1
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Bhattacharjee P, Sarkar P, Bhadra K. Evaluation of therapeutic role of harmaline: in vitro cytotoxicity targeting nucleic acids. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:519-533. [PMID: 37656039 DOI: 10.1080/10286020.2023.2251116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
Use of small molecules as valuable drugs against diseases is still an indefinable purpose due to the lack of in-detail knowledge regarding proper bio-target identification, specificity aspects, mode-mechanism of binding and proper in vitro study. Harmaline, an important beta-carboline alkaloid, shows effective anti-proliferative action against different types of human cancers and is also found to be a nucleic acid targeting natural molecule. This review sought to address the different signal pathways of apoptosis by harmaline in different cancer cell lines and simultaneously to characterize the structure activity aspects of the alkaloid with different motifs of nucleic acid to show its preference, biological efficacy and genotoxicity. The results open up new insights for the design and development of small molecule-based nucleic acid therapeutic agents.
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Affiliation(s)
| | - Paromita Sarkar
- Department of Zoology, University of Kalyani, Nadia, W. Bengal 741235, India
| | - Kakali Bhadra
- Department of Zoology, University of Kalyani, Nadia, W. Bengal 741235, India
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2
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Parmar S, Bume DD, Conelly C, Boer R, Prestwood PR, Wang Z, Labuhn H, Sinnadurai K, Feri A, Ouellet J, Homan P, Numata T, Schneekloth JS. Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581746. [PMID: 38903087 PMCID: PMC11188086 DOI: 10.1101/2024.02.23.581746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
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Affiliation(s)
- Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta Doro Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen Conelly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Peri R. Prestwood
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Zhen Wang
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | | | | | - Adeline Feri
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Philip Homan
- Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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3
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Bayazeid O, Nasibova T. Chemoinformatic analysis of alkaloids isolated from Peganum genus. Mol Divers 2021; 26:2257-2267. [PMID: 34674079 DOI: 10.1007/s11030-021-10331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Peganum genus is rich with its high phytochemical and botanical variability. Peganum species have been used as a sedative, antitumor, analgesic and antidepressant. This paper aims to study the molecular diversity of Peganum genus and to shed more light on the structure-activity relationship of the alkaloids isolated from Peganum genus. All Peganum alkaloids were grouped according to their structural properties. A chemoinformatic approach (SwissTargetPrediction) was used to determine the molecular targets of these alkaloids. To analyze and visualize the results, R software was used to generate hierarchical clustering heatmaps. The results of this study can help researchers to better understand the structure-activity relationship of Peganum alkaloids and how substitution can affect the biological activity of those alkaloids.
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Affiliation(s)
- Omer Bayazeid
- Department of Pharmacognosy, Faculty of Pharmacy, Hacettepe University, Sihhiye, 06100, Ankara, Turkey.
| | - Tohfa Nasibova
- Department of General and Toxicological Chemistry, Azerbaijan Medical University, A. Gasimzade 14, AZ1022, Baku, Azerbaijan
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4
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A comprehensive overview of β-carbolines and its derivatives as anticancer agents. Eur J Med Chem 2021; 224:113688. [PMID: 34332400 DOI: 10.1016/j.ejmech.2021.113688] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 05/05/2021] [Accepted: 07/04/2021] [Indexed: 01/13/2023]
Abstract
β-Carboline alkaloids are a family of natural and synthetic products with structural diversity and outstanding antitumor activities. This review summarizes research developments of β-carboline and its derivatives as anticancer agents, which focused on both natural and synthetic monomers as well as dimers. In addition, the structure-activity relationship (SAR) analysis of β-carboline monomers and dimers are summarized and mechanism of action of β-carboline and its derivatives are also presented. A few possible research directions, suggestions and clues for future work on the development of novel β-carboline-based anticancer agents with improved expected activities and lesser toxicity are also provided.
