUE 2017
| | - Coralie Hoareau-Aveilla
- Inserm, UMR1037 CRCT, F-31000 Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, F-31000 Toulouse, France.,CNRS, ERL5294 CRCT, F-31000 Toulouse, France.,Equipe Labelisée LIGUE 2017
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12
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Mora AK, Singh PK, Nath S. Controlled Sequestration of DNA Intercalated Drug by Polymer–Surfactant Supramolecular Assemblies. J Phys Chem B 2016; 120:4143-51. [DOI: 10.1021/acs.jpcb.5b12689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aruna K. Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Prabhat K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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13
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Vizcaíno C, Mansilla S, Portugal J. Sp1 transcription factor: A long-standing target in cancer chemotherapy. Pharmacol Ther 2015; 152:111-24. [PMID: 25960131 DOI: 10.1016/j.pharmthera.2015.05.008] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 11/25/2022]
Abstract
Sp1 (specificity protein 1) is a well-known member of a family of transcription factors that also includes Sp2, Sp3 and Sp4, which are implicated in an ample variety of essential biological processes and have been proven important in cell growth, differentiation, apoptosis and carcinogenesis. Sp1 activates the transcription of many cellular genes that contain putative CG-rich Sp-binding sites in their promoters. Sp1 and Sp3 proteins bind to similar, if not the same, DNA tracts and compete for binding, thus they can enhance or repress gene expression. Evidences exist that the Sp-family of proteins regulates the expression of genes that play pivotal roles in cell proliferation and metastasis of various tumors. In patients with a variety of cancers, high levels of Sp1 protein are considered a negative prognostic factor. A plethora of compounds can interfere with the trans-activating activities of Sp1 and other Sp proteins on gene expression. Several pathways are involved in the down-regulation of Sp proteins by compounds with different mechanisms of action, which include not only the direct interference with the binding of Sp proteins to their putative DNA binding sites, but also promoting the degradation of Sp protein factors. Down-regulation of Sp transcription factors and Sp1-regulated genes is drug-dependent and it is determined by the cell context. The acknowledgment that several of those compounds are safe enough might accelerate their introduction into clinical usage in patients with tumors that over-express Sp1.
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Affiliation(s)
- Carolina Vizcaíno
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, E-08028 Barcelona, Spain
| | - Sylvia Mansilla
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, E-08028 Barcelona, Spain
| | - José Portugal
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, E-08028 Barcelona, Spain.
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14
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Carrette LLG, Morii T, Madder A. Peptidosteroid Tweezers Revisited: DNA Binding Through an Optimised Design. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Hayes F, Kędzierska B. Regulating toxin-antitoxin expression: controlled detonation of intracellular molecular timebombs. Toxins (Basel) 2014; 6:337-58. [PMID: 24434949 PMCID: PMC3920265 DOI: 10.3390/toxins6010337] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 12/20/2013] [Accepted: 01/08/2014] [Indexed: 11/24/2022] Open
Abstract
Genes for toxin-antitoxin (TA) complexes are widely disseminated in bacteria, including in pathogenic and antibiotic resistant species. The toxins are liberated from association with the cognate antitoxins by certain physiological triggers to impair vital cellular functions. TAs also are implicated in antibiotic persistence, biofilm formation, and bacteriophage resistance. Among the ever increasing number of TA modules that have been identified, the most numerous are complexes in which both toxin and antitoxin are proteins. Transcriptional autoregulation of the operons encoding these complexes is key to ensuring balanced TA production and to prevent inadvertent toxin release. Control typically is exerted by binding of the antitoxin to regulatory sequences upstream of the operons. The toxin protein commonly works as a transcriptional corepressor that remodels and stabilizes the antitoxin. However, there are notable exceptions to this paradigm. Moreover, it is becoming clear that TA complexes often form one strand in an interconnected web of stress responses suggesting that their transcriptional regulation may prove to be more intricate than currently understood. Furthermore, interference with TA gene transcriptional autoregulation holds considerable promise as a novel antibacterial strategy: artificial release of the toxin factor using designer drugs is a potential approach to induce bacterial suicide from within.
