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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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Chowdhury S, Kanrar K, Bhuiya S, Das S. The alkaloid cryptolepine as a source of polyadenylate targeting therapeutic agent: Induction of self-assembly in the polyadenylate moiety. Arch Biochem Biophys 2021; 712:109042. [PMID: 34562470 DOI: 10.1016/j.abb.2021.109042] [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: 02/08/2021] [Revised: 09/04/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
RNAs have become a well-known target for chemotherapeutic agents in the recent years. The tails of most eukaryotic m-RNA are characterized by the presence of a long polyadenylate sequence which plays an important role in its growth and maturation. This lays emphasis on development of molecular probes that target the polyadenylate sequence. Cryptolepine (hereafter, CRP) is an indoloquinoline alkaloid well known for its anti-malarial activities. A series of spectroscopic experiments namely absorption studies, fluorimetric studies and circular dichroism studies show that cryptolepine binds with single-stranded polyriboadenylic acid (hereafter, ss-poly (rA)) with a binding constant of ∼5 × 103 M-1 at 25 °C. Moreover thermal denaturation experiments show that the bound form of polyriboadenylic acid shows a characteristic transition profile. Such a profile is indicative of the ability of cryptolepine to induce self-assembly in the polyriboadenylic acid sequence on binding to it. Such ability of CRP to modulate the structural conformation of poly (rA), which in turn may cause functional aspects of the RNA to change, may give us a chance to develop effective alkaloid based chemotherapeutic agents.
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Affiliation(s)
- Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India
| | - Kasturi Kanrar
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India
| | - Sutanwi Bhuiya
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, 700032, India.
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Jagetia GC. Anticancer Potential of Natural Isoquinoline Alkaloid Berberine. JOURNAL OF EXPLORATORY RESEARCH IN PHARMACOLOGY 2021; 000:000-000. [DOI: 10.14218/jerp.2021.00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Sarkar S, Tribedi P, Bhadra K. Structure-activity insights of harmine targeting DNA, ROS inducing cytotoxicity with PARP mediated apoptosis against cervical cancer, anti-biofilm formation and in vivo therapeutic study. J Biomol Struct Dyn 2021; 40:5880-5902. [PMID: 33480316 DOI: 10.1080/07391102.2021.1874533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Harmine exhibits pH dependent structural equilibrium and possesses numerous biological and pharmacological activities. Mode and mechanism of DNA binding and its cytotoxicity were studied by multiple spectroscopic, calorimetric, molecular docking and in vitro apoptotic as well as in vivo biochemical and histological studies. It exists as cationic (structure I) and decationic form (structure II) in the pH range 3.0-7.8 and 8.5-12.4, respectively, with a pKa of 8.0. Structure I at pH 6.8 binds strongly to DNA with a cooperative mode of binding of Kiω 1.03 × 106 M-1and stoichiometry of 5.0 nucleotide phosphates. Structure I stabilized DNA by 10 °C, showed85%quenching of fluorescence intensity, perturbation in circular dichroism, partial intercalation and enthalpy driven exothermic binding. While, structure II at pH 8.5 has very weak interaction with CT DNA. Cytotoxic potencies of structure I was tested on four different cancer cell lines along with normal embryonic cell. It showed maximum cytotoxicity with GI50of 20 µM, against HeLa causing several apoptotic induction abilities. Harmine exhibited G2M arrest with ROS induced effective role in PARP mediated apoptosis as well as anti-inflammatory action on HeLa cells. Harmine further presented MIC and antibiofilm activity against Staphylococcus aureus in presence of <160 and 30 µg/ml, respectively. Mice with post harmine treatment (30 mg/kg b.w., I.P.) showed maximum recovery from damaged to near normal architecture of cervical epithelial cells. This study may be of prospective use in a framework to design novel beta carboline compounds for improved therapeutic applications in future against cervical cancer. HighlightsHarmine exists in structure I and structure II forms in the pH 6.8 and 8.5with a pKa of 8.0.Structure I at pH 6.8 binds strongly to DNA compared to structure II.Structure I showed maximum cytotoxicity with GI50 of 20 µM against HeLa.ROS mediated cytotoxicitywithG2M arrest with PARP mediated apoptosis was studied.Harmine (30µg/ml) exhibited antibiofilm activity against Staphylococcus aureus.Post harmine dose (30 mg/kg b.w., I.P.) in mice showed recovery of cervical epithelial cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarita Sarkar
- Department of Zoology, University of Kalyani, Nadia, West Bengal, India
| | - Prosun Tribedi
- Department of Biotechnology, The Neotia University, Sarisha, West Bengal, India
| | - Kakali Bhadra
- Department of Zoology, University of Kalyani, Nadia, West Bengal, India
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Nemr MTM, Yousif MNM, Barciszewski J. Interaction of small molecules with polynucleotide repeats and frameshift site RNA. Arch Pharm (Weinheim) 2019; 352:e1900062. [PMID: 31169327 DOI: 10.1002/ardp.201900062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/17/2019] [Accepted: 04/26/2019] [Indexed: 11/11/2022]
Abstract
This mini-review describes the interaction between small molecules and RNA, in addition to its application either in treating RNA-associated diseases or detecting target molecules. In the case of RNA-associated disease treatment, the designed small molecules interact with RNA sites, forming adducts and providing successful therapeutic strategies over oligonucleotides. On the other hand, synthetically designed RNA moieties (aptamers) interact with target molecules like toxins, drugs, hormones; these interactions are useful in the detection, quantification or separation of these target moieties.