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5
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Kongkham B, Prabakaran D, Puttaswamy H. Opportunities and challenges in managing antibiotic resistance in bacteria using plant secondary metabolites. Fitoterapia 2020; 147:104762. [PMID: 33069839 DOI: 10.1016/j.fitote.2020.104762] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022]
Abstract
Development of antibiotic resistance (ABR) in bacteria and its multidimensional spread is an emerging global threat that needs immediate attention. Extensive antibiotics (AB) usage results in development of ABR in bacteria by target modification, production of AB degrading enzymes, porin modifications, efflux pumps overexpression, etc. To counter this, apart from strict regulation of AB use and behavioural changes, research and development (R&D) of newer antimicrobials are in place. One such emerging approach to combat ABR is the use of structurally and functionally diverse plant secondary metabolites (PSMs) in combination with the conventional AB. Either the PSMs are themselves antimicrobial or they potentiate the activity of the AB through a range of mechanisms. However, their use is lagging due to poor knowledge of mode of action, structure-activity relationships, pharmacokinetics, etc. This review paper discussed the opportunities and challenges in managing ABR using PSMs. Mechanisms of ABR development in bacteria and current strategies to counter them were studied and the areas where PSMs can play an important role were highlighted. The use of PSMs, both as an anti-resistance and anti-virulence agent in combination therapy to counter multi-drug resistance along with their mechanisms of action, has been discussed in detail. The difficulties in the commercialisation of PSMs and strategies to overcome them along with future priority areas of research have also been given. Following the given R&D path will definitely help in better understanding and utilising the full potential of PSMs in solving the problem of antimicrobial resistance (AMR).
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Affiliation(s)
- Bhani Kongkham
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Delhi 110016, India
| | - Duraivadivel Prabakaran
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Delhi 110016, India
| | - Hariprasad Puttaswamy
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Delhi 110016, India.
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6
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López-Morató M, Brook JD, Wojciechowska M. Small Molecules Which Improve Pathogenesis of Myotonic Dystrophy Type 1. Front Neurol 2018; 9:349. [PMID: 29867749 PMCID: PMC5968088 DOI: 10.3389/fneur.2018.00349] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/30/2018] [Indexed: 12/30/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults for which there is currently no treatment. The pathogenesis of this autosomal dominant disorder is associated with the expansion of CTG repeats in the 3'-UTR of the DMPK gene. DMPK transcripts with expanded CUG repeats (CUGexpDMPK) are retained in the nucleus forming multiple discrete foci, and their presence triggers a cascade of toxic events. Thus far, most research emphasis has been on interactions of CUGexpDMPK with the muscleblind-like (MBNL) family of splicing factors. These proteins are sequestered by the expanded CUG repeats of DMPK RNA leading to their functional depletion. As a consequence, abnormalities in many pathways of RNA metabolism, including alternative splicing, are detected in DM1. To date, in vitro and in vivo efforts to develop therapeutic strategies for DM1 have mostly been focused on targeting CUGexpDMPK via reducing their expression and/or preventing interactions with MBNL1. Antisense oligonucleotides targeted to the CUG repeats in the DMPK transcripts are of particular interest due to their potential capacity to discriminate between mutant and normal transcripts. However, a growing number of reports describe alternative strategies using small molecule chemicals acting independently of a direct interaction with CUGexpDMPK. In this review, we summarize current knowledge about these chemicals and we describe the beneficial effects they caused in different DM1 experimental models. We also present potential mechanisms of action of these compounds and pathways they affect which could be considered for future therapeutic interventions in DM1.
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Affiliation(s)
- Marta López-Morató
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - John David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Polish Academy of Sciences, Department of Molecular Genetics, Institute of Bioorganic Chemistry, Poznan, Poland
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7
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Guo L, Chen W, Cao R, Fan W, Ma Q, Zhang J, Dai B. Synthesis and structure-activity relationships of asymmetric dimeric β-carboline derivatives as potential antitumor agents. Eur J Med Chem 2018; 147:253-265. [PMID: 29448140 DOI: 10.1016/j.ejmech.2018.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 12/27/2022]
Abstract
A series of newly asymmetric dimeric β-carbolines with a spacer of 4-6 methylene units between the indole nitrogen and the harmine oxygen were synthesized. Structures of all the novel synthesized compounds were confirmed by their spectral and analytical studies. All of the synthesized compounds were screened for their in vitro cytotoxic activity against nine cancer cell lines. The results revealed that compounds 7c, 7o and 7s exhibited the highest cytotoxic activities with IC50 values of less than 20 μM against the tumor cell lines tested. Acute toxicities and antitumor efficacies of the selected compounds in mice were also evaluated, and compound 7o exhibited potent antitumor activities with the tumor inhibition rate of over 40%. The wound healing assay displayed a specific impairment in the motility of the HT-29 cells, which suggested the anti-metastatic potential of compound 7o. Moreover, compound 7o had obvious angiogenesis inhibitory effects in the chicken chorioallantoic membrane (CAM) assay. Preliminary structure-activity relationship (SAR) analysis indicated that: (1) 3-phenylpropyl substituent at the N9-position of the indole ring was the most suitable group giving rise to potent cytotoxic agents; (2) the spacer length affected the antitumor potencies, and four methylene units were more favorable.
