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Dasmahapatra U, Kumar CK, Das S, Subramanian PT, Murali P, Isaac AE, Ramanathan K, MM B, Chanda K. In-silico molecular modelling, MM/GBSA binding free energy and molecular dynamics simulation study of novel pyrido fused imidazo[4,5-c]quinolines as potential anti-tumor agents. Front Chem 2022; 10:991369. [PMID: 36247684 PMCID: PMC9566731 DOI: 10.3389/fchem.2022.991369] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022] Open
Abstract
With an alarming increase in the number of cancer patients and a variety of tumors, it is high time for intensive investigation on more efficient and potent anti-tumor agents. Though numerous agents have enriched the literature, still there exist challenges, with the availability of different targets and possible cross-reactivity. Herein we have chosen the phosphoinositide 3-kinase (PI3K) as the target of interest and investigated the potential of pyrido fused imidazo[4,5-c]quinoline derivatives to bind strongly to the active site, thereby inhibiting the progression of various types of tumors. The AutoDock, Glide and the Prime-MM/GBSA analysis are used to execute the molecular docking investigation and validation for the designed compounds. The anti-tumor property evaluations were carried out by using PASS algorithm. Based on the GLIDE score, the binding affinity of the designed molecules towards the target PI3K was evaluated. The energetics associated with static interactions revealed 1j as the most potential candidate and the dynamic investigations including RMSD, RMSF, Rg, SASA and hydrogen bonding also supported the same through relative stabilization induced through ligand interactions. Subsequently, the binding free energy of the Wortmannin and 1j complex calculated using MM-PBSA analysis. Further evaluations with PASS prediction algorithm also supported the above results. The studies reveal that there is evidence for considering appropriate pyrido fused imidazo[4,5-c]quinoline compounds as potential anti-tumor agents.
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Affiliation(s)
- Upala Dasmahapatra
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Chitluri Kiran Kumar
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Soumyadip Das
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Prathima Thimma Subramanian
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai, Tamil Nadu, India
| | - Poornimaa Murali
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Arnold Emerson Isaac
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Karuppasamy Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balamurali MM
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai, Tamil Nadu, India
- *Correspondence: Balamurali MM, ; Kaushik Chanda,
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
- *Correspondence: Balamurali MM, ; Kaushik Chanda,
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Mair S, Erharter K, Renard E, Brillet K, Brunner M, Lusser A, Kreutz C, Ennifar E, Micura R. Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA. Nucleic Acids Res 2022; 50:6038-6051. [PMID: 35687141 PMCID: PMC9226506 DOI: 10.1093/nar/gkac477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/28/2022] [Accepted: 05/20/2022] [Indexed: 12/25/2022] Open
Abstract
Nucleobase deamination, such as A-to-I editing, represents an important posttranscriptional modification of RNA. When deamination affects guanosines, a xanthosine (X) containing RNA is generated. However, the biological significance and chemical consequences on RNA are poorly understood. We present a comprehensive study on the preparation and biophysical properties of X-modified RNA. Thermodynamic analyses revealed that base pairing strength is reduced to a level similar to that observed for a G•U replacement. Applying NMR spectroscopy and X-ray crystallography, we demonstrate that X can form distinct wobble geometries with uridine depending on the sequence context. In contrast, X pairing with cytidine occurs either through wobble geometry involving protonated C or in Watson–Crick-like arrangement. This indicates that the different pairing modes are of comparable stability separated by low energetic barriers for switching. Furthermore, we demonstrate that the flexible pairing properties directly affect the recognition of X-modified RNA by reverse transcription enzymes. Primer extension assays and PCR-based sequencing analysis reveal that X is preferentially read as G or A and that the ratio depends on the type of reverse transcriptase. Taken together, our results elucidate important properties of X-modified RNA paving the way for future studies on its biological significance.
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Affiliation(s)
- Stefan Mair
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Karl Brillet
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
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Simonetti SO, Kaufman TS, Larghi EL. Conjugation of Carbohydrates with Quinolines: A Powerful Synthetic Tool. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sebastián O. Simonetti
- Instituto de Química Rosario: Instituto de Quimica Rosario Química Orgánica Suipacha 531 S2002LRK Rosario ARGENTINA
| | - Teodoro S. Kaufman
- Instituto de Química Rosario: Instituto de Quimica Rosario Química Orgánica Suipacha 531 S2002LRK Rosario ARGENTINA
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Bereiter R, Himmelstoß M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R. Impact of 3-deazapurine nucleobases on RNA properties. Nucleic Acids Res 2021; 49:4281-4293. [PMID: 33856457 PMCID: PMC8096147 DOI: 10.1093/nar/gkab256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic mutagenesis studies of functional RNAs. They were the key for our current mechanistic understanding of ribosomal peptide bond formation and of phosphodiester cleavage in recently discovered small ribozymes, such as twister and pistol RNAs. Here, we present a comprehensive study on the impact of c3A and the thus far underinvestigated 3-deazaguanosine (c3G) on RNA properties. We found that these nucleosides can decrease thermodynamic stability of base pairing to a significant extent. The effects are much more pronounced for 3-deazapurine nucleosides compared to their constitutional isomers of 7-deazapurine nucleosides (c7G, c7A). We furthermore investigated base pair opening dynamics by solution NMR spectroscopy and revealed significantly enhanced imino proton exchange rates. Additionally, we solved the X-ray structure of a c3A-modified RNA and visualized the hydration pattern of the minor groove. Importantly, the characteristic water molecule that is hydrogen-bonded to the purine N3 atom and always observed in a natural double helix is lacking in the 3-deazapurine-modified counterpart. Both, the findings by NMR and X-ray crystallographic methods hence provide a rationale for the reduced pairing strength. Taken together, our comparative study is a first major step towards a comprehensive understanding of this important class of nucleoside modifications.