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Affiliation(s)
- Mohamed T M Nemr
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Jan Barciszewski
- Department of Epigenetics, Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland.,NanoBioMedical Centre, Adam Mickiewicz University, Poznań, Poland
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Basu A, Kumar GS. Nucleic acids binding strategies of small molecules: Lessons from alkaloids. Biochim Biophys Acta Gen Subj 2018; 1862:1995-2016. [DOI: 10.1016/j.bbagen.2018.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 01/14/2023]
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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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Xiao X, Zhao B, Yang L, Liang X, Ren Y. Probe the Binding Mode of Aristololactam-β-D-glucoside to Phenylalanine Transfer RNA in Silico. ChemistrySelect 2016. [DOI: 10.1002/slct.201600603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Xingqing Xiao
- Department of Chemical and Biomolecular Engineering; North Carolina State University; Raleigh, North Carolina 27695-7905 USA
- State Key Laboratory of Chemical Engineering and Department of Chemistry; East China University of Science and Technology; Shanghai 200237 China
| | - Binwu Zhao
- Department of Chemical and Biomolecular Engineering; North Carolina State University; Raleigh, North Carolina 27695-7905 USA
| | - Li Yang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy; Wuhan Institute of Technology; Wuhan, Hubei 430073 China
- State Key Laboratory of Chemical Engineering and Department of Chemistry; East China University of Science and Technology; Shanghai 200237 China
| | - Xiaodong Liang
- Center for Energy Resources Engineering, Department of Chemical and Biochemical Engineering; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Yingqian Ren
- State Key Laboratory of Chemical Engineering and Department of Chemistry; East China University of Science and Technology; Shanghai 200237 China
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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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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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11
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Callies O, Hernández Daranas A. Application of isothermal titration calorimetry as a tool to study natural product interactions. Nat Prod Rep 2016; 33:881-904. [DOI: 10.1039/c5np00094g] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular interactions of natural products by isothermal titration calorimetry (ITC) is a potent tool to get new insights of the underpinning driving forces.
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Affiliation(s)
- O. Callies
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
| | - A. Hernández Daranas
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
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Subastri A, Ramamurthy C, Suyavaran A, Lokeswara Rao P, Preedia Babu E, Hari Krishna K, Suresh Kumar M, Thirunavukkarasu C. Probing the interaction of troxerutin with transfer RNA by spectroscopic and molecular modeling. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 153:137-44. [DOI: 10.1016/j.jphotobiol.2015.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022]
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Khan AY, Suresh Kumar G. Natural isoquinoline alkaloids: binding aspects to functional proteins, serum albumins, hemoglobin, and lysozyme. Biophys Rev 2015; 7:407-420. [PMID: 28510102 DOI: 10.1007/s12551-015-0183-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/19/2015] [Indexed: 02/04/2023] Open
Abstract
The putative anticancer alkaloids berberine, palmatine, jatrorrhizine, and sanguinarine are known to bind to nucleic acids. To develop them as potential drugs for therapeutic use, their binding affinity to functional proteins and mode of transport in the circulatory system need to be clearly understood. Towards this, many studies on their binding aspects to proteins have been reported and a considerable amount of data, mostly of biophysical nature, exists in the literature. The importance of these natural isoquinoline alkaloids and the recent literature on their interaction phenomena with functional proteins, serum albumins, hemoglobin, and lysozyme are presented in this review.
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Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700 032, India.