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Affiliation(s)
- Liang Guo
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China
| | - Wei Chen
- Xinjiang Huashidan Pharmaceutical Research Co. Ltd., 175 He Nan East Road, Urumqi 830011, PR China
| | - Rihui Cao
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, 135 Xin Gang West Road, Guangzhou 510275, PR China
| | - Wenxi Fan
- Xinjiang Huashidan Pharmaceutical Research Co. Ltd., 175 He Nan East Road, Urumqi 830011, PR China
| | - Qin Ma
- Xinjiang Huashidan Pharmaceutical Research Co. Ltd., 175 He Nan East Road, Urumqi 830011, PR China
| | - Jie Zhang
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China
| | - Bin Dai
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China.
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8
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Bhattacharjee P, Ghosh T, Sarkar S, Pandya P, Bhadra K. Binding affinity and in vitro
cytotoxicity of harmaline targeting different motifs of nucleic acids: An ultimate drug designing approach. J Mol Recognit 2017; 31. [PMID: 29243872 DOI: 10.1002/jmr.2687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/22/2017] [Accepted: 10/22/2017] [Indexed: 01/18/2023]
Affiliation(s)
| | - Tapas Ghosh
- Department of Zoology; University of Kalyani; Kalyani Nadia, West Bengal India
| | - Sarita Sarkar
- Department of Zoology; University of Kalyani; Kalyani Nadia, West Bengal India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences; Amity University; Noida Uttar Pradesh India
| | - Kakali Bhadra
- Department of Zoology; University of Kalyani; Kalyani Nadia, West Bengal India
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9
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Bhuiya S, Haque L, Goswami R, Das S. Multispectroscopic and Theoretical Exploration of the Comparative Binding Aspects of Bioflavonoid Fisetin with Triple- and Double-Helical Forms of RNA. J Phys Chem B 2017; 121:11037-11052. [DOI: 10.1021/acs.jpcb.7b07972] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Rapti Goswami
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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10
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Ray B, Agarwal S, Kadian H, Gambhir K, Sharma P, Mehrotra R. Deciphering molecular aspects of interaction between anticancer drug mitoxantrone and tRNA. J Biomol Struct Dyn 2016; 35:2090-2102. [DOI: 10.1080/07391102.2016.1213185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Bhumika Ray
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Heena Kadian
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Kaweri Gambhir
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Parag Sharma
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
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11
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Herrendorff R, Faleschini MT, Stiefvater A, Erne B, Wiktorowicz T, Kern F, Hamburger M, Potterat O, Kinter J, Sinnreich M. Identification of Plant-derived Alkaloids with Therapeutic Potential for Myotonic Dystrophy Type I. J Biol Chem 2016; 291:17165-77. [PMID: 27298317 DOI: 10.1074/jbc.m115.710616] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 11/06/2022] Open
Abstract
Myotonic dystrophy type I (DM1) is a disabling neuromuscular disease with no causal treatment available. This disease is caused by expanded CTG trinucleotide repeats in the 3' UTR of the dystrophia myotonica protein kinase gene. On the RNA level, expanded (CUG)n repeats form hairpin structures that sequester splicing factors such as muscleblind-like 1 (MBNL1). Lack of available MBNL1 leads to misregulated alternative splicing of many target pre-mRNAs, leading to the multisystemic symptoms in DM1. Many studies aiming to identify small molecules that target the (CUG)n-MBNL1 complex focused on synthetic molecules. In an effort to identify new small molecules that liberate sequestered MBNL1 from (CUG)n RNA, we focused specifically on small molecules of natural origin. Natural products remain an important source for drugs and play a significant role in providing novel leads and pharmacophores for medicinal chemistry. In a new DM1 mechanism-based biochemical assay, we screened a collection of isolated natural compounds and a library of over 2100 extracts from plants and fungal strains. HPLC-based activity profiling in combination with spectroscopic methods were used to identify the active principles in the extracts. The bioactivity of the identified compounds was investigated in a human cell model and in a mouse model of DM1. We identified several alkaloids, including the β-carboline harmine and the isoquinoline berberine, that ameliorated certain aspects of the DM1 pathology in these models. Alkaloids as a compound class may have potential for drug discovery in other RNA-mediated diseases.