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Affiliation(s)
- Finbarr Hayes
- Faculty of Life Sciences and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Barbara Kędzierska
- Faculty of Life Sciences and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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16
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17
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Ma L, Song F, Liu Z, Liu S. Study on noncovalent complexes of alkaloids with DNA duplex using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:51-58. [PMID: 23239316 DOI: 10.1002/rcm.6424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE DNA is an important molecular target in modern medicine research. Some DNA-binding ligands have been used to treat numerous diseases. Therefore, understanding the interactions of different ligands with DNA and looking for new DNA agents are necessary to develop new drugs. METHODS Electrospray ionization mass spectrometry (ESI-MS) in the negative ion mode was used to screen the noncovalent complexes between 11 alkaloids with double helix oligonucleotides at molar ratios 1:1 to 1:4. The relative binding affinities based on the fraction of bound DNA and sequence selectivities of alkaloids towards the duplex were also investigated by ESI-MS. Moreover, tandem mass spectrometry of 5-charged complex ions was used to try to determine DNA-binding modes. RESULTS Six alkaloids showed complexation with the selected DNA duplex, i.e., berberine, coptisine, peimine, aconitine, oxysophoridine and cytisine. They showed their binding affinities with d(AACTCCCGGCACAC/GTGTGCCGGGAGTT) in the order of berberine > coptisine > peimine > aconitine, oxysophoridine > cytosine; additional experiments involving collision energy proved this result. Sequence selectivities were not apparent for coptisine, peimine, aconitine and oxysophoridine with four DNA duplexes. The complexes containing berberine and coptisine underwent the predominant loss of the G base. However, for complexes containing the other four alkaloids, they dissociated via the loss of neutral drug. The results confirmed that they may have different binding modes. CONCLUSIONS According to experiment data and structural information, the binding mode of individual drugs with DNA was speculated. It was noted that the bindings of alkaloids peimine, aconitine and oxysophoridine with DNA are discovered firstly. This may give a clue to design duplex-binding ligands and be helpful for understanding biological activities of these alkaloids.
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Affiliation(s)
- Lei Ma
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, PR China
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18
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Novel mithramycins abrogate the involvement of protein factors in the transcription of cell cycle control genes. Biochem Pharmacol 2012; 84:1133-42. [DOI: 10.1016/j.bcp.2012.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/20/2012] [Accepted: 08/03/2012] [Indexed: 12/11/2022]
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19
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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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20
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Štefanišinová M, Tomečková V, Kožurková M, Ostró A, Mareková M. Study of DNA interactions with cyclic chalcone derivatives by spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 81:666-671. [PMID: 21778103 DOI: 10.1016/j.saa.2011.06.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/21/2011] [Accepted: 06/26/2011] [Indexed: 05/31/2023]
Abstract
A series of chalcone derivatives (1-4) were studied. The interaction between these ligands and calf thymus DNA was studied with UV-vis spectrophotometry, fluorescence and circular dichroism spectroscopy. The binding constants K were estimated at 0.5-4.6×10(5) M(-1). All these measurements indicated that the compounds behave as effective DNA-intercalating agents. Electrophoretic separation proved that ligands inhibited topoisomerase I at a concentration of 60 μM.
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Affiliation(s)
- M Štefanišinová
- Department of Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Košice, Trieda SNP 1, Košice 040 66, Slovak Republic.
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21
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Changes in gene expression induced by Sp1 knockdown differ from those caused by challenging Sp1 binding to gene promoters. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:327-36. [PMID: 21684359 DOI: 10.1016/j.bbagrm.2011.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/20/2011] [Accepted: 06/03/2011] [Indexed: 11/21/2022]
Abstract
C/G-rich DNA regions, which include those recognized by the Sp1 transcription factor in several gene promoters, also encompass potential binding sites for the DNA-intercalating anthracyclines doxorubicin and WP631. We explored the differences between changes in gene expression caused by the ability of these drugs to compete with Sp1 for binding to DNA and those produced by Sp1 knockdown. By quantitative RT-PCR of around 100 genes, most of them involved in control of cell cycle progression, we found that the treatment of human MDA-MB231 breast carcinoma cells with bis-anthracycline WP631 for 24 h produced a profile of gene down-regulation markedly different from the profile caused by doxorubicin treatment or by stable Sp1 knockdown. These observations are rationalized by considering a near-specific effect of WP631 on Sp1 interaction with several gene promoters, thus representing potential therapeutic targets for WP631, in contrast to a less specific effect of reducing the availability of Sp1 through RNA interference. Genes down-regulated upon each treatment were mapped to their molecular and biological functions, which documented the down-regulation, among other things, of genes involved in mRNA transcription regulation, granting us insights into the effects of challenging the transactivation of gene expression by Sp1.