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Roviello GN, Musumeci D, Roviello V, Pirtskhalava M, Egoyan A, Mirtskhulava M. Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:1338-1347. [PMID: 26199837 PMCID: PMC4505092 DOI: 10.3762/bjnano.6.138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/22/2015] [Indexed: 06/10/2023]
Abstract
The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA)) both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA) tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale (DICMaPI), Università di Napoli “Federico II”, 80125 Napoli, Italy
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Hajjawi OS. Ribonucleic acid (RNA) biosynthesis in human cancer. Cancer Cell Int 2015; 15:22. [PMID: 25717284 PMCID: PMC4339644 DOI: 10.1186/s12935-015-0167-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/20/2015] [Indexed: 12/28/2022] Open
Abstract
In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article, we review malignant tumor, with stem like properties, and recent technical advances into the phenomenon of micro-particles and micro-vesicles containing cell-free nucleic acids that circulate plasma. New areas of research have been opened into screening tumor telomerase progression, prognosis of aptamers targeting cell surface, monitoring the efficacy of anticancer therapies, oncogenic transformation of host cell, and RNA polymerases role in the cell cycle progression and differentiation.
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Affiliation(s)
- Omar S Hajjawi
- Department of Biology, Arab American University, P. O. Box 240, Jenin, Israeli Occupied Territories of Palestine
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Derry MM, Somasagara RR, Raina K, Kumar S, Gomez J, Patel M, Agarwal R, Agarwal C. Target identification of grape seed extract in colorectal cancer using drug affinity responsive target stability (DARTS) technique: role of endoplasmic reticulum stress response proteins. Curr Cancer Drug Targets 2015; 14:323-36. [PMID: 24724981 DOI: 10.2174/1568009614666140411101942] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/10/2014] [Accepted: 04/10/2014] [Indexed: 12/21/2022]
Abstract
Various natural agents, including grape seed extract (GSE), have shown considerable chemopreventive and anti-cancer efficacy against different cancers in pre-clinical studies; however, their specific protein targets are largely unknown and thus, their clinical usefulness is marred by limited scientific evidences about their direct cellular targets. Accordingly, herein, employing, for the first time, the recently developed drug affinity responsive target stability (DARTS) technique, we aimed to profile the potential protein targets of GSE in human colorectal cancer (CRC) cells. Unlike other methods, which can cause chemical alteration of the drug components to allow for detection, this approach relies on the fact that a drug bound protein may become less susceptible to proteolysis and hence the enriched proteins can be detected by Mass Spectroscopy methods. Our results, utilizing the DARTS technique followed by examination of the spectral output by LC/MS and the MASCOT data, revealed that GSE targets endoplasmic reticulum (ER) stress response proteins resulting in overall down regulation of proteins involved in translation and that GSE also causes oxidative protein modifications, specifically on methionine amino acids residues on its protein targets. Corroborating these findings, mechanistic studies revealed that GSE indeed caused ER stress and strongly inhibited PI3k-Akt-mTOR pathway for its biological effects in CRC cells. Furthermore, bioenergetics studies indicated that GSE also interferes with glycolysis and mitochondrial metabolism in CRC cells. Together, the present study identifying GSE molecular targets in CRC cells, combined with its efficacy in vast pre-clinical CRC models, further supports its usefulness for CRC prevention and treatment.
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Affiliation(s)
| | | | | | | | | | | | | | - Chapla Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd, C238, Room V20-2118, Aurora, CO 80045, USA.
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Multiple effects of berberine derivatives on colon cancer cells. BIOMED RESEARCH INTERNATIONAL 2014; 2014:924585. [PMID: 25045712 PMCID: PMC4086420 DOI: 10.1155/2014/924585] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/24/2014] [Accepted: 04/24/2014] [Indexed: 01/21/2023]
Abstract
The pharmacological use of the plant alkaloid berberine is based on its antibacterial and anti-inflammatory properties; recently, anticancer activity has been attributed to this compound. To exploit this interesting feature, we synthesized three berberine derivatives, namely, NAX012, NAX014, and NAX018, and we tested their effects on two human colon carcinoma cell lines, that is, HCT116 and SW613-B3, which are characterized by wt and mutated p53, respectively. We observed that cell proliferation is more affected by cell treatment with the derivatives than with the lead compound; moreover, the derivatives proved to induce cell cycle arrest and cell death through apoptosis, thus suggesting that they could be promising anticancer drugs. Finally, we detected typical signs of autophagy in cells treated with berberine derivatives.