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Affiliation(s)
- Ruben Herrendorff
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
| | - Maria Teresa Faleschini
- the Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Adeline Stiefvater
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
| | - Beat Erne
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
| | - Tatiana Wiktorowicz
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
| | - Frances Kern
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
| | - Matthias Hamburger
- the Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Olivier Potterat
- the Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Jochen Kinter
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
| | - Michael Sinnreich
- From the Neuromuscular Research Group, Departments of Neurology and Biomedicine, University Hospital Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and
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12
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Bhattacharjee P, Sarkar S, Pandya P, Bhadra K. Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach. J Biomol Struct Dyn 2016; 34:2722-2740. [DOI: 10.1080/07391102.2015.1126694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Spectroscopic and electrochemical studies on the interaction between luteolin and DNA. J Solid State Electrochem 2016. [DOI: 10.1007/s10008-016-3174-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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14
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Haque L, Pradhan AB, Bhuiya S, Das S. Exploring the comparative binding aspects of benzophenanthridine plant alkaloid chelerythrine with RNA triple and double helices: a spectroscopic and calorimetric approach. Phys Chem Chem Phys 2016; 17:17202-13. [PMID: 26073991 DOI: 10.1039/c5cp01737h] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A comparative study on the interaction of a benzophenanthridine alkaloid chelerythrine (CHL) with RNA triplex poly(U).poly(A)*poly(U) (hereafter U.A*U, .(dot) and *(asterisk) represent Watson-Crick and Hoogsteen base pairing respectively) and its parent duplex poly(A).poly(U) (A.U) was carried out by using a combination of various spectroscopic, viscometric and calorimetric techniques. The interaction was characterized by hypochromic and bathochromic effects in the absorption spectrum, the increase of thermal melting temperature, enhancement in solution viscosity, and perturbation in the circular dichroic spectrum. The binding constant calculated by using spectrophotometric data was in the order of 10(5) for both forms of RNA, but it was greater for triplex RNA (30.2 × 10(5) M(-1)) than duplex RNA (3.6 × 10(5) M(-1)). Isothermal titration calorimetric data are in good agreement with the spectrophotometric data. The data indicated stronger binding of CHL to the triplex structure of RNA compared to the native duplex structure. Thermal melting studies indicated greater stabilization of the Hoogsteen base paired third strand of the RNA triplex compared to its Watson-Crick strands. The mode of binding of CHL to both U.A*U and A.U was intercalation as revealed from fluorescence quenching, viscosity measurements and sensitization of the fluorescence experiment. Thermodynamic data obtained from isothermal calorimetric measurements revealed that association was favoured by both a negative enthalpy change and a positive entropy change. Taken together, our results suggest that chelerythrine binds and stabilizes the RNA triplex more strongly than its respective parent duplex. The results presented here may be useful for formulating effective antigene strategies involving benzophenanthridine alkaloids and the RNA triplex.
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Affiliation(s)
- Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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15
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Ray B, Agarwal S, Lohani N, Rajeswari MR, Mehrotra R. Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA. J Biomol Struct Dyn 2016; 34:2518-35. [DOI: 10.1080/07391102.2015.1118708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bhumika Ray
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Neelam Lohani
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Moganty R. Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
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16
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V-shaped ligand 1,3-bis(1-ethylbenzimidazol-2-yl)-2-thiapropane and manganese(II), cobalt(II) and copper(II) complexes: Synthesis, crystal structure, DNA-binding properties and antioxidant activities. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 148:252-261. [DOI: 10.1016/j.jphotobiol.2015.04.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/27/2015] [Accepted: 04/16/2015] [Indexed: 11/20/2022]
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17
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Moloudizargari M, Mikaili P, Aghajanshakeri S, Asghari MH, Shayegh J. Pharmacological and therapeutic effects of Peganum harmala and its main alkaloids. Pharmacogn Rev 2014; 7:199-212. [PMID: 24347928 PMCID: PMC3841998 DOI: 10.4103/0973-7847.120524] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 12/28/2012] [Accepted: 10/25/2013] [Indexed: 11/07/2022] Open
Abstract
Wild Syrian rue (Peganum harmala L. family Zygophyllaceae) is well-known in Iran and various parts of this plant including, its seeds, bark, and root have been used as folk medicine. Recent years of research has demonstrated different pharmacological and therapeutic effects of P. harmala and its active alkaloids, especially harmine and harmaline. Analytical studies on the chemical composition of the plant show that the most important constituents of this plant are beta-carboline alkaloids such as harmalol, harmaline, and harmine. Harmine is the most studied among these naturally occurring alkaloids. In addition to P. harmala (Syrian rue), these beta-carbolines are present in many other plants such as Banisteria caapi and are used for the treatment of different diseases. This article reviews the traditional uses and pharmacological effects of total extract and individual active alkaloids of P. harmala (Syrian rue).