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Affiliation(s)
- Raphael Bereiter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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Takeda T, Yanagi M, Suzuki A, Katoh R, Saito Y. Synthesis of ethynylpyrene-modified 3-deaza-2′-deoxyguanosines as environmentally sensitive fluorescent nucleosides: Target DNA-sequence detection via changes in the fluorescence wavelength. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Walunj MB, Tanpure AA, Srivatsan SG. Post-transcriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes. Nucleic Acids Res 2018; 46:e65. [PMID: 29546376 PMCID: PMC6009664 DOI: 10.1093/nar/gky185] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
Pd-catalyzed C-C bond formation, an important vertebra in the spine of synthetic chemistry, is emerging as a valuable chemoselective transformation for post-synthetic functionalization of biomacromolecules. While methods are available for labeling protein and DNA, development of an analogous procedure to label RNA by cross-coupling reactions remains a major challenge. Herein, we describe a new Pd-mediated RNA oligonucleotide (ON) labeling method that involves post-transcriptional functionalization of iodouridine-labeled RNA transcripts by using Suzuki-Miyaura cross-coupling reaction. 5-Iodouridine triphosphate (IUTP) is efficiently incorporated into RNA ONs at one or more sites by T7 RNA polymerase. Further, using a catalytic system made of Pd(OAc)2 and 2-aminopyrimidine-4,6-diol (ADHP) or dimethylamino-substituted ADHP (DMADHP), we established a modular method to functionalize iodouridine-labeled RNA ONs in the presence of various boronic acid and ester substrates under very mild conditions (37°C and pH 8.5). This method is highly chemoselective, and offers direct access to RNA ONs labeled with commonly used fluorescent and affinity tags and new fluorogenic environment-sensitive nucleoside probes in a ligand-controlled stereoselective fashion. Taken together, this simple approach of generating functional RNA ON probes by Suzuki-Miyaura coupling will be a very important addition to the resources and tools available for analyzing RNA motifs.
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Affiliation(s)
- Manisha B Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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Bazin HG, Bess LS, Livesay MT. Synthesis and Applications of Imidazoquinolines: A Review. ORG PREP PROCED INT 2018. [DOI: 10.1080/00304948.2018.1433427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Hélène G. Bazin
- Biomedical & Pharmaceutical Science, University of Montana, 32 Campus Drive #1552, Missoula, MT 59812, USA
| | - Laura S. Bess
- Biomedical & Pharmaceutical Science, University of Montana, 32 Campus Drive #1552, Missoula, MT 59812, USA
| | - Mark T. Livesay
- Biomedical & Pharmaceutical Science, University of Montana, 32 Campus Drive #1552, Missoula, MT 59812, USA
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Hwang GT. Single-Labeled Oligonucleotides Showing Fluorescence Changes Upon Hybridization with Target Nucleic Acids. Molecules 2018; 23:E124. [PMID: 29316733 PMCID: PMC6017082 DOI: 10.3390/molecules23010124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs) is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore. This review summarizes recent research on single-labeled oligonucleotide probes that exhibit fluorescence changes after encountering target nucleic acids, such as guanine-quenching probes, cyanine-containing probes, probes containing a fluorophore-labeled base, and microenvironment-sensitive probes.
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Affiliation(s)
- Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea.
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10
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Yanagi M, Suzuki A, Hudson RHE, Saito Y. A fluorescent 3,7-bis-(naphthalen-1-ylethynylated)-2′-deoxyadenosine analogue reports thymidine in complementary DNA by a large emission Stokes shift. Org Biomol Chem 2018; 16:1496-1507. [DOI: 10.1039/c8ob00062j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first example of a fluorescent adenosine analogue possessing simultaneous major- and minor-groove substitution selectively reports base-pairing to thymidine.
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Affiliation(s)
- Masaki Yanagi
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Azusa Suzuki
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Robert H. E. Hudson
- Department of Chemistry
- The University of Western Ontario
- London
- Canada N6A 5B7
| | - Yoshio Saito
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
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11
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Suzuki A, Yanagi M, Takeda T, Hudson RHE, Saito Y. The fluorescently responsive 3-(naphthalen-1-ylethynyl)-3-deaza-2′-deoxyguanosine discriminates cytidine via the DNA minor groove. Org Biomol Chem 2017; 15:7853-7859. [DOI: 10.1039/c7ob01931a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A newly synthesized fluorescent nucleoside 3nzG discriminates cytidine in target DNA strands by a distinct change in its emission wavelength.
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Affiliation(s)
- Azusa Suzuki
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Masaki Yanagi
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Takuya Takeda
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | | | - Yoshio Saito
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
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Yamauchi T, Takeda T, Yanagi M, Takahashi N, Suzuki A, Saito Y. C2-substituted 8-aza-7-deaza-2′-deoxyadenosines as environmentally sensitive fluorescent nucleosides for discriminating apurinic/apyrimidinic sites in DNA duplex. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2016.11.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Lee JW, Son YS, Hwang JY, Park Y, Hwang GT. pH-Responsive quencher-free molecular beacon systems containing 2′-deoxyuridine units labeled with fluorene derivatives. Org Biomol Chem 2017; 15:7165-7172. [DOI: 10.1039/c7ob01703k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
pH-Responsive oligodeoxynucleotides only exhibited dramatic increases in fluorescence upon duplex formation with their fully matched target DNAs.
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Affiliation(s)
- Ji Won Lee
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Ye-Seul Son
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Jun Yeon Hwang
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Yoojin Park
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology
- Pohang 37673
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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