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Vindry C, Vo Ngoc L, Kruys V, Gueydan C. RNA-binding protein-mediated post-transcriptional controls of gene expression: integration of molecular mechanisms at the 3' end of mRNAs? Biochem Pharmacol 2014; 89:431-40. [PMID: 24735612 DOI: 10.1016/j.bcp.2014.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 01/17/2023]
Abstract
Initially identified as an occasional and peculiar mode of gene regulation in eukaryotes, RNA-binding protein-mediated post-transcriptional control of gene expression has emerged, over the last two decades, as a major contributor in the control of gene expression. A large variety of RNA-binding proteins (RBPs) allows the recognition of very diverse messenger RNA sequences and participates in the regulation of basically all cellular processes. Nevertheless, the rapid outcome of post-transcriptional regulations on the level of gene expression has favored the expansion of this type of regulation in cellular processes prone to rapid and frequent modulations such as the control of the inflammatory response. At the molecular level, the 3'untranslated region (3'UTR) of mRNA is a favored site of RBP recruitment. RBPs binding to these regions control gene expression through two major modes of regulation, namely mRNA decay and modulation of translational activity. Recent progresses suggest that these two mechanisms are often interdependent and might result one from the other. Therefore, different RBPs binding distinct RNA subsets could share similar modes of action at the molecular level. RBPs are frequent targets of post-translational modifications, thereby disclosing numerous possibilities for pharmacological interventions. However, redundancies of the transduction pathways controlling these modifications have limited the perspectives to define RBPs as new therapeutic targets. Through the analysis of several examples of RBPs binding to 3'untranslated region of mRNA, we present here recent progress and perspectives regarding this rapidly evolving field of molecular biology.
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Affiliation(s)
- Caroline Vindry
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium
| | - Long Vo Ngoc
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium.
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Zhou J, Sayre DA, Zheng Y, Szmacinski H, Sintim HO. Unexpected complex formation between coralyne and cyclic diadenosine monophosphate providing a simple fluorescent turn-on assay to detect this bacterial second messenger. Anal Chem 2014; 86:2412-20. [PMID: 24494631 PMCID: PMC3983017 DOI: 10.1021/ac403203x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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Cyclic
diadenosine monophosphate (c-di-AMP) has emerged as an important
dinucleotide that is involved in several processes in bacteria, including
cell wall remodeling (and therefore resistance to antibiotics that
target bacterial cell wall). Small molecules that target c-di-AMP
metabolism enzymes have the potential to be used as antibiotics. Coralyne
is known to form strong complexes with polyadenine containing eight
or more adenine stretches but not with short polyadenine oligonucleotides.
Using a panel of techniques (UV, both steady state fluorescence and
fluorescence lifetime measurements, circular dichroism (CD), NMR,
and Job plots), we demonstrate that c-di-AMP, which contains only
two adenine bases is an exception to this rule and that it can form
complexes with coralyne, even at low micromolar concentrations. Interestingly,
pApA (the linear analog of c-di-AMP that also contains two adenines)
or cyclic diguanylate (c-di-GMP, another nucleotide second messenger
in bacteria) did not form any complex with coralyne. Unlike polyadenine,
which forms a 2:1 complex with coralyne, c-di-AMP forms a higher order
complex with coralyne (≥6:1). Additionally, whereas polyadenine
reduces the fluorescence of coralyne when bound, c-di-AMP enhances
the fluorescence of coralyne. We use the quenching property of halides
to selectively quench the fluorescence of unbound coralyne but not
that of coralyne bound to c-di-AMP. Using this simple selective quenching
strategy, the assay could be used to monitor the synthesis of c-di-AMP
by DisA or the degradation of c-di-AMP by YybT. Apart from the practical
utility of this assay for c-di-AMP research, this work also demonstrates
that, when administered to cells, intercalators might not only associate
with polynucleotides, such as DNA or RNA, but also could associate
with cyclic dinucleotides to disrupt or modulate signal transduction
processes mediated by these nucleotides.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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Mehta A, Sonam S, Gouri I, Loharch S, Sharma DK, Parkesh R. SMMRNA: a database of small molecule modulators of RNA. Nucleic Acids Res 2014; 42:D132-41. [PMID: 24163098 PMCID: PMC3965028 DOI: 10.1093/nar/gkt976] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/13/2013] [Accepted: 10/01/2013] [Indexed: 02/05/2023] Open
Abstract
We have developed SMMRNA, an interactive database, available at http://www.smmrna.org, with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of ∼770 unique ligands along with structural images of RNA molecules. Each ligand in the SMMRNA contains information such as Kd, Ki, IC50, ΔTm, molecular weight (MW), hydrogen donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings and 2D and 3D structures. These parameters can be explored using text search, advanced search, substructure and similarity-based analysis tools that are embedded in SMMRNA. A structure editor is provided for 3D visualization of ligands. Advance analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. Upload facility for both RNA and ligands is also provided. The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling. We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening. SMMRNA provides comprehensive resource for further design, development and refinement of small molecule modulators for selective targeting of RNA molecules.