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Szumilak M, Szulawska-Mroczek A, Koprowska K, Stasiak M, Lewgowd W, Stanczak A, Czyz M. Synthesis and in vitro biological evaluation of new polyamine conjugates as potential anticancer drugs. Eur J Med Chem 2010; 45:5744-51. [PMID: 20974504 DOI: 10.1016/j.ejmech.2010.09.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
Abstract
The synthesis of new polyamine derivatives containing dimeric quinoline (3a-c), cinnoline (4a-c) and phthalimide (7a-c and 8a-c) moieties is described. Three different polyamines: (1,4-bis(3-aminopropyl)piperazine (a), 4,9-dioxa-1,12-dodecanediamine (b), 3,3'-diamino-N-methyldipropylamine (c) were used as linkers. The new compounds were obtained according to known procedures. Their biological activity was assessed in vitro in a highly aggressive melanoma cell line A375. Polyamine diimides containing phthalimide moieties demonstrated no inhibitory activities against melanoma cells. Quinoline diamides were more efficient than cinnoline ones. Mainly cytostatic activity exerted as altered cell cycle profiles was observed at the concentrations causing about 50% reduction of adherent cell proliferation. Based on their structure as well as their biological activity, we assume that some of the newly synthesized compounds may act as DNA bisintercalators. This study might be useful for further designing and developing anticancer drugs with potent activities.
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Affiliation(s)
- Marta Szumilak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland
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23
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Selective binding of small molecules to DNA: Application and perspectives. Colloids Surf B Biointerfaces 2010; 79:1-4. [DOI: 10.1016/j.colsurfb.2010.03.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 03/31/2010] [Indexed: 11/22/2022]
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24
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Lenglet G, David-Cordonnier MH. DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences. J Nucleic Acids 2010; 2010. [PMID: 20725618 PMCID: PMC2915751 DOI: 10.4061/2010/290935] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 05/27/2010] [Accepted: 06/03/2010] [Indexed: 01/06/2023] Open
Abstract
DNA targeting drugs represent a large proportion of the actual anticancer drug pharmacopeia, both in terms of drug brands and prescription volumes. Small DNA-interacting molecules share the ability of certain proteins to change the DNA helix's overall organization and geometrical orientation via tilt, roll, twist, slip, and flip effects. In this ocean of DNA-interacting compounds, most stabilize both DNA strands and very few display helix-destabilizing properties. These types of DNA-destabilizing effect are observed with certain mono- or bis-intercalators and DNA alkylating agents (some of which have been or are being developed as cancer drugs). The formation of locally destabilized DNA portions could interfere with protein/DNA recognition and potentially affect several crucial cellular processes, such as DNA repair, replication, and transcription. The present paper describes the molecular basis of DNA destabilization, the cellular impact on protein recognition, and DNA repair processes and the latter's relationships with antitumour efficacy.
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Affiliation(s)
- Gaëlle Lenglet
- INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Team 4 Molecular and Cellular Targeting for Cancer Treatment, Institute for Research on Cancer of Lille (IRCL), Lille F-59045, France
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25
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Verzele D, Carrette LL, Madder A. Peptide scalpels for site-specific dissection of the DNA-protein interface. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e95-e146. [PMID: 24103721 DOI: 10.1016/j.ddtec.2010.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Portugal J. Evaluation of molecular descriptors for antitumor drugs with respect to noncovalent binding to DNA and antiproliferative activity. BMC Pharmacol 2009; 9:11. [PMID: 19758437 PMCID: PMC2758867 DOI: 10.1186/1471-2210-9-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 09/16/2009] [Indexed: 11/29/2022] Open
Abstract
Background Small molecules that bind reversibly to DNA are among the antitumor drugs currently used in chemotherapy. In the pursuit of a more rational approach to cancer chemotherapy based upon these molecules, it is necessary to exploit the interdependency between DNA-binding affinity, sequence selectivity and cytotoxicity. For drugs binding noncovalently to DNA, it is worth exploring whether molecular descriptors, such as their molecular weight or the number of potential hydrogen acceptors/donors, can account for their DNA-binding affinity and cytotoxicity. Results Fifteen antitumor agents, which are in clinical use or being evaluated as part of the National Cancer Institute's drug screening effort, were analyzed in silico to assess the contribution of various molecular descriptors to their DNA-binding affinity, and the capacity of the descriptors and DNA-binding constants for predicting cell cytotoxicity. Equations to predict drug-DNA binding constants and growth-inhibitory concentrations were obtained by multiple regression following rigorous statistical procedures. Conclusion For drugs binding reversibly to DNA, both their strength of binding and their cytoxicity are fairly predicted from molecular descriptors by using multiple regression methods. The equations derived may be useful for rational drug design. The results obtained agree with that compounds more active across the National Cancer Institute's 60-cell line data set tend to have common structural features.