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Affiliation(s)
- Milad Moloudizargari
- Student of Veterinary Medicine, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Peyman Mikaili
- Department of Pharmacology, Faculty of Pharmacy, Urmia University of Medical Sciences, Urmia, Iran
| | - Shahin Aghajanshakeri
- Student of Veterinary Medicine, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | | | - Jalal Shayegh
- Veterinary Medicine, Faculty of Agriculture and Veterinary, Shabestar Branch, Islamic Azad University, Shabestar, Iran
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Wu H, Pan G, Bai Y, Zhang Y, Wang H, Shi F, Wang X, Kong J. Study on synthesis, crystal structure, antioxidant and DNA-binding of mono-, di- and poly-nuclear lanthanides complexes with bis(N-salicylidene)-3-oxapentane-1,5-diamine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 135:33-43. [DOI: 10.1016/j.jphotobiol.2014.04.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
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Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol Syst Biol 2013; 9:662. [PMID: 23632384 PMCID: PMC3658274 DOI: 10.1038/msb.2013.20] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/28/2013] [Indexed: 12/14/2022] Open
Abstract
Drug-induced transcriptional modules (biclusters) were identified and annotated in three human cell lines and rat liver. These were used to assess conservation across systems and to infer and experimentally validate novel drug effects and gene functions. ![]()
Biclustering of drug-induced gene expression profiles resulted in modules of drugs and genes, which were enriched in both drug and gene annotations. Identifying drug-induced transcriptional modules separately in three human cell lines and rat liver allows assessment of their conservation across model systems. About 70% of modules are conserved across cell lines, a lower bound of 15% was estimated for their conservation across organisms, and between the in vitro and in vivo systems. Drug-induced transcriptional modules can predict novel gene functions. A conserved module associated with (chole)sterol metabolism revealed novel regulators of cellular cholesterol homeostasis; 10 of them were validated in functional imaging assays. Analysis of drugs clustered into modules can give new insights into their mechanisms of action and provide leads for drug repositioning. We predicted and experimentally validated novel cell cycle inhibitors and modulators of PPARγ, estrogen and adrenergic receptors, with potential for developing new therapies against diabetes and cancer.
In pharmacology, it is crucial to understand the complex biological responses that drugs elicit in the human organism and how well they can be inferred from model organisms. We therefore identified a large set of drug-induced transcriptional modules from genome-wide microarray data of drug-treated human cell lines and rat liver, and first characterized their conservation. Over 70% of these modules were common for multiple cell lines and 15% were conserved between the human in vitro and the rat in vivo system. We then illustrate the utility of conserved and cell-type-specific drug-induced modules by predicting and experimentally validating (i) gene functions, e.g., 10 novel regulators of cellular cholesterol homeostasis and (ii) new mechanisms of action for existing drugs, thereby providing a starting point for drug repositioning, e.g., novel cell cycle inhibitors and new modulators of α-adrenergic receptor, peroxisome proliferator-activated receptor and estrogen receptor. Taken together, the identified modules reveal the conservation of transcriptional responses towards drugs across cell types and organisms, and improve our understanding of both the molecular basis of drug action and human biology.