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Affiliation(s)
- Ankita Mehta
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Surabhi Sonam
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Isha Gouri
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Saurabh Loharch
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Deepak K. Sharma
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
| | - Raman Parkesh
- Department of Advanced Protein Science, Institute of Microbial Technology, Chandigarh-160036, India
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Yao J, Kong W, Jiang J. Learning from berberine: Treating chronic diseases through multiple targets. SCIENCE CHINA-LIFE SCIENCES 2013; 58:854-9. [PMID: 24174332 DOI: 10.1007/s11427-013-4568-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 07/04/2014] [Indexed: 11/28/2022]
Abstract
Although advances have been made, chemotherapy for chronic, multifactorial diseases such as cancers, Alzheimer's disease, cardiovascular diseases and diabetes is far from satisfactory. Agents with different mechanisms of action are required. The botanic compound berberine (BBR) has been used as an over-the-counter antibacterial for diarrhea in China for many decades. Recent clinical studies have shown that BBR may be therapeutic in various types of chronic diseases. This review addresses BBR's molecular mechanisms of action and clinical efficacy and safety in patients with type 2 diabetes, hyperlipidemia, heart diseases, cancers and inflammation. One of the advantages of BBR is its multiple-target effects in each of these diseases. The therapeutic efficacy of BBR may reflect a synergistic regulation of these targets, resulting in a comprehensive effect against these various chronic disorders. The safety of BBR may be due to its harmonious distribution into those targets. Although the single-target concept is still the principle for drug discovery and research, this review emphasizes the concept of a multiple target strategy, which may be an important approach toward the successful treatment of multifactorial chronic diseases.
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Affiliation(s)
- Jing Yao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430023, China
| | - WeiJia Kong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - JianDong Jiang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Basu A, Jaisankar P, Suresh Kumar G. Binding of the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to tRNA(phe.). PLoS One 2013; 8:e58279. [PMID: 23526972 PMCID: PMC3602459 DOI: 10.1371/journal.pone.0058279] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/01/2013] [Indexed: 12/19/2022] Open
Abstract
Background Three new analogs of berberine with aryl/arylalkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore along with berberrubine were studied for their binding to tRNAphe by wide variety of biophysical techniques like spectrophotometry, spectrofluorimetry, circular dichroism, thermal melting, viscosity and isothermal titration calorimetry. Methodology/Principal Findings Scatchard binding isotherms revealed that the cooperative binding mode of berberine was propagated in the analogs also. Thermal melting studies showed that all the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs stabilized the tRNAphe more in comparison to berberine. Circular dichroism studies showed that these analogs perturbed the structure of tRNAphe more in comparison to berberine. Ferrocyanide quenching studies and viscosity results proved the intercalative binding mode of these analogs into the helical organization of tRNAphe. The binding was entropy driven for the analogs in sharp contrast to the enthalpy driven binding of berberine. The introduction of the aryl/arylalkyl amino carbonyl methyl substituent at the 9-position thus switched the enthalpy driven binding of berberine to entropy dominated binding. Salt and temperature dependent calorimetric studies established the involvement of multiple weak noncovalent interactions in the binding process. Conclusions/Significance The results showed that 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs exhibited almost ten folds higher binding affinity to tRNAphe compared to berberine whereas the binding of berberrubine was dramatically reduced by about twenty fold in comparison to berberine. The spacer length of the substitution at the 9-position of the isoquinoline chromophore appears to be critical in modulating the binding affinities towards tRNAphe.
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Affiliation(s)
- Anirban Basu
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Gopinatha Suresh Kumar
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- * E-mail:
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Hazra S, Hossain M, Kumar GS. Studies on α-, β-, and γ-cyclodextrin inclusion complexes of isoquinoline alkaloids berberine, palmatine and coralyne. J INCL PHENOM MACRO 2013. [DOI: 10.1007/s10847-013-0301-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bansal M, Jayaram B, Mittal A. Nucleic acids in disease and disorder: Understanding the language of life emerging from the ‘ABC’ of DNA. J Biosci 2012; 37:375-8. [DOI: 10.1007/s12038-012-9226-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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