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Affiliation(s)
- José Portugal
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Baldiri Reixac, 10, E-08028 Barcelona, Spain.
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Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 2008; 9:358. [PMID: 18667070 PMCID: PMC2536678 DOI: 10.1186/1471-2164-9-358] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 07/30/2008] [Indexed: 12/02/2022] Open
Abstract
Background The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo at the transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal (IC40) concentrations of the drug to minimise general toxic effects. Results Daunorubicin affected a minor proportion (14%) of the yeast transcriptome, increasing the expression of 195 genes and reducing expression of 280 genes. Daunorubicin down-regulated genes included essentially all genes involved in the glycolytic pathway, the tricarboxylic acid cycle and alcohol metabolism, whereas transcription of ribosomal protein genes was not affected or even slightly increased. This pattern is consistent with a specific inhibition of glucose usage in treated cells, with only minor effects on proliferation or other basic cell functions. Analysis of promoters of down-regulated genes showed that they belong to a limited number of transcriptional regulatory units (regulons). Consistently, data mining showed that daunorubicin-induced changes in expression patterns were similar to those observed in yeast strains deleted for some transcription factors functionally related to the glycolysis and/or the cAMP regulatory pathway, which appeared to be particularly sensitive to daunorubicin. Conclusion The effects of daunorubicin treatment on the yeast transcriptome are consistent with a model in which this drug impairs binding of different transcription factors by competing for their DNA binding sequences, therefore limiting their effectiveness and affecting the corresponding regulatory networks. This proposed mechanism might have broad therapeutic implications against cancer cells growing under hypoxic conditions.
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Wang Z, Cui M, Song F, Lu L, Liu Z, Liu S. Evaluation of flavonoids binding to DNA duplexes by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:914-922. [PMID: 18467117 DOI: 10.1016/j.jasms.2008.04.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 05/26/2023]
Abstract
In this study, electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding interactions of ten flavonoid aglycones and ten flavonoid glycosides with DNA duplexes. Relative binding affinities of the flavonoids toward DNA duplexes were estimated based on the fraction of bound DNA. The results revealed that the 4'-OH group of flavonoid aglycones was essential for their DNA-binding properties. Flavonoid glycosides with sugar chain linked on ring A or ring B showed enhanced binding toward the duplexes over their aglycone counterparts, whereas glycosylation of the flavonol quercetin on ring C exhibited a less pronounced effect. The aglycone skeletons and other hydroxyl substitutions on the aglycone also have an effect on the fractions of bound DNA. Upon collision-induced dissociation, the complexes containing flavonoid aglycones underwent the predominant ejection of a neutral ligand molecule, suggesting an intercalative DNA-binding mode. However, for complexes containing flavonoid glycosides, the loss of nucleobase increased to different extents, indicating a stronger binding or different binding mode. The results may provide not only a deeper insight into the DNA-binding properties of flavonoids but also a useful guideline for the design of efficient DNA-binding agents for chemotherapy.
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Affiliation(s)
- Zhaofu Wang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, PR China
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29
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Peixoto P, Liu Y, Depauw S, Hildebrand MP, Boykin DW, Bailly C, Wilson WD, David-Cordonnier MH. Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication. Nucleic Acids Res 2008; 36:3341-53. [PMID: 18440973 PMCID: PMC2425483 DOI: 10.1093/nar/gkn208] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of small molecules to control gene expression could be the spearhead of future-targeted therapeutic approaches in multiple pathologies. Among heterocyclic dications developed with this aim, a phenyl-furan-benzimidazole dication DB293 binds AT-rich sites as a monomer and 5'-ATGA sequence as a stacked dimer, both in the minor groove. Here, we used a protein/DNA array approach to evaluate the ability of DB293 to specifically inhibit transcription factors DNA-binding in a single-step, competitive mode. DB293 inhibits two POU-domain transcription factors Pit-1 and Brn-3 but not IRF-1, despite the presence of an ATGA and AT-rich sites within all three consensus sequences. EMSA, DNase I footprinting and surface-plasmon-resonance experiments determined the precise binding site, affinity and stoichiometry of DB293 interaction to the consensus targets. Binding of DB293 occurred as a cooperative dimer on the ATGA part of Brn-3 site but as two monomers on AT-rich sites of IRF-1 sequence. For Pit-1 site, ATGA or AT-rich mutated sequences identified the contribution of both sites for DB293 recognition. In conclusion, DB293 is a strong inhibitor of two POU-domain transcription factors through a cooperative binding to ATGA. These findings are the first to show that heterocyclic dications can inhibit major groove transcription factors and they open the door to the control of transcription factors activity by those compounds.