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Charak S, Mehrotra R. Structural investigation of idarubicin–DNA interaction: Spectroscopic and molecular docking study. Int J Biol Macromol 2013; 60:213-8. [DOI: 10.1016/j.ijbiomac.2013.05.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 05/05/2013] [Accepted: 05/25/2013] [Indexed: 10/26/2022]
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LIN YICHIEN, TSAI JUIYING, YANG JAISING, LEE YUEHHSUAN, HAMEL ERNEST, LEE KUOHSIUNG, KUO SHENGCHU, HUANG LIJIAU. The novel synthetic compound 6-acetyl-9-(3,4,5-trimethoxybenzyl)-9H-pyrido[2,3-b]indole induces mitotic arrest and apoptosis in human COLO 205 cells. Int J Oncol 2013; 43:1596-606. [DOI: 10.3892/ijo.2013.2069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 07/29/2013] [Indexed: 11/06/2022] Open
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Kundu S, Biswas MK, Banerjee A, Bhadra K, Kumar GS, Drew MGB, Bhadra R, Ghosh P. Synthesis, structure and DNA binding studies of 9-phenyldibenzo[a,c] phenazin-9-ium. RSC Adv 2013. [DOI: 10.1039/c2ra22317a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Charak S, Shandilya M, Tyagi G, Mehrotra R. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA. Int J Biol Macromol 2012; 51:406-11. [DOI: 10.1016/j.ijbiomac.2012.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/07/2012] [Accepted: 06/10/2012] [Indexed: 11/26/2022]
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24
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Nafisi S, Manouchehri F, Bonsaii M. Study on the interaction of glycyrrhizin and glycyrrhetinic acid with RNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 111:27-34. [PMID: 22513095 DOI: 10.1016/j.jphotobiol.2012.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 03/05/2012] [Accepted: 03/13/2012] [Indexed: 11/17/2022]
Abstract
Glycyrrhizin is a well known pharmacologically bioactive natural glycoside. Glycyrrhizin (GL) has been widely used as a therapeutic agent for chronic active liver diseases. Glycyrrhetinic acid is an aglycone and an active metabolite of glycyrrhizin. This study is the first attempt to locate the binding sites of glycyrrhizin and glycyrrhetinic acid to RNA. The effect of the ligand complexation on RNA aggregation was investigated in aqueous solution at physiological conditions, using constant RNA concentration (6.25 mM) and various ligand/polynucleotide (phosphate) ratios of 1/280, 1/240, 1/120, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods as well as molecular modeling were used to determine the ligand binding modes, the binding constants, and the stability of ligands-RNA complexes in aqueous solution. Spectroscopic evidence showed that glycyrrhizin and glycyrrhetinic acid bind RNA via G-C and A-U base pairs as well as the backbone phosphate group with overall binding constants of K(GL-RNA)=3.03×10(3)M(-1), K(GA-RNA)=2.71×10(3)M(-1). The affinity of ligands-RNA binding is in the order of glycyrrhizin>glycyrrhetinic acid. RNA remains in the A-family structure, while biopolymer aggregation occurred at high triterpenoid concentrations.
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Affiliation(s)
- Shohreh Nafisi
- Department of Chemistry, Islamic Azad University, Central Tehran Branch (IAUCTB), Tehran, Iran.
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Tyagi G, Charak S, Mehrotra R. Binding of an indole alkaloid, vinblastine to double stranded DNA: A spectroscopic insight in to nature and strength of interaction. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 108:48-52. [DOI: 10.1016/j.jphotobiol.2011.12.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/07/2011] [Accepted: 12/18/2011] [Indexed: 11/17/2022]
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Bhowmik D, Hossain M, Buzzetti F, D’Auria R, Lombardi P, Kumar GS. Biophysical Studies on the Effect of the 13 Position Substitution of the Anticancer Alkaloid Berberine on Its DNA Binding. J Phys Chem B 2012; 116:2314-24. [DOI: 10.1021/jp210072a] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry
Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Maidul Hossain
- Biophysical Chemistry
Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Franco Buzzetti
- Naxospharma srl, Via G. Di Vittorio, 70 - 20026 - Novate Milanese (MI), Italy
| | - Rosaria D’Auria
- Naxospharma srl, Via G. Di Vittorio, 70 - 20026 - Novate Milanese (MI), Italy
| | - Paolo Lombardi
- Naxospharma srl, Via G. Di Vittorio, 70 - 20026 - Novate Milanese (MI), Italy
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry
Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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Nafisi S, Manouchehri F, Montazeri M. RNA adducts with Na2SeO4 and Na2SeO3 – Stability and structural features. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.09.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Charak S, Jangir DK, Tyagi G, Mehrotra R. Interaction studies of Epirubicin with DNA using spectroscopic techniques. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.06.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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