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Affiliation(s)
- Paul Peixoto
- INSERM U-837, Team 4-Molecular and cellular targeting for cancer treatment, Jean-Pierre Aubert Research Center, Institut de Recherches sur le Cancer de Lille, Place de Verdun, F-59045 Lille, IMPRT-IFR114, Lille, France
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Wang Z, Guo X, Liu Z, Cui M, Song F, Liu S. Studies on alkaloids binding to GC-rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:327-335. [PMID: 17968851 DOI: 10.1002/jms.1320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (including berberine, jatrorrhizine, palmatine, reserpine, berbamine, and tetrandrine) show complexation with the target DNA sequences. Relative binding affinities were estimated from the negative ion ESI data, and the alkaloids show a binding preference to the duplex with higher GC content. Positive ion ESI mass spectra of the complexes were also recorded and compared with those obtained in negative ion mode. Only the 1 : 1 complex with berbamine was observed with lower abundance in the positive ion mass spectrum while complexes with the other alkaloids were absolutely absent. Collision-induced dissociation (CID) experiments indicate that the complexes with the protoberberine alkaloids (berberine, jatrorrhizine, and palmatine) dissociate via base loss and covalent cleavage. In contrast, product ion spectra of the complexes with the alkaloids reserpine, berbamine, and tetrandrine show the predominant loss of a neutral alkaloid molecule, accompanied by base loss and covalent cleavage to a lesser extent. A comparison of the gas-phase behaviors of complexes with the alkaloids to those with the traditional DNA binders has suggested an intercalative binding mode of these alkaloids to the target DNA duplexes.
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Affiliation(s)
- Zhaofu Wang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, P R China
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Mansilla S, Portugal J. Sp1 transcription factor as a target for anthracyclines: effects on gene transcription. Biochimie 2008; 90:976-87. [PMID: 18226599 DOI: 10.1016/j.biochi.2007.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 12/27/2007] [Indexed: 11/28/2022]
Abstract
The analysis of how anthracyclines interfere with DNA-protein complexes, and the evaluation of their effects on gene transcription, can promote the development of new more specific anti-tumour agents. Daunorubicin and the bisintercalating anthracycline WP631 (which binds more tightly to DNA) have been compared for their ability to inhibit Sp1-DNA interactions and gene transcription. WP631 is more efficient at inhibiting transcription initiation from promoters containing an Sp1-binding site, and it is a potent inhibitor of Sp1-activated transcription both in vitro and in human cell lines. The analysis of gene expression profiles using arrays, which include several genes containing Sp1-putative binding sites, suggests that changes in the transcriptome induce cell cycle arrest and drive a time-dependent response of cells to death stimuli through distinct pathways, which rely on the anthracycline used and its concentration.
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Affiliation(s)
- Sylvia Mansilla
- Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Josep Samitier 1-5, E-08028 Barcelona, Spain
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32
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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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Gong J, Vaidyanathan VG, Yu X, Kensler TW, Peterson LA, Sturla SJ. Depurinating acylfulvene-DNA adducts: characterizing cellular chemical reactions of a selective antitumor agent. J Am Chem Soc 2007; 129:2101-11. [PMID: 17256933 DOI: 10.1021/ja0665951] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.
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Affiliation(s)
- Jiachang Gong
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Majumder P, Pradhan SK, Devi PG, Pal S, Dasgupta D. Chromatin as a target for the DNA-binding anticancer drugs. Subcell Biochem 2007; 41:145-89. [PMID: 17484128 PMCID: PMC7121056 DOI: 10.1007/1-4020-5466-1_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Chemotherapy has been a major approach to treat cancer. Both constituents of chromatin, chromosomal DNA and the associated chromosomal histone proteins are the molecular targets of the anticancer drugs. Small DNA binding ligands, which inhibit enzymatic processes with DNA substrate, are well known in cancer chemotherapy. These drugs inhibit the polymerase and topoisomerase activity. With the advent in the knowledge of chromatin chemistry and biology, attempts have shifted from studies of the structural basis of the association of these drugs or small ligands (with the potential of drugs) with DNA to their association with chromatin and nucleosome. These drugs often inhibit the expression of specific genes leading to a series of biochemical events. An overview will be given about the latest understanding of the molecular basis of their action. We shall restrict to those drugs, synthetic or natural, whose prime cellular targets are so far known to be chromosomal DNA.
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Affiliation(s)
- Parijat Majumder
- Biophysics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-I, Bidhannagar, Kolkata-700 064, India
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